Human papillomavirus (HPV) vaccines

Abstract

Disclosed herein are vaccine compositions that include HPV MHC epitope-encoding cassettes and / or full-length HPV proteins. Also disclosed are nucleotides, cells, and methods associated with the compositions including their use as vaccines.

Description

HUMAN PAPILLOMAVIRUS (HPV) VACCINESCROSS REFERENCE TO RELATED APPLICATIONS

[0001] Not applicable.SEQUENCE LISTING

[0002] The instant application contains a Sequence Listing which has been submitted via Patent Center and is hereby incorporated herein by reference in its entirety. Said .XML copy, created on November 7, 2022, is named GSO-006D2, and is 538 Kb in size.BACKGROUND

[0003] Malignancies, such as cervical cancer, arising from human papillomavirus (HPV) infections remain a global health issue despite the advent of prophylactic HPV vaccinations (e.g., Gardasil®, Cervarix®). Specifically, there is still a need for HPV vaccines for women from low middle income countries (LMIC) with persistent HPV infection (non-malignant), as well as a continued need for therapeutic HPV vaccinations for additional indivduals.

[0004] An additional question for antigen vaccine design in infectious disease settings is which of the many proteins present generate the “best” therapeutic antigens, e.g., which HPV antigens that can stimulate immunity.

[0005] In addition to the challenges of current antigen prediction methods certain challenges also exist with the available vector systems that can be used for antigen delivery in humans, many of which are derived from humans. For example, many humans have pre-existing immunity to human viruses as a result of previous natural exposure, and this immunity can be a major obstacle to the use of recombinant human viruses for antigen delivery in vaccination strategies, such as in cancer treatment or vaccinations against infectious diseases.

[0006] While some progress has been made in vaccinations strategies addressing the above problems, improvements are still needed, particularly for clinical applications, such as improved vaccine potency and efficacy, such as the need for a HPV vaccine that stimulates robust T cell immunity in humans, including, but not limited to, women at risk for HPV-associated malignancies (e.g., cervical cancer).SUMMARY

[0007] Provided herein is a human papillomavirus (HPV) vaccine comprising at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide, wherein the encoded immunogenic polypeptide comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in any one of Tables C1-C8; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8; or- any one of the polypeptide sequences of the cassette sequences set forth in Table D; or- an HPV-derived E6 / E7 fusion protein comprising an HPV E6 derived polypeptide and an HPV E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the polypeptide sequences shown in Table A; or- combinations thereof.

[0008] Also provided herein is a composition for delivery of an antigen expression system, comprising (a) one or more vectors, the one or more vectors comprising a vector backbone, wherein the vector backbone comprises (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) an antigen cassette, optionally wherein the antigen cassette is inserted into the vector backbone when present, and wherein the antigen cassette comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in any one of Tables C1-C8; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8; or- any one of the polypeptide sequences of the cassette sequences set forth in Table D; or- an HPV-derived E6 / E7 fusion protein comprising an HPV E6 derived polypeptide and an HPV E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the polypeptide sequences shown in Table A; or- combinations thereof; and wherein each of the HPV derived nucleic acid sequences comprises; (I) optionally, a 5’ linker sequence, and (II) optionally, a 3’ linker sequence; (ii) optionally, a second promoter nucleotide sequence operably linked to one or more of the three HPV derived nucleic acid sequences; and (iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence; (iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and (v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone optionally wherein the exogenous poly(A) sequence comprises an SV40 poIy(A) signal sequence or a Bovine Growth Hormone (BGH) poly(A) signal sequence.

[0009] Also provided herein is a composition for delivery of an antigen expression system, wherein the antigen expression system comprises (a) one or more vectors, the one or more vectors comprising a vector backbone, wherein the vector backbone comprises a chimpanzee adenovirus vector, optionally wherein the chimpanzee adenovirus vector is a ChAdV68 vector, or an alphavirus vector, optionally wherein the alphavirus vector is a Venezuelan equine encephalitis virus vector, and wherein the vector backbone comprises (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone such that the antigen cassette is operably linked to the at least one promoter nucleotide sequence, and wherein the antigen cassette comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in any one of Tables C1-C8; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8; or- any one of the polypeptide sequences of the cassette sequences set forth in Table D; or- an HPV-derived E6 / E7 fusion protein comprising an HPV E6 derived polypeptide and an HPV E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the polypeptide sequences shown in Table A; or- combinations thereof; and

[0010] Also provided herein is a composition for delivery of an antigen expression system, comprising: the antigen expression system, wherein the antigen expression system comprises: (a) a vector backbone, wherein the vector backbone comprises an alphavirus vector, optionally wherein the alphavirus vector is a Venezuelan equine encephalitis virus vector, and wherein the vector backbone comprises: (i) a subgenomic promoter nucleotide sequence, and (ii) a polyadenylation (poly(A)) sequence; and (b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone such that the antigen cassette is operably linked to the subgenomic promoter nucleotide sequence, and wherein the antigen cassette comprises, in order from 5’ to 3’: (i) a nucleotide sequence encoding a first HPV-derived nucleic acid sequence; (ii)a 2A ribosome skipping sequence element; and (iii) a nucleotide sequence encoding a second HPV-derived nucleic acid sequence, and optionally wherein (a) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV strain and a second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV strain, or (b) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV protein and the second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV protein, optionally wherein the first HPV protein and the second HPV protein are derived from the same HPV strain.

[0011] Also provided herein is a composition for delivery of an antigen expression system, comprising the antigen expression system, wherein the antigen expression system comprises (a) a vector backbone, wherein the vector backbone comprises an alphavirus vector, optionally wherein the alphavirus vector is a Venezuelan equine encephalitis virus vector, and wherein the vector backbone comprises (i) a first subgenomic promoter nucleotide sequence, and (ii) a polyadenylation (poly(A)) sequence; and (b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone such that the antigen cassette is operably linked to the subgenomic promoter nucleotide sequence, and wherein the antigen cassette comprises, in order from 5’ to 3’: (i) a nucleotide sequence encoding a first HPV-derived nucleic acid sequence; (ii) a second subgenomic promoter nucleotide sequence; and (iii) a nucleotide sequence encoding a second HPV-derived nucleic acid sequence, and optionally wherein (a) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV strain and a second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV strain, or (b) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV protein and the second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV protein, optionally wherein the first HPV protein and the second HPV protein are derived from the same HPV strain.

[0012] In some aspects, the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl, and an HPV16-derived E6 / E7 fusion protein comprising an HPV 16 E6 derived polypeptide and an HPV 16 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV16-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2, and an HPV18-derived E6 / E7 fusion protein comprising an HPV18 E6 derived polypeptide and an HPV18 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV18-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3, and an HPV31 -derived E6 / E7 fusion protein comprising an HPV31 E6 derived polypeptide and an HPV31 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV31 -derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4, and an HPV33-derived E6 / E7 fusion protein comprising an HPV33 E6 derived polypeptide and an HPV33 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV33-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5, and an HPV35-derived E6 / E7 fusion protein comprising an HPV35 E6 derived polypeptide and an HPV35 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV35-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6, and an HPV45-derived E6 / E7 fusion protein comprising an HPV45 E6 derived polypeptide and an HPV45 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV45-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7, and an HPV52-derived E6 / E7 fusionprotein comprising an HPV52 E6 derived polypeptide and an HPV52 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV52-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8, and an HPV58-derived E6 / E7 fusion protein comprising an HPV58 E6 derived polypeptide and an HPV58 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV58-derived polypeptide sequences shown in Table A; or- combinations thereof.

[0013] In some aspects, the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl, and an HPV16-derived E6 / E7 fusion protein comprising an HPV16 E6 derived polypeptide and an HPV 16 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV16-derived polypeptide sequences shown in Table A; and at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2, and an HPV18-derived E6 / E7 fusion protein comprising an HPV18 E6 derived polypeptide and an HPV18 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV18-derived polypeptide sequences shown in Table A.

[0014] In some aspects, the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl, and an HPV16-derived E6 / E7 fusion protein comprising an HPV16 E6 derived polypeptide and an HPV16 E7 derived polypeptide, wherein the HPV-derived fusion protein comprises any one of the HPV16-derived polypeptide sequences shown in Table A; and each of the polypeptide sequences as set forth in Tables C2, and an HPV 18-derived E6 / E7 fusion protein comprising an HPV18 E6 derived polypeptide and an HPV18 E7 derived polypeptide, wherein the HPV-derived fusion protein comprises any one of the HPV18-derived polypeptide sequences shown in Table A.

[0015] In some aspects, the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide compriseseach of the polypeptide sequences as set forth in Tables Cl; and at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2.

[0016] In some aspects, the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises: at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; and at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; and at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; and at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6.

[0017] Also provided herein is a HPV vaccine, wherein the vaccine comprises a selfamplifying alphavirus-based expression system comprising: (A) one or more vectors, wherein the one or more vectors comprises: (a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises: (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises: (i) one or more of the HPV derived nucleic acid sequences provided herein, wherein the immunogenic polypeptide optionally comprises a N-terminal linker and / or a C-terminal linker; (ii) optionally, a second promoter nucleotide sequence operably linked to the HPV derived nucleic acid sequence; and (iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence; (iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and (v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone, optionally wherein the exogenous poly(A) sequence comprises an SV40 poly(A) signal sequence or a Bovine Growth Hormone (BGH) poly(A) signal sequence; and (B) a lipid-nanoparticle (LNP), wherein the LNP encapsulates the self- amplifying alphavirus-based expression system.

[0018] In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises at least lOpg or 20 pg of each of the one or more vectors. In some aspects, the composition for delivery of the self- amplifying alphavirus-based expression systemcomprises between 10 pg- 20 pg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises 20pg or less of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises between 10-30pg or between 10-100pg of each of the one or more vectors.

[0019] In some aspects, the composition comprises at least two HPV-derived nucleic acid sequences, wherein a first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV strain and a second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV strain. In some aspects, the first HPV strain and the second HPV strain are each selected from the group consisting of: HPV16, HPV18, HPV31, HPV33, HPV35, HPV45, HPV52, and HPV58. In some aspects, the first HPV strain and the second HPV strain are HPV16 and HPV18.

[0020] In some aspects, the immunogenic polypeptide is derived from an HPV early (E) protein selected from the group consisting of: HPV El, HPV E2, HPV E5, HPV E6, HPV E7, and combinations thereof. In some aspects, the composition comprises the HPV derived nucleic acid sequence encodes at least one immunogenic polypeptide derived from each of HPV El, HPV E2, HPV E5, HPV E6, and HPV E7.

[0021] In some aspects, the composition further comprises a non-HPV derived nucleic acid sequence encoding at least one immunogenic polypeptide derived from an infectious disease other than HPV, optionally wherein the infectious disease is selected from the group consisting of: a pathogen, a virus, a bacteria, a fungus, and a parasite.

[0022] In some aspects, the RNA alphavirus backbone comprises one or more elements obtained from the sequence of SEQ ID NO: 3 or SEQ ID NO:5, optionally wherein the one or more elements are selected from the group consisting of the sequences necessary for nonstructural protein-mediated amplification, the 26S promoter nucleotide sequence, the poly (A) sequence, and the nsPl-4 genes of the sequence set forth in SEQ ID NO: 3 or SEQ ID NO:5, optionally the RNA alphavirus backbone comprises the sequence set forth in the sequences selected from the group consisting of SEQ ID NOs:6-9.

[0023] Also provided herein is a method for stimulating an immune response in a subject, the method comprising administering to the subject the composition for delivery of the selfamplifying alphavirus-based expression systems provided herein. In some aspects, the method comprises administering at least two doses of the composition for delivery of the self-amplifying alphavirus-based expression system. In some aspects, the at least two doses comprises a priming dose and at least one boosting dose. In some aspects, the at least two doses are administered on days 1 and day 28 or later. In some aspects, the at least two doses are administered on days 1and on or after week 4. In some aspects, the at least two doses comprise the same antigen cassette.

[0024] In some aspects, the method further comprises administration of a chimpanzee adenovirus (ChAdV)-based expression system, wherein the composition for delivery of the ChAdV-based expression system comprises the ChAdV-based expression system, wherein the ChAdV-based expression system comprises a viral particle comprising a ChAdV vector, wherein the ChAdV vector comprises (a) a ChAdV backbone, wherein the ChAdV backbone comprises: (i) at least one promoter nucleotide sequence, and (ii) at least one poly adenylation (poly(A)) sequence; and (b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide.

[0025] In some aspects, the ChAdV-based expression system is administered as a priming dose. In some aspects, the antigen cassette of the ChAdV-based expression system is the same as the antigen cassette of the self-amplifying alphavirus-based expression system.

[0026] Also provided herein is a HPV vaccine comprising a chimpanzee adenovirus (ChAdV)-based expression system, wherein the composition for delivery of the ChAdV-based expression system comprises: (a) a ChAdV backbone, wherein the ChAdV backbone comprises (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and (b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises (i) one or more of the HPV derived nucleic acid sequences provided herein, wherein the immunogenic polypeptide optionally comprises a N-terminal linker and / or a C-terminal linker; (ii) optionally, a second promoter nucleotide sequence operably linked to the HPV derived nucleic acid sequence; and (iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence; (iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and (v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone, optionally wherein the exogenous poly(A) sequence comprises an SV40 poly(A) signal sequence or a Bovine Growth Hormone (BGH) poly(A) signal sequence, and wherein the cassette is operably linked to the at least one promoter nucleotide sequence and the at least one poly(A) sequence.

[0027] In some aspects, the composition for delivery of the ChAdV-based expression system comprises at least IxlO11of the viral particles. In some aspects, the composition for delivery of the ChAdV-based expression system comprises between IxlO11and IxlO12. In some aspects, the composition for delivery of the ChAdV-based expression system comprises IxlO11, 3xl0n, orvp / mL.

[0028] In some aspects, the ChAdV backbone comprises at least nucleotides 2 to 36,518 of the sequence set forth in SEQ ID NO: 1, wherein the nucleotides 2 to 36,518 lack: (1) nucleotides 577 to 3403 of the sequence shown in SEQ ID NO: 1 corresponding to an El deletion; (2) nucleotides 27,125 to 31,825 of the sequence shown in SEQ ID NO:1 corresponding to an E3 deletion; and (3) optionally nucleotides 34,916 to 35,642 of the sequence shown in SEQ ID NO:1 corresponding to a partial E4 deletion; optionally wherein the antigen cassette is inserted within the El deletion.

[0029] Also provided herein is a method for stimulating an immune response in a subject, the method comprising administering to the subject the composition for delivery of the ChAdV- based expression systems provided herein.

[0030] In some aspects, the the ChAdV-based expression system is administered as a priming dose. In some aspects, the method further comprises administration of a composition for delivery of a self-amplifying alphavirus-based expression system, wherein the composition for delivery of the self-amplifying alphavirus-based expression system comprises (A) the selfamplifying alphavirus-based expression system, wherein the self-amplifying alphavirus-based expression system comprises one or more vectors, wherein the one or more vectors comprises(a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises (i) at least one promoter nucleotide sequence, and (ii) at least one polyadenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide.

[0031] In some aspects, the antigen cassette of the ChAdV-based expression system is the same as the antigen cassette of the self- amplifying alphavirus-based expression system.

[0032] In some aspects, the composition for delivery of the expression system is formulated in a pharmaceutical composition comprising a pharmaceutically acceptable carrier.

[0033] Also provided herein is a kit comprising the composition for delivery of the expression systems provided herein.

[0034] Also provided herein is a method for stimulating an immune response in a subject, the method comprising administering to the subject any one of the HPV vaccines provided herein.

[0035] Also provided herein is a method for stimulating an immune response in a subject, the method comprising administering to the subject any one of the HPV vaccines provided herein. In some aspects, the subject is at risk for one or more of cervical cancer, anal cancer,oropharyngeal cancer, oral cancer, penile cancer, vaginal cancer, and / or vulvar cancer. In some aspects, the subject is diagnosed as HPV positive. In some aspects, the subject is diagnosed as having cervical intraepithelial neoplasia (CIN1).

[0036] Also provided for herein is a method for stimulating an immune response in a subject, the method comprising administering to the subject a composition for delivery of a selfamplifying alphavirus-based expression system and administering to the subject a composition for delivery of a chimpanzee adenovirus (ChAdV)-based expression system, and wherein either: a. the composition for delivery of the ChAdV-based expression system comprises the ChAdV- based expression system, wherein the ChAdV-based expression system comprises a viral particle comprising a ChAdV vector, and wherein the composition comprises IxlO12or less of the viral particles, b. wherein the composition for delivery of the self-amplifying alphavirusbased expression system comprises the self-amplifying alphavirus-based expression system, wherein the self-amplifying alphavirus-based expression system comprises one or more vectors, and wherein the composition comprises at least lOpg of each of the one or more vectors, or c. the composition for delivery of the ChAdV-based expression system comprises the ChAdV- based expression system, wherein the ChAdV-based expression system comprises a viral particle comprising a ChAdV vector, and wherein the composition comprises IxlO12or less of the viral particles and wherein the composition for delivery of the self-amplifying alphavirusbased expression system comprises the self-amplifying alphavirus-based expression system, wherein the self-amplifying alphavirus-based expression system comprises one or more vectors, and wherein the composition comprises at least lOpg of each of the one or more vectors.

[0037] In some aspects, the composition for delivery of the ChAdV-based expression system is administered as a priming dose and the composition for delivery of the self-amplifying alphavirus-based expression system is administered as one or more boosting doses.

[0038] In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises at least 3 pg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises at least lOpg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises at least 30pg of each of the one or more vectors. In some aspects, the composition for delivery of the selfamplifying alphavirus-based expression system comprises at least lOOpg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirusbased expression system comprises at least 300pg of each of the one or more vectors. In some aspects, the composition for delivery of the self- amplifying alphavirus-based expression system comprises at least 400 pg, at least 500pg, at least 600pg, at least 700pg, at least 800pg, at least900(ig, at least lOOOpg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises between 10-30pg, 10-lOOpg, 10-300pg, 30-100pg, 30-300|ig, or 100-300pg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises between 3-lOpg, 3-30pg, 3- lOOpg, 3-300pg, 10-30pg, or 100-300pg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises between 10-500pg, lO-lOOOpg, 30-500pg, 30- lOOOpg, or 500-1000pg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises lOpg, 30pg, lOOpg, or 300pg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises 400pg, 500 pg. 600pg, 700pg, 800pg, 900pg, or lOOOpg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises less than or equal to 300pg of each of the one or more vectors. In some aspects, the composition for delivery of the self-amplifying alphavirus-based expression system comprises less than or equal to lOOpg of each of the one or more vectors. In some aspects, the composition for delivery of the self- amplifying alphavirus-based expression system comprises less than or equal to 30pg of each of the one or more vectors. A dose of can represent the total content of RNA / samRNA administered. A dose of can represent the total content of RNA / samRNA administered and include only a single distinct samRNA construct.

[0039] In some aspects, an ordered sequence of one or more of the HPV derived nucleic acid sequences encoding the immunogenic polypeptide is described in the formula, from 5’ to 3’, comprising:Pa-(L5b-Nc-L3d)X-(G5e-Uf)Y-G3g wherein P comprises the second promoter nucleotide sequence, where a = 0 or 1, N comprises one of the HPV derived nucleic acid sequences, where c = 1, optionally wherein each N encodes a polypeptide sequence as set forth in Tables C1-C8, L5 comprises the 5’ linker sequence, where b = 0 or 1, L3 comprises the 3’ linker sequence, where d = 0 or 1, G5 comprises one of the at least one nucleic acid sequences encoding a GPGPG amino acid linker (SEQ ID NO: 56), where e = 0 or 1, G3 comprises one of the at least one nucleic acid sequences encoding a GPGPG amino acid linker (SEQ ID NO: 56), where g = 0 or 1, U comprises one of the at least one MHC class II epitope-encoding nucleic acid sequence, where f = 1, X = 1 to 400, where for each X the corresponding Nc is a HPV derived nucleic acid sequence, and Y = 0, 1, or 2, where for each Y the corresponding Uf is a universal MHC class II epitope-encoding nucleic acid sequence,optionally wherein the at least one universal sequence comprises at least one of Tetanus toxoid and PADRE, or a MHC class II HPV derived epitope-encoding nucleic acid sequence.

[0040] In some aspects, for each X the corresponding Nc is a distinct HPV derived nucleic acid sequence. In some aspects, for each Y the corresponding Uf is a distinct MHC class II HPV derived nucleic acid sequence. In some aspects, b = 1, d = 1, e = 1, g = 1, h = 1, X = 18, Y = 2, (i) the vector backbone comprises a ChAdV68 vector, a = 1, P is a CMV promoter, the at least one second poly(A) sequence is present, wherein the second poly(A) sequence is an exogenous poly(A) sequence to the vector backbone, and optionally wherein the exogenous poly(A) sequence comprises an SV40 poly(A) signal sequence or a BGH poly(A) signal sequence, or (ii) the vector backbone comprises a Venezuelan equine encephalitis virus vector, a = 0, and the antigen cassette is operably linked to an endogenous 26S promoter, and the at least one polyadenylation poly(A) sequence is a poly(A) sequence of at least 80 consecutive A nucleotides provided by the backbone, each N encodes a MHC class I epitope 7-15 amino acids in length, a MHC class II epitope, an epitope capable of stimulating a B cell response, or combinations thereof, L5 is a native 5’ linker sequence that encodes a native N-terminal amino acid sequence of the epitope, and wherein the 5’ linker sequence encodes a peptide that is at least 3 amino acids in length, L3 is a native 3’ linker sequence that encodes a native C-terminal amino acid sequence of the epitope, and wherein the 3’ linker sequence encodes a peptide that is at least 3 amino acids in length, and U is each of a PADRE class II sequence and a Tetanus toxoid MHC class II sequence.

[0041] In some aspects, the composition further comprises a nanoparticulate delivery vehicle. In some aspects, the nanoparticulate delivery vehicle is a lipid nanoparticle (LNP). In some aspects, the LNP comprises ionizable amino lipids. In some aspects, the ionizable amino lipids comprise MC3-like (dilinoleylmethyl-4-dimethylaminobutyrate) molecules. In some aspects, the nanoparticulate delivery vehicle encapsulates the antigen expression system.

[0042] In some aspects, the antigen cassette is integrated between the at least one promoter nucleotide sequence and the at least one poly (A) sequence. In some aspects, the at least one promoter nucleotide sequence is operably linked to the HPV derived nucleic acid sequence.

[0043] In some aspects, the one or more vectors comprise one or more +-stranded RNA In some aspects, the one or more +-stranded RNA vectors comprise a 5’ 7-methylguanosine (m7g) cap. In some aspects, the one or more +-stranded RNA vectors are produced by in vitro transcription. In some aspects, the one or more vectors are self-replicating within a mammalian cell.

[0044] In some aspects, the backbone comprises at least one nucleotide sequence of an Aura virus, a Fort Morgan virus, a Venezuelan equine encephalitis virus, a Ross River virus, a SemlikiForest virus, a Sindbis virus, or a Mayaro virus. In some aspects, the backbone comprises at least one nucleotide sequence of a Venezuelan equine encephalitis virus. In some aspects, the backbone comprises at least sequences for nonstructural protein-mediated amplification, a 26S promoter sequence, a poly(A) sequence, a nonstructural protein 1 (nsPl) gene, a nsP2 gene, a nsP3 gene, and a nsP4 gene encoded by the nucleotide sequence of the Aura virus, the Fort Morgan virus, the Venezuelan equine encephalitis virus, the Ross River virus, the Semliki Forest virus, the Sindbis virus, or the Mayaro virus. In some aspects, the backbone comprises at least sequences for nonstructural protein-mediated amplification, a 26S promoter sequence, and a poly(A) sequence encoded by the nucleotide sequence of the Aura virus, the Fort Morgan virus, the Venezuelan equine encephalitis virus, the Ross River virus, the Semliki Forest virus, the Sindbis virus, or the Mayaro virus. In some aspects, sequences for nonstructural protein- mediated amplification are selected from the group consisting of: an alphavirus 5’ UTR, a 51-nt CSE, a 24-nt CSE, a 26S subgenomic promoter sequence, a 19-nt CSE, an alphavirus 3’ UTR, or combinations thereof. In some aspects, the backbone does not encode structural virion proteins capsid, E2 and El. In some aspects, the antigen cassette is inserted in place of structural virion proteins within the nucleotide sequence of the Aura virus, the Fort Morgan virus, the Venezuelan equine encephalitis virus, the Ross River virus, the Semliki Forest virus, the Sindbis virus, or the Mayaro virus. In some aspects, the Venezuelan equine encephalitis virus comprises the sequence of SEQ ID NO:3 or SEQ ID NO:5. In some aspects, the Venezuelan equine encephalitis virus comprises the sequence of SEQ ID NO:3 or SEQ ID NO:5 further comprising a deletion between base pair 7544 and 11176. In some aspects, the backbone comprises the sequence set forth in SEQ ID NO:6 or SEQ ID NO:7. In some aspects, the antigen cassette is inserted at position 7544 to replace the deletion between base pairs 7544 and 11176 as set forth in the sequence of SEQ ID NO:3 or SEQ ID NO:5. In some aspects, the insertion of the antigen cassette provides for transcription of a polycistronic RNA comprising the nsPl-4 genes and the at least one HPV derived nucleic acid sequence, wherein the nsPl-4 genes and the at least one HPV derived nucleic acid sequence are in separate open reading frames. In some aspects, the at least one promoter nucleotide sequence is the native 26S promoter nucleotide sequence encoded by the backbone.

[0045] In some aspects, the backbone comprises at least one nucleotide sequence of a chimpanzee adenovirus vector, optionally wherein the chimpanzee adenovirus vector is a ChAdV68 vector. In some aspects, the ChAdV68 vector backbone comprises the sequence set forth in SEQ ID NO:1. In some aspects, the ChAdV68 vector backbone comprises the sequence set forth in SEQ ID NO: 1, except that the sequence is fully deleted or functionally deleted in at least one gene selected from the group consisting of the chimpanzee adenovirus E1A, E1B,E2A, E2B, E3, E4, LI, L2, L3, L4, and L5 genes of the sequence set forth in SEQ ID NO: 1, optionally wherein the sequence is fully deleted or functionally deleted in: (1) E1A and E1B; (2) El A, E1B, and E3; or (3) El A, E1B, E3, and E4 of the sequence set forth in SEQ ID NO:1. In some aspects, the ChAdV68 vector backbone comprises a gene or regulatory sequence obtained from the sequence of SEQ ID NO: 1, optionally wherein the gene is selected from the group consisting of the chimpanzee adenovirus inverted terminal repeat (ITR), E1A, E1B, E2A, E2B, E3, E4, LI, L2, L3, L4, and L5 genes of the sequence set forth in SEQ ID NO:1. In some aspects, the ChAdV68 vector backbone comprises a partially deleted E4 gene comprising a deleted or partially-deleted E4orf2 region and a deleted or partially-deleted E4orf3 region, and optionally a deleted or partially-deleted E4orf4 region. In some aspects, the ChAdV68 vector backbone comprises at least nucleotides 2 to 36,518 of the sequence set forth in SEQ ID NO: 1 and further comprising: (1) an El deletion of at least nucleotides 577 to 3403 of the sequence shown in SEQ ID NO:1, (2) an E3 deletion of at least nucleotides 27,125 to 31,825 of the sequence shown in SEQ ID NO: 1, and (3) an E4 deletion of at least nucleotides 34,916 to 35,642 of the sequence shown in SEQ ID NO:1; optionally wherein the antigen cassette is inserted within the El deletion. In some aspects, the ChAdV68 vector backbone comprises the sequence set forth in SEQ ID NO:57 (“chAd68-Empty-E4deleted”), optionally wherein the antigen cassette is inserted within the El deletion. In some aspects, the ChAdV68 vector backbone comprises one or more deletions between base pair number 577 and 3403 or between base pair 456 and 3014, and optionally wherein the vector further comprises one or more deletions between base pair 27,125 and 31,825 or between base pair 27,816 and 31,333 of the sequence set forth in SEQ ID NO:1. In some aspects, the ChAdV68 vector backbone comprises one or more deletions between base pair number 3957 and 10346, base pair number 21787 and 23370, and base pair number 33486 and 36193 of the sequence set forth in SEQ ID NO:1. In some aspects, the wherein the cassette is inserted in the ChAdV backbone at the El region, E3 region, and / or any deleted AdV region that allows incorporation of the cassette. In some aspects, the ChAdV backbone is generated from one of a first generation, a second generation, or a helper-dependent adenoviral vector

[0046] In some aspects, the at least one promoter nucleotide sequence is selected from the group consisting of: a CMV, a SV40, an EF-1, a RSV, a PGK, a HSA, a MCK, and a EBV promoter sequence. In some aspects, the at least one promoter nucleotide sequence is a CMV promoter sequence. In some aspects, the at least one promoter nucleotide sequence is an exogenous RNA promoter. In some aspects, the second promoter nucleotide sequence is a 26S promoter nucleotide sequence or a CMV promoter nucleotide sequence. In some aspects, the second promoter nucleotide sequence comprises multiple 26S promoter nucleotide sequences ormultiple CMV promoter nucleotide sequences, wherein each 26S promoter nucleotide sequence or CMV promoter nucleotide sequence provides for transcription of one or more of the separate open reading frames.

[0047] In some aspects, one or more of the cassettes are at least 100, 200, 300, 400, 500, 600, 700, 800, or 900 nucleotides in length. In some aspects, one or more of the cassettes are at least 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, or 10000 nucleotides in length. In some aspects, the one or more vectors are capable of driving expression of a cassette that is at least 3500 nucleotides in length. In some aspects, the one or more vectors are capable of driving expression of a cassette that is at least 6000 nucleotides in length.

[0048] In some aspects, at least one of the at least one HPV derived nucleic acid sequences encodes a polypeptide sequence or portion thereof that is presented by MHC class I. In some aspects, at least one of the at least one HPV derived nucleic acid sequences encodes a polypeptide sequence or portion thereof that is presented by MHC class II. In some aspects, at least one of the at least one HPV derived nucleic acid sequences encodes a polypeptide sequence or portion thereof capable of stimulating a B cell response, optionally wherein the polypeptide sequence or portion thereof capable of stimulating a B cell response comprises a full-length protein, a protein domain, a protein subunit, or an antigenic fragment predicted or known to be capable of being bound by an antibody.

[0049] In some aspects, each HPV derived nucleic acid sequence is linked directly to one another. In some aspects, at least one of the at least one HPV derived nucleic acid sequences is linked to a distinct HPV derived nucleic acid sequence with a nucleic acid sequence encoding a linker. In some aspects, the linker links In some aspects, the linker is selected from the group consisting of: (1) consecutive glycine residues, at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues in length; (2) consecutive alanine residues, at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues in length; (3) two arginine residues (RR); (4) alanine, alanine, tyrosine (AAY); (5) a consensus sequence at least 2, 3, 4, 5, 6, 7, 8 , 9, or 10 amino acid residues in length that is processed efficiently by a mammalian proteasome; (6) one or more native sequences flanking the antigen derived from the cognate protein of origin and that is at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 2-20 amino acid residues in length; and (7) a furin or TEV cleavage sequence. In some aspects, the linker links two MHC class II sequences or an MHC class II sequence to an MHC class I sequence. In some aspects, the linker comprises the sequence GPGPG (SEQ ID NO: 56).

