Methods and compositions for pandemic influenza vaccine

Abstract

Provided herein are RNA molecules encoding viral replication proteins and antigenic proteins or fragments thereof. Also provided herein are compositions that include RNA molecules encoding viral replication proteins and antigenic proteins or fragments thereof, and lipids. RNA molecules and compositions including them are useful for inducing immune responses.

Description

METHODS AND COMPOSITIONS FOR PANDEMIC INFLUENZA VACCINE CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of priority of U.S. Provisional Application No. 63 / 676,888, filed July 29, 2024, the entire contents of which are incorporated herein by reference. STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

[0002] This invention was made with government support under Contract No. 75A50122C00007 awarded by the Biomedical Advanced Research and Development Authority (BARDA). The US government has certain rights in the invention INCORPORATION OF SEQUENCE LISTING

[0003] The Sequence Listing titled 207653-607601_SL.xml, which was created on May 12, 2025 and is 231,393 bytes in size, is hereby incorporated by reference in its entirety. TECHNICAL FIELD

[0004] The present disclosure relates generally to inducing immune responses against infectious agents, such as influenza viruses, and more specifically to RNA molecules and lipid nanoparticles as vaccines. BACKGROUND

[0005] Influenza viruses cause epidemics almost every winter. Influenza infection results in various disease states, from sub-clinical infections to severe viral pneumonia. The severity of the disease is affected by the age of the host, their immune status, and / or the site of infection. Vaccination plays a critical role in controlling seasonal influenza epidemics. Highly pathogenic H5N1, an influenza A subtype with pandemic potential, circulates in avian and mammalian populations. Most humans are immunologically naïve to these highly pathogenic viruses leading to the potential of severe morbidity and mortality if these viruses begin to spread efficiently in the human population. Vaccines that specifically target hemagglutinin do not generate robust responses against the neuraminidase, another influenza virion surface protein that has sialidase activity.

[0006] Self-replicating ribonucleic acids (RNAs), e.g., RNAs derived from viral replicons, and messenger RNAs (mRNAs) are useful for expression of proteins, such as heterologous proteins, for a variety of purposes, such as expression of therapeutic proteins and expression of antigens for vaccines. A desirable property of replicons is the ability for sustained expression of the protein. Few treatments for infections caused by viruses and eukaryotic organisms are available, andresistance to antibiotics for the treatment of bacterial infections is increasing. In addition, rapid responses, including rapid vaccine development, are often required to effectively control emerging infectious diseases and pandemics. SUMMARY

[0007] In view of the foregoing, there exists a need for the prevention and / or treatment of infectious diseases, such as influenza. Various aspects of the present disclosure address this need, and provide other advantages as well.

[0008] The present disclosure provides RNA molecules that are useful for inducing immune responses. Both self-replicating RNA molecules and messenger RNA (mRNA) molecules are provided, as well as polynucleotides encoding the same.

[0009] In some aspects, the present disclosure provides self-replicating RNA molecules (saRNA) encoding both a hemagglutinin (HA) polypeptide and a neuraminidase (NA) polypeptide. In some embodiments, encoding both HA and NA provides one or more of the following advantages: (1) providing additional sequences other than hemagglutinin that could be the target of T cell responses; (2) improving effectiveness over hemagglutinin alone; and (3) decreasing risk of escape mutants from antigenic shift by one antigen alone.

[0010] In one aspects, provided herein is a composition comprising a self-replicating RNA molecule comprising the following in a 5’ to 3’ direction: (a) a 5’ untranslated region (UTR); (b) a sequence encoding one or more viral replication proteins; (c) a first subgenomic promoter (sgP); (d) a first Kozak sequence; (e) a sequence encoding a first avian influenza virus protein; (f) a second sgP; (g) a second Kozak sequence; (h) a sequence encoding a second avian influenza virus protein; (i) a 3’ UTR; and (j) a poly(A) tail. In some embodiments, the first and second avian influenza virus proteins together comprise a hemagglutinin (HA) polypeptide and a neuraminidase (NA) polypeptide of the same strain of avian influenza virus.

[0011] In some embodiments, the avian influenza virus is an H5N1 influenza virus. In some embodiments, the H5N1 influenza virus is a strain of A / Indonesia / 5 / 2005. In some embodiments, the one or more viral replication proteins are alphavirus proteins. In some embodiments, the alphavirus proteins are Venezuelan Equine Encephalitis Virus (VEEV) proteins. In some embodiments, the one or more viral replication proteins comprise an alphavirus nonstructural protein 1 (nsP1), an alphavirus nonstructural protein 2 (nsP2), an alphavirus nonstructural protein 3 (nsP3), and an alphavirus nonstructural protein 4 (nsP4). In some embodiments, the sequence encoding one or more viral replication proteins comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, atleast 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 4.

[0012] In some embodiments, the HA polypeptide comprises an antigenic polypeptide of HA. In some embodiments, the HA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO: 11. In some embodiments, the HA polypeptide is encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by SEQ ID NO: 3. In some embodiments, the HA polypeptide is encoded by the RNA sequence encoded by any one of SEQ ID NOs: 3, or 13-19. In some embodiments, the HA polypeptide comprises one or more of R224C, K228C, K404I, 342-345del, N27D, N39D, N100D, N170D, N181D, N209D, N302D, or N500D, relative to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises: (i) R224C and K228C, relative to SEQ ID NO: 11; (ii) R224C, K228C, and K404I, relative to SEQ ID NO: 11; (iii) N27D, N39D, N100D, N170D, N181D, N209D, and N302D, relative to SEQ ID NO: 11; (iv) N170D and N181D, relative to SEQ ID NO: 11; or (v) N27D, N39D, N170D, N181D, N302D, and N500D, relative to SEQ ID NO: 11.