[0050] In some aspects, at least one sequence of the at least one HPV derived nucleic acid sequences is linked, operably or directly, to a separate or contiguous sequence that enhances the expression, stability, cell trafficking, processing and presentation, and / or immunogenicity of theat least one HPV derived nucleic acid sequences. In some aspects, the separate or contiguous sequence comprises at least one of: a ubiquitin sequence, a ubiquitin sequence modified to increase proteasome targeting (e.g., the ubiquitin sequence contains a Gly to Ala substitution at position 76), an immunoglobulin signal sequence (e.g., IgK), a major histocompatibility class I sequence, lysosomal-associated membrane protein (LAMP)-l, human dendritic cell lysosomal- associated membrane protein, and a major histocompatibility class II sequence; optionally wherein the ubiquitin sequence modified to increase proteasome targeting is A76.

[0051] In some aspects, at least one of the at least one HPV derived nucleic acid sequences encodes two or more distinct polypeptides predicted or validated to be capable of presentation by at least one HLA allele.

[0052] In some aspects, each of the at least one HPV derived nucleic acid sequences encodes a polypeptide sequence or portion thereof that is less than 50%, less than 49%, less than 48%, less than 47%, less than 46%, less than 45%, less than 45%, less than 43%, less than 42%, less than 41%, less than 40%, less than 39%, less than 38%, less than 37%, less than 36%, less than 35%, less than 34%, or less than 33% of the translated, corresponding full-length HPV protein.

[0053] In some aspects, each of the at least one HPV derived nucleic acid sequences encodes a polypeptide sequence or portion thereof that does not encode a functional protein, functional protein domain, functional protein subunit, or functional protein fragment of the translated, corresponding HPV protein.

[0054] In some aspects, two or more of the at least one HPV derived nucleic acid sequences are derived from the same HPV gene. In some aspects, the two or more HPV derived nucleic acid sequences derived from the same HPV gene are ordered such that a first nucleic acid sequence cannot be immediately followed by or linked to a second nucleic acid sequence if the second nucleic acid sequence follows first nucleic acid sequence in the corresponding HPV gene.

[0055] In some aspects, the at least one HPV derived nucleic acid sequence comprises at least 2-10, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleic acid sequences. In some aspects, the at least one HPV derived nucleic acid sequence comprises at least 11-20, 15-20, 11-100, 11-200, 11-300, 11-400, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or up to 400 nucleic acid sequences. In some aspects, the at least one HPV derived nucleic acid sequence comprises at least 2-400 nucleic acid sequences and wherein at least two of the HPV derived nucleic acid sequences encode polypeptide sequences or portions thereof that are (1) presented by MHC class I, (2) presented by MHC class II, and / or (3) capable of stimulating a B cell response. In some aspects, at least two of the HPV derived nucleic acid sequences encode polypeptide sequences or portionsthereof that are (1) presented by MHC class I, (2) presented by MHC class II, and / or (3) capable of stimulating a B cell response class.

[0056] In some aspects, when administered to the subject and translated, at least one of the antigens encoded by the at least one HPV derived nucleic acid sequence are presented on antigen presenting cells resulting in an immune response targeting at least one of the antigens on a HPV infected cell surface. In some aspects, when administered to the subject and translated, at least one of the antigens encoded by the at least one HPV derived nucleic acid sequence results in an antibody response targeting at least one of the antigens on a HPV virus. In some aspects, the at least one HPV derived nucleic acid sequences when administered to the subject and translated, at least one of the MHC class I or class II antigens are presented on antigen presenting cells resulting in an immune response targeting at least one of the antigens on a HPV infected cell surface, and optionally wherein the expression of each of the at least one HPV derived nucleic acid sequences is driven by the at least one promoter nucleotide sequence.

[0057] In some aspects, each MHC class I epitope-encoding HPV derived nucleic acid sequence encodes a polypeptide sequence between 8 and 35 amino acids in length, optionally 9- 17, 9-25, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 amino acids in length. In some aspects, the at least one MHC class II epitopeencoding nucleic acid sequence is present. In some aspects, the at least one MHC class II epitope-encoding nucleic acid sequence is present and comprises at least one MHC class II HPV derived nucleic acid sequence. In some aspects, the at least one MHC class II epitope-encoding nucleic acid sequence is 12-20, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 20-40 amino acids in length. In some aspects, the at least one MHC class II epitope-encoding nucleic acid sequence is present and comprises at least one universal MHC class II epitope-encoding nucleic acid sequence, optionally wherein the at least one universal sequence comprises at least one of Tetanus toxoid and PADRE, and / or at least one MHC class II HPV derived epitope-encoding nucleic acid sequence.

[0058] In some aspects, the at least one promoter nucleotide sequence or the second promoter nucleotide sequence is inducible. In some aspects, the at least one promoter nucleotide sequence or the second promoter nucleotide sequence is non- inducible. In some aspects, the at least one poly(A) sequence comprises a poly(A) sequence native to the backbone. In some aspects, the at least one poly(A) sequence comprises a poly(A) sequence exogenous to the backbone.

[0059] In some aspects, the at least one poly(A) sequence is operably linked to at least one of the at least one HPV derived nucleic acid sequences. In some aspects, the at least one poly(A) sequence is at least 20 , at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, or atleast 90 consecutive A nucleotides. In some aspects, the at least one poly(A) sequence is at least 80 consecutive A nucleotides. In some aspects, the at least one second poly(A) sequence is present. In some aspects, the at least one second poly(A) sequence comprises an SV40 poly(A) signal sequence or a Bovine Growth Hormone (BGH) poly(A) signal sequence, or a combination of two more SV40 poly (A) signal sequences or BGH poly (A) signal sequence. In some aspects, the at least one second poly(A) sequence comprises two or more second poly(A) sequences, optionally wherein the two or more second poly(A) sequences comprises two or more SV40 poly(A) signal sequences two or more BGH poly(A) signal sequences, or a combination of SV40 poly(A) signal sequences and BGH poly(A) signal sequences.

[0060] In some aspects, the antigen cassette further comprises at least one of: an intron sequence, an exogenous intron sequence, a Constitutive Transport Element (CTE), a RNA Transport Element (RTE), a woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) sequence, an internal ribosome entry sequence (IRES) sequence, a nucleotide sequence encoding a 2A self cleaving peptide sequence, a nucleotide sequence encoding a Furin cleavage site, or a sequence in the 5 ’ or 3 ’ non-coding region known to enhance the nuclear export, stability, or translation efficiency of mRNA that is operably linked to at least one of the at least one HPV derived nucleic acid sequences.

[0061] In some aspects, the antigen cassette further comprises a reporter gene, including but not limited to, green fluorescent protein (GFP), a GFP variant, secreted alkaline phosphatase, luciferase, a luciferase variant, or a detectable peptide or epitope. In some aspects, the detectable peptide or epitope is selected from the group consisting of an HA tag, a Flag tag, a His-tag, or a V5 tag.

[0062] In some aspects, the one or more vectors further comprises one or more nucleic acid sequences encoding at least one immune modulator. In some aspects, the immune modulator is an anti-CTLA4 antibody or an antigen-binding fragment thereof, an anti-PD-1 antibody or an antigen-binding fragment thereof, an anti-PD-Ll antibody or an antigen-binding fragment thereof, an anti-4- IBB antibody or an antigen-binding fragment thereof, or an anti-OX-40 antibody or an antigen-binding fragment thereof. In some aspects, the antibody or antigenbinding fragment thereof is a Fab fragment, a Fab’ fragment, a single chain Fv (scFv), a single domain antibody (sdAb) either as single specific or multiple specificities linked together (e.g., camelid antibody domains), or full-length single-chain antibody (e.g., full-length IgG with heavy and light chains linked by a flexible linker). In some aspects, the heavy and light chain sequences of the antibody are a contiguous sequence separated by either a self-cleaving sequence such as 2A or IRES ; or the heavy and light chain sequences of the antibody are linked by a flexible linker such as consecutive glycine residues. In some aspects, the immunemodulator is a cytokine. In some aspects, the cytokine is at least one of IL-2, IL-7, IL-12, IL-15, or IL-21 or variants thereof of each.

[0063] In some aspects, a MHC class I or MHC class II epitope-encoding HPV derived nucleic acid sequence is selected by performing the steps of: (a) obtaining at least one of exome, transcriptome, or whole genome HPV nucleotide sequencing data from a HPV virus or HPV infected cell, wherein the HPV nucleotide sequencing data is used to obtain data representing peptide sequences of each of a set of antigens; (b) inputting the peptide sequence of each antigen into a presentation model to generate a set of numerical likelihoods that each of the antigens is presented by one or more of the MHC alleles on a HPV infected cell surface, the set of numerical likelihoods having been identified at least based on received mass spectrometry data; and (c) selecting a subset of the set of antigens based on the set of numerical likelihoods to generate a set of selected antigens which are used to generate the MHC class I or MHC class II epitope-encoding HPV derived nucleic acid sequence.

[0064] In some aspects, each MHC class I or MHC class II epitope-encoding HPV derived nucleic acid sequences is selected by performing the steps of: (a) obtaining at least one of exome, transcriptome, or whole genome HPV nucleotide sequencing data from a HPV virus or HPV infected cell, wherein the HPV nucleotide sequencing data is used to obtain data representing peptide sequences of each of a set of antigens; (b) inputting the peptide sequence of each antigen into a presentation model to generate a set of numerical likelihoods that each of the antigens is presented by one or more of the MHC alleles on a HPV infected cell surface, the set of numerical likelihoods having been identified at least based on received mass spectrometry data; and (c) selecting a subset of the set of antigens based on the set of numerical likelihoods to generate a set of selected antigens which are used to generate the at least 18 HPV derived nucleic acid sequences. In some aspects, a number of the set of selected antigens is 2-20. In some aspects, the presentation model represents dependence between: (a) presence of a pair of a particular one of the MHC alleles and a particular amino acid at a particular position of a peptide sequence; and (b) likelihood of presentation on a HPV infected cell surface, by the particular one of the MHC alleles of the pair, of such a peptide sequence comprising the particular amino acid at the particular position. In some aspects, selecting the set of selected antigens comprises selecting antigens that have an increased likelihood of being presented on a HPV infected cell surface relative to unselected antigens based on the presentation model, optionally wherein the selected antigens have been validated as being presented by one or more specific HLA alleles. In some aspects, selecting the set of selected antigens comprises selecting antigens that have an increased likelihood of being capable of inducing a HPV specific immune response in the subject relative to unselected antigens based on the presentation model. In some aspects,selecting the set of selected antigens comprises selecting antigens that have an increased likelihood of being capable of being presented to naive T cells by professional antigen presenting cells (APCs) relative to unselected antigens based on the presentation model, optionally wherein the APC is a dendritic cell (DC). In some aspects, selecting the set of selected antigens comprises selecting antigens that have a decreased likelihood of being subject to inhibition via central or peripheral tolerance relative to unselected antigens based on the presentation model. In some aspects, selecting the set of selected antigens comprises selecting antigens that have a decreased likelihood of being capable of inducing an autoimmune response to normal tissue in the subject relative to unselected antigens based on the presentation model. In some aspects, exome or transcriptome HPV nucleotide sequencing data is obtained by performing sequencing on a HPV virus or HPV infected tissue or cell. In some aspects, the sequencing is next generation sequencing (NGS) or any massively parallel sequencing approach.

[0065] In some aspects, the antigen cassette comprises junctional epitope sequences formed by adjacent sequences in the antigen cassette. In some aspects, at least one or each junctional epitope sequence has an affinity of greater than 500 nM for MHC. In some aspects, each junctional epitope sequence is non- self.

[0066] In some aspects, each of the MHC class I and / or MHC class II epitopes is predicted or validated to be capable of presentation by at least one HLA allele present in at least 5% of a population. In some aspects, each of the MHC class I and / or MHC class II epitopes is predicted or validated to be capable of presentation by at least one HLA allele, wherein each antigen / HLA pair has an antigen / HLA prevalence of at least 0.01% in a population. In some aspects, each of the MHC class I and / or MHC class II epitopes is predicted or validated to be capable of presentation by at least one HLA allele, wherein each antigen / HLA pair has an antigen / HLA prevalence of at least 0.1 % in a population.

[0067] In some aspects, the antigen cassette does not encode a non-therapeutic MHC class I or class II epitope nucleic acid sequence comprising a translated, wild-type nucleic acid sequence, wherein the non-therapeutic epitope is predicted to be displayed on an MHC allele of the subject. In some aspects, the non-therapeutic predicted MHC class I or class II epitope sequence is a junctional epitope sequence formed by adjacent sequences in the antigen cassette.

[0068] In some aspects, the prediction is based on presentation likelihoods generated by inputting sequences of the non-therapeutic epitopes into a presentation model. In some aspects, an order of the at least one HPV derived nucleic acid sequences in the antigen cassette is determined by a series of steps comprising: (a) generating a set of candidate antigen cassette sequences corresponding to different orders of the at least one HPV derived nucleic acid sequences; (b) determining, for each candidate antigen cassette sequence, a presentation scorebased on presentation of non-therapeutic epitopes in the candidate antigen cassette sequence; and (c) selecting a candidate cassette sequence associated with a presentation score below a predetermined threshold as the antigen cassette sequence for an antigen vaccine.

[0069] Also provided for herein is a pharmaceutical composition any of the compositions provided herein and a pharmaceutically acceptable carrier. In some aspects, the composition further comprises an adjuvant. In some aspects, the composition further comprises an immune modulator. In some aspects, the immune modulator is an anti-CTLA4 antibody or an antigenbinding fragment thereof, an anti-PD- 1 antibody or an antigen-binding fragment thereof, an anti- PD-L1 antibody or an antigen-binding fragment thereof, an anti-4- IBB antibody or an antigenbinding fragment thereof, or an anti-OX-40 antibody or an antigen-binding fragment thereof.

[0070] Also provided herein is an isolated nucleotide sequence or set of isolated nucleotide sequences comprising the antigen cassette of any of the compositions described herein and one or more elements obtained from the sequence of SEQ ID NO: 3 or SEQ ID NO:5, optionally wherein the one or more elements are selected from the group consisting of the sequences necessary for nonstructural protein-mediated amplification, the 26S promoter nucleotide sequence, the poly(A) sequence, and the nsPl-4 genes of the sequence set forth in SEQ ID NO:3 or SEQ ID NO: 5, and optionally wherein the nucleotide sequence is cDNA. In some aspects, the sequence or set of isolated nucleotide sequences comprises the antigen cassette of any of the above composition claims inserted at position 7544 of the sequence set forth in SEQ ID NO:6 or SEQ ID NO:7. In some aspects, the isolated sequence further comprises: a T7 or SP6 RNA polymerase promoter nucleotide sequence 5’ of the one or more elements obtained from the sequence of SEQ ID NO:3 or SEQ ID NO:5; and optionally, one or more restriction sites 3’ of the poly(A) sequence. In some aspects, the antigen cassette of any of the compositions provided herein is inserted at position 7563 of SEQ ID NO:8 or SEQ ID NO:9.

[0071] Also provided herein is an isolated nucleotide sequence or set of isolated nucleotide sequences comprising the antigen cassette of any of the compositions provided herein and one or more elements obtained from the sequence of SEQ ID NO:1 or SEQ ID NO:57 (“chAd68- Empty-E4deleted”), optionally wherein the one or more elements are selected from the group consisting of the chimpanzee adenovirus inverted terminal repeat (ITR), E1A, E1B, E2A, E2B, E3, E4, LI, L2, L3, L4, and L5 genes of the sequence set forth in SEQ ID NO:1, and optionally wherein the nucleotide sequence is cDNA. In some aspects, the sequence or set of isolated nucleotide sequences comprises the antigen cassette of any of the compositions provided herein inserted within the El deletion of the sequence set forth in SEQ ID NO:57 (“chAd68-Empty- E4deleted”). In some aspects, the isolated sequence further comprises: a T7 or SP6 RNA polymerase promoter nucleotide sequence 5’ of the one or more elements obtained from thesequence of SEQ ID NO:1 or SEQ ID NO:57 (“chAd68-Empty-E4deleted”); and optionally, one or more restriction sites 3 ’ of the poly( A) sequence.

[0072] Also provided herein is a vector or set of vectors comprising any of the isolated nucleotide sequences or set of isolated nucleotide sequences provided herein.

[0073] Also provided herein is an isolated cell comprising any of the isolated nucleotide sequences or set of isolated nucleotide sequences provided herein, optionally wherein the cell is a BHK-21, CHO, HEK293 or variants thereof, 911, HeLa, A549, LP-293, PER.C6, or AEl-2a cell.

[0074] Also provided herein is a kit comprising any of the compositions provided herein and instructions for use.

[0075] Also provided herein is a method for treating a HPV infection or preventing a HPV infection in a subject, the method comprising administering to the subject any of the compositions or pharmaceutical compositions provided herein. In some aspects, the HPV derived nucleic acid sequence encodes at least one immunogenic polypeptide corresponding to a polypeptide encoded by a HPV subtype the subject is infected with or at risk for infection by.

[0076] In some aspects, any of the methods described herein comprises a homologous prime / boost strategy. In some aspects, any of the methods described herein comprises a heterologous prime / boost strategy. In some aspects, the heterologous prime / boost strategy comprises an identical antigen cassette encoded by different vaccine platforms. In some aspects, the heterologous prime / boost strategy comprises different antigen cassettes encoded by the same vaccine platform. In some aspects, the heterologous prime / boost strategy comprises different antigen cassettes encoded by different vaccine platforms. In some aspects, the different antigen cassettes comprise a E6 / E7 fusion protein-encoding cassette and a separate T cell epitope encoding cassette. In some aspects, the different antigen cassettes comprise cassettes encoding distinct epitopes and / or antigens derived from different strains of HPV.

[0077] Also provided herein is a method for inducing an immune response in a subject, the method comprising administering to the subject any of the compositions or pharmaceutical compositions provided herein. In some aspects, the subject expresses at least one HLA allele predicted or known to present a MHC class I or MHC class II epitope encoded by the at least one HPV derived nucleic acid sequence. In some aspects, the subject expresses at least one HLA allele predicted or known to present a MHC class I epitope encoded by the at least one HPV derived nucleic acid sequence, and wherein the MHC class I epitope comprises at least one MHC class I epitope comprising a polypeptide sequence as set forth in Table A. In some aspects, the subject express at least one HLA allele predicted or known to present a MHC class II epitope encoded by the at least one HPV derived nucleic acid sequence, and wherein the MHCclass II epitope comprises at least one MHC class II epitope comprising a polypeptide sequence as set forth in Table B. In some aspects, the composition is administered intramuscularly (IM), intradermally (ID), subcutaneously (SC), or intravenously (IV). In some aspects, the composition is administered intramuscularly

[0078] In some aspects, the method further comprises administration of one or more immune modulators, optionally wherein the immune modulator is administered before, concurrently with, or after administration of the composition or pharmaceutical composition. In some aspects, the one or more immune modulators are selected from the group consisting of: an anti-CTLA4 antibody or an antigen-binding fragment thereof, an anti-PD- 1 antibody or an antigen-binding fragment thereof, an anti-PD-Ll antibody or an antigen-binding fragment thereof, an anti-4-lBB antibody or an antigen-binding fragment thereof, or an anti-OX-40 antibody or an antigenbinding fragment thereof. In some aspects, the immune modulator is administered intravenously (IV), intramuscularly (IM), intradermally (ID), or subcutaneously (SC). In some aspects, the subcutaneous administration is near the site of the composition or pharmaceutical composition administration or in close proximity to one or more vector or composition draining lymph nodes.

[0079] In some aspects, the method further comprises administering to the subject a second vaccine composition. In some aspects, the second vaccine composition is administered prior to the administration of the first composition or pharmaceutical composition. In some aspects, the second vaccine composition is administered subsequent to the administration of any of the compositions or pharmaceutical compositions provided herein. In some aspects, the second vaccine composition is the same as the first composition or pharmaceutical composition administered. In some aspects, the second vaccine composition is different from the first composition or pharmaceutical composition administered. In some aspects, the second vaccine composition comprises a chimpanzee adenovirus vector encoding at least one HPV derived nucleic acid sequence. In some aspects, the at least one HPV derived nucleic acid sequence encoded by the chimpanzee adenovirus vector is the same as the at least one HPV derived nucleic acid sequence of any of the compositions provided herein.

[0080] Also provided herein is a method of manufacturing the one or more vectors of any of the above composition claims, the method comprising: (a) obtaining a linearized DNA sequence comprising the backbone and the antigen cassette; (b) in vitro transcribing the linearized DNA sequence by addition of the linearized DNA sequence to an in vitro transcription reaction containing all the necessary components to transcribe the linearized DNA sequence into RNA, optionally further comprising in vitro addition of the m7g cap to the resulting RNA; and (c) isolating the one or more vectors from the in vitro transcription reaction. In some aspects, the linearized DNA sequence is generated by linearizing a DNA plasmid sequence or byamplification using PCR. In some aspects, the DNA plasmid sequence is generated using one of bacterial recombination or full genome DNA synthesis or full genome DNA synthesis with amplification of synthesized DNA in bacterial cells. In some aspects, isolating the one or more vectors from the in vitro transcription reaction involves one or more of phenol chloroform extraction, silica column based purification, or similar RNA purification methods.

[0081] Also provided herein is a method of manufacturing the composition of any of the above composition claims for delivery of the antigen expression system, the method comprising: (a) providing components for the nanoparticulate delivery vehicle; (b) providing the antigen expression system; and (c) providing conditions sufficient for the nanoparticulate delivery vehicle and the antigen expression system to produce the composition for delivery of the antigen expression system. In some aspects, the conditions are provided by microfluidic mixing.

[0082] Also provided herein is a method of manufacturing an adenovirus vector disclosed herein, the method comprising: obtaining a plasmid sequence comprising the at least one promoter sequence and the antigen cassette; transfecting the plasmid sequence into one or more host cells; and isolating the adenovirus vector from the one or more host cells.

[0083] In some aspects, isolating comprises: lysing the host cell to obtain a cell lysate comprising the adenovirus vector; and purifying the adenovirus vector from the cell lysate.

[0084] In some aspects, the plasmid sequence is generated using one of bacterial recombination or full genome DNA synthesis or full genome DNA synthesis with amplification of synthesized DNA in bacterial cells. In some aspects, the one or more host cells are at least one of CHO, HEK293 or variants thereof, 911, HeLa, A549, LP-293, PER.C6, and AEl-2a cells. In some aspects, purifying the adenovirus vector from the cell lysate involves one or more of chromatographic separation, centrifugation, virus precipitation, and filtration.

[0085] In some aspects, any of the above compositions further comprise a nanoparticulate delivery vehicle. The nanoparticulate delivery vehicle, in some aspects, may be a lipid nanoparticle (LNP). In some aspects, the LNP comprises ionizable amino lipids. In some aspects, the ionizable amino lipids comprise MC3-like (dilinoleylmethyl- 4- dimethylaminobutyrate ) molecules. In some aspects, the nanoparticulate delivery vehicle encapsulates the antigen expression system.

[0086] In some aspects, any of the above compositions further comprise a plurality of LNPs, wherein the LNPs comprise: the antigen expression system; a cationic lipid; a non-cationic lipid; and a conjugated lipid that inhibits aggregation of the LNPs, wherein at least about 95% of the LNPs in the plurality of LNPs either: have a non-lamellar morphology; or are electron-dense.

[0087] In some aspects, the non-cationic lipid is a mixture of (1) a phospholipid and (2) cholesterol or a cholesterol derivative.

[0088] In some aspects, the conjugated lipid that inhibits aggregation of the LNPs is a polyethyleneglycol (PEG)-lipid conjugate. In some aspects, the PEG-lipid conjugate is selected from the group consisting of: a PEG-diacylglycerol (PEG-DAG) conjugate, a PEG dialkyloxypropyl (PEG-DAA) conjugate, a PEG-phospholipid conjugate, a PEG-ceramide (PEG-Cer) conjugate, and a mixture thereof. In some aspects the PEG-DAA conjugate is a member selected from the group consisting of: a PEG-didecyloxypropyl (Cio) conjugate, a PEG- dilauryloxypropyl (C12) conjugate, a PEG-dimyristyloxypropyl (C14) conjugate, a PEG- dipalmityloxypropyl (Cie) conjugate, a PEG-distearyloxypropyl (Cis) conjugate, and a mixture thereof.

[0089] In some aspects, the antigen expression system is fully encapsulated in the LNPs.

[0090] In some aspects, the non-lamellar morphology of the LNPs comprises an inverse hexagonal (I I / / ) or cubic phase structure.

[0091] In some aspects, the cationic lipid comprises from about 10 mol % to about 50 mol % of the total lipid present in the LNPs. In some aspects, the cationic lipid comprises from about 20 mol % to about 50 mol % of the total lipid present in the LNPs. In some aspects, the cationic lipid comprises from about 20 mol % to about 40 mol % of the total lipid present in the LNPs.

[0092] In some aspects, the non-cationic lipid comprises from about 10 mol % to about 60 mol % of the total lipid present in the LNPs. In some aspects, the non-cationic lipid comprises from about 20 mol % to about 55 mol % of the total lipid present in the LNPs. In some aspects, the non-cationic lipid comprises from about 25 mol % to about 50 mol % of the total lipid present in the LNPs.

[0093] In some aspects, the conjugated lipid comprises from about 0.5 mol % to about 20 mol % of the total lipid present in the LNPs. In some aspects, the conjugated lipid comprises from about 2 mol % to about 20 mol % of the total lipid present in the LNPs. In some aspects, the conjugated lipid comprises from about 1.5 mol % to about 18 mol % of the total lipid present in the LNPs.

[0094] In some aspects, greater than 95% of the LNPs have a non-lamellar morphology. In some aspects, greater than 95% of the LNPs are electron dense.

[0095] In some aspects, any of the above compositions further comprise a plurality of LNPs, wherein the LNPs comprise: a cationic lipid comprising from 50 mol % to 65 mol % of the total lipid present in the LNPs; a conjugated lipid that inhibits aggregation of LNPs comprising from 0.5 mol % to 2 mol % of the total lipid present in the LNPs; and a non-cationic lipid comprising either: a mixture of a phospholipid and cholesterol or a derivative thereof, wherein the phospholipid comprises from 4 mol % to 10 mol % of the total lipid present in the LNPs and the cholesterol or derivative thereof comprises from 30 mol % to 40 mol % of the total lipid presentin the LNPs; a mixture of a phospholipid and cholesterol or a derivative thereof, wherein the phospholipid comprises from 3 mol % to 15 mol % of the total lipid present in the LNPs and the cholesterol or derivative thereof comprises from 30 mol % to 40 mol % of the total lipid present in the LNPs; or up to 49.5 mol % of the total lipid present in the LNPs and comprising a mixture of a phospholipid and cholesterol or a derivative thereof, wherein the cholesterol or derivative thereof comprises from 30 mol % to 40 mol % of the total lipid present in the LNPs.

[0096] In some aspects, any of the above compositions further comprise a plurality of LNPs, wherein the LNPs comprise: a cationic lipid comprising from 50 mol % to 85 mol % of the total lipid present in the LNPs; a conjugated lipid that inhibits aggregation of LNPs comprising from 0.5 mol % to 2 mol % of the total lipid present in the LNPs; and a non-cationic lipid comprising from 13 mol % to 49.5 mol % of the total lipid present in the LNPs.

[0097] In some aspects, the phospholipid comprises dipalmitoylphosphatidylcholine (DPPC), distearoylphosphatidylcholine (DSPC), or a mixture thereof.

[0098] In some aspects, the conjugated lipid comprises a polyethyleneglycol (PEG)-lipid conjugate. In some aspects, the PEG-lipid conjugate comprises a PEG-diacylglycerol (PEGDAG) conjugate, a PEG-dialkyloxypropyl (PEG-DAA) conjugate, or a mixture thereof. In some aspects, the PEG-DAA conjugate comprises a PEG-dimyristyloxypropyl (PEG-DMA) conjugate, a PEG-distearyloxypropyl (PEG-DSA) conjugate, or a mixture thereof. In some aspects, the PEG portion of the conjugate has an average molecular weight of about 2,000 daltons.

[0099] In some aspects, the conjugated lipid comprises from 1 mol % to 2 mol % of the total lipid present in the LNPs.

[0100] In some aspects, the LNP comprises a compound having a structure of:or a pharmaceutically acceptable salt, tautomer, prodrug or stereoisomer thereof, wherein:L1and L2are each independently -0(C=0)-, -(C=0)0-, -C(=0)-, -0-, -S(0)x-, -S-S-, -C(=0)S-, - SC(=0)-, - RaC(=0)-, -C(=0) Ra-, - RaC(=0) Ra-, -OC(=0) Ra-, - RaC(=0)0- or a direct bond; G1is Ci-C2alkylene, - (C=0)-, -0(C=0)-, -SC(=0)-, - RaC(=0)- or a direct bond: -C(=0)-, -(C=0)0-, - C(=0)S-, -C(=0) Ra- or a direct bond; G is Ci-Ce alkylene; Rais H or C1-C12 alkyl; RlaandRlbare, at each occurrence, independently either: (a) H or C1-C12 alkyl; or (b) Rlais H or Ci- C12 alkyl, and Rlbtogether with the carbon atom to which it is bound is taken together with an adjacent Rlband the carbon atom to which it is bound to form a carbon-carbon double bond; R2aand R2bare, at each occurrence, independently either: (a) H or C1-C12 alkyl; or (b) R2ais H or C1-C12 alkyl, and R2btogether with the carbon atom to which it is bound is taken together with an adjacent R2band the carbon atom to which it is bound to form a carbon-carbon double bond; R3aand R3bare, at each occurrence, independently either (a): H or C1-C12 alkyl; or (b) R3ais H or Ci-C 12 alkyl, and R3btogether with the carbon atom to which it is bound is taken together with an adjacent R and the carbon atom to which it is bound to form a carbon-carbon double bond; R4aand R4bare, at each occurrence, independently either: (a) H or Cl -Cl 2 alkyl; or (b) R4ais H or C1-C12 alkyl, and R4btogether with the carbon atom to which it is bound is taken together with an adjacent R4band the carbon atom to which it is bound to form a carboncarbon double bond; Rsand R6are each independently H or methyl; R7is C4-C20 alkyl; R8and R9are each independently Cl -Cl 2 alkyl; or R8and R9, together with the nitrogen atom to which they are attached, form a 5, 6 or 7-membered heterocyclic ring; a, b, c and d are each independently an integer from 1 to 24; and x is 0, 1 or 2.

[0101] In some aspects, the LNP comprises a compound having a structure of Formula II:II or a pharmaceutically acceptable salt, tautomer, prodrug or stereoisomer thereof, wherein: L1and L2are each independently -0(C=0)-, -(C=0)0- or a carbon-carbon double bond; Rlaand Rlbare, at each occurrence, independently either (a) H or C1-C12 alkyl, or (b) Rlais H or Ci- C12 alkyl, and Rlbtogether with the carbon atom to which it is bound is taken together with an adjacent Rlband the carbon atom to which it is bound to form a carbon-carbon double bond; R2aand R2bare, at each occurrence, independently either (a) H or C1-C12 alkyl, or (b) R2ais H or Ci-C 12 alkyl, and R2btogether with the carbon atom to which it is bound is taken together with an adjacent R2band the carbon atom to which it is bound to form a carbon-carbon double bond; R3aand R3bare, at each occurrence, independently either (a) H or C1-C12 alkyl, or (b) R3ais H or C1-C12 alkyl, and Rbtogether with the carbon atom to which it is bound is taken together with an adjacent R3band the carbon atom to which it is bound to form a carbon-carbon double bond; R4aand R4bare, at each occurrence, independently either (a) H or C1-C12 alkyl, or (b) R4ais H orC1-C12 alkyl, and R4btogether with the carbon atom to which it is bound is taken together with an adjacent R4band the carbon atom to which it is bound to form a carbon-carbon double bond; R5and R6are each independently methyl or cycloalkyl; R7is, at each occurrence, independently H or Ci-C 12 alkyl; R8and R9are each independently unsubstituted C1-C12 alkyl; or R8and R9, together with the nitrogen atom to which they are attached, form a 5, 6 or 7-membered heterocyclic ring comprising one nitrogen atom; a and d are each independently an integer from 0 to 24; b and c are each independently an integer from 1 to 24; and e is 1 or 2, provided that: at least one of Rla, R2a, R3aor R4ais C1-C12 alkyl, or at least one of L1or L2is -0(C=0)- or - (C=0)0-; and Rlaand Rlbare not isopropyl when a is 6 or n-butyl when a is 8.

[0102] In some aspects, any of the above compositions further comprise one or more excipients comprising a neutral lipid, a steroid, and a polymer conjugated lipid. In some aspects, the neutral lipid comprises at least one of l,2-Distearoyl-sn-glycero-3-phosphocholine (DSPC), l,2-Dipalmiloyl-.S7?-glycero-3-phosphocholine (DPPC), l,2-Dimyristoyl-5n-glycero-3- phosphocholine (DMPC), l-Palmitoyl-2-oleoyl-.yn-glycero-3 -phosphocholine (POPC), 1,2- dioleoyl-OT-gdycero-3-phosphocholine (DOPC), and l,2-Dioleoyl-.vn-glycero-3- phosphoethanolamine (DOPE). In some aspects, the neutral lipid is DSPC.

[0103] In some aspects, the molar ratio of the compound to the neutral lipid ranges from about 2:1 to about 8: 1.

[0104] In some aspects, the steroid is cholesterol. In some aspects, the molar ratio of the compound to cholesterol ranges from about 2:1 to 1:1.

[0105] In some aspects, the polymer conjugated lipid is a pegylated lipid. In some aspects, the molar ratio of the compound to the pegylated lipid ranges from about 100: 1 to about 25: 1. In some aspects, the pegylated lipid is PEG-DAG, a PEG polyethylene (PEG-PE), a PEG- succinoyl-diacylglycerol (PEG-S-DAG), PEG-cer or a PEG dialkyoxypropylcarbamate. In some aspects, the pegylated lipid has the following structure III:III or a pharmaceutically acceptable salt, tautomer or stereoisomer thereof, wherein: R10and R11are each independently a straight or branched, saturated or unsaturated alkyl chain containing from 10 to 30 carbon atoms, wherein the alkyl chain is optionally interrupted by one or more ester bonds; and z has a mean value ranging from 30 to 60. In some aspects, R10and R11are each independently straight, saturated alkyl chains having 12 to 16 carbon atoms. In some aspects, the average z is about 45.start here

[0106] In some aspects, the LNP self- ssembles into non-bilayer structures when mixed with polyanionic nucleic acid. In some aspects, the non-bilayer structures have a diameter between 60nm and 120nm. In some aspects, the non-bilayer structures have a diameter of about 70nm, about 80nm, about 90nm, or about lOOnm. In some aspects, wherein the nanoparticulate delivery vehicle has a diameter of about lOOnm.

[0107] Also provided for herein is a vector or set of vectors comprising any of the nucleotide sequence described herein. Also disclosed herein is a vector comprising an isolated nucleotide sequence disclosed herein.

[0108] Also provided for herein is an isolated cell comprising any of the nucleotide sequences or set of isolated nucleotide sequences described herein, optionally wherein the cell is a BHK-21, CHO, HEK293 or variants thereof, 911, HeLa, A549, LP-293, PER.C6, or AEl-2a cell.

[0109] Also provided for herein is a kit comprising any of the compositions described herein and instructions for use. Also disclosed herein is a kit comprising a vector or a composition disclosed herein and instructions for use.

[0110] Also provided for herein is a method for treating a subject having one or more of cervical cancer, anal cancer, oropharyngeal cancer, oral cancer, penile cancer, vaginal cancer, and / or vulvar cancer, the method comprising administering to the subject any of the compositions or any of the pharmaceutical compositions described herein.

[0111] Also provided for herein is a method for treating a subject infected with or at risk for infection by HPV, the method comprising administering to the subject any of the compositions or any of the pharmaceutical compositions described herein.

[0112] Also provided for herein is a method for stimulating an immune response in a subject, the method comprising administering to the subject any of the compositions or any of the pharmaceutical compositions described herein.

[0113] Also disclosed herein is a method for treating a subject, the method comprising administering to the subject a vector disclosed herein or a pharmaceutical composition disclosed herein.

[0114] Also disclosed herein is a method of manufacturing the one or more vectors of any of the above compositions.

[0115] Also disclosed herein is a method of manufacturing any of the compositions disclosed herein.BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

[0116] These and other features, aspects, and advantages of the present invention will become better understood with regard to the following description, and accompanying drawings, where:

[0117] Figures (FIGS.) 1A-C present architectures of samRNA vaccine constructs for individual HPV strains based on either double promoter systems (FIG. 1A and FIG. IB) or an internal ribosomal skip site (FIG. 1C) to facilitate the combination of E6E7 and T Cell Epitope Cassette (TCE) inclusion on a single nucleic acid backbone. Filled black boxes indicate an IgG expression leader sequence and unfilled white boxes indicate an internal furin cleavage site.

[0118] FIG. 2 shows immunogenicity results as assessed by ELISpot in C57 / B16 mice for antigens HPV16 and HPV 18 on individual samRNA vaccine constructs according to architectures found in FIG. 1A and FIG. IB, respectively.

[0119] FIGS. 3A-B present architectures of ChAd vaccine constructs for individual HPV strains based on an internal ribosomal skip site with E6E7 in either the first (FIG. 3A) or second (FIG. 3B) position to facilitate the combination of E6E7 and T Cell Epitope Cassette (TCE) inclusion on a single nucleic acid backbone. Filled black boxes indicate an IgG expression leader sequence and unfilled white boxes indicate an internal furin cleavage site.

[0120] FIG. 4 shows immunogenicity results as assessed by ELISpot in C57 / B16 mice for antigens HP VI 6 or HPV 18 E6E7 and T Cell Epitope cassettes on single ChAd vectors utilizing architectures from FIG. 3A.

[0121] FIGS. 5A-C present architectures for inclusion of HPV16 and HPV18 E6E7 and T Cell Epitope cassettes on single samRNA vectors. These architectures utilize a dual promoter system to either include single E6E7 and TCE’ s with internal ribosomal skip sites on each promoter (FIG. 4A) or a fusion of the two TCE’s expressed on either the first (FIG. 4B) or second (FIG. 4C) promoter. Filled black boxes indicate an IgG expression leader sequence and unfilled white boxes indicate an internal furin cleavage site.

[0122] FIG. 6 shows immunogenicity results as assessed by ELISpot in C57 / B16 mice for antigens HPV16 or HPV 18 E6E7 and T Cell Epitope for either the multi-strain samRNA vaccine construct for HPV 16 and HPV18 (format architecture of FIG. 5 A) or as a combination of separate single-strain samRNA vaccine constructs for each of HPV16 and HPV18 (Blended). Note: Data compiled from separate experiments.

[0123] FIGS. 7A-B present architectures for inclusion of HPV 16 & HPV 18 E6E7 and T Cell Epitope cassettes on single ChAd vectors. These architectures utilize fused E6E7 proteins from both HPV16 & HPV18 as well as fused T Cell Epitope cassettes from both viruses, with the fused E6E7’s as the first (FIG. 7A) or second (FIG. 7B) component of an internal ribosomalskip site containing sequence. Filled black boxes indicate an IgG expression leader sequence and unfdled white boxes indicate an internal furin cleavage site.

[0124] FIG. 8 shows immunogenicity results as assessed by ELISpot in C57 / B16 mice for antigens HP VI 6 or HPV 18 E6E7 and T Cell Epitope for either a multi-strain ChAd vaccine construct for HPV 16 and HPV 18 (format architecture of FIG. 7A) or as a combination of separate single-strain ChAd vaccine constructs for each of HPV16 and HPV18 (Blended).

[0125] FIG. 9 shows immunogenicity results as assessed by ELISpot in C57 / B16 mice for the indicated prime / boost experiments: Mice primed with either samRNA (left), or ChAd (2ndfrom left) vectors encoding antigens for both HPV 16 and HPV 18 were subsequently boosted at d28 with either samRNA (middle, right) at day 28 or ChAd (2ndfrom right) at 4 months.

[0126] FIG. 10 shows immunogenicity results as assessed by ELISpot against included E6 / E7 and T Cell Epitope antigens in C57 / B16 and FVB mice for samRNA (left) and ChAd (right) based blended vaccines encoding the antigens for HPV35 or HPV45.

[0127] FIG. 11 shows immunogenicity results as assessed by ELISpot against included E6 / E7 and T Cell Epitope antigens in C57 / B16 and FVB mice for samRNA (left) and ChAd (right) based blended vaccines encoding the antigens for HPV31 or HPV33.

[0128] FIG. 12 shows immunogenicity results as assessed by ELISpot against included E6 / E7 and T Cell Epitope antigens in C57 / B16 and FVB mice for samRNA (left) and ChAd (right) based blended vaccines encoding the antigens for HPV52 or HPV58.

[0129] FIG. 13 shows a Phase lb study design in females age 25-55 who are HPV 16 / 18 positive with CIN1.

[0130] FIG. 14 shows a Phase lb study design in females age 25-55 who are HPV 16 / 18 positive.

[0131] FIG. 15A shows an illustration of an algorithm performing several ranking iterations used to construct a concatenated T-cell epitope cassette.

[0132] FIG. 15A shows an illustration of calculating coverage provided by a given epitope by the frequencies of haplotypes in a reference population that cover at least one allele associated with the epitope used to construct a concatenated T-cell epitope cassette.

[0133] FIG. 16 shows the performance of performance of epitope prediction and inclusion in an exemplary HPV16 TCE cassette design, as assessed using mass-spectrometry verification of presentation of predicted epitopes in HLA monoallelic lines.

[0134] FIG. 17 shows performance of population coverage for an exemplary HPV 16 TCE cassette design.DETAILED DESCRIPTIONI. Definitions

[0135] In general, terms used in the claims and the specification are intended to be construed as having the plain meaning understood by a person of ordinary skill in the art. Certain terms are defined below to provide additional clarity. In case of conflict between the plain meaning and the provided definitions, the provided definitions are to be used.

[0136] As used herein the term “antigen” is a substance that stimulates an immune response. An antigen can be a neoantigen. An antigen can be a “shared antigen” that is an antigen found among a specific population, e.g., a specific population of HPV patients with or at risk of infection for an infectious disease.

[0137] As used herein the term “antigen-based vaccine” is a vaccine composition based on one or more antigens, e.g., a plurality of antigens. The vaccines can be nucleotide-based (e.g., virally based, RNA based, or DNA based), protein-based (e.g., peptide based), or a combination thereof.

[0138] As used herein the term “candidate antigen” is a mutation or other aberration giving rise to a sequence that may represent an antigen.

[0139] As used herein the term “coding region” is the portion(s) of a gene that encode protein.

[0140] As used herein the term “coding mutation” is a mutation occurring in a coding region.

[0141] As used herein the term “ORF” means open reading frame.

[0142] As used herein the term “missense mutation” is a mutation causing a substitution from one amino acid to another.

[0143] As used herein the term “nonsense mutation” is a mutation causing a substitution from an amino acid to a stop codon or causing removal of a canonical start codon.

[0144] As used herein the term “frameshift mutation” is a mutation causing a change in the frame of the protein.

[0145] As used herein the term “indel” is an insertion or deletion of one or more nucleic acids.

[0146] As used herein, the term percent "identity," in the context of two or more nucleic acid or polypeptide sequences, refer to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill)or by visual inspection. Depending on the application, the percent "identity" can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.

[0147] For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters. Alternatively, sequence similarity or dissimilarity can be established by the combined presence or absence of particular nucleotides, or, for translated sequences, amino acids at selected sequence positions (e.g., sequence motifs).

[0148] Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTF1T, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally Ausubel et al., infra).

[0149] One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.

[0150] As used herein the term “non-stop or read-through” is a mutation causing the removal of the natural stop codon.

[0151] As used herein the term “epitope” is the specific portion of an antigen typically bound by an antibody or T cell receptor.

[0152] As used herein the term “immunogenic” is the ability to stimulate an immune response, e.g., via T cells, B cells, or both.

[0153] As used herein the term “HLA binding affinity” “MHC binding affinity” means affinity of binding between a specific antigen and a specific MHC allele.

[0154] As used herein the term “bait” is a nucleic acid probe used to enrich a specific sequence of DNA or RNA from a sample.

[0155] As used herein the term “variant” is a difference between a subject’ s nucleic acids and the reference human genome used as a control.

[0156] As used herein the term “variant call” is an algorithmic determination of the presence of a variant, typically from sequencing.

[0157] As used herein the term “polymorphism” is a germline variant, i.e., a variant found in all DNA-bearing cells of an individual.

[0158] As used herein the term “somatic variant” is a variant arising in non-germline cells of an individual.

[0159] As used herein the term “allele” is a version of a gene or a version of a genetic sequence or a version of a protein.

[0160] As used herein the term “HLA type” is the complement of HLA gene alleles.

[0161] As used herein the term “nonsense-mediated decay” or “NMD” is a degradation of an mRNA by a cell due to a premature stop codon.

[0162] As used herein the term “exome” is a subset of the genome that codes for proteins. An exome can be the collective exons of a genome.

[0163] As used herein the term “logistic regression” is a regression model for binary data from statistics where the logit of the probability that the dependent variable is equal to one is modeled as a linear function of the dependent variables.

[0164] As used herein the term “neural network” is a machine learning model for classification or regression consisting of multiple layers of linear transformations followed by element-wise nonlinearities typically trained via stochastic gradient descent and back- propagation.

[0165] As used herein the term “proteome” is the set of all proteins expressed and / or translated by a cell, group of cells, or individual.

[0166] As used herein the term “peptidome” is the set of all peptides presented by MHC-I or MHC-II on the cell surface. The peptidome may refer to a property of a cell or a collection of cells (e.g., the infectious disease peptidome, meaning the union of the peptidomes of all cells that are infected by the infectious disease).

[0167] As used herein the term “ELIS POT” means Enzyme-linked immunosorbent spot assay - which is a common method for monitoring immune responses in humans and animals.

[0168] As used herein the term “dextramers” is a dextran-based peptide-MHC multimers used for antigen-specific T-cell staining in flow cytometry.

[0169] As used herein the term “tolerance or immune tolerance” is a state of immune nonresponsiveness to one or more antigens, e.g. self-antigens.

[0170] As used herein the term “central tolerance” is a tolerance affected in the thymus, either by deleting self-reactive T-cell clones or by promoting self-reactive T-cell clones to differentiate into immunosuppressive regulatory T-cells (Tregs).

[0171] As used herein the term “peripheral tolerance” is a tolerance affected in the periphery by downregulating or anergizing self-reactive T-cells that survive central tolerance or promoting these T cells to differentiate into Tregs.

[0172] The term “sample” can include a single cell or multiple cells or fragments of cells or an aliquot of body fluid, taken from a subject, by means including venipuncture, excretion, ejaculation, massage, biopsy, needle aspirate, lavage sample, scraping, surgical incision, or intervention or other means known in the art.

[0173] The term “subject” encompasses a cell, tissue, or organism, human or non-human, whether in vivo, ex vivo, or in vitro, male or female. The term subject is inclusive of mammals including humans.

[0174] The term “mammal” encompasses both humans and non-humans and includes but is not limited to humans, non-human primates, canines, felines, murines, bovines, equines, and porcines.

[0175] The term “clinical factor” refers to a measure of a condition of a subject, e.g., disease activity or severity. “Clinical factor” encompasses all markers of a subject’s health status, including non-sample markers, and / or other characteristics of a subject, such as, without limitation, age and gender. A clinical factor can be a score, a value, or a set of values that can be obtained from evaluation of a sample (or population of samples) from a subject or a subject under a determined condition. A clinical factor can also be predicted by markers and / or other parameters such as gene expression surrogates. Clinical factors can include infection type (e.g., human papillomavirus species), infection sub-type (e.g., HPV strain), and medical history.

[0176] The term “antigen-encoding nucleic acid sequences derived from an infection” refers to nucleic acid sequences obtained from infected cells or an infectious disease organism, e.g. via RT-PCR; or sequence data obtained by sequencing the infected cell or infectious disease organism and then synthesizing the nucleic acid sequences using the sequencing data, e.g., via various synthetic or PCR-based methods known in the art. Derived sequences can include nucleic acid sequence variants, such as sequence-optimized nucleic acid sequence variants (e.g., codon-optimized and / or otherwise optimized for expression), that encode the same polypeptide sequence as the corresponding native infectious disease organism nucleic acid sequence.Derived sequences can include nucleic acid sequence variants that encode a modified infectious disease organism polypeptide sequence having one or more (e.g., 1, 2, 3, 4, or 5) mutations relative to a native infectious disease organism polypeptide sequence. For example, a modified polypeptide sequence can have one or more missense mutations relative to the native polypeptide sequence of an infectious disease organism protein.

[0177] The term “HPV nucleic acid sequence encoding an immunogenic polypeptide” refers to nucleic acid sequences obtained from a HPV virus, e.g. via RT-PCR; or sequence data obtained by sequencing a HPV virus or a HPV virus infected cell, and then synthesizing the nucleic acid sequences using the sequencing data, e.g., via various synthetic or PCR-based methods known in the art. Derived sequences can include nucleic acid sequence variants, such as sequence-optimized nucleic acid sequence variants (e.g., codon-optimized and / or otherwise optimized for expression), that encode the same polypeptide sequence as the corresponding native HPV nucleic acid sequence. Derived sequences can include nucleic acid sequence variants that encode a modified HPV polypeptide sequence having one or more (e.g., 1, 2, 3, 4, or 5) mutations relative to a native HPV polypeptide sequence. For example, a modified HPV polypeptide sequence can have one or more mutations, such as one or more deletions that render proteins inactive.

[0178] The term “alphavirus” refers to members of the family Togaviridae, and are positivesense single-stranded RNA viruses. Alphaviruses are typically classified as either Old World, such as Sindbis, Ross River, Mayaro, Chikungunya, and Semliki Forest viruses, or New World, such as eastern equine encephalitis, Aura, Fort Morgan, or Venezuelan equine encephalitis and its derivative strain TC-83. Alphaviruses are typically self-replicating RNA viruses.

[0179] The term “alphavirus backbone” refers to minimal sequence(s) of an alphavirus that allow for self-replication of the viral genome. Minimal sequences can include conserved sequences for nonstructural protein- mediated amplification, a nonstructural protein 1 (nsPl) gene, a nsP2 gene, a nsP3 gene, a nsP4 gene, and a polyA sequence, as well as sequences for expression of subgenomic viral RNA including a subgenomic promoter (e.g., a 26S promoter element).

[0180] The term “sequences for nonstructural protein-mediated amplification” includes alphavirus conserved sequence elements (CSE) well known to those in the art. CSEs include, but are not limited to, an alphavirus 5’ UTR, a 51-nt CSE, a 24-nt CSE, a subgenomic promoter sequence (e.g. , a 26S subgenomic promoter sequence), a 19-nt CSE, and an alphavirus 3’ UTR.

[0181] The term “RNA polymerase” includes polymerases that catalyze the production of RNA polynucleotides from a DNA template. RNA polymerases include, but are not limited to, bacteriophage derived polymerases including T3, T7, and SP6.

[0182] The term “lipid” includes hydrophobic and / or amphiphilic molecules. Lipids can be cationic, anionic, or neutral. Lipids can be synthetic or naturally derived, and in some instances biodegradable. Lipids can include cholesterol, phospholipids, lipid conjugates including, but not limited to, polyethyleneglycol (PEG) conjugates (PEGylated lipids), waxes, oils, glycerides,fats, and fat-soluble vitamins. Lipids can also include dilinoleylmethyl- 4- dimethylaminobutyrate (MC3) and MC3-like molecules.

[0183] The term “lipid nanoparticle” or “LNP” includes vesicle like structures formed using a lipid containing membrane surrounding an aqueous interior, also referred to as liposomes. Lipid nanoparticles includes lipid-based compositions with a solid lipid core stabilized by a surfactant. The core lipids can be fatty acids, acylglycerols, waxes, and mixtures of these surfactants. Biological membrane lipids such as phospholipids, sphingomyelins, bile salts (sodium taurocholate), and sterols (cholesterol) can be utilized as stabilizers. Lipid nanoparticles can be formed using defined ratios of different lipid molecules, including, but not limited to, defined ratios of one or more cationic, anionic, or neutral lipids. Lipid nanoparticles can encapsulate molecules within an outer-membrane shell and subsequently can be contacted with target cells to deliver the encapsulated molecules to the host cell cytosol. Lipid nanoparticles can be modified or functionalized with non- lipid molecules, including on their surface. Lipid nanoparticles can be single-layered (unilamellar) or multi-layered (multilamellar). Lipid nanoparticles can be complexed with nucleic acid. Unilamellar lipid nanoparticles can be complexed with nucleic acid, wherein the nucleic acid is in the aqueous interior. Multilamellar lipid nanoparticles can be complexed with nucleic acid, wherein the nucleic acid is in the aqueous interior, or to form or sandwiched between

[0184] Abbreviations: MHC: major histocompatibility complex; HLA: human leukocyte antigen, or the human MHC gene locus; NGS: next-generation sequencing; PPV: positive predictive value; TSNA: tumor-specific neoantigen; FFPE: formalin-fixed, paraffin-embedded; NMD: nonsense-mediated decay; NSCLC: non-small-cell lung cancer; DC: dendritic cell.

[0185] It should be noted that, as used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.

[0186] Unless specifically stated or otherwise apparent from context, as used herein the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.

[0187] Any terms not directly defined herein shall be understood to have the meanings commonly associated with them as understood within the art of the invention. Certain terms are discussed herein to provide additional guidance to the practitioner in describing the compositions, devices, methods and the like of aspects of the invention, and how to make or use them. It will be appreciated that the same thing may be said in more than one way.Consequently, alternative language and synonyms may be used for any one or more of the terms discussed herein. No significance is to be placed upon whether or not a term is elaborated or discussed herein. Some synonyms or substitutable methods, materials and the like are provided. Recital of one or a few synonyms or equivalents does not exclude use of other synonyms or equivalents, unless it is explicitly stated. Use of examples, including examples of terms, is for illustrative purposes only and does not limit the scope and meaning of the aspects of the invention herein.

[0188] All references, issued patents and patent applications cited within the body of the specification are hereby incorporated by reference in their entirety, for all purposes.IL Antigen Identification

[0189] Research methods for NGS analysis of tumor and normal exome and transcriptomes have been described and applied in the antigen identification space.6,14,15Certain optimizations for greater sensitivity and specificity for antigen identification in the clinical setting can be considered. These optimizations can be grouped into two areas, those related to laboratory processes and those related to the NGS data analysis. The research methods described can also be applied to identification of antigens in other settings, such as identification of identifying antigens from an infectious disease organism (e.g., HPV), an infection in a subject, or an infected cell of a subject. Examples of optimizations are known to those skilled in the art, for example the methods described in more detail in US Pat No. 10,055,540, US Application Pub. No. US20200010849A1, international patent application publications WO / 2018 / 195357 and WO / 2018 / 208856, US App. No. 16 / 606,577, and international patent application PCT / US2020 / 021508, each herein incorporated by reference, in their entirety, for all purposes.

[0190] Methods for identifying antigens (e.g., antigens derived from an infectious disease organism) include identifying antigens that are likely to be presented on a cell surface e.g., presented by MHC on an infected cell or an immune cell, including professional antigen presenting cells such as dendritic cells), and / or are likely to be immunogenic. As an example, one such method may comprise the steps of: obtaining at least one of exome, transcriptome or whole genome nucleotide sequencing and / or expression data from an infected cell or an infectious disease organism (e.g., HPV), wherein the nucleotide sequencing data and / or expression data is used to obtain data representing peptide sequences of each of a set of antigens (e.g. , antigens derived from the infectious disease organism); inputting the peptide sequence of each antigen into one or more presentation models to generate a set of numerical likelihoods that each of the antigens is presented by one or more MHC alleles on a cell surface, such as an infected cell of the subject, the set of numerical likelihoods having been identified at least basedon received mass spectrometry data; and selecting a subset of the set of antigens based on the set of numerical likelihoods to generate a set of selected antigens.IV. Antigens

[0191] Antigens can include nucleotides or polypeptides. For example, an antigen can be an RNA sequence that encodes for a polypeptide sequence. Antigens useful in vaccines can therefore include nucleotide sequences or polypeptide sequences.

[0192] Disclosed herein are peptides and nucleic acid sequences encoding immunogenic peptides derived from any polypeptide associated with HPV, a HPV infection in a subject, or a HPV infected cell of a subject. Antigens can be derived from nucleotide sequences or polypeptide sequences of a HPV virus. Immunogenic polypeptide sequences of HPV include, but are not limited to, MHC class I epitopes shown in Tables C1-C9, which can include polypeptides sequences in Tables C1-C9 that contain one or more predicted HPV MHC class I epitopes and / or one or more HPV MHC class I epitopes validated in the literature. Immunogenic polypeptide sequences of HPV include HPV MHC class I epitopes validated by mass- spectrometry to be presented by one or more HL A alleles, including one or more HL A alleles of a target vaccine demographic. Immunogenic polypeptide sequences of HPV include, but are not limited to, multiple MHC class I epitopes (or multiple HPV polypeptides that contain one or more predicted HPV MHC class I epitopes and / or one or more HPV MHC class I epitopes) that are concatenated into a single polypeptide, e.g. in a cassette. Illustrative non-limitating examples of concatenated HPV MHC class I epitopes are shown in Table D. HPV MHC class I epitopes can include epitopes from any protein encoded by HPV, including but not limited to any early (E) region encoding proteins E1-E7 or late (L) region encoding structural proteins L1-L2. HPV MHC class I epitopes can include epitopes from one or more of HPV proteins E1-E7. HPV MHC class I epitopes can include epitopes only from one or more of HPV proteins E1-E7. HPV MHC class I epitopes can include epitopes from one or more of HPV proteins El, E2, E5, E6, and E7. HPV MHC class 1 epitopes can include epitopes from at least each of HPV proteins El, E2, E5, E6, and E7. HPV MHC class I epitopes can include epitopes from at least each of and limited to HPV proteins El, E2, E5, E6, and E7.

[0193] Immunogenic polypeptide sequences of HPV include, but are not limited to, HPV proteins (e.g., full-length HPV proteins), including HPV proteins that contain one or more predicted HPV MHC class I epitopes and / or one or more HPV MHC class I epitopes validated in the literature. Full-length HPV proteins can include any early (E) region encoding proteins E1-E7 or late (L) region encoding structural proteins L1-L2. Full-length HPV proteins can include one or more of any early (E) region encoding proteins E1-E7. Full-length HPV proteinscan include only one or more of early (E) region encoding proteins E1-E7. Full-length HPV proteins can include E6. Full-length HPV proteins can include E7. Full-length HPV proteins can include E6 and E7. Full-length HPV proteins can include only E6 and E7. Full-length HPV proteins can be modified from their naturally occurring sequences, for example as shown in the non-limiing illustrative modifications shown in Table B. Modifications can include, but are not limited to, deletions or other substitutions that inactivate a protein or otherwise make a protein non-functional or reduce the function of a protein, e.g., to improve the safety of a vaccine. HPV protein modifications can include one or more of the modifications shown in Table B. HPV protein modifications can include each of the modifications shown in Table B for a respective HPV protein.

[0194] Full-length HPV proteins can include a fusion protein (e.g., two or more proteins modified to be co-expressed as a single polypeptide, including through use of a peptide linker) of one or more full-length HPV proteins. A HPV fusion protein can include one or more full- length HPV proteins E1-E7. In an illustrative non-limiting example, a HPV fusion protein can include HPV proteins E6 and E7 modified to be co-expressed as a single polypeptide, such as in the illustrative examples shown in Table A.

[0195] Immunogenic polypeptide sequences can include full-length HPV proteins in combination with multiple MHC class I epitopes concatenated into a single polypeptide. In an illustrative non-limiting example, immunogenic polypeptide sequences can include full-length HPV proteins E6 and E7 (e.g., a HPV fusion protein can including HPV proteins E6 and E7 modified to be co-expressed as a single polypeptide, such as in the illustrative examples shown in Table A) in combination with multiple MHC class I epitopes concatenated into a single polypeptide, such as one or more of the polypeptides sequences in Tables C1-C9 or each of the polypeptides sequences shown in Tables C1-C9 (e.g., any one of the polypeptides sequences shown in Table D). Where immunogenic polypeptide sequences include full-length HPV proteins in combination with multiple MHC class I epitopes concatenated into a single polypeptide, the selection of the multiple MHC class I epitopes concatenated into the single polypeptide can exclude those peptides encoded in the full-length HPV proteins. In an illustrative non-limiting example, when immunogenic polypeptide sequences include both of full-length HPV E6 and E7 proteins, multiple MHC class I epitopes concatenated into a single polypeptide can include only immunogenic polypeptide sequences derived from HPV proteins other than E6 and E7.

[0196] Vaccines can be designed to encode at least one HPV-derived immunogenic polypeptide corresponding to a polypeptide encoded by a HPV strain the subject is infected with or at risk for infection by, such as for use in prophylactic vaccines for a specific demographic orgeographic population at risk for infection by the specific HPV strain. Specific HPV strains include, but are not limited to, HPV strains HPV16, HPV18, HPV31, HPV33, HPV35, HPV45, HPV52, and HPV58. Specific HPV strains for a specific demographic or geographic population can include HPV strains generally found in women from low middle income countries (LMIC) with persistent HPV infection, such as HPV31, HPV33, HPV35, HPV45, HPV52, and HPV58.

[0197] Vaccines can be designed to encode at least one HPV-derived immunogenic polypeptide corresponding to a polypeptide encoded by at least two or more HPV strains. Vaccines can be designed to encode at least one HPV-derived immunogenic polypeptide corresponding to two or more HPV strains selected from HPV16, HPV18, HPV31, HPV33, HPV35, HPV45, HPV52, and HPV58. Vaccines can be designed to encode at least one HPV- derived immunogenic polypeptide derived from each of HPV16 and HPV18. Vaccines can be designed to encode at least one HPV-derived immunogenic polypeptide derived from each of HPV16, HPV18, HPV35, and HPV45. Vaccines can be designed to encode at least one HPV- derived immunogenic polypeptide derived from each of HPV35 and HPV45. Vaccines can be designed to encode at least one HPV-derived immunogenic polypeptide derived from at least each of HPV35 and HPV45. Vaccines can be designed to encode at least one HPV-derived immunogenic polypeptide derived from each of HPV31, HPV33, HPV35, HPV45, HPV52, and HPV58. Vaccines can be designed to encode at least one HPV-derived immunogenic polypeptide derived from at least each of HPV31, HPV33, HPV35, HPV45, HPV52, and HPV58.