[0013] In some embodiments, the NA polypeptide comprises an antigenic polypeptide of NA. In some embodiments, the NA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO: 10. In some embodiments, the NA polypeptide is encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by SEQ ID NO: 2. In some embodiments, the NA polypeptide is encoded by the RNA sequence encoded by any one of SEQ ID NO: 2, or 20-25. In some embodiments, the NA polypeptide comprises one or more of 48InsPCNQSIITYENNTWVNQTYVN (SEQ ID NO: 12), N68S, V79P, H80L, I86V, T111Q, N126S, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, N215S, Q388M, R399V, relative to SEQ ID NO: 10. In some embodiments, the NA polypeptide comprises: (i) V79P, H80L, C141V, E145S, S152A, V157I, S176T, V185I, Q388M, and R399V, relative to SEQ ID NO: 10; (ii) V79P, C141V, E145S, S152A, V157I, S176T, V185I, relative to SEQ ID NO: 10; (iii) V79P, H80L, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, Q388M, and R399V, relative to SEQ ID NO: 10; (iv) V79P, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, and V185I, relative to SEQ ID NO. 10; or (v) N68S, N126S, N215S, relative to SEQ ID NO: 10.

[0014] In some embodiments, the 5’ UTR comprises a viral 5’ UTR, a non-viral 5’ UTR, or a combination of viral and non-viral 5’ UTR sequences. In some embodiments, the 5’ UTR comprises an alphavirus 5’ UTR. In some embodiments, the alphavirus 5’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 5’ UTR sequence. In some embodiments, the 5’UTR comprises the RNA sequence encoded by SEQ ID NO: 5. In some embodiments, the 3’ UTR comprises a viral 3’ UTR, a non-viral 3’ UTR, or a combination of viral and non-viral 3’ UTR sequences. In some embodiments, the 3’ UTR comprises an alphavirus 3’ UTR sequence. In some embodiments, the alphavirus 3’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 3’ UTR sequence. In some embodiments, the 3’ UTR comprises the RNA sequence encoded by SEQ ID NO: 7. In some embodiments, the sgP comprises a sequence having at least 90%, at least 95%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 6. In some embodiments, the first and second Kozak sequences comprise GCCACC.

[0015] In some embodiments, the RNA molecule comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 1. In some embodiments, the RNA molecule comprises a sequence encoded by any one of SEQ ID NO: 1-9 or 13-25. In some embodiments, the RNA molecule comprises a sequence encoded by SEQ ID NO: 1.

[0016] In one aspect, the present disclosure provides a composition comprising a DNA molecule encoding an RNA molecule of any of the compositions disclosed herein. In some embodiments, the DNA molecule comprises a promoter. In some embodiments, the promoter is a T7 promoter.

[0017] In some embodiments, compositions disclosed herein further comprise an ionizable cationic lipid. In some embodiments, the ionizable cationic lipid has a structure of Formula I: (I) or a pharmaceutically acceptable salt or solvate thereof, wherein R5and R6are each independently selected from the group consisting of a linear or branched C1-C31 alkyl, C2-C31 alkenyl or C2-C31 alkynyl and cholesteryl; L5and L6are each independently selected from the group consisting of a linear C1-C20alkyl and C2-C20alkenyl; X5is -C(O)O-, whereby -C(O)O-R6is formed or -OC(O)- whereby -OC(O)-R6is formed; X6is -C(O)O- whereby -C(O)O-R5is formed or -OC(O)- whereby -OC(O)-R5is formed; X7is S or O; L7is absent or lower alkyl; R4is a linear or branched C1-C6alkyl; and R7and R8are each independently selected from the group consisting of a hydrogen and a linear or branched C1-C6 alkyl.

[0018] In some embodiments, the ionizable cationic lipid is selected from Table 6. In some embodiments, the ionizable cationic lipid is Compound-77: Compound-77. In some embodiments, the ionizable cationic lipid is Compound-90: Compound-90.

[0019] In one aspect, provided herein are methods of vaccinating a subject against an avian influenza (e.g., an H5N1 influenza, such as A / Indonesia / 5 / 2005), the method comprising administering to the subject any of the compositions disclosed herein.

[0020] In one aspect, the present disclosure provides uses of any of the compositions disclosed herein in the preparation of a medicament for vaccinating a subject against an avian influenza (e.g., an H5N1 influenza, such as A / Indonesia / 5 / 2005). BRIEF DESCRIPTION OF THE DRAWINGS

[0021] FIG.1 shows a schematic of a self-amplifying mRNA (also referred to as “sa-mRNA” or “saRNA” or “self-replicating RNA”) for expression of a hemagglutinin (HA) protein and a neuraminidase (NA) protein for an avian influenza virus.

[0022] FIGS.2A-2C show exemplary results for HA inhibition (FIG.2A), NA inhibition (FIG. 2B), and microneutralization titer (FIG.2C) assays for mice vaccinated intramuscularly with sa-mRNA constructs for expression of a HA protein and / or a NA protein from avian influenza strain H5N1 A / Indonesia / 5 / 2005. x axis indicates order and presence of HA and / or NA proteins. Vaccination with phosphate buffered saline (PBS) was used as a control.

[0023] FIGS.3A-3C show exemplary results for HA inhibition (FIG.3A), NA inhibition (FIG. 3B), and microneutralization titer (FIG.3C) assays for ferrets vaccinated intramuscularly with an sa-mRNA construct for expression of a HA protein and a NA protein from avian influenza strain H5N1 A / Indonesia / 5 / 2005 (Construct 1). Vaccination with a trimeric HA protein (rHA) from an A / Indonesia / 5 / 2005 plus Addavax adjuvant was used as a control.