[0198] Vaccine strategies can also include use of multiple separate vaccines used in combination to separately express multiple HPV-derived immunogenic polypeptides. Such a strategy can be called a “blended” vaccination strategy. Vaccine strategies can also include use of multiple separate vaccines used in combination to separately express multiple HPV-derived immunogenic polypeptides, where the separately expressed HPV-derived immunogenic polypeptides are derived from distinct HPV strains, such as in the non-limting illustrative example of a first vaccine that encodes HPV-derived immunogenic polypeptides derived from HPV 16 and a second vaccine that encodes HPV-derived immunogenic polypeptides derived from HPV18. Vaccine strategies can also include use of multiple separate vaccines used in combination to separately express multiple HPV-derived immunogenic polypeptides, where the separately expressed HPV-derived immunogenic polypeptides are derived from distinct HPV proteins, such as in the non-limting illustrative example of a first vaccine that encodes HPV- derived immunogenic polypeptides derived from HPV E6 and / or E7 and a second vaccine that encodes HPV-derived immunogenic polypeptides derived from El, E2, and E5 (e.g., concatenated into a single polypeptide, such as in a cassette). Vaccine strategies can also includeuse of multiple separate vaccines used in combination to separately express multiple HPV- derived immunogenic polypeptides, where the separately expressed HPV-derived immunogenic polypeptides are derived from distinct HPV proteins that include distinct proteins from multiple HPV strains, such as in the non-limting illustrative example of a first vaccine that encodes HPV- derived immunogenic polypeptides derived from HPV E6 and / or E7 from both HPV 16 and HPV 18 and a second vaccine that encodes HPV-derived immunogenic polypeptides derived from El, E2, and E5 from both HPV16 and HPV18 (e.g., concatenated into a single polypeptide for HPV 16 and concatenated into a single polypeptide for HPV 18).

[0199] Vaccines can be designed to encode at least one immunogenic polypeptide corresponding to a polypeptide encoded by HPV and at least one immunogenic polypeptide corresponding to a polypeptide encoded by a an infectious disease other than HPV, e.g., polypeptide sequences of an infectious disease organism that can include, but are not limited to, a pathogen-derived peptide, a virus-derived peptide, a bacteria-derived peptide, a fungus -derived peptide, and / or a parasite-derived peptide. Infectious disease organism include, but are not limited to, Severe acute respiratory syndrome-related coronavirus (SARS), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Ebola, HIV, Hepatitis B virus (HBV), influenza, Hepatitis C virus (HCV), Cytomegalovirus (CMV), Chikungunya virus, Respiratory syncytial virus (RSV), Dengue virus, a orthymyxoviridae family virus, and tuberculosis.

[0200] Antigens can be selected that are predicted to be presented on the cell surface of a cell, such as an infected cell or an immune cell, including professional antigen presenting cells such as dendritic cells. Antigens can be selected that are predicted to be immunogenic. Exemplary antigens predicted using the methods described herein to be presented on the cell surface by an MHC include predicted and / or previously validated MHC class I epitopes shown in Tables C1-C9..

[0201] Antigens can be selected that have been validated to be presented by a specific HLA and / or stimulate an immune response, such as previously reported / validated in the literature (for example, as in Nelde et al. [Nature Immunology volume 22, pages 74-85 2021], Tarke et al. 2021, or Schelien et al. [bioRxiv 2020.08.13.249433]). The magnitude of stimulation of an immune response can be used to guide epitope / antigen selection, such as to select epitopes that stimulate as robust an immune response as possible, including when cassettes have a size constraint. As an illustrative non-limiting example of magnitude based-selection, the following can be used (1) An individual’s magnitude is the sum of all epitope magnitudes across their respective diplotype alleles; (2) Each epitopes magnitude = (magnitude of response) x (Frequency of positive response / 100),; (3) exclusion of epitopes other than those from starting proteins that span mutations with >5% frequency, optionally with mutations allowed in flankingregions; and / or (4) cassette order determined to minimize unintended junction epitopes across adjacent frames, as well as minimize consecutive frames in the same protein to reduce chance of functional protein fragments, as described herein.

[0202] A cassette can be constructed to encode one or more validated epitopes and / or at least 4, 5, 6, or 7 predicted epitopes, wherein at least 85%, 90%, or 95% of a population carries at least one HLA validated to present at least one of the one or more validated epitopes and / or at least one HLA predicted to present each of the at least 4, 5, 6, or 7 predicted epitopes. A cassette can be constructed to encode one or more validated epitopes and at least 4, 5, 6, or 7 predicted epitopes, wherein at least 85%, 90%, or 95% of a population carries at least one HLA validated to present at least one of the one or more validated epitopes or at least one HLA predicted to present each of the at least 4, 5, 6, or 7 predicted epitopes.

[0203] One or more polypeptides encoded by an antigen nucleotide sequence can comprise at least one of: a binding affinity with MHC with an IC50 value of less than lOOOnM, for MHC Class I peptides a length of 8-15, 8, 9, 10, 11, 12, 13, 14, or 15 amino acids, presence of sequence motifs within or near the peptide promoting proteasome cleavage, and presence or sequence motifs promoting TAP transport. For MHC Class II peptides a length 6-30, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 amino acids, presence of sequence motifs within or near the peptide promoting cleavage by extracellular or lysosomal proteases (e.g., cathepsins) or HLA-DM catalyzed HLA binding.

[0204] One or more antigens can be presented on the surface of an infected cell (e.g. , a HPV infected cell).

[0205] One or more antigens can be immunogenic in a subject having or suspected to have an infection (e.g., a HPV infection, such as a persistent HPV infection), e.g., capable of stimulating a T cell response in the subject. One or more antigens can be immunogenic in a subject at risk of an infection (e.g., a HPV infection, such as a persistent HPV infection), e.g., capable of stimulating a T cell response in the subject that provides immunological protection (i.e., immunity) against the infection, e.g., such as stimulating the production of memory T cells.

[0206]

[0207] One or more antigens can include a combination of antigens capable of stimulating a T cell response (e.g., peptides including predicted T cell epitope sequences) and distinct antigens capable of stimulating a B cell response (e.g., full-length proteins, protein subunits, protein domains).

[0208] One or more antigens that stimulate an autoimmune response in a subject can be excluded from consideration in the context of vaccine generation for a subject.

[0209] The size of at least one antigenic peptide molecule (e.g., an epitope sequence) can comprise, but is not limited to, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120 or greater amino molecule residues, and any range derivable therein. In specific embodiments the antigenic peptide molecules are equal to or less than 50 amino acids.

[0210] Antigenic peptides and polypeptides can be: for MHC Class 1 15 residues or less in length and usually consist of between about 8 and about 11 residues, particularly 9 or 10 residues; for MHC Class II, 6-30 residues, inclusive.

[0211] If desirable, a longer peptide can be designed in several ways. In one case, when presentation likelihoods of peptides on HLA alleles are predicted or known, a longer peptide could consist of either: (1) individual presented peptides with an extensions of 2-5 amino acids toward the N- and C-terminus of each corresponding gene product; (2) a concatenation of some or all of the presented peptides with extended sequences for each. In another case, when sequencing reveals a long (>10 residues) epitope sequence present, a longer peptide would consist of: (3) the entire stretch of novel infectious disease-specific amino acids— thus bypassing the need for computational or in vitro test-based selection of the strongest HLA-presented shorter peptide. In both cases, use of a longer peptide allows endogenous processing by patient cells and may lead to more effective antigen presentation leading to increased T cell responses. Longer peptides can also include a full-length protein, a protein subunit, a protein domain, and combinations thereof of a peptide, such as those expressed in an infectious disease organism. Longer peptides (e.g. , full-length protein, protein subunit, or protein domain) and combinations thereof can be included to stimulate a B cell response.

[0212] Antigenic peptides and polypeptides can be presented on an HLA protein. In some aspects antigenic peptides and polypeptides are presented on an HLA protein with greater affinity than a wild-type peptide. In some aspects, an antigenic peptide or polypeptide can have an IC50 of at least less than 5000 nM, at least less than 1000 nM, at least less than 500 nM, at least less than 250 nM, at least less than 200 nM, at least less than 150 nM, at least less than 100 nM, at least less than 50 nM or less.

[0213] In some aspects, antigenic peptides and polypeptides do not stimulate an autoimmune response and / or invoke immunological tolerance when administered to a subject.

[0214] Also provided are compositions comprising at least two or more antigenic peptides. In some embodiments the composition contains at least two distinct peptides. At least two distinct peptides can be derived from the same polypeptide. By distinct polypeptides is meant that the peptide vary by length, amino acid sequence, or both. The peptides can be derived from any polypeptide known to or suspected to be associated with an infectious disease organism, or peptides derived from any polypeptide known to or have been found to have altered expression in an infected cell in comparison to a normal cell or tissue (e.g., an infectious disease polynucleotide or polypeptide, including infectious disease polynucleotides or polypeptides with expression restricted to a host cell).

[0215] Antigenic peptides and polypeptides having a desired activity or property can be modified to provide certain desired attributes, e.g., improved pharmacological characteristics, while increasing or at least retaining substantially all of the biological activity of the unmodified peptide to bind the desired MHC molecule and activate the appropriate T cell. For instance, antigenic peptide and polypeptides can be subject to various changes, such as substitutions, either conservative or non-conservative, where such changes might provide for certain advantages in their use, such as improved MHC binding, stability or presentation. By conservative substitutions is meant replacing an amino acid residue with another which is biologically and / or chemically similar, e.g., one hydrophobic residue for another, or one polar residue for another. The substitutions include combinations such as Gly, Ala; Vai, He, Leu, Met; Asp, Glu; Asn, Gin; Ser, Thr; Lys, Arg; and Phe, Tyr. The effect of single amino acid substitutions may also be probed using D-amino acids. Such modifications can be made using well known peptide synthesis procedures, as described in e.g., Merrifield, Science 232:341-347 (1986), Barany & Merrifield, The Peptides, Gross & Meienhofer, eds. (N.Y., Academic Press), pp. 1-284 (1979); and Stewart & Young, Solid Phase Peptide Synthesis, (Rockford, Ill., Pierce), 2d Ed. (1984).

[0216] Modifications of peptides and polypeptides with various amino acid mimetics or unnatural amino acids can be particularly useful in increasing the stability of the peptide and polypeptide in vivo. Stability can be assayed in a number of ways. For instance, peptidases and various biological media, such as human plasma and serum, have been used to test stability. See, e.g., Verhoef el al., Eur. J. Drug Metab Pharmacokin. 11:291-302 (1986). Half-life of the peptides can be conveniently determined using a 25% human serum (v / v) assay. The protocol is generally as follows. Pooled human serum (Type AB, non-heat inactivated) is delipidated by centrifugation before use. The serum is then diluted to 25% with RPMI tissue culture media and used to test peptide stability. At predetermined time intervals a small amount of reaction solution is removed and added to either 6% aqueous trichloracetic acid or ethanol. The cloudy reactionsample is cooled (4 degrees C) for 15 minutes and then spun to pellet the precipitated serum proteins. The presence of the peptides is then determined by reversed-phase HPLC using stability-specific chromatography conditions.

[0217] The peptides and polypeptides can be modified to provide desired attributes other than improved serum half-life. For instance, the ability of the peptides to stimulate CTL activity can be enhanced by linkage to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Immunogenic peptides / T helper conjugates can be linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus can be a hetero- or homooligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues. Alternatively, the peptide can be linked to the T helper peptide without a spacer.

[0218] Polypeptides encoding antigens can be modified to alter processing of the polypeptides, such as protease cleavage and / or other post- translation processing. Polypeptides encoding antigens can be modified such that the antigen favors a specific conformation. Polypeptides encoding antigens can be modified such that the mutations (e.g., one or more missense mutations) disrupt a specific conformation in the antigen, such as through the introduction of prolines that disrupt secondary and tertiary structures (e.g. , alpha-helix or betasheet formation). Altering, reducing, or eliminating processing or conformation changes may, in some instances, bias the antigen to favor states favorable to neutralizing antibody production. Illustrative non-limiting modifications for specific HPV proteins include those shown in Table B for HPV proteins E7 and E7. Modified polypeptide sequences can be at least 60%, 70%, 80%, or 90% identical to a native HPV polypeptide sequence. Modified polypeptide sequences can be at least 91%, 92%, 93%, or 94% identical to a native HPV polypeptide sequence. Modified polypeptide sequences can be at least 95%, 96%, 97%, 98%, or 99% identical to a native HPV polypeptide sequence. Modified polypeptide sequences can be at least 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical to a native HPV polypeptide sequence.

[0219] An antigenic peptide can be linked to the T helper peptide either directly or via a spacer either at the amino or carboxy terminus of the peptide. The amino terminus of either the antigenic peptide or the T helper peptide can be acylated. Exemplary T helper peptides include tetanus toxoid 830-843, influenza 307-319, malaria circumsporozoite 382-398 and 378-389.

[0220] Proteins or peptides can be made by any technique known to those of skill in the art, including the expression of proteins, polypeptides or peptides through standard molecular biological techniques, the isolation of proteins or peptides from natural sources, or the chemical synthesis of proteins or peptides. The nucleotide and protein, polypeptide and peptide sequences corresponding to various genes have been previously disclosed, and can be found at computerized databases known to those of ordinary skill in the art. One such database is the National Center for Biotechnology Information's Genbank and GenPept databases located at the National Institutes of Health website. The coding regions for known genes can be amplified and / or expressed using the techniques disclosed herein or as would be known to those of ordinary skill in the art. Alternatively, various commercial preparations of proteins, polypeptides and peptides are known to those of skill in the art.

[0221] In a further aspect, an antigen includes a nucleic acid (e.g. polynucleotide) that encodes an antigenic peptide or portion thereof. The polynucleotide can be, e.g., DNA, cDNA, PNA, CNA, RNA (e.g., mRNA), either single- and / or double-stranded, or native or stabilized forms of polynucleotides, such as, e.g., polynucleotides with a phosphorothioate backbone, or combinations thereof and it may or may not contain introns. A polynucleotide sequence encoding an antigen can be sequence-optimized to improve expression, such as through improving transcription, translation, post-transcriptional processing, and / or RNA stability. For example, polynucleotide sequence encoding an antigen can be codon-optimized. “Codonoptimization” herein refers to replacing infrequently used codons, with respect to codon bias of a given organism, with frequently used synonymous codons. Polynucleotide sequences can be optimized to improve post-transcriptional processing, for example optimized to reduce unintended splicing, such as through removal of splicing motifs (e.g. , canonical and / or cryptic / non-canonical splice donor, branch, and / or acceptor sequences) and / or introduction of exogenous splicing motifs e.g. , splice donor, branch, and / or acceptor sequences) to bias favored splicing events. Exogenous intron sequences include, but are not limited to, those derived from SV40 (e.g. , an SV40 mini-intron) and derived from immunoglobulins (e.g., human P-globin gene). Exogenous intron sequences can be incorporated between a promoter / enhancer sequence and the antigen(s) sequence. Exogenous intron sequences for use in expression vectors are described in more detail in Callendret et al. (Virology. 2007 Jul 5; 363(2): 288-302), herein incorporated by reference for all purposes. Polynucleotide sequences can be optimized to improve transcript stability, for example through removal of RNA instability motifs (e.g., AU- rich elements and 3’ UTR motifs) and / or repetitive nucleotide sequences. Polynucleotide sequences can be optimized to improve accurate transcription, for example through removal of cryptic transcriptional initiators and / or terminators. Polynucleotide sequences can be optimizedto improve translation and translational accuracy, for example through removal of cryptic AUG start codons, premature polyA sequences, and / or secondary structure motifs. Polynucleotide sequences can be optimized to improve nuclear export of transcripts, such as through addition of a Constitutive Transport Element (CTE), RNA Transport Element (RTE), or Woodchuck Posttranscriptional Regulatory Element (WPRE). Nuclear export signals for use in expression vectors are described in more detail in Callendret et al. (Virology. 2007 Jul 5; 363(2): 288-302), herein incorporated by reference for all purposes. Polynucleotide sequences can be optimized with respect to GC content, for example to reflect the average GC content of a given organism. Sequence optimization can balance one or more sequence properties, such as transcription, translation, post-transcriptional processing, and / or RNA stability. Sequence optimization can generate an optimal sequence balancing each of transcription, translation, post-transcriptional processing, and RNA stability. Sequence optimization algorithms are known to those of skill in the art, such as GeneArt (Thermo Fisher), Codon Optimization Tool (IDT), Cool Tool, SGI- DNA (La Jolla California). One or more regions of an antigen-encoding protein can be sequence-optimized separately.

[0222] A method disclosed herein can also include identifying one or more T cells that are antigen- specific for at least one of the antigens in the subset. In some embodiments, the identification comprises co-culturing the one or more T cells with one or more of the antigens in the subset under conditions that expand the one or more antigen-specific T cells. In further embodiments, the identification comprises contacting the one or more T cells with a tetramer comprising one or more of the antigens in the subset under conditions that allow binding between the T cell and the tetramer. In even further embodiments, the method disclosed herein can also include identifying one or more T cell receptors (TCR) of the one or more identified T cells. In certain embodiments, identifying the one or more T cell receptors comprises sequencing the T cell receptor sequences of the one or more identified T cells. The method disclosed herein can further comprise genetically engineering a plurality of T cells to express at least one of the one or more identified T cell receptors; culturing the plurality of T cells under conditions that expand the plurality of T cells; and infusing the expanded T cells into the subject. In some embodiments, genetically engineering the plurality of T cells to express at least one of the one or more identified T cell receptors comprises cloning the T cell receptor sequences of the one or more identified T cells into an expression vector; and transfecting each of the plurality of T cells with the expression vector. In some embodiments, the method disclosed herein further comprises culturing the one or more identified T cells under conditions that expand the one or more identified T cells; and infusing the expanded T cells into the subject.

[0223] Also disclosed herein is an isolated T cell that is antigen- specific for at least one selected antigen in the subset.

[0224] A still further aspect provides an expression vector capable of expressing a polypeptide or portion thereof. Expression vectors for different cell types are well known in the art and can be selected without undue experimentation. Generally, DNA is inserted into an expression vector, such as a plasmid, in proper orientation and correct reading frame for expression. If necessary, DNA can be linked to the appropriate transcriptional and translational regulatory control nucleotide sequences recognized by the desired host, although such controls are generally available in the expression vector. The vector is then introduced into the host through standard techniques. Guidance can be found e.g. in Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.V. Vaccine Compositions

[0225] Also disclosed herein is an immunogenic composition, e.g., a vaccine composition, capable of raising a specific immune response, e.g., an infectious disease organism-specific immune response. Vaccine compositions typically comprise one or a plurality of antigens, e.g., selected using a method described herein. Vaccine compositions can also be referred to as vaccines.

[0226] A vaccine can contain between 1 and 30 peptides, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 different peptides, 6, 7, 8, 9, 10 11, 12, 13, or 14 different peptides, or 12, 13 or 14 different peptides. Peptides can include post-translational modifications. A vaccine can contain between 1 and 100 or more nucleotide sequences, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100 or more different nucleotide sequences, 6, 7, 8, 9, 10 11, 12, 13, or 14 different nucleotide sequences, or12, 13 or 14 different nucleotide sequences. A vaccine can contain between 1 and 30 antigen sequences, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100 or more different antigen sequences, 6, 7, 8, 9, 10 11, 12, 13, or 14 different antigen sequences, or 12, 13 or 14 different antigen sequences.

[0227] A vaccine can contain between 1 and 30 antigen-encoding nucleic acid sequences, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82,83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100 or more different antigenencoding nucleic acid sequences, 6, 7, 8, 9, 10 11, 12, 13, or 14 different antigen-encoding nucleic acid sequences, or 12, 13 or 14 different antigen-encoding nucleic acid sequences. Antigen-encoding nucleic acid sequences can refer to the antigen encoding portion of an “antigen cassette.” Features of an antigen cassette are described in greater detail herein. An antigen-encoding nucleic acid sequence can contain one or more epitope-encoding nucleic acid sequences (e.g., an antigen-encoding nucleic acid sequence encoding concatenated T cell epitopes).

[0228] A vaccine can contain between 1 and 30 distinct epitope-encoding nucleic acid sequences, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100 or more distinct epitope-encoding nucleic acid sequences, 6, 7, 8, 9, 10 11, 12, 13, or 14 distinct epitopeencoding nucleic acid sequences, or 12, 13 or 14 distinct epitope-encoding nucleic acid sequences. Epitope-encoding nucleic acid sequences can refer to sequences for individual epitope sequences, such as each of the T cell epitopes in an antigen-encoding nucleic acid sequence encoding concatenated T cell epitopes.

[0229] A vaccine can contain at least two repeats of an epitope-encoding nucleic acid sequence. A used herein, a “repeat” refers to two or more iterations of an identical nucleic acid epitope-encoding nucleic acid sequence (inclusive of the optional 5’ linker sequence and / or the optional 3 ’ linker sequences described herein) within an antigen-encoding nucleic acid sequence. In one example, the antigen-encoding nucleic acid sequence portion of a cassette encodes at least two repeats of an epitope-encoding nucleic acid sequence. In further non-limiting examples, the antigen-encoding nucleic acid sequence portion of a cassette encodes more than one distinct epitope, and at least one of the distinct epitopes is encoded by at least two repeats of the nucleic acid sequence encoding the distinct epitope (z.<?., at least two distinct epitopeencoding nucleic acid sequences). In illustrative non-limiting examples, an antigen-encoding nucleic acid sequence encodes epitopes A, B, and C encoded by epitope-encoding nucleic acid sequences epitope-encoding sequence A (EA), epitope-encoding sequence B (EB), and epitopeencoding sequence C (Ec), and examplary antigen-encoding nucleic acid sequences havingrepeats of at least one of the distinct epitopes are illustrated by, but is not limited to, the formulas below:- Repeat of one distinct epitope (repeat of epitope A):EA-EB-EC-EA; orEA-EA-EB-ECRepeat of multiple distinct epitopes (repeats of epitopes A, B, and C): EA-EB-EC-EA-EB-EC; or EA-EA-EB -EB-EC-ECMultiple repeats of multiple distinct epitopes (repeats of epitopes A, B, and C): EA-EB-EC-EA-EB-EC-EA-EB-EC; or EA-EA-EA-EB-EB-EB-EC-EC-EC

[0230] The above examples are not limiting and the antigen-encoding nucleic acid sequences having repeats of at least one of the distinct epitopes can encode each of the distinct epitopes in any order or frequency. For example, the order and frequency can be a random arangement of the distinct epitopes, e.g., in an example with epitopes A, B, and C, by the formula EA-EB-EC-EC-EA-EB-EA-EC-EA-EC-EC-EB.

[0231] Also provided for herein is an antigen-encoding cassette, the antigen-encoding cassette having at least one antigen-encoding nucleic acid sequence described, from 5’ to 3’, by the formula:(Ex-(ENn)y)Zwhere E represents a nucleotide sequence comprising at least one of the at least one distinct epitope-encoding nucleic acid sequences, n represents the number of separate distinct epitope-encoding nucleic acid sequences and is any integer including 0,ENrepresents a nucleotide sequence comprising the separate distinct epitope-encoding nucleic acid sequence for each corresponding n, for each iteration of z: x = 0 or 1, y = 0 or 1 for each n, and at least one of x or y = 1, and z = 2 or greater, wherein the antigen-encoding nucleic acid sequence comprises at least two iterations of E, a given EN, or a combination thereof.

[0232] Each E or ENcan independently comprise any epitope-encoding nucleic acid sequence described herein (e.g. , a nucleotide sequence encoding a polypeptide sequence as set forth in Tables C1-C9). For example, Each E or ENcan independently comprises a nucleotide sequence described, from 5’ to 3’, by the formula (L5b-Nc-L3d), where N comprises the distinct epitope-encoding nucleic acid sequence associated with each E or EN, where c = 1 , L5 comprisesa 5’ linker sequence, where b = 0 or 1, and L3 comprises a 3’ linker sequence, where d = 0 or 1. Epitopes and linkers that can be used are further described herein..

[0233] Repeats of an epitope-encoding nucleic acid sequences (inclusive of optional 5 ’ linker sequence and / or the optional 3 ’ linker sequences) can be linearly linked directly to one another (e.g. , EA-EA-. .. as illustrated above). Repeats of an epitope-encoding nucleic acid sequences can be separated by one or more additional nucleotides sequences. In general, repeats of an epitope-encoding nucleic acid sequences can be separated by any size nucleotide sequence applicable for the compositions described herein. In one example, repeats of an epitopeencoding nucleic acid sequences can be separated by a separate distinct epitope-encoding nucleic acid sequence (e.g., EA-EB-EC-EA..., as illustrated above). In examples where repeats are separated by a single separate distinct epitope-encoding nucleic acid sequence, and each epitopeencoding nucleic acid sequences (inclusive of optional 5’ linker sequence and / or the optional 3’ linker sequences) encodes a peptide 25 amino acids in length, the repeats can be separated by 75 nucleotides, such as in antigen-encoding nucleic acid represented by EA-EB-EA. . EA is separated by 75 nucleotides. In an illustrative example, an antigen-encoding nucleic acid having the sequenceVTNTEMFVTAPDNLGYMYEVQWPGQTQPQIANCSVYDFFVWLHYYSVRDTVTNTEMF VTAPDNLGYMYEVQWPGQTQPQIANCSVYDFFVWLHYYSVRDT encoding repeats of 25mer antigens Trpl (VTNTEMFVTAPDNLGYMYEVQWPGQ) and Trp2 (TQPQIANCSVYDFFVWLHYYSVRDT), the repeats of Trpl are separated by the 25mer Trp2 and thus the repeats of the Trpl epitope-encoding nucleic acid sequences are separated the 75 nucleotide Trp2 epitope-encoding nucleic acid sequence. In examples where repeats are separated by 2, 3, 4, 5, 6, 7, 8, or 9 separate distinct epitope-encoding nucleic acid sequence, and each epitope-encoding nucleic acid sequences (inclusive of optional 5 ’ linker sequence and / or the optional 3 ’ linker sequences) encodes a peptide 25 amino acids in length, the repeats can be separated by 150, 225, 300, 375, 450, 525, 600, or 675 nucleotides, respectively.

[0234] In one embodiment, different peptides and / or polypeptides or nucleotide sequences encoding them are selected so that the peptides and / or polypeptides capable of associating with different MHC molecules, such as different MHC class I molecules and / or different MHC class II molecules. In some aspects, one vaccine composition comprises coding sequence for peptides and / or polypeptides capable of associating with the most frequently occurring MHC class I molecules and / or different MHC class II molecules. Hence, vaccine compositions can comprise different fragments capable of associating with at least 2 preferred, at least 3 preferred, or at least 4 preferred MHC class I molecules and / or different MHC class II molecules.

[0235] The vaccine composition can stimulate a specific cytotoxic T-cell response and a specific helper T-cell response.

[0236] A combination of vaccine compositions can stimulate a specific cytotoxic T-cell response and / or a specific helper T-cell response. Vaccine compositions can be homologous and stimulate T-cell response and / or a specific helper T-cell response in combination. Vaccine compositions can be homologous and stimulate a specific T-cell response and a specific helper T-cell response in combination. Vaccine compositions can be heterologous and stimulate a specific T-cell response and / or a specific helper T-cell response in combination. Vaccine compositions can be heterologous and stimulate a specific T-cell response and a specific helper T-cell response in combination. Heterologous vaccines include an identical antigen cassette encoded by different vaccine platforms, e.g., a viral vaccine (e.g., a ChAdV-based platform) and a mRNA vaccine (e.g., a SAM-based platform). Heterologous vaccines include different antigen cassettes (e.g., aE6 / E7 fusion protein cassette and a separate T cell epitope encoding cassette, and / or epitopes / antigens derived from different HPV strains, such as E6 / E7 fusion protein variants from a HPV16 strain and a HPV18 strain) encoded by the same vaccine platform, e.g., either a viral vaccine (e.g., a ChAdV-based platform) or a mRNA vaccine (e.g., a SAM-based platform). Heterologous vaccines include different antigen cassettes (e.g., an E6 / E7 fusion protein cassette and a separate T cell epitope encoding cassette, and / or epitopes / antigens derived from different HPV strains, such as E6 / E7 fusion protein variants from a HPV16 strain and a HPV18 strain) encoded by different vaccine platforms, e.g., a viral vaccine (e.g., a ChAdV- based platform) and a mRNA vaccine (e.g. , a SAM-based platform).

[0237] A vaccine composition can further comprise an adjuvant and / or a carrier. Examples of useful adjuvants and carriers are given herein below. A composition can be associated with a carrier such as e.g. a protein or an antigen-presenting cell such as, e.g., a dendritic cell (DC) capable of presenting the peptide to a T-cell.

[0238] Adjuvants are any substance whose admixture into a vaccine composition increases or otherwise modifies the immune response to an antigen. Carriers can be scaffold structures, for example a polypeptide or a polysaccharide, to which an antigen, is capable of being associated. Optionally, adjuvants are conjugated covalently or non-covalently.

[0239] The ability of an adjuvant to increase an immune response to an antigen is typically manifested by a significant or substantial increase in an immune-mediated reaction, or reduction in disease symptoms. For example, an increase in humoral immunity is typically manifested by a significant increase in the titer of antibodies raised to the antigen, and an increase in T-cell activity is typically manifested in increased cell proliferation, or cellular cytotoxicity, orcytokine secretion. An adjuvant may also alter an immune response, for example, by changing a primarily humoral or Th response into a primarily cellular, or Th response.

[0240] Suitable adjuvants include, but are not limited to 1018 ISS, alum, aluminum salts, Amplivax, AS 15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, GM-CSF, IC30, IC31, Imiquimod, ImuFact 1MP321, IS Patch, ISS, 1SCOMATR1X, Juvlmmune, LipoVac, MF59, monophosphoryl lipid A, Montanide IMS 1312, Montanide ISA 206, Montanide ISA 50V, Montanide ISA-51, OK-432, OM-174, OM-197-MP-EC, ONTAK, PepTel vector system, PLG microparticles, resiquimod, SRL172, Virosomes and other Virus-like particles, YF-17D, VEGF trap, R848, beta-glucan, Pam3Cys, Aquila's QS21 stimulon (Aquila Biotech, Worcester, Mass., USA) which is derived from saponin, mycobacterial extracts and synthetic bacterial cell wall mimics, and other proprietary adjuvants such as Ribi's Detox. Quil or Superfos. Adjuvants such as incomplete Freund's or GM-CSF are useful. Several immunological adjuvants (e.g., MF59) specific for dendritic cells and their preparation have been described previously (Dupuis M, et al., Cell Immunol. 1998; 186(1): 18-27; Allison A C; Dev Biol Stand. 1998; 92:3-11). Also cytokines can be used. Several cytokines have been directly linked to influencing dendritic cell migration to lymphoid tissues (e.g., TNF-alpha), accelerating the maturation of dendritic cells into efficient antigen-presenting cells for T-lymphocytes (e.g., GM-CSF, IL-1 and IL-4) (U.S. Pat. No. 5,849,589, specifically incorporated herein by reference in its entirety) and acting as immunoadjuvants (e.g., IL-12) (Gabrilovich D I, et al., J Immunother Emphasis Tumor Immunol. 1996 (6):414-418).

[0241] CpG immunostimulatory oligonucleotides have also been reported to enhance the effects of adjuvants in a vaccine setting. Other TLR binding molecules such as RNA binding TLR 7, TLR 8 and / or TLR 9 may also be used.

[0242] Other examples of useful adjuvants include, but are not limited to, chemically modified CpGs (e.g. CpR, Idera), Poly(I:C)(e.g. polyi:CI2U), non-CpG bacterial DNA or RNA as well as immunoactive small molecules and antibodies such as cyclophosphamide, sunitinib, bevacizumab, celebrex, NCX-4016, sildenafil, tadalafil, vardenafil, sorafinib, XL- 999, CP- 547632, pazopanib, ZD2171, AZD2171, ipilimumab, tremelimumab, and SC58175, which may act therapeutically and / or as an adjuvant. The amounts and concentrations of adjuvants and additives can readily be determined by the skilled artisan without undue experimentation. Additional adjuvants include colony-stimulating factors, such as Granulocyte Macrophage Colony Stimulating Factor (GM-CSF, sargramostim).

[0243] A vaccine composition can comprise more than one different adjuvant. Furthermore, a therapeutic composition can comprise any adjuvant substance including any of the above orcombinations thereof. It is also contemplated that a vaccine and an adjuvant can be administered together or separately in any appropriate sequence.

[0244] A carrier (or excipient) can be present independently of an adjuvant. The function of a carrier can for example be to increase the molecular weight of a particular mutant to increase activity or immunogenicity, to confer stability, to increase the biological activity, or to increase serum half-life. Furthermore, a carrier can aid presenting peptides to T-cells. A carrier can be any suitable carrier known to the person skilled in the art, for example a protein or an antigen presenting cell. A carrier protein could be but is not limited to keyhole limpet hemocyanin, serum proteins such as transferrin, bovine serum albumin, human serum albumin, thyroglobulin or ovalbumin, immunoglobulins, or hormones, such as insulin or palmitic acid. For immunization of humans, the carrier is generally a physiologically acceptable carrier acceptable to humans and safe. However, tetanus toxoid and / or diphtheria toxoid are suitable carriers. Alternatively, the carrier can be dextrans for example Sepharose.

[0245] Cytotoxic T-cells (CTLs) recognize an antigen in the form of a peptide bound to an MHC molecule rather than the intact foreign antigen itself. The MHC molecule itself is located at the cell surface of an antigen presenting cell. Thus, an activation of CTLs is possible if a trimeric complex of peptide antigen, MHC molecule, and APC is present. Correspondingly, it may enhance the immune response if not only the peptide is used for activation of CTLs, but if additionally APCs with the respective MHC molecule are added. Therefore, in some embodiments a vaccine composition additionally contains at least one antigen presenting cell.

[0246] Antigens can also be included in viral vector-based vaccine platforms, such as vaccinia, fowlpox, self-replicating alphavirus, marabavirus, adenovirus (See, e.g., Tatsis et al., Adenoviruses, Molecular Therapy (2004) 10, 616 — 629), or lentivirus, including but not limited to second, third or hybrid second / third generation lentivirus and recombinant lentivirus of any generation designed to target specific cell types or receptors (See, e.g., Hu et al., Immunization Delivered by Lentiviral Vectors for Cancer and Infectious Diseases, Immunol Rev. (2011) 239(1): 45-61, Sakuma et al., Lentiviral vectors: basic to translational, Biochem J. (2012) 443(3) :603-l 8, Cooper et al., Rescue of splicing-mediated intron loss maximizes expression in lentiviral vectors containing the human ubiquitin C promoter, Nucl. Acids Res. (2015) 43 (1): 682-690, Zufferey et al., Self-Inactivating Lentivirus Vector for Safe and Efficient In Vivo Gene Delivery, J. Virol. (1998) 72 (12): 9873-9880). Dependent on the packaging capacity of the above mentioned viral vector-based vaccine platforms, this approach can deliver one or more nucleotide sequences that encode one or more antigen peptides. The sequences may be flanked by non-mutated sequences, may be separated by linkers or may be preceded with one or more sequences targeting a subcellular compartment (See, e.g., Gros et al., Prospective identificationof neoantigen-specific lymphocytes in the peripheral blood of melanoma patients, Nat Med. (2016) 22 (4):433-8, Stronen et al., Targeting of cancer neoantigens with donor-derived T cell receptor repertoires, Science. (2016) 352 (6291): 1337-41, Lu et al., Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions, Clin Cancer Res. (2014) 20( 13):3401-10). Upon introduction into a host, infected cells express the antigens, and thereby stimulate a host immune (e.g., CTL) response against the peptide(s). Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al. (Nature 351:456-460 (1991)). A wide variety of other vaccine vectors useful for therapeutic administration or immunization of antigens, e.g., Salmonella typhi vectors, and the like will be apparent to those skilled in the art from the description herein.V.A. Antigen Cassette

[0247] The methods employed for the selection of one or more antigens, the cloning and construction of a “cassette” and its insertion into a viral vector are within the skill in the art given the teachings provided herein. By "antigen cassette" or “cassette” is meant the combination of a selected antigen or plurality of antigens (e.g., antigen-encoding nucleic acid sequences) and the other regulatory elements necessary to transcribe the antigen(s) and express the transcribed product. The selected antigen or plurality of antigens can refer to distinct epitope sequences, e.g., an antigen-encoding nucleic acid sequence in the cassette can encode an epitope-encoding nucleic acid sequence (or plurality of epitope-encoding nucleic acid sequences) such that the epitopes are transcribed and expressed. An antigen or plurality of antigens can be operatively linked to regulatory components in a manner which permits transcription. Such components include conventional regulatory elements that can drive expression of the antigen(s) in a cell transfected with the viral vector. Thus the antigen cassette can also contain a selected promoter which is linked to the antigen(s) and located, with other, optional regulatory elements, within the selected viral sequences of the recombinant vector. A cassette can have one or more antigen-encoding nucleic acid sequences, such as a cassette containing multiple antigen-encoding nucleic acid sequences each independently operably linked to separate promoters and / or linked together using other multicistonic systems, such as 2A ribosome skipping sequence elements (e.g., E2A, P2A, F2A, or T2A sequences) or Internal Ribosome Entry Site (IRES) sequence elements. A linker can also have a cleavage site, such as a TEV or furin cleavage site. Linkers with cleavage sites can be used in combination with other elements, such as those in a multicistronic system. In a non-limiting illustrative example, a furin protease cleavage site can be used in conjuction with a 2A ribosome skipping sequence elementsuch that the furin protease cleavage site is configured to facilitate removal of the 2A sequence following translation. In a cassette containing more than one antigen-encoding nucleic acid sequences, each antigen-encoding nucleic acid sequence can contain one or more epitopeencoding nucleic acid sequences (e.g., an antigen-encoding nucleic acid sequence encoding concatenated T cell epitopes). In illustrative examples of multicistronic formats, cassettes encoding HPV antigens are configured as follows: (1) endogenous 26S promoter - E6 / E7 fusion protein - T2A - concatenated T-cell epitopes (TCE), or (2) endogenous 26S promoter - E6 / E7 fusion protein - 26S promoter - concatenated TCE.. Combinations of multicistronic formats can also be used, such as in illustrative example: endogenous 26S promoter - HPV 16 E6 / E7 fusion protein - T2A - HPV 16 concatenated TCE - 26S promoter - HPV18 E6 / E7 fusion protein - T2A - HPV 18 concatenated TCE.

[0248] Useful promoters can be constitutive promoters or regulated (inducible) promoters, which will enable control of the amount of antigen(s) to be expressed. For example, a desirable promoter is that of the cytomegalovirus immediate early promoter / enhancer [see, e.g., Boshart et al, Cell, 41:521-530 (1985)]. Another desirable promoter includes the Rous sarcoma virus LTR promoter / enhancer. Still another promoter / enhancer sequence is the chicken cytoplasmic betaactin promoter [T. A. Kost et al, Nucl. Acids Res., 11(23):8287 (1983)]. Other suitable or desirable promoters can be selected by one of skill in the art.

[0249] The antigen cassette can also include nucleic acid sequences heterologous to the viral vector sequences including sequences providing signals for efficient polyadenylation of the transcript (poly(A), poly-A or pA) and introns with functional splice donor and acceptor sites. A common poly-A sequence which is employed in the exemplary vectors of this invention is that derived from the papovavirus SV-40. The poly-A sequence generally can be inserted in the cassette following the antigen-based sequences and before the viral vector sequences. A common intron sequence can also be derived from SV-40, and is referred to as the SV-40 T intron sequence. An antigen cassette can also contain such an intron, located between the promoter / enhancer sequence and the antigen(s). Selection of these and other common vector elements are conventional [see, e.g., Sambrook et al, "Molecular Cloning. A Laboratory Manual.", 2d edit., Cold Spring Harbor Laboratory, New York (1989) and references cited therein] and many such sequences are available from commercial and industrial sources as well as from Genbank.

[0250] An antigen cassette can have one or more antigens. For example, a given cassette can include 1-10, 1-20, 1-30, 10-20, 15-25, 15-20, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more antigens. Antigens can be linked directly to one another. Antigens canalso be linked to one another with linkers. Antigens can be in any orientation relative to one another including N to C or C to N.

[0251] As described elsewhere, the antigen cassette can be located in the site of any selected deletion in the viral vector backbone, such as the site of the El gene region deletion or E3 gene region deletion of a ChAd-based vector or the deleted structural proteins of a VEE backbone, among others which may be selected.

[0252] The antigen encoding sequence (e.g., cassette or one or more of the nucleic acid sequences encoding an immunogenic polypeptide in the cassette) can be described using the following formula to describe the ordered sequence of each element, from 5’ to 3’:Pa-(L5b-Nc-L3d)x-(G5e-Uf)Y-G3gwherein P comprises the second promoter nucleotide sequence, where a = 0 or 1, where c = 1, N comprises one of the HPV derived nucleic acid sequences described herein, optionally wherein each N encodes a polypeptide sequence as set forth in Tables C1-C9, L5 comprises the 5’ linker sequence, where b = 0 or 1, L3 comprises the 3’ linker sequence, where d = 0 or 1, G5 comprises one of the at least one nucleic acid sequences encoding a GPGPG amino acid linker (SEQ ID NO: 56), where e = 0 or 1, G3 comprises one of the at least one nucleic acid sequences encoding a GPGPG amino acid linker (SEQ ID NO: 56), where g = 0 or 1, U comprises one of the at least one MHC class II epitope-encoding nucleic acid sequence, where f = 1, X = 1 to 400, where for each X the corresponding Ncis a HPV derived nucleic acid sequence, and Y = 0, I, or 2, where for each Y the corresponding Uf is a (1 ) universal MHC class II epitope-encoding nucleic acid sequence, optionally wherein the at least one universal sequence comprises at least one of Tetanus toxoid and PADRE, or (2) a MHC class II HPV derived epitope-encoding nucleic acid sequence. In some aspects, for each X the corresponding Ncis a distinct HPV derived nucleic acid sequence. In some aspects, for each Y the corresponding Uf is a distinct universal MHC class II epitope-encoding nucleic acid sequence or a distinct MHC class II HPV derived epitope-encoding nucleic acid sequence. The above antigen encoding sequence formula in some instances only describes the portion of an antigen cassette encoding concatenated epitope sequences, such as concatenated T cell epitopes. For example, in cassettes encoding concatenated T cell epitopes and one or more full-length HPV proteins, the above antigen encoding sequence formula describes the concatenated T cell epitopes and separately the cassette encodes one or more full-length HPV proteins that are linked optionally using a multicistonic system, such as 2A ribosome skipping sequence elements (e.g. , E2A, P2A, F2A, or T2A sequences), a Internal Ribosome Entry Site (IRES) sequence elements, and / or independently operably linked to a separate promoter.

[0253] In one example, elements present include where b = l, d = l, e = l, g = l, h = l, X = 18, Y = 2, and the vector backbone comprises a ChAdV68 vector, a = 1, P is a CMV promoter, the at least one second poly(A) sequence is present, wherein the second poly(A) sequence is an exogenous poly(A) sequence to the vector backbone, and optionally wherein the exogenous poly(A) sequence comprises an SV40 poly(A) signal sequence or a BGH poly(A) signal sequence, and each N encodes a MHC class I epitope 7-15 amino acids in length, a MHC class II epitope, an epitope capable of stimulating a B cell response, or combinations thereof, L5 is a native 5’ linker sequence that encodes a native N-terminal amino acid sequence of the epitope, and wherein the 5’ linker sequence encodes a peptide that is at least 3 amino acids in length, L3 is a native 3 ’ linker sequence that encodes a native C-terminal amino acid sequence of the epitope, and wherein the 3 ’ linker sequence encodes a peptide that is at least 3 amino acids in length, and U is each of a PADRE class II sequence and a Tetanus toxoid MHC class II sequence. The above antigen encoding sequence formula in some instances only describes the portion of an antigen cassette encoding concatenated epitope sequences, such as concatenated T cell epitopes.

[0254] In one example, elements present include where b = 1, d = 1, e = 1, g = 1, h = 1, X = 18, Y = 2, and the vector backbone comprises a Venezuelan equine encephalitis virus vector, a = 0, and the antigen cassette is operably linked to an endogenous 26S promoter, and the at least one polyadenylation poly(A) sequence is a poly(A) sequence of at least 80 consecutive A nucleotides provided by the backbone, and each N encodes a MHC class I epitope 7-15 amino acids in length, a MHC class II epitope, an epitope capable of stimulating a B cell response, or combinations thereof, L5 is a native 5’ linker sequence that encodes a native N-terminal amino acid sequence of the epitope, and wherein the 5’ linker sequence encodes a peptide that is at least 3 amino acids in length, L3 is a native 3’ linker sequence that encodes a native C-terminal amino acid sequence of the epitope, and wherein the 3’ linker sequence encodes a peptide that is at least 3 amino acids in length, and U is each of a PADRE class II sequence and a Tetanus toxoid MHC class II sequence.

[0255] The antigen encoding sequence can be described using the following formula to describe the ordered sequence of each element, from 5’ to 3’:(Pa-(L5b-Nc-L3d)x)z-(P2h-(G5e-Uf)Y)w-G3g wherein P and P2 comprise promoter nucleotide sequences, N comprises one of the HPV derived nucleic acid sequences described herein (e.g., N encodes a polypeptide sequence as set forth in Tables C1-C9), L5 comprises a 5’ linker sequence, L3 comprises a 3’ linker sequence, G5 comprises a nucleic acid sequences encoding an amino acid linker, G3 comprises one of the at least one nucleic acid sequences encoding an amino acid linker, U comprises an MHC class IIepitope-encoding nucleic acid sequence, where for each X the corresponding Nc is a HPV derived nucleic acid sequence, where for each Y the corresponding Uf is a (1) universal MHC class II epitope-encoding nucleic acid sequence, optionally wherein the at least one universal sequence comprises at least one of Tetanus toxoid and PADRE, or (2) a MHC class II HPV derived epitope-encoding nucleic acid sequence. The composition and ordered sequence can be further defined by selecting the number of elements present, for example where a = 0 or 1, where b = 0 or 1, where c = 1, where d = 0 or 1, where e = 0 or 1, where f = 1, where g = 0 or 1, where h = 0 or 1, X = 1 to 400, Y = 0, 1, 2, 3, 4 or 5, Z = 1 to 400, and W = 0, 1, 2, 3, 4 or 5.

[0256] In one example, elements present include where a = 0, b = 1, d = 1, e = 1, g = 1, h = 0, X = 10, Y = 2, Z = 1, and W = 1, describing where no additional promoter is present (e.g. only the promoter nucleotide sequence provided by the vector backbone, such as an RNA alphavirus backbone, is present), 10 epitopes are present, a 5’ linker is present for each N, a 3’ linker is present for each N, 2 MHC class II epitopes are present, a linker is present linking the two MHC class II epitopes, a linker is present linking the 5’ end of the two MHC class II epitopes to the 3’ linker of the final MHC class I epitope, and a linker is present linking the 3’ end of the two MHC class II epitopes to the to the vector backbone. Examples of linking the 3 ’ end of the antigen cassette to the vector backbone include linking directly to the 3’ UTR elements provided by the vector backbone, such as a 3’ 19-nt CSE. Examples of linking the 5’ end of the antigen cassette to the vector backbone include linking directly to a promoter or 5’ UTR element of the vector backbone, such as a 26S promoter sequence, an alphavirus 5’ UTR, a 51 -nt CSE, or a 24-nt CSE of an alphavirus vector backbone.

[0257] Other examples include: where a = 1 describing where a promoter other than the promoter nucleotide sequence provided by the vector backbone is present; where a = 1 and Z is greater than 1 where multiple promoters other than the promoter nucleotide sequence provided by the vector backbone are present each driving expression of 1 or more distinct MHC class I epitope encoding nucleic acid sequences; where h = 1 describing where a separate promoter is present to drive expression of the MHC class II epitope-encoding nucleic acid sequences; and where g = 0 describing the MHC class II epitope-encoding nucleic acid sequence, if present, is directly linked to the vector backbone.

[0258] Other examples include where each MHC class I epitope that is present can have a 5’ linker, a 3 ’ linker, neither, or both. In examples where more than one MHC class I epitope is present in the same antigen cassette, some MHC class I epitopes may have both a 5’ linker and a 3’ linker, while other MHC class I epitopes may have either a 5’ linker, a 3’ linker, or neither. In other examples where more than one MHC class I epitope is present in the same antigencassette, some MHC class I epitopes may have either a 5’ linker or a 3’ linker, while other MHC class I epitopes may have either a 5’ linker, a 3’ linker, or neither.

[0259] In examples where more than one MHC class II epitope is present in the same antigen cassette, some MHC class II epitopes may have both a 5’ linker and a 3’ linker, while other MHC class 11 epitopes may have either a 5 ’ linker, a 3 ’ linker, or neither. In other examples where more than one MHC class II epitope is present in the same antigen cassette, some MHC class II epitopes may have either a 5 ’ linker or a 3 ’ linker, while other MHC class II epitopes may have either a 5’ linker, a 3’ linker, or neither.

[0260] Other examples include where each antigen that is present can have a 5’ linker, a 3’ linker, neither, or both. In examples where more than one antigen is present in the same antigen cassette, some antigens may have both a 5’ linker and a 3’ linker, while other antigens may have either a 5’ linker, a 3’ linker, or neither. In other examples where more than one antigen is present in the same antigen cassette, some antigens may have either a 5’ linker or a 3’ linker, while other antigens may have either a 5’ linker, a 3’ linker, or neither.

[0261] The promoter nucleotide sequences P and / or P2 can be the same as a promoter nucleotide sequence provided by the vector backbone, such as a RNA alphavirus backbone. For example, the promoter sequence provided by the vector backbone, Pn and P2, can each comprise a 26S subgenomic promoter or a CMV promoter. The promoter nucleotide sequences P and / or P2 can be different from the promoter nucleotide sequence provided by the vector backbone, as well as can be different from each other.

[0262] The 5’ linker L5 can be a native sequence or a non-natural sequence. Non-natural sequence include, but are not limited to, AAY, RR, and DPP. The 3’ linker L3 can also be a native sequence or a non-natural sequence. Additionally, L5 and L3 can both be native sequences, both be non-natural sequences, or one can be native and the other non-natural. For each X, the amino acid linkers can be 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97,98, 99, 100 or more amino acids in length. For each X, the amino acid linkers can be also be at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 amino acids in length.

[0263] The amino acid linker G5, for each Y, can be 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100 or more amino acids in length. For each Y, the amino acid linkers can be also be at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 amino acids in length.

[0264] The amino acid linker G3 can be 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95,96, 97, 98, 99, 100 or more amino acids in length. G3 can be also be at least 3, at least 4, at least5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 amino acids in length.

[0265] For each X, each N can encode a MHC class I epitope, a MHC class II epitope, an epitope capable of stimulating a B cell response, or a combination thereof. For each X, N can encode a combination of a MHC class I epitope, a MHC class II epitope, and an epitope capable of stimulating a B cell response. For each X, N can encode a combination of a MHC class I epitope and a MHC class II epitope. For each X, N can encode a combination of a MHC class I epitope and an epitope capable of stimulating a B cell response. For each X, N can encode a combination of a MHC class II epitope and an epitope capable of stimulating a B cell response. For each X, each N can encode a MHC class I epitope 7-15 amino acids in length. For each X, each N can also encodes a MHC class I epitope 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 amino acids in length. For each X, each N can also encodes a MHC class I epitope at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, or at least 30 amino acids in length. For each X, each N can encode a MHC class II epitope. For each X, each N can encode an epitope capable of stimulating a B cell response.

[0266] The cassette encoding the one or more antigens can be 700 nucleotides or less. The cassette encoding the one or more antigens can be 700 nucleotides or less and encode 2 distinct epitope-encoding nucleic acid sequences (e.g., encode 2 distinct HPV derived nucleic acidsequence encoding an immunogenic polypeptide). The cassette encoding the one or more antigens can be 700 nucleotides or less and encode at least 2 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be 700 nucleotides or less and encode 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be 700 nucleotides or less and encode at least 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be 700 nucleotides or less and include 1-10, 1-5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more antigens.

[0267] The cassette encoding the one or more antigens can be between 375-700 nucleotides in length. The cassette encoding the one or more antigens can be between 375-700 nucleotides in length and encode 2 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be between 375-700 nucleotides in length and encode at least 2 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be between 375-700 nucleotides in length and encode 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens be between 375-700 nucleotides in length and encode at least 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be between 375-700 nucleotides in length and include 1- 10, 1-5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more antigens.

[0268] The cassette encoding the one or more antigens can be 600, 500, 400, 300, 200, or 100 nucleotides in length or less. The cassette encoding the one or more antigens can be 600, 500, 400, 300, 200, or 100 nucleotides in length or less and encode 2 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be 600, 500, 400, 300, 200, or 100 nucleotides in length or less and encode at least 2 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be 600, 500, 400, 300, 200, or 100 nucleotides in length or less and encode 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be 600, 500, 400, 300, 200, or 100 nucleotides in length or less and encode at least 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be 600, 500, 400, 300, 200, or 100 nucleotides in length or less and include 1-10, 1-5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more antigens.

[0269] The cassette encoding the one or more antigens can be between 375-600, between 375-500, or between 375-400 nucleotides in length. The cassette encoding the one or more antigens can be between 375-600, between 375-500, or between 375-400 nucleotides in length and encode 2 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be between 375-600, between 375-500, or between 375-400 nucleotides in length and encode at least 2 distinct epitope-encoding nucleic acid sequences. The cassetteencoding the one or more antigens can be between 375-600, between 375-500, or between 375- 400 nucleotides in length and encode 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be between 375-600, between 375-500, or between 375-400 nucleotides in length and encode at least 3 distinct epitope-encoding nucleic acid sequences. The cassette encoding the one or more antigens can be between 375-600, between 375-500, or between 375-400 nucleotides in length and include 1-10, 1-5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more antigens.V.B. Additional Considerations for Vaccine Design and Manufacture

[0270] After all of the above antigen filters are applied, more candidate antigens may still be available for vaccine inclusion than the vaccine technology can support. Additionally, uncertainty about various aspects of the antigen analysis may remain and tradeoffs may exist between different properties of candidate vaccine antigens. Thus, in place of predetermined filters at each step of the selection process, an integrated multi-dimensional model can be considered that places candidate antigens in a space with at least the following axes and optimizes selection using an integrative approach.1. Risk of auto-immunity or tolerance (risk of germline) (lower risk of auto-immunity is typically preferred)2. Probability of sequencing artifact (lower probability of artifact is typically preferred)3. Probability of immunogenicity (higher probability of immunogenicity is typically preferred)4. Probability of presentation (higher probability of presentation is typically preferred)5. Gene expression (higher expression is typically preferred)6. Coverage of HLA genes (larger number of HLA molecules involved in the presentation of a set of antigens may lower the probability that an infected cell will escape immune attack via downregulation or mutation of HLA molecules)7. Coverage of HLA classes (covering both HLA-I and HLA-II may increase the probability of therapeutic response and decrease the probability of infectious disease escape)

[0271] Additionally, optionally, antigens can be deprioritized (e.g., excluded) from the vaccination if they are predicted to be presented by HLA alleles lost or inactivated in either all or part of the patient’ s infected cell. HLA allele loss can occur by either somatic mutation, loss of heterozygosity, or homozygous deletion of the locus. Methods for detection of HLA allele somatic mutation are well known in the art, e.g. (Shukla et al., 2015). Methods for detection of somatic LOH and homozygous deletion (including for HLA locus) are likewise well described. (Carter et al., 2012; McGranahan et al., 2017; Van Loo et al., 2010). Antigens can also be deprioritized if mass-spectrometry data indicates a predicted antigen is not presented by a predicted HLA allele.V.C. Self-Amplifying RNA Vectors

[0272] In general, all self-amplifying RNA (SAM) vectors contain a self-amplifying backbone derived from a self-replicating virus. The term “self-amplifying backbone” refers to minimal sequence(s) of a self-replicating virus that allows for self-replication of the viral genome. For example, minimal sequences that allow for self-replication of an alphavirus can include conserved sequences for nonstructural protein-mediated amplification (e.g., a nonstructural protein 1 (nsPl) gene, a nsP2 gene, a nsP3 gene, a nsP4 gene, and / or a polyA sequence). A self- amplifying backbone can also include sequences for expression of subgenomic viral RNA (e.g. , a 26S promoter element for an alphavirus). SAM vectors can be positive-sense RNA polynucleotides or negative-sense RNA polynucleotides, such as vectors with backbones derived from positive-sense or negative-sense self-replicating viruses. Self-replicating viruses include, but are not limited to, alphaviruses, flaviviruses e.g., Kunjin virus), measles viruses, and rhabdoviruses (e.g., rabies virus and vesicular stomatitis virus). Examples of SAM vector systems derived from self-replicating viruses are described in greater detail in Lundstrom (Molecules. 2018 Dec 13;23(12). pii: E3310. doi: 10.3390 / molecules23123310), herein incorporated by reference for all purposes.V.C.l. Alphavirus Biology

[0273] Alphaviruses are members of the family Togaviridae, and are positive-sense single stranded RNA viruses. Members are typically classified as either Old World, such as Sindbis, Ross River, Mayaro, Chikungunya, and Semliki Forest viruses, or New World, such as eastern equine encephalitis, Aura, Fort Morgan, or Venezuelan equine encephalitis virus and its derivative strain TC-83 (Strauss Microbrial Review 1994). A natural alphavirus genome is typically around 12kb in length, the first two-thirds of which contain genes encoding nonstructural proteins (nsPs) that form RNA replication complexes for self-replication of the viral genome, and the last third of which contains a subgenomic expression cassette encoding structural proteins for virion production (Frolov RNA 2001).

[0274] A model lifecycle of an alphavirus involves several distinct steps (Strauss Microbrial Review 1994, Jose Future Microbiol 2009). Following virus attachment to a host cell, the virion fuses with membranes within endocytic compartments resulting in the eventual release of genomic RNA into the cytosol. The genomic RNA, which is in a plus-strand orientation and comprises a 5’ methylguanylate cap and 3’ polyA tail, is translated to produce non-structural proteins nsPl-4 that form the replication complex. Early in infection, the plus-strand is then replicated by the complex into a minus-stand template. In the current model, the replication complex is further processed as infection progresses, with the resulting processed complexswitching to transcription of the minus-strand into both full-length positive-strand genomic RNA, as well as the 26S subgenomic positive-strand RNA containing the structural genes. Several conserved sequence elements (CSEs) of alphavirus have been identified to potentially play a role in the various RNA replication steps including; a complement of the 5’ UTR in the replication of plus-strand RNAs from a minus-strand template, a 51 -nt CSE in the replication of minus-strand synthesis from the genomic template, a 24-nt CSE in the junction region between the nsPs and the 26S RNA in the transcription of the subgenomic RNA from the minus-strand, and a 3’ 19-nt CSE in minus-strand synthesis from the plus-strand template.

[0275] Following the replication of the various RNA species, virus particles are then typically assembled in the natural lifecycle of the virus. The 26S RNA is translated and the resulting proteins further processed to produce the structural proteins including capsid protein, glycoproteins El and E2, and two small polypeptides E3 and 6K (Strauss 1994). Encapsidation of viral RNA occurs, with capsid proteins normally specific for only genomic RNA being packaged, followed by virion assembly and budding at the membrane surface.V.C.2. Alphavirus as a delivery vector

[0276] Alphaviruses (including alphavirus sequences, features, and other elements) can be used to generate alphavirus-based delivery vectors (also be referred to as alphavirus vectors, alphavirus viral vectors, alphavirus vaccine vectors, self-replicating RNA (srRNA) vectors, or self-amplifying RNA (samRNA) vectors). Alphaviruses have previously been engineered for use as expression vector systems (Pushko 1997, Rheme 2004). Alphaviruses offer several advantages, particularly in a vaccine setting where heterologous antigen expression can be desired. Due to its ability to self-replicate in the host cytosol, alphavirus vectors are generally able to produce high copy numbers of the expression cassette within a cell resulting in a high level of heterologous antigen production. Additionally, the vectors are generally transient, resulting in improved biosafety as well as reduced induction of immunological tolerance to the vector. The public, in general, also lacks pre-existing immunity to alphavirus vectors as compared to other standard viral vectors, such as human adenovirus. Alphavirus based vectors also generally result in cytotoxic responses to infected cells. Cytotoxicity, to a certain degree, can be important in a vaccine setting to properly illicit an immune response to the heterologous antigen expressed. However, the degree of desired cytotoxicity can be a balancing act, and thus several attenuated alphaviruses have been developed, including the TC-83 strain of VEE. Thus, an example of an antigen expression vector described herein can utilize an alphavirus backbone that allows for a high level of antigen expression, stimulates a robust immune response to antigen, does not stimulate an immune response to the vector itself, and can be used in a safe manner. Furthermore, the antigen expression cassette can be designed to stimulate differentlevels of an immune response through optimization of which alphavirus sequences the vector uses, including, but not limited to, sequences derived from VEE or its attenuated derivative TC- 83.

[0277] Several expression vector design strategies have been engineered using alphavirus sequences (Pushko 1997). In one strategy, a alphavirus vector design includes inserting a second copy of the 26S promoter sequence elements downstream of the structural protein genes, followed by a heterologous gene (Frolov 1993). Thus, in addition to the natural non-structural and structural proteins, an additional subgenomic RNA is produced that expresses the heterologous protein. In this system, all the elements for production of infectious virions are present and, therefore, repeated rounds of infection of the expression vector in non-infected cells can occur.

[0278] Another expression vector design makes use of helper virus systems (Pushko 1997). In this strategy, the structural proteins are replaced by a heterologous gene. Thus, following selfreplication of viral RNA mediated by still intact non-structural genes, the 26S subgenomic RNA provides for expression of the heterologous protein. Traditionally, additional vectors that expresses the structural proteins are then supplied in trans, such as by co-transfection of a cell line, to produce infectious virus. A system is described in detail in USPN 8,093,021, which is herein incorporated by reference in its entirety, for all purposes. The helper vector system provides the benefit of limiting the possibility of forming infectious particles and, therefore, improves biosafety. In addition, the helper vector system reduces the total vector length, potentially improving the replication and expression efficiency. Thus, an example of an antigen expression vector described herein can utilize an alphavirus backbone wherein the structural proteins are replaced by an antigen cassette, the resulting vector both reducing biosafety concerns, while at the same time promoting efficient expression due to the reduction in overall expression vector size.V.C.3. Self-Amplifying Virus Production in vitro

[0279] A convenient technique well-known in the art for RNA production is in vitro transcription (IVT). In this technique, a DNA template of the desired vector is first produced by techniques well-known to those in the art, including standard molecular biology techniques such as cloning, restriction digestion, ligation, gene synthesis, and polymerase chain reaction (PCR).

[0280] The DNA template contains a RNA polymerase promoter at the 5’ end of the sequence desired to be transcribed into RNA (e.g., SAM). Promoters include, but are not limited to, bacteriophage polymerase promoters such as T3, T7, KI 1, or SP6. Depending on the specific RNA polymerase promoter sequence chosen, additional 5’ nucleotides can transcribed in addition to the desired sequence. For example, the canonical T7 promoter can be referred to bythe sequence TAATACGACTCACTATAGG, in which an IVT reaction using the DNA template TAATACGACTCACTATAGGN for the production of desired sequence N will result in the mRNA sequence GG-N. In general, and without wishing to be bound by theory, T7 polymerase more efficiently transcribes RNA transcripts beginning with guanosine. In instances where additional 5’ nucleotides are not desired (e.g., no additional GG), the RNA polymerase promoter contained in the DNA template can be a sequence the results in transcripts containing only the 5’ nucleotides of the desired sequence, e.g., a SAM having the native 5’ sequence of the self-replicating virus from which the SAM vector is derived. For example, a minimal T7 promoter can be referred to by the sequence TAATACGACTCACTATA, in which an IVT reaction using the DNA template TAATACGACTCACTATAN for the production of desired sequence N will result in the mRNA sequence N. Likewise, a minimal SP6 promoter referred to by the sequence ATTTAGGTGACACTATA can be used to generate transcripts without additional 5’ nucleotides. In a typical IVT reaction, the DNA template is incubated with the appropriate RNA polymerase enzyme, buffer agents, and nucleotides (NTPs).