[0024] FIG. 4 shows exemplary results for HA inhibition (left graph), NA inhibition (middle graph), and microneutralization titer (right graph) assays for mice vaccinated intramuscularly with an sa-mRNA construct for expression of a HA protein and a NA protein from avian influenza strain H5N1 A / Indonesia / 5 / 2005 formulated with Compound-77 or Compound-90. Administration of phosphate buffered saline (PBS) was used as a control.

[0025] FIG. 5 shows exemplary results from HA inhibition assays for mice vaccinated intramuscularly with an sa-mRNA construct for expression of a wildtype (WT) and mutant HA proteins from avian influenza strain H5N1 A / Indonesia / 5 / 2005, formulated with Compound-77. Administration of phosphate buffered saline (PBS) was used as a control.

[0026] FIG. 6 shows exemplary results from HA inhibition assays for mice vaccinated intramuscularly with an sa-mRNA construct for expression of a wildtype (WT) and mutant NA proteins from avian influenza strain H5N1 A / Indonesia / 5 / 2005, formulated with Compound-77. Administration of phosphate buffered saline (PBS) was used as a control.

[0027] FIGS. 7A-7B show exemplary levels of binding antibodies against H5N1 A / Indonesia / 5 / 2005 HA assessed from naïve BALB / c mice immunized with 1 µg (FIG.7A) or 5 µg (FIG.7B) of sa-mRNA constructs for expression of a HA protein and / or a NA protein from avian influenza strain H5N1 A / Indonesia / 5 / 2005. x axis indicates order and presence of HA and / or NA proteins.

[0028] FIGS. 8A-8B show exemplary levels of binding antibodies against H5N1 A / Indonesia / 5 / 2005 NA assessed from naïve BALB / c mice immunized with 1 µg (FIG.8A) or 5 µg (FIG.8B) of sa-mRNA constructs for expression of a HA protein and / or a NA protein from avian influenza strain H5N1 A / Indonesia / 5 / 2005. x axis indicates order and presence of HA and / or NA proteins.

[0029] FIGS.9A-9I show exemplary results from assays performed in ferret homologous viral challenge models to assess the efficacy of vaccination with Construct 1 compared to vaccination with recombinant protein (Recombinant HA) + adjuvant. FIG. 9A is a diagram of the experimental design for the illustrated results. FIG.9B is a graph showing percent survival of thesubjects post-viral challenge (arrow indicating results for unvaccinated ferrets). FIG. 9C is a graph showing percent weight change of the ferrets post-viral challenge. FIG. 9D is a graph showing the average body temperature of each group of ferrets post-viral challenge. FIGs.9E and 9F are graphs showing nasal wash titer and tissue viral titer, respectively, of each group of ferrets post-viral challenge (bars in groups of 4 from left to right correspond to groups in the legend listed from top to bottom, respectively). FIGs. 9G and 9H are graphs showing exemplary results of hemagglutinin inhibition assays and enzyme-linked lectin assays, respectively (bars in groups of 4 from left to right correspond to groups in the legend listed from top to bottom, respectively). FIG.9I is a graph showing exemplary results of microneutralization assays (bars from left to right correspond to groups in the legend listed from top to bottom, respectively).

[0030] FIGS. 10A-10I show exemplary results from assays performed in ferret heterologous viral challenge models to assess the efficacy of vaccination with Construct 1 compared to vaccination with recombinant protein (recombinant A / Indonesia / 5 / 2005 HA, or recombinant A / Vietnam / 1203 / 2004 HA) + adjuvant. FIG.10A is a diagram of the experimental design for the illustrated results. FIG.10B is a graph showing percent survival of the ferrets post-viral challenge. FIG.10C is a graph showing percent weight change of the ferrets post-viral challenge. FIG.10D is a graph showing the average body temperature of each group of ferrets post-viral challenge. FIGs.10E and 10F are graphs showing nasal wash titer and tissue viral titer, respectively, post- viral challenge (bars within each group of 4 from left to right correspond to results for PBS, Construct 1, Recombinant HA (Indonesia / 05), and Recombinant HA (Vietnam / 04), respectively). FIG. 10G provides graphs showing exemplary results of hemagglutinin inhibition assays, comparing results for inhibition of Vietnam / 04 HA (left) to Indonesia / 05 HA (right). FIG. 10H provides graphs showing exemplary results of neuraminidase inhibition assays, comparing results for inhibition of Vietnam / 04 NA (left) to Indonesia / 05 NA (right). FIG. 10I provides graphs showing exemplary results of microneutralization assays against Vietnam / 04 (left) and Indonesia / 05 (right).

[0031] FIGs. 11A-11C are exemplary micrographs of stained lung tissue sections from vaccinated and unvaccinated ferrets following viral challenge. DETAILED DESCRIPTION

[0032] The present disclosure relates to RNAs, e.g., self-replicating RNAs and messenger RNAs (mRNAs), and nucleic acids encoding the same for expression of transgenes such as antigenic proteins, for example. Also provided herein are methods of administration (e.g., to a host, such as a mammalian subject) of RNAs, whereby the RNA is translated in vivo and the heterologous protein-coding sequence is expressed and, e.g., can elicit an immune response to theheterologous protein-coding sequence in the recipient or provide a therapeutic effect, including induction of an immune response, where the heterologous protein-coding sequence is a therapeutic or an antigenic protein. RNAs, e.g., self-replicating RNAs and messenger RNAs (mRNAs), provided herein are useful as vaccines that can be rapidly generated and that can be effective at low and / or single doses. The present disclosure further relates to methods of inducing an immune response using RNAs provided herein.

[0033] In some embodiments, an immune response can be elicited against influenza. Immunogens include, but are not limited to, those derived from type A influenza strains (such as H5N1).

[0034] Self-replicating RNAs are described, for example, in U.S. 2018 / 0036398, the contents of which are incorporated herein by reference in their entirety. Definitions

[0035] As used herein, the term “fragment,” when referring to a protein or nucleic acid, for example, means any shorter sequence than the full-length protein or nucleic acid. Accordingly, any sequence of a nucleic acid or protein other than the full-length nucleic acid or protein sequence can be a fragment. In some aspects, a protein fragment includes an epitope. In other aspects, a protein fragment is an epitope.

[0036] As used herein, the term “nucleic acid” refers to any deoxyribonucleic acid (DNA) molecule, ribonucleic acid (RNA) molecule, or nucleic acid analogues. A DNA or RNA molecule can be double-stranded or single-stranded and can be of any size. Exemplary nucleic acids include, but are not limited to, chromosomal DNA, plasmid DNA, cDNA, cell-free DNA (cfDNA), mitochondrial DNA, chloroplast DNA, viral DNA, mRNA, tRNA, rRNA, long non-coding RNA, siRNA, micro RNA (miRNA or miR), hnRNA, and viral RNA. Exemplary nucleic analogues include peptide nucleic acid, morpholino- and locked nucleic acid, glycol nucleic acid, and threose nucleic acid. As used herein, the term “nucleic acid molecule” is meant to include fragments of nucleic acid molecules as well as any full-length or non-fragmented nucleic acid molecule, for example. As used herein, the terms “nucleic acid” and “nucleic acid molecule” can be used interchangeably, unless context clearly indicates otherwise.

[0037] As used herein, the term “polynucleotide” refers to a nucleic acid sequence that includes at least two nucleotide monomers. The term “polynucleotide” can refer to polymers of DNA, RNA, nucleic acid analogues, or combinations of these. A “polynucleotide” can be double- stranded or single-stranded and can be of any size. A polynucleotide can be a separate nucleic acid molecule or be a part of a nucleic acid molecule. Accordingly, the term “polynucleotide” can refer to a nucleic acid molecule or to a region of a nucleic acid molecule.

[0038] As used herein, the term “protein” refers to any polymeric chain of amino acids. The terms “peptide” and “polypeptide” can be used interchangeably with the term protein, unless context clearly indicates otherwise, and can also refer to a polymeric chain of amino acids. The term “protein” encompasses native or artificial proteins, protein fragments and polypeptide analogs of a protein sequence. A protein may be monomeric or polymeric. The term “protein” encompasses fragments and variants (including fragments of variants) thereof, unless otherwise contradicted by context.

[0039] Amino acid mutations are indicated by the form “AxxB,” relative to a reference sequence, where “B” is the amino acid that replaces amino acid “A” at position “xx” of the reference sequence. In cases where a variant polypeptide with one or more specified mutations and the reference sequence are not otherwise 100% identical to one another, the position of one or more of the amino acid substitutions indicated for the corresponding variant may shift (e.g., in the case of insertion or deletion of one or more amino acids), but still be contained within the resulting variant. For example, the cysteine substitution corresponding to “R224C” (at position 224 relative to SEQ ID NO: 10) may be present, but at a different position (and possibly represent a change from a different starting amino acid) in the resulting variant. Whether an amino acid corresponds to an indicated substitution, albeit at a different position, can be determined by sequence alignment. In general, an alignment showing identity or similarity of one or more amino acids flanking the amino acid substitution will allow the variant amino acid in a homologous query sequence to be positioned locally with respect to the corresponding variant of a reference sequence to confirm the presence of the substitution, albeit at a shifted numerical position in a given polypeptide chain. In some embodiments, a region comprising at least three to fifteen amino acids, including the substituted position, will locally align with the corresponding variant of the reference sequence with a relatively high percent identity or similarity, including at the position of the substituted amino acid along the corresponding variant sequence (e.g., 90%, 95%, or 100% identity). In some embodiments, the one or more amino acid substitutions (e.g. all or less than all of the amino acid substitutions) indicated by a corresponding variant of the reference sequence is considered to be present in a given variant, even if occurring at a different physical position along a polypeptide chain, if the sequence of the polypeptide being compared aligns to the corresponding variant with an identical amino acid at the indicated position along the corresponding variant sequence when using a BLASTP alignment algorithm with default parameters. Alignments can also be used to identify a position in a starting sequence that should be modified in order to arrive at a polypeptide corresponding to a variant polypeptide disclosed herein, including in cases where the position and / or identity of the starting amino acid to be modified is different from that of the corresponding variant. In general, two amino acids are considered to be similar if having chemicalproperties sufficiently similar for contributing to an alignment using default parameters. In some embodiments, a given amino acid variant is considered present when at least fifteen amino acids (including the variant position) aligns to the indicated numbered position of the reference sequence (modified to contain the indicated variant) with 100% identity, using a BLASTP alignment algorithm with default parameters.