[0281] The resulting RNA polynucleotide can optionally be further modified including, but limited to, addition of a 5’ cap structure such as 7-methylguanosine or a related structure, and optionally modifying the 3’ end to include a poly adenylate (poly A) tail. In a modified IVT reaction, RNA is capped with a 5’ cap structure co-transcriptionally through the addition of cap analogues during IVT. Cap analogues can include dinucleotide (m7G-ppp-N) cap analogues or trinucleotide (m7G-ppp-N-N) cap analogues, where N represents a nucleotide or modified nucleotide (e.g., ribonucleosides including, but not limited to, adenosine, guanosine, cytidine, and uradine). Exemplary cap analogues and their use in IVT reactions are also described in greater detail in U.S. Pat. No. 10,519,189, herein incorporated by reference for all purposes. As discussed, T7 polymerase more efficiently transcribes RNA transcripts beginning with guanosine. To improve transcription efficiency in templates that do not begin with guanosine, a trinucleotide cap analogue (m7G-ppp-N-N) can be used. The trinucleotide cap analogue can increase transcription efficiency 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20- fold or more relative to an IVT reaction using a dinucleotide cap analogue (m7G-ppp-N).

[0282] A 5’ cap structure can also be added following transcription, such as using a vaccinia capping system (e.g., NEB Cat. No. M2080) containing mRNA 2’-O-methyltransferase and S- Adenosyl methionine.

[0283] The resulting RNA polynucleotide can optionally be further modified separately from or in addition to the capping techniques described including, but limited to, modifying the 3’ end to include a poly adenylate (poly A) tail.

[0284] The RNA can then be purified using techniques well-known in the field, such as phenol-chloroform extraction.V.C.4. Delivery via lipid nanoparticle

[0285] An important aspect to consider in vaccine vector design is immunity against the vector itself (Riley 2017). This may be in the form of preexisting immunity to the vector itself, such as with certain human adenovirus systems, or in the form of developing immunity to the vector following administration of the vaccine. The latter is an important consideration if multiple administrations of the same vaccine are performed, such as separate priming and boosting doses, or if the same vaccine vector system is to be used to deliver different antigen cassettes.

[0286] In the case of alphavirus vectors, the standard delivery method is the previously discussed helper virus system that provides capsid, El, and E2 proteins in trans to produce infectious viral particles. However, it is important to note that the El and E2 proteins are often major targets of neutralizing antibodies (Strauss 1994). Thus, the efficacy of using alphavirus vectors to deliver antigens of interest to target cells may be reduced if infectious particles are targeted by neutralizing antibodies.

[0287] An alternative to viral particle mediated gene delivery is the use of nanomaterials to deliver expression vectors (Riley 2017). Nanomaterial vehicles, importantly, can be made of non-immunogenic materials and generally avoid stimulating immunity to the delivery vector itself. These materials can include, but are not limited to, lipids, inorganic nanomaterials, and other polymeric materials. Lipids can be cationic, anionic, or neutral. The materials can be synthetic or naturally derived, and in some instances biodegradable. Lipids can include fats, cholesterol, phospholipids, lipid conjugates including, but not limited to, polyethyleneglycol (PEG) conjugates (PEGylated lipids), waxes, oils, glycerides, and fat soluble vitamins.

[0288] Lipid nanoparticles (LNPs) are an attractive delivery system due to the amphiphilic nature of lipids enabling formation of membranes and vesicle like structures (Riley 2017). In general, these vesicles deliver the expression vector by absorbing into the membrane of target cells and releasing nucleic acid into the cytosol. In addition, LNPs can be further modified or functionalized to facilitate targeting of specific cell types. Another consideration in LNP design is the balance between targeting efficiency and cytotoxicity. Lipid compositions generally include defined mixtures of cationic, neutral, anionic, and amphipathic lipids. In some instances, specific lipids are included to prevent LNP aggregation, prevent lipid oxidation, or provide functional chemical groups that facilitate attachment of additional moieties. Lipid composition can influence overall LNP size and stability. In an example, the lipid composition comprises dilinoleylmethyl- 4-dimethylaminobutyrate (MC3) or MC3-like molecules. MC3 and MC3-likelipid compositions can be formulated to include one or more other lipids, such as a PEG or PEG- conjugated lipid, a sterol, or neutral lipids.

[0289] Nucleic-acid vectors, such as expression vectors, exposed directly to serum can have several undesirable consequences, including degradation of the nucleic acid by serum nucleases or off-target stimulation of the immune system by the free nucleic acids. Therefore, encapsulation of the alphavirus vector can be used to avoid degradation, while also avoiding potential off-target effects. In certain examples, an alphavirus vector is fully encapsulated within the delivery vehicle, such as within the aqueous interior of an LNP. Encapsulation of the alphavirus vector within an LNP can be carried out by techniques well-known to those skilled in the art, such as microfluidic mixing and droplet generation carried out on a microfluidic droplet generating device. Such devices include, but are not limited to, standard T-junction devices or flow-focusing devices. In an example, the desired lipid formulation, such as MC3 or MC3-like containing compositions, is provided to the droplet generating device in parallel with the alphavirus delivery vector and other desired agents, such that the delivery vector and desired agents are fully encapsulated within the interior of the MC3 or MC3-like based LNP. In an example, the droplet generating device can control the size range and size distribution of the LNPs produced. For example, the LNP can have a size ranging from 1 to 1000 nanometers in diameter, e.g., 1, 10, 50, 100, 500, or 1000 nanometers. Following droplet generation, the delivery vehicles encapsulating the expression vectors can be further treated or modified to prepare them for administration.V.D. Chimpanzee adenovirus (ChAd)V.D.l. Viral delivery with chimpanzee adenovirus

[0290] Vaccine compositions for delivery of one or more antigens (e.g., via an antigen cassette) can be created by providing adenovirus nucleotide sequences of chimpanzee origin, a variety of novel vectors, and cell lines expressing chimpanzee adenovirus genes. A nucleotide sequence of a chimpanzee C68 adenovirus (also referred to herein as ChAdV68) can be used in a vaccine composition for antigen delivery (See SEQ ID NO: 1). Use of C68 adenovirus derived vectors is described in further detail in USPN 6,083,716, which is herein incorporated by reference in its entirety, for all purposes.

[0291] In a further aspect, provided herein is a recombinant adenovirus comprising the DNA sequence of a chimpanzee adenovirus such as C68 and an antigen cassette operatively linked to regulatory sequences directing its expression. The recombinant virus is capable of infecting a mammalian, preferably a human, cell and capable of expressing the antigen cassette product in the cell. In this vector, the native chimpanzee El gene, and / or E3 gene, and / or E4 gene can bedeleted. An antigen cassette can be inserted into any of these sites of gene deletion. The antigen cassette can include an antigen against which a primed immune response is desired.

[0292] In another aspect, provided herein is a mammalian cell infected with a chimpanzee adenovirus such as C68.

[0293] In still a further aspect, a novel mammalian cell line is provided which expresses a chimpanzee adenovirus gene (e.g., from C68) or functional fragment thereof.

[0294] In still a further aspect, provided herein is a method for delivering an antigen cassette into a mammalian cell comprising the step of introducing into the cell an effective amount of a chimpanzee adenovirus, such as C68, that has been engineered to express the antigen cassette.

[0295] Still another aspect provides a method for stimulating an immune response in a mammalian host. The method can comprise the step of administering to the host an effective amount of a recombinant chimpanzee adenovirus, such as C68, comprising an antigen cassette that encodes one or more antigens from the infection against which the immune response is targeted.

[0296] Still another aspect provides a method for stimulating an immune response in a mammalian host to treat or prevent a disease in a subject, such as an infectious disease. The method can comprise the step of administering to the host an effective amount of a recombinant chimpanzee adenovirus, such as C68, comprising an antigen cassette that encodes one or more antigens, such as from the infectious disease against which the immune response is targeted.

[0297] Also disclosed is a non-simian mammalian cell that expresses a chimpanzee adenovirus gene obtained from the sequence of SEQ ID NO: 1. The gene can be selected from the group consisting of the adenovirus E1A, E1B, E2A, E2B, E3, E4, LI, L2, L3, L4 and L5 of SEQ ID NO: 1.

[0298] Also disclosed is a nucleic acid molecule comprising a chimpanzee adenovirus DNA sequence comprising a gene obtained from the sequence of SEQ ID NO: 1. The gene can be selected from the group consisting of said chimpanzee adenovirus E1A, E1B, E2A, E2B, E3, E4, LI, L2, L3, L4 and L5 genes of SEQ ID NO: 1. In some aspects the nucleic acid molecule comprises SEQ ID NO: 1. In some aspects the nucleic acid molecule comprises the sequence of SEQ ID NO: 1, lacking at least one gene selected from the group consisting of E1A, E1B, E2A, E2B, E3, E4, LI, L2, L3, L4 and L5 genes of SEQ ID NO: 1.

[0299] Also disclosed is a vector comprising a chimpanzee adenovirus DNA sequence obtained from SEQ ID NO: 1 and an antigen cassette operatively linked to one or more regulatory sequences which direct expression of the cassette in a heterologous host cell, optionally wherein the chimpanzee adenovirus DNA sequence comprises at least the cis-elements necessary for replication and virion encapsidation, the czs-elements flanking the antigen cassette and regulatory sequences. In some aspects, the chimpanzee adenovirus DNA sequence comprises a gene selected from the group consisting of El A, E1B, E2A, E2B, E3, E4, LI, L2, L3, L4 and L5 gene sequences of SEQ ID NO: 1. In some aspects the vector can lack the E1A and / or E1B gene.

[0300] Also disclosed herein is an adenovirus vector comprising: a partially deleted E4 gene comprising a deleted or partially-deleted E4orf2 region and a deleted or partially-deleted E4orf3 region, and optionally a deleted or partially-deleted E4orf4 region. The partially deleted E4 can comprise an E4 deletion of at least nucleotides 34,916 to 35,642 of the sequence shown in SEQ ID NO:1, and wherein the vector comprises at least nucleotides 2 to 36,518 of the sequence set forth in SEQ ID NO:1. The partially deleted E4 can comprise an E4 deletion of at least a partial deletion of nucleotides 34,916 to 34,942 of the sequence shown in SEQ ID NO: 1, at least a partial deletion of nucleotides 34,952 to 35,305 of the sequence shown in SEQ ID NO: 1, and at least a partial deletion of nucleotides 35,302 to 35,642 of the sequence shown in SEQ ID NO:1, and wherein the vector comprises at least nucleotides 2 to 36,518 of the sequence set forth in SEQ ID NO:1 The partially deleted E4 can comprise an E4 deletion of at least nucleotides 34,980 to 36,516 of the sequence shown in SEQ ID NO:1, and wherein the vector comprises at least nucleotides 2 to 36,518 of the sequence set forth in SEQ ID NO:1. The partially deleted E4 can comprise an E4 deletion of at least nucleotides 34,979 to 35,642 of the sequence shown in SEQ ID NO:1, and wherein the vector comprises at least nucleotides 2 to 36,518 of the sequence set forth in SEQ ID NO: 1. The partially deleted E4 can comprise an E4 deletion of at least a partial deletion of E40rf2, a fully deleted E40rf3, and at least a partial deletion of E40rf4. The partially deleted E4 can comprise an E4 deletion of at least a partial deletion of E40rf2, at least a partial deletion of E40rf3, and at least a partial deletion of E40rf4. The partially deleted E4 can comprise an E4 deletion of at least a partial deletion of E4Orf 1 , a fully deleted E40rf2, and at least a partial deletion of E40rf3. The partially deleted E4 can comprise an E4 deletion of at least a partial deletion of E40rf2 and at least a partial deletion of E40rf3.The partially deleted E4 can comprise an E4 deletion between the start site of E4Orfl to the start site of E40rf5. The partially deleted E4 can be an E4 deletion adjacent to the start site of E4Orfl. The partially deleted E4 can be an E4 deletion adjacent to the start site of E40rf2. The partially deleted E4 can be an E4 deletion adjacent to the start site of E40rf3. The partially deleted E4 can be an E4 deletion adjacent to the start site of E40rf4. The E4 deletion can be at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1100, at least 1200, at least 1300, at least 1400, at least 1500, at least 1600, at least 1700, at least 1800, at least 1900, or at least 2000 nucleotides. The E4 deletion canbe at least 700 nucleotides. The E4 deletion can be at least 1500 nucleotides. The E4 deletion can be 50 or less, 100 or less, 200 or less, 300 or less, 400 or less, 500 or less, 600 or less, 700 or less, 800 or less, 900 or less, 1000 or less, 1100 or less, 1200 or less, 1300 or less, 1400 or less, 1500 or less, 1600 or less, 1700 or less, 1800 or less, 1900 or less, or 2000 or less nucleotides.The E4 deletion can be 750 nucleotides or less. The E4 deletion can be at least 1550 nucleotides or less.

[0301] Also disclosed herein is a host cell transfected with a vector disclosed herein such as a C68 vector engineered to expression an antigen cassette. Also disclosed herein is a human cell that expresses a selected gene introduced therein through introduction of a vector disclosed herein into the cell.

[0302] Also disclosed herein is a method for delivering an antigen cassette to a mammalian cell comprising introducing into said cell an effective amount of a vector disclosed herein such as a C68 vector engineered to expression the antigen cassette.

[0303] Also disclosed herein is a method for producing an antigen comprising introducing a vector disclosed herein into a mammalian cell, culturing the cell under suitable conditions and producing the antigen.V.D.2. El-Expressing Complementation Cell Lines

[0304] To generate recombinant chimpanzee adenoviruses (Ad) deleted in any of the genes described herein, the function of the deleted gene region, if essential to the replication and infectivity of the virus, can be supplied to the recombinant virus by a helper virus or cell line, i.e., a complementation or packaging cell line. For example, to generate a replication-defective chimpanzee adenovirus vector, a cell line can be used which expresses the El gene products of the human or chimpanzee adenovirus; such a cell line can include HEK293 or variants thereof. The protocol for the generation of the cell lines expressing the chimpanzee El gene products (Examples 3 and 4 of USPN 6,083,716) can be followed to generate a cell line which expresses any selected chimpanzee adenovirus gene.

[0305] An AAV augmentation assay can be used to identify a chimpanzee adenovirus El- expressing cell line. This assay is useful to identify El function in cell lines made by using the El genes of other uncharacterized adenoviruses, e.g., from other species. That assay is described in Example 4B of USPN 6,083,716.

[0306] A selected chimpanzee adenovirus gene, e.g., El, can be under the transcriptional control of a promoter for expression in a selected parent cell line. Inducible or constitutive promoters can be employed for this purpose. Among inducible promoters are included the sheep metallothionine promoter, inducible by zinc, or the mouse mammary tumor virus (MMTV)promoter, inducible by a glucocorticoid, particularly, dexamethasone. Other inducible promoters, such as those identified in International patent application WO95 / 13392, incorporated by reference herein can also be used in the production of packaging cell lines. Constitutive promoters in control of the expression of the chimpanzee adenovirus gene can be employed also.

[0307] A parent cell can be selected for the generation of a novel cell line expressing any desired C68 gene. Without limitation, such a parent cell line can be HeLa [ATCC Accession No. CCL 2], A549 [ATCC Accession No. CCL 185], KB [CCL 17], Detroit [e.g., Detroit 510, CCL 72] and WI-38 [CCL 75] cells. Other suitable parent cell lines can be obtained from other sources. Parent cell lines can include CHO, HEK293 or variants thereof, 911, HeLa, A549, LP- 293, PER.C6, or AEl-2a.

[0308] An El-expressing cell line can be useful in the generation of recombinant chimpanzee adenovirus El deleted vectors. Cell lines constructed using essentially the same procedures that express one or more other chimpanzee adenoviral gene products are useful in the generation of recombinant chimpanzee adenovirus vectors deleted in the genes that encode those products. Further, cell lines which express other human Ad El gene products are also useful in generating chimpanzee recombinant Ads.V.D.3. Recombinant Viral Particles as Vectors

[0309] The compositions disclosed herein can comprise viral vectors, that deliver at least one antigen to cells. Such vectors comprise a chimpanzee adenovirus DNA sequence such as C68 and an antigen cassette operatively linked to regulatory sequences which direct expression of the cassette. The C68 vector is capable of expressing the cassette in an infected mammalian cell. The C68 vector can be functionally deleted in one or more viral genes. An antigen cassette comprises at least one antigen under the control of one or more regulatory sequences such as a promoter. Optional helper viruses and / or packaging cell lines can supply to the chimpanzee viral vector any necessary products of deleted adenoviral genes.

[0310] The term "functionally deleted" means that a sufficient amount of the gene region is removed or otherwise altered, e.g., by mutation or modification, so that the gene region is no longer capable of producing one or more functional products of gene expression. Mutations or modifications that can result in functional deletions include, but are not limited to, nonsense mutations such as introduction of premature stop codons and removal of canonical and non- canonical start codons, mutations that alter mRNA splicing or other transcriptional processing, or combinations thereof. If desired, the entire gene region can be removed.

[0311] Modifications of the nucleic acid sequences forming the vectors disclosed herein, including sequence deletions, insertions, and other mutations may be generated using standard molecular biological techniques and are within the scope of this invention.V.D.4. Construction of The Viral Plasmid Vector

[0312] The chimpanzee adenovirus C68 vectors useful in this invention include recombinant, defective adenoviruses, that is, chimpanzee adenovirus sequences functionally deleted in the Ela or Elb genes, and optionally bearing other mutations, e.g., temperaturesensitive mutations or deletions in other genes. It is anticipated that these chimpanzee sequences are also useful in forming hybrid vectors from other adenovirus and / or adeno-associated virus sequences. Homologous adenovirus vectors prepared from human adenoviruses are described in the published literature [see, for example, Kozarsky T and TT, cited above, and references cited therein, U.S. Pat. No. 5,240,846].

[0313] In the construction of useful chimpanzee adenovirus C68 vectors for delivery of an antigen cassette to a human (or other mammalian) cell, a range of adenovirus nucleic acid sequences can be employed in the vectors. A vector comprising minimal chimpanzee C68 adenovirus sequences can be used in conjunction with a helper virus to produce an infectious recombinant virus particle. The helper virus provides essential gene products required for viral infectivity and propagation of the minimal chimpanzee adenoviral vector. When only one or more selected deletions of chimpanzee adenovirus genes are made in an otherwise functional viral vector, the deleted gene products can be supplied in the viral vector production process by propagating the virus in a selected packaging cell line that provides the deleted gene functions in trans.V.D.5. Recombinant Minimal Adenovirus

[0314] A minimal chimpanzee Ad C68 virus is a viral particle containing just the adenovirus cis-elements necessary for replication and virion encapsidation. That is, the vector contains the cis-acting 5' and 3' inverted terminal repeat (ITR) sequences of the adenoviruses (which function as origins of replication) and the native 5' packaging / enhancer domains (that contain sequences necessary for packaging linear Ad genomes and enhancer elements for the El promoter). See, for example, the techniques described for preparation of a "minimal" human Ad vector in International Patent Application WO96 / 13597 and incorporated herein by reference.V.D.6. Other Defective Adenoviruses

[0315] Recombinant, replication-deficient adenoviruses can also contain more than the minimal chimpanzee adenovirus sequences. These other Ad vectors can be characterized bydeletions of various portions of gene regions of the virus, and infectious virus particles formed by the optional use of helper viruses and / or packaging cell lines.

[0316] As one example, suitable vectors may be formed by deleting all or a sufficient portion of the C68 adenoviral immediate early gene Ela and delayed early gene E lb, so as to eliminate their normal biological functions. Replication-defective El-deleted viruses are capable of replicating and producing infectious virus when grown on a chimpanzee adenovirus- transformed, complementation cell line containing functional adenovirus Ela and Elb genes which provide the corresponding gene products in trans. Based on the homologies to known adenovirus sequences, it is anticipated that, as is true for the human recombinant El-deleted adenoviruses of the art, the resulting recombinant chimpanzee adenovirus is capable of infecting many cell types and can express antigen(s), but cannot replicate in most cells that do not carry the chimpanzee El region DNA unless the cell is infected at a very high multiplicity of infection.

[0317] As another example, all or a portion of the C68 adenovirus delayed early gene E3 can be eliminated from the chimpanzee adenovirus sequence which forms a part of the recombinant virus.

[0318] Chimpanzee adenovirus C68 vectors can also be constructed having a deletion of the E4 gene. Still another vector can contain a deletion in the delayed early gene E2a.

[0319] Deletions can also be made in any of the late genes LI through L5 of the chimpanzee C68 adenovirus genome. Similarly, deletions in the intermediate genes IX and IVa2 can be useful for some purposes. Other deletions may be made in the other structural or non-structural adenovirus genes.

[0320] The above discussed deletions can be used individually, i.e., an adenovirus sequence can contain deletions of El only. Alternatively, deletions of entire genes or portions thereof effective to destroy or reduce their biological activity can be used in any combination. For example, in one exemplary vector, the adenovirus C68 sequence can have deletions of the El genes and the E4 gene, or of the El, E2a and E3 genes, or of the El and E3 genes, or of El, E2a and E4 genes, with or without deletion of E3, and so on. As discussed above, such deletions can be used in combination with other mutations, such as temperature-sensitive mutations, to achieve a desired result.

[0321] The cassette comprising antigen(s) be inserted optionally into any deleted region of the chimpanzee C68 Ad virus. Alternatively, the cassette can be inserted into an existing gene region to disrupt the function of that region, if desired.V.D.7. Helper Viruses

[0322] Depending upon the chimpanzee adenovirus gene content of the viral vectors employed to carry the antigen cassette, a helper adenovirus or non-replicating virus fragment can be used to provide sufficient chimpanzee adenovirus gene sequences to produce an infective recombinant viral particle containing the cassette.

[0323] Useful helper viruses contain selected adenovirus gene sequences not present in the adenovirus vector construct and / or not expressed by the packaging cell line in which the vector is transfected. A helper virus can be replication-defective and contain a variety of adenovirus genes in addition to the sequences described above. The helper virus can be used in combination with the El -expressing cell lines described herein.

[0324] For C68, the "helper" virus can be a fragment formed by clipping the C terminal end of the C68 genome with SspI, which removes about 1300 bp from the left end of the virus. This clipped virus is then co-transfected into an El -expressing cell line with the plasmid DNA, thereby forming the recombinant virus by homologous recombination with the C68 sequences in the plasmid.

[0325] Helper viruses can also be formed into poly-cation conjugates as described in Wu et al, J. Biol. Chem., 264:16985-16987 (1989); K. J. Fisher and J. M. Wilson, Biochem. J., 299:49 (Apr. 1, 1994). Helper virus can optionally contain a reporter gene. A number of such reporter genes are known to the art. The presence of a reporter gene on the helper virus which is different from the antigen cassette on the adenovirus vector allows both the Ad vector and the helper virus to be independently monitored. This second reporter is used to enable separation between the resulting recombinant virus and the helper virus upon purification.V.D.8. Assembly of Viral Particle and Infection of a Cell Line

[0326] Assembly of the selected DNA sequences of the adenovirus, the antigen cassette, and other vector elements into various intermediate plasmids and shuttle vectors, and the use of the plasmids and vectors to produce a recombinant viral particle can all be achieved using conventional techniques. Such techniques include conventional cloning techniques of cDNA, in vitro recombination techniques (e.g., Gibson assembly), use of overlapping oligonucleotide sequences of the adenovirus genomes, polymerase chain reaction, and any suitable method which provides the desired nucleotide sequence. Standard transfection and co-transfection techniques are employed, e.g., CaPO4 precipitation techniques or liposome-mediated transfection methods such as lipofectamine. Other conventional methods employed include homologous recombination of the viral genomes, plaquing of viruses in agar overlay, methods of measuring signal generation, and the like.

[0327] For example, following the construction and assembly of the desired antigen cassette-containing viral vector, the vector can be transfected in vitro in the presence of a helper virus into the packaging cell line. Homologous recombination occurs between the helper and the vector sequences, which permits the adenovirus-antigen sequences in the vector to be replicated and packaged into virion capsids, resulting in the recombinant viral vector particles.

[0328] The resulting recombinant chimpanzee C68 adenoviruses are useful in transferring an antigen cassette to a selected cell. In in vivo experiments with the recombinant virus grown in the packaging cell lines, the El -deleted recombinant chimpanzee adenovirus demonstrates utility in transferring a cassette to a non-chimpanzee, preferably a human, cell.V.D.9. Use of the Recombinant Virus Vectors

[0329] The resulting recombinant chimpanzee C68 adenovirus containing the antigen cassette (produced by cooperation of the adenovirus vector and helper virus or adenoviral vector and packaging cell line, as described above) thus provides an efficient gene transfer vehicle which can deliver antigen(s) to a subject in vivo or ex vivo.

[0330] The above-described recombinant vectors are administered to humans according to published methods for gene therapy. A chimpanzee viral vector bearing an antigen cassette can be administered to a patient, preferably suspended in a biologically compatible solution or pharmaceutically acceptable delivery vehicle. A suitable vehicle includes sterile saline. Other aqueous and non-aqueous isotonic sterile injection solutions and aqueous and non-aqueous sterile suspensions known to be pharmaceutically acceptable carriers and well known to those of skill in the art may be employed for this purpose.

[0331] The chimpanzee adenoviral vectors are administered in sufficient amounts to transduce the human cells and to provide sufficient levels of antigen transfer and expression to provide a therapeutic benefit without undue adverse or with medically acceptable physiological effects, which can be determined by those skilled in the medical arts. Conventional and pharmaceutically acceptable routes of administration include, but are not limited to, direct delivery to the liver, intranasal, intravenous, intramuscular, subcutaneous, intradermal, oral and other parental routes of administration. Routes of administration may be combined, if desired.

[0332] Dosages of the viral vector will depend primarily on factors such as the condition being treated, the age, weight and health of the patient, and may thus vary among patients. The dosage will be adjusted to balance the therapeutic benefit against any side effects and such dosages may vary depending upon the therapeutic application for which the recombinant vector is employed. The levels of expression of antigen(s) can be monitored to determine the frequency of dosage administration.

[0333] Recombinant, replication defective adenoviruses can be administered in a "pharmaceutically effective amount", that is, an amount of recombinant adenovirus that is effective in a route of administration to transfect the desired cells and provide sufficient levels of expression of the selected gene to provide a vaccinal benefit, i.e., some measurable level of protective immunity. C68 vectors comprising an antigen cassette can be co- administered with adjuvant. Adjuvant can be separate from the vector (e.g., alum) or encoded within the vector, in particular if the adjuvant is a protein. Adjuvants are well known in the art.

[0334] Conventional and pharmaceutically acceptable routes of administration include, but are not limited to, intranasal, intramuscular, intratracheal, subcutaneous, intradermal, rectal, oral and other parental routes of administration. Routes of administration may be combined, if desired, or adjusted depending upon the immunogen or the disease. For example, in prophylaxis of rabies, the subcutaneous, intratracheal and intranasal routes are preferred. The route of administration primarily will depend on the nature of the disease being treated.

[0335] The levels of immunity to antigen(s) can be monitored to determine the need, if any, for boosters. Following an assessment of antibody titers in the serum, for example, optional booster immunizations may be desiredVI. Therapeutic and Manufacturing Methods

[0336] Also provided is a method of inducing an infectious disease organism-specific (e.g. a HPV specific) immune response in a subject, vaccinating against an infectious disease organism, treating and / or alleviating a symptom of an infection associated with an infectious disease organism in a subject by administering to the subject one or more antigens such as a plurality of antigens identified using methods disclosed herein.

[0337] In some aspects, a subject has been diagnosed with an infection or is at risk of an infection (e.g. one or more of cervical cancer, anal cancer, oropharyngeal cancer, oral cancer, penile cancer, vaginal cancer, and / or vulvar cancer due to a HPV infection), such as age, geographical / travel, and / or work-related increased risk of or predisposition to an infection, or at risk to a seasonal and / or novel disease infection.

[0338] In some aspects, a subject is immunocompromised, such as diagnosed with and / or suspected of having cancer. A subject can include those treated with a therapy resulting in immunosuppression. For example, a subject can include those diagnosed with a hematopoietic malignancy and treated with a hematopoietic cell targeting therapy, such as a B cell malignancy treated with an anti-CD20 therapy (e.g., rituximab). In another example, a subject can include those diagnosed with multiple sclerosis [e.g., Relapsing-remitting multiple sclerosis (RRMS),Secondary-progressive multiple sclerosis (SPMS), or Primary-progressive multiple sclerosis (PPMS)] and treated with an anti-CD20 therapy.

[0339] An antigen can be administered in an amount sufficient to stimulate a CTL response. An antigen can be administered in an amount sufficient to stimulate a T cell response. An antigen can be administered in an amount sufficient to stimulate a B cell response.

[0340] An antigen can be administered alone or in combination with other therapeutic agents. Therapeutic agents can include those that target an infectious disease organism, such as an anti-viral or antibiotic agent.

[0341] The optimum amount of each antigen to be included in a vaccine composition and the optimum dosing regimen can be determined. For example, an antigen or its variant can be prepared for intravenous (i.v.) injection, sub-cutaneous (s.c.) injection, intradermal (i.d.) injection, intraperitoneal (i.p.) injection, intramuscular (i.m.) injection. Methods of injection include s.c., i.d., i.p., i.m., and i.v. Methods of DNA or RNA injection include i.d., i.m., s.c., i.p. and i.v. Other methods of administration of the vaccine composition are known to those skilled in the art.

[0342] A vaccine can be compiled so that the selection, number and / or amount of antigens present in the composition is / are tissue, infectious disease, and / or patient-specific. For instance, the exact selection of peptides can be guided by expression patterns of the parent proteins in a given tissue or guided by mutation or disease status of a patient. The selection can be dependent on the specific infectious disease (e.g. the specific HPV strain the subject is infected with or at risk for infection by), the status of the disease, the goal of the vaccination (e.g. , preventative or targeting an ongoing disease), earlier treatment regimens, the immune status of the patient, and, of course, the HLA-haplotype of the patient. Furthermore, a vaccine can contain individualized components, according to personal needs of the particular patient. Examples include varying the selection of antigens according to the expression of the antigen in the particular patient or adjustments for secondary treatments following a first round or scheme of treatment.

[0343] A patient can be identified for administration of an antigen vaccine through the use of various diagnostic methods, e.g., patient selection methods described further below. Patient selection can involve identifying mutations in, or expression patterns of, one or more genes. Patient selection can involve identifying the infectious disease of an ongoing infection (e.g. the presence of a HPV infection and / or the specific HPV strain). Patient selection can involve identifying risk of an infection by an infectious disease. In some cases, patient selection involves identifying the haplotype of the patient. The various patient selection methods can be performed in parallel, e.g., a sequencing diagnostic can identify both the mutations and the haplotype of a patient. The various patient selection methods can be performed sequentially, e.g. , onediagnostic test identifies the mutations and separate diagnostic test identifies the haplotype of a patient, and where each test can be the same (e.g., both high-throughput sequencing) or different (e.g. , one high-throughput sequencing and the other Sanger sequencing) diagnostic methods.

[0344] For a composition to be used as a vaccine for an infectious disease, antigens with similar normal self-peptides that are expressed in high amounts in normal tissues can be avoided or be present in low amounts in a composition described herein. On the other hand, if it is known that the infected cell of a patient expresses high amounts of a certain antigen, the respective pharmaceutical composition for treatment of this infection can be present in high amounts and / or more than one antigen specific for this particularly antigen or pathway of this antigen can be included.

[0345] Compositions comprising an antigen can be administered to an individual already having (e.g., diagnosed with) an infection. In therapeutic applications, compositions are administered to a patient in an amount sufficient to stimulate an effective CTL response to the infectious disease organism antigen and to cure or at least partially arrest symptoms and / or complications. An amount adequate to accomplish this is defined as "therapeutically effective dose." Amounts effective for this use will depend on, e.g., the composition, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician. It should be kept in mind that compositions can generally be employed in serious disease states, that is, life-threatening or potentially life threatening situations, especially when the infectious disease organism has induced organ damage and / or other immune pathology. In such cases, in view of the minimization of extraneous substances and the relative nontoxic nature of an antigen, it is possible and can be felt desirable by the treating physician to administer substantial excesses of these compositions.

[0346] For therapeutic use, administration can begin at the detection or treatment of an infection. This can be followed by boosting doses until at least symptoms are substantially abated and for a period thereafter.

[0347] The pharmaceutical compositions (e.g., vaccine compositions) for therapeutic treatment are intended for parenteral, topical, nasal, oral or local administration. A pharmaceutical compositions can be administered parenterally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. The compositions can be administered to target specific infected tissues and / or cells of a subject. Disclosed herein are compositions for parenteral administration which comprise a solution of the antigen and vaccine compositions are dissolved or suspended in an acceptable carrier, e.g., an aqueous carrier. A variety of aqueous carriers can be used, e.g., water, buffered water, 0.9% saline, 0.3% glycine, hyaluronic acid andthe like. These compositions can be sterilized by conventional, well known sterilization techniques, or can be sterile filtered. The resulting aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

[0348] Antigens can also be administered via liposomes, which target them to a particular cells tissue, such as lymphoid tissue. Liposomes are also useful in increasing half-life. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations the antigen to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to, e.g., a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes filled with a desired antigen can be directed to the site of lymphoid cells, where the liposomes then deliver the selected therapeutic / immunogenic compositions. Liposomes can be formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka et al., Ann. Rev. Biophys. Bioeng. 9; 467 (1980), U.S. Pat. Nos. 4,235,871, 4,501,728, 4,501,728, 4,837,028, and 5,019,369.

[0349] For targeting to the immune cells, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension can be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

[0350] For therapeutic or immunization purposes, nucleic acids encoding a peptide and optionally one or more of the peptides described herein can also be administered to the patient. A number of methods are conveniently used to deliver the nucleic acids to the patient. For instance, the nucleic acid can be delivered directly, as "naked DNA". This approach is described, for instance, in Wolff et al., Science 247: 1465-1468 (1990) as well as U.S. Pat. Nos. 5,580,859 and 5,589,466. The nucleic acids can also be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Particles comprised solely of DNA can be administered.Alternatively, DNA can be adhered to particles, such as gold particles. Approaches for delivering nucleic acid sequences can include viral vectors, mRNA vectors, and DNA vectors with or without electroporation.

[0351] The nucleic acids can also be delivered complexed to cationic compounds, such as cationic lipids. Lipid-mediated gene delivery methods are described, for instance, in 9618372WOAWO 96 / 18372; 9324640WOAWO 93 / 24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682-691 (1988); U.S. Pat. No. 5,279,833 Rose U.S. Pat. No. 5,279,833; 9106309WOAWO 91 / 06309; and Feigner et al., Proc. Natl. Acad. Sci. USA 84: 7413-7414 (1987).

[0352] Antigens can also be included in viral vector-based vaccine platforms, such as vaccinia, fowlpox, self-replicating alphavirus, marabavirus, adenovirus (See, e.g., Tatsis et al., Adenoviruses, Molecular Therapy (2004) 10, 616 — 629), or lentivirus, including but not limited to second, third or hybrid second / third generation lentivirus and recombinant lentivirus of any generation designed to target specific cell types or receptors (See, e.g., Hu et al., Immunization Delivered by Lentiviral Vectors for Cancer and Infectious Diseases, Immunol Rev. (2011) 239(1): 45-61, Sakuma et al., Lentiviral vectors: basic to translational, Biochem J. (2012) 443(3):603-18, Cooper et al., Rescue of splicing-mediated intron loss maximizes expression in lentiviral vectors containing the human ubiquitin C promoter, Nucl. Acids Res. (2015) 43 (1): 682-690, Zufferey et al., Self-Inactivating Lentivirus Vector for Safe and Efficient In Vivo Gene Delivery, J. Virol. (1998) 72 (12): 9873-9880). Dependent on the packaging capacity of the above mentioned viral vector-based vaccine platforms, this approach can deliver one or more nucleotide sequences that encode one or more antigen peptides. The sequences may be flanked by non-mutated sequences, may be separated by linkers or may be preceded with one or more sequences targeting a subcellular compartment (See, e.g., Gros et al., Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients, Nat Med. (2016) 22 (4):433-8, Stronen et al., Targeting of cancer neoantigens with donor-derived T cell receptor repertoires, Science. (2016) 352 (6291): 1337-41, Lu et al., Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions, Clin Cancer Res. (2014) 20( 13):3401-10). Upon introduction into a host, infected cells express the antigens, and thereby stimulate a host immune (e.g., CTL) response against the peptide(s). Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al. (Nature 351:456-460 (1991)). A wide variety of other vaccine vectors useful for therapeutic administration or immunization of antigens, e.g., Salmonella typhi vectors, and the like will be apparent to those skilled in the art from the description herein.

[0353] A means of administering nucleic acids uses minigene constructs encoding one or multiple epitopes. To create a DNA sequence encoding the selected CTL epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes are reverse translated. A human codon usage table is used to guide the codon choice for each amino acid. These epitopeencoding DNA sequences are directly adjoined, creating a continuous polypeptide sequence. To optimize expression and / or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequence that could be reverse translated and included in the minigene sequence include: helper T lymphocyte, epitopes, a leader (signal) sequence, and an endoplasmic reticulum retention signal. In addition, MHC presentation of CTL epitopes can be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL epitopes. The minigene sequence is converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) are synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides are joined using T4 DNA ligase. This synthetic minigene, encoding the CTL epitope polypeptide, can then cloned into a desired expression vector.

[0354] Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate- buffer saline (PBS). A variety of methods have been described, and new techniques can become available. As noted above, nucleic acids are conveniently formulated with cationic lipids. In addition, glycolipids, fusogenic liposomes, peptides and compounds referred to collectively as protective, interactive, non-condensing (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.

[0355] Also disclosed is a method of manufacturing a vaccine, comprising performing the steps of a method disclosed herein; and producing a vaccine comprising a plurality of antigens or a subset of the plurality of antigens.

[0356] Antigens disclosed herein can be manufactured using methods known in the art. For example, a method of producing an antigen or a vector (e.g., a vector including at least one sequence encoding one or more antigens) disclosed herein can include culturing a host cell under conditions suitable for expressing the antigen or vector wherein the host cell comprises at least one polynucleotide encoding the antigen or vector, and purifying the antigen or vector. Standard purification methods include chromatographic techniques, electrophoretic, immunological, precipitation, dialysis, filtration, concentration, and chromatofocusing techniques.

[0357] Host cells can include a Chinese Hamster Ovary (CHO) cell, NSO cell, yeast, or a HEK293 cell. Host cells can be transformed with one or more polynucleotides comprising at least one nucleic acid sequence that encodes an antigen or vector disclosed herein, optionally wherein the isolated polynucleotide further comprises a promoter sequence operably linked to the at least one nucleic acid sequence that encodes the antigen or vector. In certain embodiments the isolated polynucleotide can be cDNA.VII. Antigen Use and Administration

[0358] A vaccination protocol can be used to dose a subject with one or more antigens and / or epitopes. A priming vaccine and a boosting vaccine can be used to dose the subject.

[0359] The priming vaccine can be based on C68 (e.g., the sequences shown in SEQ ID NO:1 or 2) or srRNA (e.g., the sequences shown in SEQ ID NO:3 or 4) and the boosting vaccine can be based on C68 (e.g., the sequences shown in SEQ ID NO: 1 or 2) or srRNA / samRNA (e.g., the sequences shown in SEQ ID NO: 3 or 4). Each vector typically includes a cassette that includes antigens and / or epitopes. Cassettes can include about 20 epitopes (or antigens from which the epitopes are derived), separated by spacers such as the natural sequence that normally surrounds each epitope or other non-natural spacer sequences such as AAY. Cassettes can also include MHCII antigens / epitopes such a tetanus toxoid antigen and PADRE antigen, which can be considered universal class II antigens. Cassettes can also include a targeting sequence such as a ubiquitin targeting sequence.

[0360] A priming vaccine can be injected (e.g., intramuscularly) in a subject. Bilateral injections per dose can be used. For example, one or more injections of ChAdV68 (C68) can be used (e.g., total dose IxlO12viral particles); one or more injections of self- amplifying RNA (samRNA or SAM), such as a dose of 3 pg, lOpg, 30pg, lOOpg, or 300pg RNA can be used. A SAM priming dose of 30pg or less can be used. A SAM priming dose of lOpg or less can be used. A SAM priming dose of 3 pg or less can be used. One or more injections of samRNA at a dose of 30pg or less can be used. A dose of 30pg or less can represent the total content of RNA / samRNA administered. A dose of 30pg or less can represent the total content of RNA / samRNA administered and include only a single distinct samRNA construct. A SAM prime of between 10-30pg, 10-100pg, 10-300pg, 30-100pg, 30-300pg, or 100-300pg RNA can be administered. A SAM prime of between 10-500pg, lO-lOOOpg, 30-500pg, 30-1000pg, or 500-1000pg RNA can be administered. A SAM prime of at least 400pg, at least 500pg, at least 600pg, at least 700pg, at least 800pg, at least 900pg, at least lOOOpg RNA can be administered. A SAM prime of lOpg, 30pg, lOOpg, or 300pg RNA can be administered. A SAM prime of 300 pg RNA can be administered. A SAM prime of lOOpg RNA can be administered. A SAMprime of 30pg RNA can be administered. A SAM prime of 20 pg RNA can be administered. A SAM prime of lOpg RNA can be administered. A SAM prime of 3|ig RNA can be administered. A SAM prime of at least 300pg RNA can be administered. A SAM prime of at least lOOpg RNA can be administered. A SAM prime of at least 30pg RNA can be administered. A SAM prime of at least lOpg RNA can be administered. A SAM prime of at least 3pg RNA can be administered. A SAM prime of less than or equal to 300 pg RNA can be administered. A SAM prime of less than or equal to lOOpg RNA can be administered. For ChAdV68 priming, IxlO12or less of viral particles can be administered. For ChAdV68 priming, 3x 10" or less of the viral particles can be administered. For ChAdV68 priming, at least IxlO11of the viral particles can be administered. For ChAdV68 priming, between IxlO11and IxlO12, between 3xl0nand IxlO12, or between IxlO11and 3x10'1of the viral particles can be administered. For ChAdV68 priming, IxlO11, 3xl0n, or IxlO12of the viral particles can be administered. For ChAdV68 priming, the viral particles can be at a concentration of at 5xl0nvp / mL.

[0361] A vaccine boost (boosting vaccine) can be injected (e.g., intramuscularly) after prime vaccination. A boosting vaccine can be administered about every 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks, e.g., every 4 weeks and / or 8 weeks after the prime. A boosting vaccine can be administered 4 weeks after the prime. A boosting vaccine can be administered a month after the prime. A boosting vaccine can be administered 28 days after the prime. A boosting vaccine can be administered 28 days after the prime. A boosting vaccine can be administered 113 days after the prime. A boosting vaccine can be administered at least 4 weeks after the prime. A boosting vaccine can be administered at least a month after the prime. A boosting vaccine can be administered at least 28 days after the prime. A boosting vaccine can be administered at least 28 days after the prime. A boosting vaccine can be administered at least 113 days after the prime. A boosting vaccine can be administered between 28 to 113 days after the prime. Bilateral injections per dose can be used. For example, one or more injections of ChAdV68 (C68) can be used (e.g., total dose IxlO12viral particles); one or more injections of self- amplifying RNA (samRNA or SAM), such as a dose of 3 pg, lOpg, 30pg, lOOpg, or 300pg RNA can be used. A SAM boosting dose of 30pg or less can be used. A SAM boosting dose of lOpg or less can be used. A SAM boosting dose of 3pg or less can be used. One or more injections of samRNA at a dose of 30pg or less can be used. A dose of 30pg or less can represent the total content of RNA / samRNA administered. A dose of 30pg or less can represent the total content of RNA / samRNA administered and include only a single distinct samRNA construct. A SAM boost of between 10-30pg, 10-100pg, 10-300pg, 30-100pg, 30-300pg, or 100-300pg RNA can be administered. A SAM boost of between 10-500pg, 10-lOOOpg, 30-500pg, 30-1000pg, or 500- lOOOpg RNA can be administered. A SAM boost of at least 400pg, at least 500pg, at least600(ig, at least 700pg, at least 800pg, at least 900(tg, at least lOOOpg RNA can be administered. A SAM boost of lOpg, 30(ig, 100(ig, or 300pg RNA can be administered. A SAM boost of 300pg RNA can be administered. A SAM boost of lOOjrg RNA can be administered. A SAM boost of 30pg RNA can be administered. A SAM boost of 20[ig RNA can be administered. A SAM boost of lOpg RNA can be administered. A SAM boost of 3 pg RNA can be administered. A SAM boost of at least 300pg RNA can be administered. A SAM boost of at least lOOpg RNA can be administered. A SAM boost of at least 30pg RNA can be administered. A SAM boost of at least lOpg RNA can be administered. A SAM boost of at least 3(ig RNA can be administered. A SAM boost of less than or equal to 300(ig RNA can be administered. A SAM boost of less than or equal to lOOpg RNA can be administered. A vaccine boost can include the same antigen cassette (e.g., encode the same HPV immunogenic polypeptide) as a priming dose. A vaccine boost can include a different antigen cassette as a priming dose. A vaccine boost can include the same composition as a priming dose. Any of the samRNA-based and / or ChAdV68-based vaccine composition described herein can be used in combination with commercially available HPV vaccines, e.g., Gardasil® and / or Cervarix®.

[0362] A dose of can represent the total content of RNA / samRNA administered. A dose of can represent the total content of RNA / samRNA administered and include only a single distinct samRNA construct.

[0363] Immune monitoring can be performed before, during, and / or after vaccine administration. Such monitoring can inform safety and efficacy, among other parameters.

[0364] To perform immune monitoring, PBMCs are commonly used. PBMCs can be isolated before prime vaccination, and after prime vaccination (e.g. 4 weeks and 8 weeks). PBMCs can be harvested just prior to boost vaccinations and after each boost vaccination (e.g. 4 weeks and 8 weeks).

[0365] Immune responses, such as T cell responses and B cells responses, can be assessed as part of an immune monitoring protocol. For example, the ability of a vaccine composition described herein to stimulate an immune response can be monitored and / or assessed. As used herein, “stimulate an immune response” refers to any increase in a immune response, such as initiating an immune response (e.g., a priming vaccine stimulating the initiation of an immune response in a naive subject) or enhancement of an immune response (e.g., a boosting vaccine stimulating the enhancement of an immune response in a subject having a pre-existing immune response to an antigen, such as a pre-existing immune response initiated by a priming vaccine). Enhancing an immune response can include stimulating an immune response in a convalescent subject (e.g. , a boosting vaccine stimulating the enhancement of an immune response in a subject with persistent HPV infection, e.g., non-malignant). A subject can include an HIVpositive subject. T cell responses can be measured using one or more methods known in the art such as ELISpot, intracellular cytokine staining, cytokine secretion and cell surface capture, T cell proliferation, MHC multimer staining, or by cytotoxicity assay. T cell responses to epitopes encoded in vaccines can be monitored from PBMCs by measuring induction of cytokines, such as IFN-gamma, using an ELISpot assay. Specific CD4 or CD8 T cell responses to epitopes encoded in vaccines can be monitored from PBMCs by measuring induction of cytokines captured intracellularly or extracellularly, such as IFN-gamma, using flow cytometry. Specific CD4 or CD8 T cell responses to epitopes encoded in the vaccines can be monitored from PBMCs by measuring T cell populations expressing T cell receptors specific for epitope / MHC class I complexes using MHC multimer staining. Specific CD4 or CD8 T cell responses to epitopes encoded in the vaccines can be monitored from PBMCs by measuring the ex vivo expansion of T cell populations following 3H-thymidine, bromodeoxyuridine and carboxyfluoresceine-diacetate- succinimidylester (CFSE) incorporation. The antigen recognition capacity and lytic activity of PBMC-derived T cells that are specific for epitopes encoded in vaccines can be assessed functionally by chromium release assay or alternative colorimetric cytotoxicity assays.

[0366] B cell responses can be measured using one or more methods known in the art such as assays used to determine B cell differentiation (e.g., differentiation into plasma cells), B cell or plasma cell proliferation, B cell or plasma cell activation (e.g. , upregulation of costimulatory markers such as CD80 or CD86), antibody class switching, and / or antibody production (e.g., an ELISA).

[0367] Vaccination regimens can include assessing neutralizing antibody titers against the vaccine composition of interest, such as a ChAdV68-based vaccine. For example, a ChAdV68- based vaccine can be administered as a priming dose, and re-administration of the ChAdV68- based vaccine as a boosting dose follows determining ChAdV-specific neutralizing antibody titers are below a neutralization threshold prior to re-administration. The neutralizing antibody titer can be an NT50 value calculated as a minimum dilution of sera from the immunized subject that neutralizes a ChAdV virus by 50%. Determining the neutralizing antibody titer can include the steps of: (1) contacting one or more dilutions of sera from the immunized subject with a ChAdV virus under conditions sufficient for neutralization of the ChAdV virus; and (2) assessing neutralization of the ChAdV virus relative to a non-neutralized virus.VIII. Isolation and Detection of HLA Peptides

[0368] Isolation of HLA-peptide molecules was performed using classic immunoprecipitation (IP) methods after lysis and solubilization of the tissue sample (55-58).Examples and methods are described in more detail in international patent application publication WO / 2018 / 208856, herein incorporated by reference, in its entirety, for all purposes.IX. Presentation Model

[0369] Presentation models can be used to identify likelihoods of peptide presentation in subjects. Various presentation models are known to those skilled in the art, for example the presentation models described in more detail in US Pat No. 10,055,540, US Application Pub. No. US20200010849A1 and US20110293637, and international patent application publications WO / 2018 / 195357, WO / 2018 / 208856, and WO2016187508, each herein incorporated by reference, in their entirety, for all purposes. An exemplary epitope presentation model, and methods for using the same, in a viral context is described in International PCT Application Publication WO2023196966A1, herein incorporated by reference for all purposes.X. Training Module

[0370] Training modules can be used to construct one or more presentation models based on training data sets that generate likelihoods of whether peptide sequences will be presented by MHC alleles associated with the peptide sequences. Various training modules are known to those skilled in the art, for example the presentation models described in more detail in US Pat No. 10,055,540, US Application Pub. No. US20200010849A1, and international patent application publications WO / 2018 / 195357 and WO / 2018 / 208856, each herein incorporated by reference, in their entirety, for all purposes. An exemplary training model for prediction, and methods for using the same, in a viral context is described in International PCT Application Publication WO2023196966A1, herein incorporated by reference for all purposes. A training module can construct a presentation model to predict presentation likelihoods of peptides on a per-allele basis. A training module can also construct a presentation model to predict presentation likelihoods of peptides in a multiple- allele setting where two or more MHC alleles are present.XL Prediction Module

[0371] A prediction module can be used to receive sequence data and select candidate antigens in the sequence data using a presentation model. Specifically, the sequence data may be DNA sequences, RNA sequences, and / or protein sequences extracted from infected cells patients or infectious disease organisms themselves (e.g., HPV). A prediction module may identify candidate antigens that are pathogen-derived peptides (e.g., HPV derived), such as by comparing sequence data extracted from normal tissue cells of a patient with the sequence data extracted from infected cells of the patient to identify portions containing one or more infectiousdisease organism associated antigens. A prediction module may identify candidate antigens that are expressed in an infected cell or infected tissue in comparison to a normal cell or tissue by comparing sequence data extracted from normal tissue cells of a patient with the sequence data extracted from infected tissue cells of the patient to identify expressed candidate antigens (e.g., identifying expressed polynucleotides and / or polypeptides specific to an infectious disease).

[0372] A presentation module can apply one or more presentation model to processed peptide sequences to estimate presentation likelihoods of the peptide sequences. Specifically, the prediction module may select one or more candidate antigen peptide sequences that are likely to be presented on infected cell HLA molecules by applying presentation models to the candidate antigens. In one implementation, the presentation module selects candidate antigen sequences that have estimated presentation likelihoods above a predetermined threshold. In another implementation, the presentation model selects the N candidate antigen sequences that have the highest estimated presentation likelihoods (where N is generally the maximum number of epitopes that can be delivered in a vaccine). A vaccine including the selected candidate antigens for a given patient can be injected into the patient to stimulate immune responses.

[0373] An exemplary epitope prediction module using an epitope presentation, and methods for using the same, in a viral context is described in International PCT Application Publication WO2023196966A1, herein incorporated by reference for all purposes.XLB. Cassette Design ModuleXLB.l Overview

[0374] A cassette design module can be used to generate a vaccine cassette sequence based on selected candidate peptides for injection into a patient. For example, a cassette design module can be used to generate a sequence encoding concatenated epitope sequences, such as concatenated T cell epitopes. Various cassette design modules are known to those skilled in the art, for example the cassette design modules described in more detail in US Pat No. 10,055,540, US Application Pub. No. US20200010849A1, and international patent application publications WO / 2018 / 195357 and WO / 2018 / 208856, each herein incorporated by reference, in their entirety, for all purposes.

[0375] A set of therapeutic epitopes may be generated based on the selected peptides determined by a prediction module associated with presentation likelihoods above a predetermined threshold, where the presentation likelihoods are determined by the presentation models. However it is appreciated that in other embodiments, the set of therapeutic epitopes may be generated based on any one or more of a number of methods (alone or in combination), for example, based on binding affinity or predicted binding affinity to HLA class I or class IIalleles of the patient, binding stability or predicted binding stability to HLA class I or class II alleles of the patient, random sampling, and the like.

[0376] Therapeutic epitopes may correspond to selected peptides themselves. Therapeutic epitopes may also include C- and / or N-terminal flanking sequences in addition to the selected peptides. N- and C-terminal flanking sequences can be the native N- and C-terminal flanking sequences of the therapeutic vaccine epitope in the context of its source protein. Therapeutic epitopes can represent a fixed-length epitope Therapeutic epitopes can represent a variablelength epitope, in which the length of the epitope can be varied depending on, for example, the length of the C- or N-flanking sequence. For example, the C-terminal flanking sequence and the N-terminal flanking sequence can each have varying lengths of 2-5 residues, resulting in 16 possible choices for the epitope.

[0377] A cassette design module can also generate cassette sequences by taking into account presentation of junction epitopes that span the junction between a pair of therapeutic epitopes in the cassette. Junction epitopes are novel non-self but irrelevant epitope sequences that arise in the cassette due to the process of concatenating therapeutic epitopes and linker sequences in the cassette. The novel sequences of junction epitopes are different from the therapeutic epitopes of the cassette themselves.

[0378] A cassette design module can generate a cassette sequence that reduces the likelihood that junction epitopes are presented in the patient. Specifically, when the cassette is injected into the patient, junction epitopes have the potential to be presented by HLA class I or HLA class II alleles of the patient, and stimulate a CD8 or CD4 T-cell response, respectively. Such reactions are often times undesirable because T-cells reactive to the junction epitopes have no therapeutic benefit, and may diminish the immune response to the selected therapeutic epitopes in the cassette by antigenic competition.76

[0379] A cassette design module can iterate through one or more candidate cassettes, and determine a cassette sequence for which a presentation score of junction epitopes associated with that cassette sequence is below a numerical threshold. The junction epitope presentation score is a quantity associated with presentation likelihoods of the junction epitopes in the cassette, and a higher value of the junction epitope presentation score indicates a higher likelihood that junction epitopes of the cassette will be presented by HLA class I or HLA class II or both.

[0380] In one embodiment, a cassette design module may determine a cassette sequence associated with the lowest junction epitope presentation score among the candidate cassette sequences.

[0381] A cassette design module may iterate through one or more candidate cassette sequences, determine the junction epitope presentation score for the candidate cassettes, and identify an optimal cassette sequence associated with a junction epitope presentation score below the threshold.

[0382] A cassette design module may further check the one or more candidate cassette sequences to identify if any of the junction epitopes in the candidate cassette sequences are self-epitopes for a given patient for whom the vaccine is being designed. To accomplish this, the cassette design module checks the junction epitopes against a known database such as BLAST. In one embodiment, the cassette design module may be configured to design cassettes that avoid junction self-epitopes.

[0383] A cassette design module can perform a brute force approach and iterate through all or most possible candidate cassette sequences to select the sequence with the smallest junction epitope presentation score. However, the number of such candidate cassettes can be prohibitively large as the capacity of the vaccine increases. For example, for a vaccine capacity of 20 epitopes, the cassette design module has to iterate through ~1018possible candidate cassettes to determine the cassette with the lowest junction epitope presentation score. This determination may be computationally burdensome (in terms of computational processing resources required), and sometimes intractable, for the cassette design module to complete within a reasonable amount of time to generate the vaccine for the patient. Moreover, accounting for the possible junction epitopes for each candidate cassette can be even more burdensome. Thus, a cassette design module may select a cassette sequence based on ways of iterating through a number of candidate cassette sequences that are significantly smaller than the number of candidate cassette sequences for the brute force approach.

[0384] A cassette design module can generate a subset of randomly or at least pseudo- randomly generated candidate cassettes, and selects the candidate cassette associated with a junction epitope presentation score below a predetermined threshold as the cassette sequence. Additionally, the cassette design module may select the candidate cassette from the subset with the lowest junction epitope presentation score as the cassette sequence. For example, the cassette design module may generate a subset of ~1 million candidate cassettes for a set of 20 selected epitopes, and select the candidate cassette with the smallest junction epitope presentation score. Although generating a subset of random cassette sequences and selecting a cassette sequence with a low junction epitope presentation score out of the subset may be sub- optimal relative to the brute force approach, it requires significantly less computational resources thereby making its implementation technically feasible. Further, performing the brute force method as opposed to this more efficient technique may only result in a minor oreven negligible improvement injunction epitope presentation score, thus making it not worthwhile from a resource allocation perspective. A cassette design module can determine an improved cassette configuration by formulating the epitope sequence for the cassette as an asymmetric traveling salesman problem (TSP). Given a list of nodes and distances between each pair of nodes, the TSP determines a sequence of nodes associated with the shortest total distance to visit each node exactly once and return to the original node. For example, given cities A, B, and C with known distances between each other, the solution of the TSP generates a closed sequence of cities, for which the total distance traveled to visit each city exactly once is the smallest among possible routes. The asymmetric version of the TSP determines the optimal sequence of nodes when the distance between a pair of nodes are asymmetric. For example, the “distance” for traveling from node A to node B may be different from the “distance” for traveling from node B to node A. By solving for an improved optimal cassette using an asymmetric TSP, the cassette design module can find a cassette sequence that results in a reduced presentation score across the junctions between epitopes of the cassette. The solution of the asymmetric TSP indicates a sequence of therapeutic epitopes that correspond to the order in which the epitopes should be concatenated in a cassette to minimize the junction epitope presentation score across the junctions of the cassette. A cassette sequence determined through this approach can result in a sequence with significantly less presentation of junction epitopes while potentially requiring significantly less computational resources than the random sampling approach, especially when the number of generated candidate cassette sequences is large. Illustrative examples of different computational approaches and comparisons for optimizing cassette design are described in more detail in US Pat No. 10,055,540, US Application Pub. No. US20200010849A1, and international patent application publications WO / 2018 / 195357 and WO / 2018 / 208856, each herein incorporated by reference, in their entirety, for all purposes.

[0385] A cassette design module can also generate cassette sequences by taking into account additional protein sequences encoded in the vaccine. For example, a cassette design module used to generate a sequence encoding concatenated T cell epitopes can take into account T cell epitopes already encoded by additional protein sequences present in the vaccine (e.g. , full-length protein sequences), such as by removing T cell epitopes already encoded by the additional protein sequences from the list of candidate sequences.

[0386] A cassette design module can also generate cassette sequences by taking into account the size of the sequences. Without wishing to be bound by theory, in general, increased cassette size can negatively impact vaccine aspects, such as vaccine production and / or vaccine efficacy. In one example, the cassette design module can take into accountoverlapping sequences, such as overlapping T cell epitope sequences. In general, a single sequence containing overlapping T cell epitope sequences (also referred to as a “frame”) is more efficient than separately linking individual T cell epitope sequences as it reduces the sequence size needed to encode the multiple peptides. Accordingly, in an illustrative example, a cassette design module used to generate a sequence encoding concatenated T cell epitopes can take into account the cost / benefit of extending a candidate T cell epitope to encode one or more additional T cell epitopes, such as determining the benefit gained in additional population coverage for an MHC presenting the additional T cell epitope versus the cost of increasing the size of the sequence.

[0387] A cassette design module can also generate cassette sequences by taking into account the magnitude of stimulation of an immune response generated by validated epitopes.

[0388] A cassette design module can also generate cassette sequences by taking into account presentation of encoded epitopes across a population, for example that at least one immunogenic epitope is presented by at least one HLA across a proportion of a population, for example by at least 85%, 90%, or 95% of a population (e.g., HLA-A, HLA-B and HLA-C genes over four major ethnic groups, namely European (EUR), African American (AFA), Asian and Pacific Islander (APA) and Hispanic (HIS)). As an illustrative non-limiting example, a cassette design module can also generate cassette sequences such that at least one HLA is present at least across 85%, 90%, or 95% of a population that presents at least one validated epitope or presents at least 4, 5, 6, or 7 predicted epitopes.

[0389] A cassette design module can also generate cassette sequences by taking into account other aspects that improve potential safety, such as limiting encoding or the potential to encode a functional protein, functional protein domain, functional protein subunit, or functional protein fragment potentially presenting a safety risk. In some cases, a cassette design module can limit sequence size of encoded peptides such that are less than 50%, less than 49%, less than 48%, less than 47%, less than 46%, less than 45%, less than 45%, less than 43%, less than 42%, less than 41%, less than 40%, less than 39%, less than 38%, less than 37%, less than 36%, less than 35%, less than 34%, or less than 33% of the translated, corresponding full-length protein. In some cases, a cassette design module can limit sequence size of encoded peptides such that a single contiguous sequence is less than 50% of the translated, corresponding full-length protein, but more than one sequence may be derived from the same translated, corresponding full-length protein and together encode more than 50%. In an illustrative example, if a single sequence containing overlapping T cell epitope sequences (“frame”) is larger than 50% of the translated, corresponding full-length protein, the frame can be split into multiple frames (e.g. , fl, f2 etc.) such that each frame is less than 50% of the translated, corresponding full-length protein. Acassette design module can also limit sequence size of encoded peptides such that a single contiguous sequence is less than 49%, less than 48%, less than 47%, less than 46%, less than 45%, less than 45%, less than 43%, less than 42%, less than 41%, less than 40%, less than 39%, less than 38%, less than 37%, less than 36%, less than 35%, less than 34%, or less than 33% of the translated, corresponding full-length protein. Where multiple frames from the same gene are encoded, the multiple frames can have overlapping sequences with each other, in other words each separately encode the same sequence. Where multiple frames from the same gene are encoded, the two or more nucleic acid sequences derived from the same gene can be ordered such that a first nucleic acid sequence cannot be immediately followed by or linked to a second nucleic acid sequence if the second nucleic acid sequence follows, immediately or not, the first nucleic acid sequence in the corresponding gene. For example, if there are 3 frames within the same gene (f 1 ,f2,f3 in increasing order of amino acid position):The following cassette orderings are not allowed: o fl immediately followed by f2 o f2 immediately followed by f3 o fl immediately followed by f3The following cassette orderings are allowed: o f3 immediately followed by f2 o f2 immediately followed by flXIII. Example Computer

[0390] A computer can be used for any of the computational methods described herein. One skilled in the art will recognize a computer can have different architectures. Examples of computers are known to those skilled in the art, for example the computers described in more detail in US Pat No. 10,055,540, US Application Pub. No. US20200010849A1, and international patent application publications WO / 2018 / 195357 and WO / 2018 / 208856, each herein incorporated by reference, in their entirety, for all purposes.XIV. Examples

[0391] Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for.