[0040] In general, “sequence identity” or “sequence homology,” which can be used interchangeably, refer to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Typically, techniques for determining sequence identity include determining the nucleotide sequence of a polynucleotide and / or determining the amino acid sequence encoded thereby or the amino acid sequence of a polypeptide, and comparing these sequences to a second nucleotide or amino acid sequence. As used herein, the term “percent (%) sequence identity” or “percent (%) identity,” also including “percent homology,” refers to the percentage of amino acid residues or nucleotides in a sequence that are identical with the amino acid residues or nucleotides in a reference sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Thus, two or more sequences (polynucleotide or amino acid) can be compared by determining their “percent identity,” also referred to as “percent homology.” The percent identity to a reference sequence (e.g., nucleic acid or amino acid sequences), which may be a sequence within a longer molecule (e.g., polynucleotide or polypeptide), may be calculated as the number of exact matches between two optimally aligned sequences divided by the length of the reference sequence and multiplied by 100. Percent identity may also be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul, Proc. Natl. Acad. Sci. USA 87:2264-2268 (1990) and as discussed in Altschul et al., J. Mol. Biol.215:403-410 (1990); Karlin and Altschul, Proc. Natl. Acad. sci. USA 90:5873-5877 (1993); and Altschul et al., Nucleic Acids Res.25:3389-3402 (1997). Briefly, the BLAST program defines identity as the number of identical aligned symbols (i.e., nucleotides or amino acids), divided by the total number of symbols in the shorter of the two sequences. The program may be used to determine percent identity over the entire length of the sequences being compared. Default parameters are provided to optimize searches with short query sequences, for example, with the blastp program. The program also allows use of an SEG filter to mask-off segments of the query sequences as determined by the SEG program of Wootton and Federhen, Computers and Chemistry 17: 149-163 (1993). Ranges of desired degrees of sequence identity are approximately 80% to 100% and integer values in between. Percent identities betweena reference sequence and a claimed sequence can be at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, at least 99.5%, or at least 99.9%. In general, an exact match indicates 100% identity over the length of the reference sequence. Additional programs and methods for comparing sequences and / or assessing sequence identity include the Needleman- Wunsch algorithm (see, e.g., the EMBOSS Needle aligner available at ebi.ac.uk / Tools / psa / emboss needle / , optionally with default settings), the Smith-Waterman algorithm (see, e.g., the EMBOSS Water aligner available at ebi.ac.uk / Tools / psa / emboss water / , optionally with default settings), the similarity search method of Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85, 2444, or computer programs which use these algorithms (GAP, BESTFIT, FASTA, BLAST P, BLAST N and TFASTA in Wisconsin Genetics Software Package, Genetics Computer Group. 575 Science Drive, Madison, Wis.). In some aspects, reference to percent sequence identity refers to sequence identity as measured using BLAST (Basic Local Alignment Search Tool). In other aspects, ClustalW is used for multiple sequence alignment. Optimal alignment may be assessed using any suitable parameters of a chosen algorithm, including default parameters.

[0041] As used herein, “homologous sequences” refers to sequences that share sequence similarity and / or structural similarity (Pearson, 2013, An Introduction to Sequence similarity (“Homology”) Searching, Current Protoc Bioinformatics, 42:3.1.1-3.1.8). Accordingly, homologous sequences share common evolutionary ancestry or are derived from a common sequence. Homologous sequences can also share structural or sequence similarity to an intermediate sequence. Homologous sequences can have similar functions, i.e., have functional similarity. Homology can be inferred based on nucleic acid and / or amino acid sequence, with protein similarity searches generally having greater sensitivity than nucleic acid sequence searches. Homology can also be inferred for amino acid sequences that include similar amino acids, i.e., amino acids with similar physiochemical properties, rather than identical amino acids over at least a region of sequence. The terms “homologous sequences,” “homologues,” and “homologous nucleic acid” and / or “homologous protein” can be used interchangeably, unless context clearly indicated otherwise.

[0042] As used herein, the term “drug” or “medicament,” means a pharmaceutical formulation or composition as described herein.

[0043] As used herein, the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, references to “the method” includes one or more methods, and / or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.

[0044] “About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of +20%, or ±10%, or ±5%, or even ±1% from the specified value, as such variations are appropriate for the disclosed methods or to perform the disclosed methods.

[0045] The term “expression” refers to the process by which a nucleic acid sequence or a polynucleotide is transcribed from a DNA template (such as into mRNA or other RNA transcript) and / or the process by which a transcribed mRNA or other RNA is subsequently translated into peptides, polypeptides, or proteins. Transcripts and encoded polypeptides may be collectively referred to as “gene product.”

[0046] As used herein, the terms “self-replicating RNA,” “self-transcribing and self-replicating RNA,” “self-amplifying RNA” (saRNA, samRNA, or sa-mRNA), and “replicon” may be used interchangeably, unless context clearly indicates otherwise. Generally, the term “replicon” or “viral replicon” refers to a self-replicating subgenomic RNA derived from a viral genome that includes viral genes encoding non-structural proteins important for viral replication and that lacks viral genes encoding structural proteins. A self-replicating RNA can encode further subgenomic RNAs that are not able to self-replicate. A self-replicating RNA can also be referred to as a “STARRTM” or STARR® RNA.

[0047] As used herein, “operably linked,” “operable linkage,” “operatively linked,” or grammatical equivalents thereof refer to juxtaposition of genetic elements, e.g., a promoter, an enhancer, a polyadenylation sequence, etc., wherein the elements are in a relationship permitting them to operate in the expected manner. For instance, a regulatory element, which can comprise promoter and / or enhancer sequences, is operatively linked to a coding region if the regulatory element helps initiate transcription of the coding sequence. There may be intervening residues between the regulatory element and coding region so long as this functional relationship is maintained. RNA Molecules

[0048] In some aspects, provided herein are RNA molecules comprising the following in a 5’ to 3’ direction: (a) a 5’ untranslated region (UTR); (b) a sequence encoding one or more viral replication proteins; (c) a first subgenomic promoter (sgP); (d) a first Kozak sequence; (e) a sequence encoding a first avian influenza virus protein; (f) a second sgP; (g) a second Kozak sequence; (h) a sequence encoding a second avian influenza virus protein; (i) a 3’ UTR; and (j) a poly(A) tail. In some embodiments, the first and second avian influenza virus proteins together comprise a hemagglutinin (HA) polypeptide and a neuraminidase (NA) polypeptide of the same strain of avian influenza virus (or variant / mutant thereof). In some embodiments, the avianinfluenza virus is an H5N1 influenza virus. In some embodiments, the H5N1 influenza virus is a strain of A / Indonesia / 5 / 2005 (or variant / mutant thereof).

[0049] In some aspects, provided herein are compositions comprising the RNA molecules described herein. In some embodiments, the composition comprises an RNA molecule comprising the following in a 5’ to 3’ direction: (a) a 5’ untranslated region (UTR); (b) a sequence encoding one or more viral replication proteins; (c) a first subgenomic promoter (sgP); (d) a first Kozak sequence; (e) a sequence encoding a first avian influenza virus protein; (f) a second sgP; (g) a second Kozak sequence; (h) a sequence encoding a second avian influenza virus protein; (i) a 3’ UTR; and (j) a poly(A) tail. In some embodiments, the first and second avian influenza virus proteins together comprise a hemagglutinin (HA) polypeptide and a neuraminidase (NA) polypeptide of the same strain of avian influenza virus (or variant / mutant thereof). In some embodiments, the avian influenza virus is an H5N1 influenza virus. In some embodiments, the H5N1 influenza virus is a strain of A / Indonesia / 5 / 2005 (or variant / mutant thereof).

[0050] In some embodiments, the one or more viral replication proteins are alphavirus proteins. In yet further embodiments, the alphavirus proteins are from Venezuelan Equine Encephalitis Virus (VEEV).

[0051] In some embodiments, the one or more viral replication proteins comprise an alphavirus nonstructural protein 1 (nsP1), an alphavirus nonstructural protein 2 (nsP2), an alphavirus nonstructural protein 3 (nsP3), an alphavirus nonstructural protein 4 (nsP4), or any combination thereof. In some embodiments, the sequence encoding one or more viral replication proteins comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 4. In some embodiments, the sequence encoding one or more viral replication proteins comprises a sequence having at least 90% identity to the RNA sequence encoded by SEQ ID NO: 4. In some embodiments, the sequence encoding one or more viral replication proteins comprises a sequence having at least 95% identity to the RNA sequence encoded by SEQ ID NO: 4. In some embodiments, the sequence encoding one or more viral replication proteins comprises a sequence that differs from SEQ ID NO: 4, but encodes proteins having the same protein sequence encoded thereby. In some embodiments, the sequence encoding one or more viral replication proteins comprises the RNA sequence encoded by SEQ ID NO: 4.

[0052] In some embodiments, the HA polypeptide comprises an antigenic polypeptide of an HA. In some embodiments, the HA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO: 11. In some embodiments, the HA polypeptideis encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by any one of SEQ ID NOs: 3 or 13-19. In some embodiments, the HA polypeptide comprises one or more of R224C, K228C, K404I, 342-345del, N27D, N39D, N100D, N170D, N181D, N209D, N302D, or N500D, relative to SEQ ID NO: 11.

[0053] In some embodiments, the NA polypeptide comprises an antigenic polypeptide of a NA. In some embodiments, the NA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO: 10. In some embodiments, the NA polypeptide is encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by any one of SEQ ID NOs: 2 or 20-25. In some embodiments, the NA polypeptide comprises one or more of 48InsPCNQSIITYENNTWVNQTYVN (SEQ ID NO: 12), N68S, V79P, H80L, I86V, T111Q, N126S, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, N215S, Q388M, R399V, relative to SEQ ID NO: 10.

[0054] In some embodiments, the 5’ UTR comprises a viral 5’ UTR, a non-viral 5’ UTR, or a combination of viral and non-viral 5’ UTR sequences. In some embodiments, the 5’ UTR comprises an alphavirus 5’ UTR. In some embodiments, the alphavirus 5’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 5’ UTR sequence. In some embodiments, the 5’ UTR comprises the RNA sequence encoded by SEQ ID NO: 5.

[0055] In some embodiments, the 3’ UTR comprises a viral 3’ UTR, a non-viral 3’ UTR, or a combination of viral and non-viral 3’ UTR sequences. In some embodiments, the 3’ UTR comprises an alphavirus 3’ UTR sequence. In some embodiments, the alphavirus 3’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 3’ UTR sequence. In some embodiments, the 3’ UTR comprises the RNA sequence encoded by SEQ ID NO: 7.

[0056] In some embodiments, one or both of the sgP comprises an alphavirus sgP sequence. In some embodiments, the alphavirus sgP comprises a VEEV sgP sequence. In some embodiments, one or both of the sgP comprises a sequence having at least 90%, at least 95%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 6. In some embodiments, one or both of the sgP comprises the RNA sequence encoded by SEQ ID NO: 6.

[0057] In some embodiments, one or both of the Kozak sequences comprises GCCACC.

[0058] In some embodiments, the RNA molecule includes a poly-A tail. The poly-A tail may be transcribed directly from a template polynucleotide, or may be added post-transcriptionally. The poly-A tail may have any of a variety of lengths, such as 20-300 nucleotides (SEQ ID NO: 156). In some embodiments, the poly-A tail is about 90 nucleotides in length. In some embodiments, the poly-A tail is about 130 nucleotides in length. In some embodiments, the poly- A tail is encoded by an RNA encoded by the sequence of SEQ ID NO: 8 or 9. In some embodiments, the poly-A tail is less than 100 nucleotides in length (SEQ ID NO: 157) (e.g., 20-99 nucleotides in length). In some embodiments, the poly-A tail is less than 90, 80, 75, 70, 65, 60, 55, or 50 nucleotides in length (SEQ ID NO: 158).