[0392] The practice of the present invention will employ, unless otherwise indicated, conventional methods of protein chemistry, biochemistry, recombinant DNA techniques andpharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., T.E. Creighton, Proteins: Structures and Molecular Properties (W.H. Freeman and Company, 1993); A.L. Lehninger, Biochemistry (Worth Publishers, Inc., current addition); Sambrook, et al., Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Methods In Enzymology (S. Colowick and N. Kaplan eds., Academic Press, Inc.); Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pennsylvania: Mack Publishing Company, 1990); Carey and Sundberg Advanced Organic Chemistry 3rdEd. (Plenum Press) Vols A and B(1992).XIV.A. HPV MHC Epitope Prediction and Vaccine Cassette Construction

[0393] The first step in the vaccine design was to obtain a set of potential epitopes to be included in the vaccine, which are short amino-acid sequences with length 8 through 12. Two sets of epitopes were defined: predicted using prediction algorithms; and validated, which are experimentally identified epitopes documented in the literature or in public databases.

[0394] CD8+ epitopes were predicted using a machine learning EDGE platform (see US Pat No. 10,055,540, herein incorporated by reference for all purposes), which was shown to be best- in-class [Bulik-Sullivan et al. (2018). The amino acid sequences of all CD8+ epitopes identified using the machine learning EDGE platform for each of HPV strains 16, 18, 31, 33, 35, 45, 52, and 58 are shown in Tables G1-G8 and Tables Q1-Q8 of the Appendix, respectively. The Appendix is hereby incorporated by reference, in its entirety, for all purposes. Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification. Nature Biotechnology 2018, 37(1), herein incorporated by reference for all purposes]. In particular, for HPV prediction, an EDGE platform was used (see International PCT Application Publication WO2023196966A1, herein incorporated by reference for all purposes). Initial selection for inclusion in a TCE cassette was limited to El, E2, and E5 given the general considerations that those proteins have evidence of eliciting immune responses in addition to E6 and E7 — which are separately included in their entirety - as well as providing the greatest number of potential epitopes.

[0395] Each epitope selected is associated to one or more class I HLA allele, which were either predicted or experimentally demonstrated to present the respective epitope in the surface of antigen presentation cells.

[0396] The set of validated epitopes was aligned to the reference proteome, requiring an additional set of k flanking amino acids on either side of the epitope. The proteome regions containing aligned epitopes were defined as the initial footprint and characterized the building foundation of the vaccine cassette (FIG. 15A). The initial footprint was constrained byparameters that specify the minimum proportion of the epitope length (min_proportion ) that have a minimum required number of overlapping (min_overlap) epitopes necessary to accept an epitope as part of the initial footprint or not. These two parameters controled the size of the initial footprint.

[0397] In the next step, the algorithm performed several ranking iterations that consider all remaining validated and predicted epitopes. In each iteration, every epitope was ranked by the fraction c / f where c is the added population coverage provided by the epitope and f is the total increase in cassette size as consequence of the epitope addition. The epitope with the lowest value was added to the cassette and the process repeated until a maximum cassette design was reached or until all epitopes were included in the cassette (FIG. 15A).

[0398] The coverage provided by a given epitope is calculated by the frequencies of haplotypes in a reference population that cover at least one allele associated with the epitope (FIG. 15B). As reference populations, we used the haplotypes of the ancestry groups African- American (AFA), Hispanic (HIS), Asian-Pacific Islanders (API) and Europeans (EUR) as provided by the US National Marrow Donor Program (bioinformatics.bethematchclinical.org / WorkArea / DownloadAsset.aspx?id=6379).

[0399] Further evaluation was performed to assess cassette design and prediction. As an illustration, the TCE cassette for HPV16 was assessed using mass-spectrometry verification of presentation of predicted epitopes in HLA monoallelic lines. FIG. 16 shows the overall performance that 85 of 214 predicted epitopes were at least provisionally validated to be presented by a single HLA. For the 20 alleles tested for the HLA lines created at the time of assesment, a minimum of 2 unique TCEs was detected for each cell line tested.

[0400] Further, the performance of population coverage was assessed. Population coverage was estimated by counting how many epitopes-HLA pairs are required for individuals to be protected (degree of protection). Predicted epitopes received a smaller weight than validated epitopes in the population coverage estimation. By updating the validated epitopes with the mass-spectrometry data, as shown in FIG. 17, an improvement in population coverage estimates was observed, even for higher degree of protection levels.XIV.B. HPV Vaccine Design

[0401] A series of vaccines against HPV were designed to assess efficacy for eliciting T cell responses. Initial HPV vaccines were designed targeting HPV strains HPV 16 and HPV18 that included E6 and E7 whole fusions and T cell epitope (TCE) sequences from El, E2 and E5.HPV strains 16 and 18 were initially chosen for assessment (e.g., as a proof of principal) given they are common in US / Europe.

[0402] HPV genomes contain ORFs that are all transcribed from a single DNA strand that include the early (E) region encoding proteins E1-E7, the late (L) region encoding structural proteins L1-L2, and a generally non-coding long control region (LCR) region. HPV antigens E6 and E7 were chosen for inclusion in their entirety (except for deletions and other modifications described below, e.g., in Table B) as a fusion protein given they are generally considered to be the most highly expressed proteins post-transformation, as well as due to their contribution to the oncogenic process and expression within transformed cell. Additional epitopes from El, E2 and E5 were identified for inclusion in a T-cell epitope (TCE) cassette using a combination of published clinical epitopes and epitopes identified using the mass-spectrometry trained MHC I epitope identification algorithms described herein (see also the machine learning EDGE platform described in US Pat No. 10,055,540 and Bulik-Sullivan et al. [Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification. Nature Biotechnology 2018, 57(1)], each of which is herein incorporated by reference for all purposes). The epitopes were selected based on their ability to provide broad HLA coverage for major global populations, including those in specific low middle income countries, with an initial focus on covering HLA diversity within Sub-Saharan Africa (but noteworthy later determined that cassettes were predicted to cover global diversity more broadly, e.g., see FIG. 17).

[0403] The E6 / E7 fusion proteins linked by a Furin cleavage site for each of HPV strains 16, 18, 31, 33, 35, 45, 52, and 58 are shown in Table A, including with leader sequences for expression, with both amino acid and nucleotide sequences provided, where nucleotide sequences were codon optimized. The E6 and E7 proteins also featured additional modifications referred to by amino acid position relative to the identified wildtype strain sequence, as shown in Table B, which include deletions to render the respective proteins inactive, e.g., for safety considerations. The amino acid sequences selected for inclusion in the TCE cassettes with their protein origin (both HPV gene and frame) for each of HPV strains 16, 18, 31, 33, 35, 45, 52, and 58 are shown in Tables C1-C8, respectively. The full TCE cassette sequences for each of HPV strains 16, 18, 31, 33, 35, 45, 52, and 58 are shown in Table D, including with leader sequences and universal MHC Class II PADRE sequence (inclusive of GPGPG linkers), with both amino acid and nucleotide sequences provided.

[0404] Vaccines were constructed using both an alphavirus-based self- amplifying mRNA (samRNA) vector and a chimpanzee adenovirus (ChAd) vector, as described below. For vaccines expressing a combination of an E6 / E7 fusion protein and TCE cassette from a single HPV strain, the E6 / E7 fusion protein and TCE cassette were expressed from separate alphavirus subgenomic promoters (SGP or “26S”) in samRNA contructs, and expressed using a T2A ribosome skipping sequence element in ChAd constructs. The order of the E6 / E7 fusion proteinand the TCE cassette for the initial vaccines assessed for each of individual HPV strains 16, 18, 31, 33, 35, 45, 52, and 58 is shown in Table E.

[0405] Multi-strain vaccines encoding E6 / E7 fusion proteins and TCE cassettes from both HPV16 and HPV18 were also constructed and assessed. For samRNA multi-strain vaccines, a combination of separate alphavirus subgenomic promoters (SGP / 26S) and T2A ribosome skipping sequence elements was used, with the initial construct assessed having the following format: 18.E6E7-T2A-16.TCE-18.TCE-SGP-16.E6E7. For ChAd multi-strain vaccines, a T2A ribosome skipping sequence element was used, with the initial construct assessed having the following format: 16.E6E7-18.E6E7-T2A-16.TCE-18.TCE.

[0406] Representative sequences for full-length cassettes and vectors are shown in Table F,Table A - E6 / E7 Fusion Proteins SequencesTable B - E6 / E7 ModificationsTable Cl - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV16Table C2 - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV18Table C3 - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV31Table C4 - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV33Table C5 - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV35Table C6 - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV45Table C7 - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV52Table C8 - Selected Sequences for T-cell Epitope (TCE) Cassette for HPV58Table D - T-ccll Epitope (TCE) Cassette SequencesTable E - Single HPV Strain Formats AssessedTable F - Certain HPV Cassette and Vector SequencesSAM Vectors

[0407] A RNA alphavirus backbone for the antigen expression system was generated from a self-replicating Venezuelan Equine Encephalitis (VEE) virus (Kinney, 1986, Virology 152: 400- 413) by deleting the structural proteins of VEE located 3’ of the 26S sub-genomic promoter (VEE sequences 7544 to 11,175 deleted; numbering based on Kinney et al 1986; SEQ ID NO:6). To generate the self-amplifying mRNA (“SAM”) vector, the deleted sequences are replaced by antigen sequences. A representative SAM vector containing 20 model antigens is “VEE-MAG25mer” (SEQ ID NO:4). The vectors featuring the antigen cassettes described having the MAG25mer cassette can be replaced by the HPV cassettes and / or full-length proteins described herein.In vitro transcription to generate SAM

[0408] For in vivo studies: SAM vectors were generated as “AU-SAM” vectors. A modified T7 RNA polymerase promoter (TAATACGACTCACTATA), which lacks the canonical 3’ dinucleotide GG, was added to the 5’ end of the SAM vector to generate the in vitro transcription template DNA (7544 to 11,175 deleted without an inserted antigen cassette).Reaction conditions are described below:lx transcription buffer (40 mM Tris-HCL [pH7.9], 10 mM dithiothreitol, 2 mM spermidine, 0.002% Triton X-100, and 27 mM magnesium chloride) using final concentrations of lx T7 RNA polymerase mix (E2040S); 0.025 mg / mL DNA transcription template (linearized by restriction digest); 8 mM CleanCap Reagent AU (Cat. No. N-7114) and 10 mM each of ATP, cytidine triphosphate (CTP), GTP, and uridine triphosphate (UTP)Transcription reactions were incubated at 37°C for 2 hr and treated with final 2 U DNase I (AM2239) / 0.001 mg DNA transcription template in DNase I buffer for 1 hr at 37°C. SAM was purified by RNeasy Maxi (QIAGEN, 75162)

[0409] Alternatively to co-transcriptional addition of a 5’ cap structure, a 7-methylguanosine or a related 5’ cap structure can be enzymatically added following transcription using a vaccinia capping system (NEB Cat. No. M2080) containing mRNA 2’-O-methyltransferase and S- Adenosyl methionine.Adenoviral Vectors

[0410] A modified ChAdV68 vector (“chAd68-Empty-E4deleted” SEQ ID NO:57) for the antigen expression system was generated based on AC_000011.1 with El (nt 577 to 3403), E3 (nt 27,125- 31,825), and E4 region (nt 34,916 to 35,642) sequences deleted and the corresponding ATCC VR-594 (Independently sequenced Full-Length VR-594 C68 SEQ ID NO: 10) nucleotides substituted at five positions. Specifically, a transcriptionally reglated E4- deletion ChAdV68 vector was used. Relevant ChAdV68 vectors and sequences are described in U.S. Pat. No. 11,591,619, herein incorporated by reference for all purposes. The full-length ChAdV68 AC_000011.1 sequence with corresponding ATCC VR-594 nucleotides substituted at five positions is referred to as “ChAdV68.5WTnt” (SEQ ID NO: 1). Antigen cassettes under the control of the CMV promoter / enhancer are inserted in place of deleted El sequences.Adenoviral Production in 293F cells

[0411] ChAdV68 virus production are performed in 293F cells grown in 293 FreeStyle™ (ThermoFisher) media in an incubator at 8% CO2. On the day of infection cells are diluted to 106cells per mL, with 98% viability and 400 mL are used per production run in IL Shake flasks (Corning). 4 mL of the tertiary viral stock with a target MOI of >3.3 is used per infection. The cells are incubated for 48-72h until the viability was <70% as measured by Trypan blue. The infected cells are then harvested by centrifugation, full speed bench top centrifuge and washed in 1XPBS, re-centrifuged and then re-suspended in 20 mL of lOmM Tris pH7.4. The cell pellet is lysed by freeze thawing 3X and clarified by centrifugation at 4,300Xg for 5 minutes.Adenoviral Purification by CsCl centrifugation

[0412] Viral DNA is purified by CsCl centrifugation. Two discontinuous gradient runs are performed. The first to purify virus from cellular components and the second to further refine separation from cellular components and separate defective from infectious particles.

[0413] 10 mL of 1.2 (26.8g CsCl dissolved in 92 mL of 10 mM Tris pH 8.0) CsCl is added to polyallomer tubes. Then 8 mL of 1.4 CsCl (53g CsCl dissolved in 87 mL of 10 mM Tris pH 8.0) is carefully added using a pipette delivering to the bottom of the tube. The clarified virus is carefully layered on top of the 1.2 layer. If needed more 10 mM Tris is added to balance the tubes. The tubes are then placed in a SW-32Ti rotor and centrifuged for 2h 30 min at 10°C. The tube are then removed to a laminar flow cabinet and the virus band pulled using an 18 gauge needle and a 10 mL syringe. Care is taken not to remove contaminating host cell DNA and protein. The band is then diluted at least 2X with 10 mM Tris pH 8.0 and layered as before on a discontinuous gradient as described above. The run is performed as described before except that this time the run is performed overnight. The next day the band is pulled with care to avoid pulling any of the defective particle band. The virus is then dialyzed using a Slide-a-LyzerTMCassette (Pierce) against ARM buffer (20 mM Tris pH 8.0, 25 mM NaCl, 2.5% Glycerol). This is performed 3X, Ih per buffer exchange. The virus is then aliquoted for storage at -80°C.Adenoviral Viral Assays

[0414] VP concentration i...

Claims

CLAIMSWhat is claimed is:

1. A human papillomavirus (HPV) vaccine comprising at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide, wherein the encoded immunogenic polypeptide comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in any one of Tables C1-C8; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8; or- any one of the polypeptide sequences of the cassette sequences set forth in Table D; or- an HPV-derived E6 / E7 fusion protein comprising an HPV E6 derived polypeptide and an HPV E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the polypeptide sequences shown in Table A; or- combinations thereof.

2. The composition of claim 1 , wherein the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl, and an HPV16-derived E6 / E7 fusion protein comprising an HPV 16 E6 derived polypeptide and an HPV 16 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV16-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2, and an HPV 18-derived E6 / E7 fusion protein comprising an HPV 18 E6 derived polypeptide and an HPV 18 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV18-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3, and an HPV31 -derived E6 / E7 fusion protein comprising an HPV31 E6 derived polypeptide and an HPV31 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV31-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4, and an HPV33-derived E6 / E7 fusion protein comprising an HPV33 E6 derived polypeptide and an HPV33 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV33-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of thepolypeptide sequences as set forth in Tables C5, and an HPV35-derived E6 / E7 fusion protein comprising an HPV35 E6 derived polypeptide and an HPV35 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV35-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6, and an HPV45-derived E6 / E7 fusion protein comprising an HPV45 E6 derived polypeptide and an HPV45 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV45-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7, and an HPV52-derived E6 / E7 fusion protein comprising an HPV52 E6 derived polypeptide and an HPV52 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV52-derived polypeptide sequences shown in Table A; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8, and an HPV58-derived E6 / E7 fusion protein comprising an HPV58 E6 derived polypeptide and an HPV58 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV58-derived polypeptide sequences shown in Table A; or- combinations thereof.

3. The composition of claim 1, wherein the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl, and an HPV16-derived E6 / E7 fusion protein comprising an HPV 16 E6 derived polypeptide and an HPV 16 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV16-derived polypeptide sequences shown in Table A; and- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of thepolypeptide sequences as set forth in Tables C2, and an HPV18-derived E6 / E7 fusion protein comprising an HPV 18 E6 derived polypeptide and an HPV 18 E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the HPV18-derived polypeptide sequences shown in Table A.

4. The composition of claim 1, wherein the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises:- each of the polypeptide sequences as set forth in Tables Cl, and an HPV16-derived E6 / E7 fusion protein comprising an HPV 16 E6 derived polypeptide and an HPV16 E7 derived polypeptide, wherein the HPV-derived fusion protein comprises any one of the HPV16-derived polypeptide sequences shown in Table A; and- each of the polypeptide sequences as set forth in Tables C2, and an HPV 18-derived E6 / E7 fusion protein comprising an HPV 18 E6 derived polypeptide and an HPV 18 E7 derived polypeptide, wherein the HPV-derived fusion protein comprises any one of the HPV 18-derived polypeptide sequences shown in Table A.

5. The composition of claim 1, wherein the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; and- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2.

6. The composition of claim 1, wherein the at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; and- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; and- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; and- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6.

7. A HPV vaccine, wherein the vaccine comprises a self-amplifying alphavirus-based expression system comprising:(A) one or more vectors, wherein the one or more vectors comprises:(a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises:(i) at least one promoter nucleotide sequence, and(ii) at least one polyadenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises:(i) one or more of the HPV derived nucleic acid sequences of any of the above claims, wherein the immunogenic polypeptide optionally comprises a N-terminal linker and / or a C-terminal linker;(ii) optionally, a second promoter nucleotide sequence operably linked to the HPV derived nucleic acid sequence; and(iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence;(iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and(v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone, optionally wherein the exogenous poly(A) sequence comprises an SV40 poly(A) signal sequence or a Bovine Growth Hormone (BGH) poly (A) signal sequence; and(B) a lipid-nanoparticle (LNP), wherein the LNP encapsulates the self-amplifying alphavirus-based expression system.

8. The composition of claim 7, wherein the composition for delivery of the self-amplifying alphavirus-based expression system comprises at least lOpg or 20 pg of each of the one or more vectors.

9. The composition of claim 7, wherein the composition for delivery of the self- amplifying alphavirus-based expression system comprises between 10pg-20pg of each of the one or more vectors.

10. The composition of claim 7, wherein the composition for delivery of the self-amplifying alphavirus-based expression system comprises 20pg or less of each of the one or more vectors.

11. The composition of claim 7, wherein the composition for delivery of the self- amplifying alphavirus-based expression system comprises between 10-30pg or between 10-100pg of each of the one or more vectors.

12. The composition of any of claims 1-11, wherein the composition comprises at least two HPV-derived nucleic acid sequences, wherein a first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV strain and a second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV strain.

13. The composition of claim 12, wherein the first HPV strain and the second HPV strain are each selected from the group consisting of: HPV16, HPV18, HPV31, HPV33, HPV35, HPV45, HPV52, and HPV58.

14. The composition of claim 13, wherein the first HPV strain and the second HPV strain are HPV16 and HPV18.

15. The composition of any of the above claims, wherein the immunogenic polypeptide is derived from an HPV early (E) protein selected from the group consisting of: HPV El, HPV E2, HPV E5, HPV E6, HPV E7, and combinations thereof.

16. The composition of any of the above claims, wherein the composition comprises the HPV derived nucleic acid sequence encodes at least one immunogenic polypeptide derived from each of HPV El, HPV E2, HPV E5, HPV E6, and HPV E7.

17. The composition of any of the above claims, wherein the composition further comprises a non-HPV derived nucleic acid sequence encoding at least one immunogenic polypeptide derived from an infectious disease other than HPV, optionally wherein the infectious disease is selected from the group consisting of: a pathogen, a virus, a bacteria, a fungus, and a parasite.

18. The composition of any one of the above claims, wherein the RNA alphavirus backbone comprises one or more elements obtained from the sequence of SEQ ID NO:3 or SEQ ID NO:5, optionally wherein the one or more elements are selected from the group consisting of the sequences necessary for nonstructural protein-mediated amplification, the 26S promoter nucleotide sequence, the poly(A) sequence, and the nsPl-4 genes of the sequence set forth in SEQ ID NO:3 or SEQ ID NO:5, optionally the RNA alphavirus backbone comprises the sequence set forth in the sequences selected from the group consisting of SEQ ID NOs:6-9.

19. A method for stimulating an immune response in a subject, the method comprising administering to the subject the composition for delivery of the self-amplifying alphavirus-based expression system of any one of the above claims.

20. The method of claim 19, wherein the method comprises administering at least two doses of the composition for delivery of the self-amplifying alphavirus-based expression system.

21. The method of claim 20, wherein the at least two doses comprises a priming dose and at least one boosting dose.

22. The method of claim 20 or 21, wherein the at least two doses are administered on days 1 and day 28 or later.

23. The method of claim 20 or 21, wherein the at least two doses are administered on days 1 and on or after week 4.

24. The method of any one of claims 20-23, wherein the at least two doses comprise the same antigen cassette.

25. The method of any one of claims 19-24, wherein the method further comprises administration of a chimpanzee adenovirus (ChAdV)-based expression system, wherein the composition for delivery of the ChAdV-based expression system comprises:the ChAdV-based expression system, wherein the ChAdV-based expression system comprises a viral particle comprising a ChAdV vector, wherein the ChAdV vector comprises:(a) a ChAdV backbone, wherein the ChAdV backbone comprises:(i) at least one promoter nucleotide sequence, and(ii) at least one polyadenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide.

26. The method of claim 25, wherein the ChAdV-based expression system is administered as a priming dose.

27. The method of claim 26, wherein the antigen cassette of the ChAdV-based expression system is the same as the antigen cassette of the self-amplifying alphavirus-based expression system.

28. A HPV vaccine comprising a chimpanzee adenovirus (ChAdV)-based expression system, wherein the composition for delivery of the ChAdV-based expression system comprises:(a) a ChAdV backbone, wherein the ChAdV backbone comprises:(i) at least one promoter nucleotide sequence, and(ii) at least one polyadenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises:(i) one or more of the HPV derived nucleic acid sequences of any of the above claims, wherein the immunogenic polypeptide optionally comprises a N-terminal linker and / or a C-terminal linker;(ii) optionally, a second promoter nucleotide sequence operably linked to the HPV derived nucleic acid sequence; and(iii) optionally, at least one MHC class If epitope-encoding nucleic acid sequence;(iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and(v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone, optionally wherein the exogenous poly(A) sequence comprises an SV40 poly(A) signal sequence or a Bovine Growth Hormone (BGH) poly(A) signal sequence, and wherein the cassette is operably linked to the at least one promoter nucleotide sequence and the at least one poly(A) sequence.

29. The composition of claim 28, wherein the composition for delivery of the ChAdV-based expression system comprises at least IxlO11of the viral particles.

30. The composition of claim 28, wherein the composition for delivery of the ChAdV-based expression system comprises between IxlO11and IxlO12.

31. The composition of claim 28, wherein the composition for delivery of the ChAdV-based expression system comprises IxlO11, 3xl0n, or IxlO12of the viral particles.

32. The composition of any one of claims 28-31, wherein the viral particles are at a concentration of 5x1011vp / mL.

33. The composition of any one of claims 28-32, wherein the ChAdV backbone comprises at least nucleotides 2 to 36,518 of the sequence set forth in SEQ ID NO:1, wherein the nucleotides 2 to 36,518 lack: (1) nucleotides 577 to 3403 of the sequence shown in SEQ ID NO:1 corresponding to an El deletion; (2) nucleotides 27,125 to 31,825 of the sequence shown in SEQ ID NO:1 corresponding to an E3 deletion; and (3) optionally nucleotides 34,916 to 35,642 of the sequence shown in SEQ ID NO:1 corresponding to a partial E4 deletion; optionally wherein the antigen cassette is inserted within the El deletion.

34. A method for stimulating an immune response in a subject, the method comprising administering to the subject the composition for delivery of the ChAdV-based expression system of any one of the above claims 28-33.

35. The method of claim 34, wherein the the ChAdV-based expression system is administered as a priming dose.

36. The method of claim 34 or 35, wherein the method further comprises administration of a composition for delivery of a self- amplifying alphavirus-based expression system,wherein the composition for delivery of the self-amplifying alphavirus-based expression system comprises:(A) the self-amplifying alphavirus-based expression system, wherein the selfamplifying alphavirus-based expression system comprises one or more vectors, wherein the one or more vectors comprises:(a) an RNA alphavirus backbone, wherein the RNA alphavirus backbone comprises:(i) at least one promoter nucleotide sequence, and(ii) at least one polyadenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone, and wherein the antigen cassette comprises at least one HPV derived nucleic acid sequence encoding an immunogenic polypeptide.

37. The method of claim 36, wherein the antigen cassette of the ChAdV-based expression system is the same as the antigen cassette of the self-amplifying alphavirus-based expression system.

38. The composition of any one of the above claims, wherein the composition for delivery of the expression system is formulated in a pharmaceutical composition comprising a pharmaceutically acceptable carrier.

39. A kit comprising the composition for delivery of the expression system of any one of the above claims, and instructions for use.

40. A method for stimulating an immune response in a subject, the method comprising administering to the subject any one of the above HPV vaccines.

41. A composition for delivery of an antigen expression system, comprising:(a) one or more vectors, the one or more vectors comprising: a vector backbone, wherein the vector backbone comprises:(i) at least one promoter nucleotide sequence, and(ii) at least one polyadenylation (poly(A)) sequence; and(b) an antigen cassette, optionally wherein the antigen cassette is inserted into the vector backbone when present, and wherein the antigen cassette comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in any one of Tables C1-C8; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8; or- any one of the polypeptide sequences of the cassette sequences set forth in Table D; or- an HPV-derived E6 / E7 fusion protein comprising an HPV E6 derived polypeptide and an HPV E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the polypeptide sequences shown in Table A; or- combinations thereof; and wherein each of the HPV derived nucleic acid sequences comprises;(I) optionally, a 5’ linker sequence, and(II) optionally, a 3’ linker sequence;(ii) optionally, a second promoter nucleotide sequence operably linked to one or more of the three HPV derived nucleic acid sequences; and(iii) optionally, at least one MHC class II epitope-encoding nucleic acid sequence;(iv) optionally, at least one nucleic acid sequence encoding a GPGPG amino acid linker sequence (SEQ ID NO:56); and(v) optionally, at least one second poly(A) sequence, wherein the second poly(A) sequence is a native poly(A) sequence or an exogenous poly(A) sequence to the vector backbone optionally wherein the exogenous poly(A) sequence comprises an SV40 poly(A) signal sequence or a Bovine Growth Hormone (BGH) poly(A) signal sequence.

42. A composition for delivery of an antigen expression system, wherein the antigen expression system comprises:(a) one or more vectors, the one or more vectors comprising: a vector backbone, wherein the vector backbone comprises a chimpanzee adenovirus vector, optionally wherein the chimpanzee adenovirus vector is a ChAdV68 vector, or an alphavirus vector, optionally wherein the alphavirus vector is a Venezuelan equine encephalitis virus vector, and wherein the vector backbone comprises:(i) at least one promoter nucleotide sequence, and(ii) at least one poly adenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone such that the antigen cassette is operably linked to the at least one promoter nucleotide sequence, and wherein the antigen cassette comprises:- at least one MHC class I epitope comprising a polypeptide sequence as set forth in any one of Tables C1-C8; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables Cl, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables Cl; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C2, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C2; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C3, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C3; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C4, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C4; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C5, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C5; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C6, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C6; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C7, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C7; or- at least one MHC class I epitope comprising a polypeptide sequence as set forth in Tables C8, optionally wherein the immunogenic polypeptide comprises each of the polypeptide sequences as set forth in Tables C8; or- any one of the polypeptide sequences of the cassette sequences set forth in Table D; or- an HPV-derived E6 / E7 fusion protein comprising an HPV E6 derived polypeptide and an HPV E7 derived polypeptide, optionally wherein the HPV-derived fusion protein comprises any one of the polypeptide sequences shown in Table A; or- combinations thereof; and43. A composition for delivery of an antigen expression system, comprising: the antigen expression system, wherein the antigen expression system comprises:(a) a vector backbone, wherein the vector backbone comprises an alphavirus vector, optionally wherein the alphavirus vector is a Venezuelan equine encephalitis virus vector, and wherein the vector backbone comprises:(i) a subgenomic promoter nucleotide sequence, and(ii) a polyadenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone such that the antigen cassette is operably linked to the subgenomic promoter nucleotide sequence, and wherein the antigen cassette comprises, in order from 5’ to 3’:(i) a nucleotide sequence encoding a first HPV-derived nucleic acid sequence;(ii) a 2A ribosome skipping sequence element; and(iii) a nucleotide sequence encoding a second HPV-derived nucleic acid sequence, and optionally wherein(a) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV strain and a second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV strain, or(b) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV protein and the second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV protein, optionally wherein the first HPV protein and the second HPV protein are derived from the same HPV strain.

44. A composition for delivery of an antigen expression system, comprising: the antigen expression system, wherein the antigen expression system comprises:(a) a vector backbone, wherein the vector backbone comprises an alphavirus vector, optionally wherein the alphavirus vector is a Venezuelan equine encephalitis virus vector, and wherein the vector backbone comprises:(i) a first subgenomic promoter nucleotide sequence, and(ii) a polyadenylation (poly(A)) sequence; and(b) an antigen cassette, wherein the antigen cassette is inserted into the vector backbone such that the antigen cassette is operably linked to the subgenomic promoter nucleotide sequence, and wherein the antigen cassette comprises, in order from 5’ to 3’:(i) a nucleotide sequence encoding a first HPV-derived nucleic acid sequence;(ii) a second subgenomic promoter nucleotide sequence; and(iii) a nucleotide sequence encoding a second HPV-derived nucleic acid sequence, and optionally wherein(a) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV strain and a second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV strain, or(b) the first HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a first HPV protein and the second HPV-derived nucleic acid sequence encodes an immunogenic polypeptide derived from a second HPV protein, optionally wherein the first HPV protein and the second HPV protein are derived from the same HPV strain.

45. A method for stimulating an immune response in a subject, the method comprising administering to the subject any one of the above compositions.

46. The method of claim 45, wherein the subject is at risk for one or more of cervical cancer, anal cancer, oropharyngeal cancer, oral cancer, penile cancer, vaginal cancer, and / or vulvar cancer.

47. The method of claim 45 or 46, wherein the subject is diagnosed as HPV positive.

48. The method of any one of claims 45-47, wherein the subject is diagnosed as having cervical intraepithelial neoplasia (C1N 1).

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