[0059] In some aspects, the RNA molecules disclosed herein are self-replicating RNA molecules. In some embodiments, the RNA molecule comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 1. In some embodiments, the RNA molecule has at least 80% sequence identity (e.g., at least 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity) to the RNA sequence encoded by SEQ ID NO: 1. In some embodiments, the RNA molecule has at least 90% sequence identity to the RNA sequence encoded by SEQ ID NO: 1. In some embodiments, the RNA molecule has at least 95% sequence identity to the RNA sequence encoded by SEQ ID NO: 1. In some embodiments, the RNA molecule comprises the RNA sequence encoded by SEQ ID NO: 1.

[0060] In some embodiments, the compositions disclosed herein comprise DNA molecules encoding any of the RNA molecules disclosed herein. In some embodiments, each of the DNA molecules comprise a promoter. In further embodiments, the promoter of each DNA molecule is located 5’ of a 5’ UTR. In yet further embodiments, the promoter is a T7 promoter. Codon Optimization

[0061] In some embodiments, compositions provided herein encode one or more viral replication proteins include codon-optimized sequences. As a result, protein-coding sequences provided herein may be substantially varied and still encode the same protein. As used herein, the term “codon-optimized” means a polynucleotide, nucleic acid sequence, or coding sequence has been redesigned as compared to a wild-type or reference polynucleotide, nucleic acid sequence, or coding sequence by choosing different codons without altering the amino acid sequence of the encoded protein. Accordingly, codon-optimization generally refers to replacement of codons with synonymous codons to optimize expression of a protein while keeping the amino acid sequence of the translated protein the same. Codon optimization of a sequence can increase protein expression levels (Gustafsson et al., Codon bias and heterologous protein expression. 2004, Trends Biotechnol 22: 346-53) of the encoded proteins, for example, and provide other advantages. Variables such as codon usage preference as measured by codon adaptation index (CAI), for example, the presence or frequency of U and other nucleotides, mRNA secondary structures, cis-regulatory sequences, GC content, and other variables may correlate with protein expression levels (Villalobos et al., Gene Designer: a synthetic biology tool for constructing artificial DNA segments. 2006, BMC Bioinformatics 7:285). Polynucleotides can be codon-optimized before modifying miRNA binding sites. miRNA binding sites can be modified to replace one or more codons with synonymous codons.

[0062] Any method of codon optimization can be used to codon optimize polynucleotides and nucleic acid molecules provided herein, and any variable can be altered by codon optimization. Accordingly, any combination of codon optimization methods can be used. Exemplary methods include the high codon adaptation index (CAI) method, the Low U method, and others. The CAI method chooses a most frequently used synonymous codon for an entire protein coding sequence. As an example, the most frequently used codon for each amino acid can be deduced from 74,218 protein-coding genes from a human genome. The Low U method targets U-containing codons that can be replaced with a synonymous codon with fewer U moieties, generally without changing other codons. If there is more than one choice for replacement, the more frequently used codon can be selected. Any polynucleotide, nucleic acid sequence, or codon sequence provided herein can be codon-optimized.

[0063] In some embodiments, the nucleotide sequence of any region of the RNA or DNA templates described herein may be codon optimized, including, for example, nucleotide sequences encoding viral replication proteins, hemagglutinin proteins, neuraminidase proteins, or any combination thereof. Preferably, the primary cDNA template may include reducing the occurrence or frequency of appearance of certain nucleotides in the template strand. For example, the occurrence of a nucleotide in a template may be reduced to a level below 25% of said nucleotides in the template. In further examples, the occurrence of a nucleotide in a template may be reduced to a level below 20% of said nucleotides in the template. In some examples, the occurrence of a nucleotide in a template may be reduced to a level below 16% of said nucleotides in the template. Preferably, the occurrence of a nucleotide in a template may be reduced to a level below 15%, and preferably may be reduced to a level below 12% of said nucleotides in the template.

[0064] In some embodiments, the nucleotide reduced is uridine. For example, the present disclosure provides nucleic acids with altered uracil content wherein at least one codon in the wild-type sequence has been replaced with an alternative codon to generate a uracil-altered sequence. Altered uracil sequences can have at least one of the following properties: (i) an increase or decrease in global uracil content (i.e., the percentage of uracil of the total nucleotide content in the nucleic acid of a section of the nucleic acid, e.g., the open reading frame); (ii) an increase or decrease in local uracil content (i.e., changes in uracil content are limited to specific subsequences); (iii) a change in uracil distribution without a change in the global uracil content;(iv) a change in uracil clustering (e.g., number of clusters, location of clusters, or distance between clusters); or (v) combinations thereof.

[0065] In some embodiments, the percentage of uracil nucleobases in the nucleic acid sequence is reduced with respect to the percentage of uracil nucleobases in the wild-type nucleic acid sequence. For example, 30% of nucleobases may be uracil in the wild-type sequence but the nucleobases that are uracil are preferably lower than 15%, preferably lower than 12% and preferably lower than 10% of the nucleobases in the nucleic acid sequences of the disclosure. The percentage uracil content can be determined by dividing the number of uracil in a sequence by the total number of nucleotides and multiplying by 100.

[0066] In some embodiments, the percentage of uracil nucleobases in a subsequence of the nucleic acid sequence is reduced with respect to the percentage of uracil nucleobases in the corresponding subsequence of the wild-type sequence. For example, the wild-type sequence may have a 5′-end region (e.g., 30 codons) with a local uracil content of 30%, and the uracil content in that same region could be reduced to preferably 15% or lower, preferably 12% or lower and preferably 10% or lower in the nucleic acid sequences of the disclosure. These subsequences can also be part of the wild-type sequences of the heterologous 5’ and 3’ UTR sequences of the present disclosure.

[0067] In some embodiments, codons in the nucleic acid sequence of the disclosure reduce or modify, for example, the number, size, location, or distribution of uracil clusters that could have deleterious effects on protein translation. Although lower uracil content is desirable in certain aspects, the uracil content, and in particular the local uracil content, of some subsequences of the wild-type sequence can be greater than the wild-type sequence and still maintain beneficial features (e.g., increased expression).

[0068] In some embodiments, the uracil-modified sequence induces a lower Toll-Like Receptor (TLR) response when compared to the wild-type sequence. Several TLRs recognize and respond to nucleic acids. Double-stranded (ds)RNA, a frequent viral constituent, has been shown to activate TLR3. Single-stranded (ss)RNA activates TLR7. RNA oligonucleotides, for example RNA with phosphorothioate internucleotide linkages, are ligands of human TLR8. DNA containing unmethylated CpG motifs, characteristic of bacterial and viral DNA, activate TLR9.

[0069] As used herein, the term “TLR response” is defined as the recognition of single-stranded RNA by a TLR7 receptor, and preferably encompasses the degradation of the RNA and / or physiological responses caused by the recognition of the single-stranded RNA by the receptor. Methods to determine and quantify the binding of an RNA to a TLR7 are known in the art. Similarly, methods to determine whether an RNA has triggered a TLR7-mediated physiologicalresponse (e.g., cytokine secretion) are well known in the art. In some embodiments, a TLR response can be mediated by TLR3, TLR8, or TLR9 instead of TLR7. Suppression of TLR7- mediated response can be accomplished via nucleoside modification. RNA undergoes over a hundred different nucleoside modifications in nature. Human rRNA, for example, has ten times more pseudouracil (′P) and 25 times more 2′-O-methylated nucleosides than bacterial rRNA. Bacterial RNA contains no nucleoside modifications, whereas mammalian RNAs have modified nucleosides such as 5-methylcytidine (m5C), N6-methyladenosine (m6A), inosine and many 2′- O-methylated nucleosides in addition to N7-methylguanosine (m7G).

[0070] In some embodiments, the uracil content of polynucleotides disclosed herein is less than about 50%, 49%, 48%, 47%, 46%, 45%, 44%, 43%, 42%, 41%, 40%, 39%, 38%, 37%, 36%, 35%, 34%, 33%, 32%, 31%, 30%, 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1% of the total nucleobases in the sequence in the reference sequence. In some embodiments, the uracil content of polynucleotides disclosed herein is between about 5% and about 25%. In some embodiments, the uracil content of polynucleotides disclosed herein is between about 15% and about 25%.

[0071] In some embodiments, the nucleotide that is increased or decreased is a nucleotide other than or in addition to uracil. Sequences with altered nucleotide content can have (i) an increase or decrease in local C content (i.e., changes in cytosine content are limited to specific subsequences); (ii) an increase or decrease in local G content (i.e., changes in guanosine content are limited to specific subsequences); or (iii) a combination thereof.

[0072] In some embodiments, polynucleotides of nucleic acid molecules provided herein comprise a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to the RNA sequence encoded by SEQ ID NO: 4. In some embodiments, polynucleotides of nucleic acid molecules provided herein comprise the RNA sequence encoded by SEQ ID NO: 4. Intergenic Region

[0073] In some embodiments, polynucleotides provided herein (e.g., polynucleotides encoding an NA polypeptide and polynucleotides ending an HA polypetide) are included in the same (i.e., a single) or in separate nucleic acid molecules. In some embodiments, polynucleotides of nucleic acid molecules provided herein are included in a single nucleic acid molecule. In some embodiments, a polynucleotide encoding an NA polypeptide is located 5’ of a polynucleotide encoding an HA polypeptide.

[0074] In some embodiments, a first polynucleotide (e.g., a polynucleotide that encodes one or more viral replication proteins, or a polynucleotide encoding an NA polypeptide or an HA polypeptide) and a second polynucleotide (e.g., a polynucleotide encoding an NA polypeptide or an HA polypeptide) are included in the same (i.e., a single) nucleic acid molecule. In some embodiments, a nucleic acid molecule herein includes first, second, and third polynucleotides (e.g., a polynucleotide encoding one or more viral replication proteins, a polynucleotide encoding an NA polypeptide, and a polynucleotide encoding an HA polypeptide). Sequentially located polynucleotides of nucleic acid molecules provided herein can be contiguous, i.e., adjacent to each other without nucleotides in between. In one aspect, an intergenic region is located between sequential polynucleotides (e.g., a first polynucleotide and a second polynucleotide, and / or between a second polynucleotide and a third polynucleotide). As used herein, the terms “intergenic region” and “intergenic sequence” can be used interchangeably, unless context clearly indicates otherwise.

[0075] An intergenic region located between polynucleotides can be of any length and can have any nucleotide sequence. As an example, the intergenic region between two polynucleotides can include about one nucleotide, about two nucleotides, about three nucleotides, about four nucleotides, about five nucleotides, about six nucleotides, about seven nucleotides, about eight nucleotides, about nine nucleotides, about ten nucleotides, about 11 nucleotides, about 12 nucleotides, about 13 nucleotides, about 14 nucleotides, about 15 nucleotides, about 16 nucleotides, about 17 nucleotides, about 18 nucleotides, about 19 nucleotides, about 20 nucleotides, about 21 nucleotides, about 22 nucleotides, about 23 nucleotides, about 24 nucleotides, about 25 nucleotides, about 26 nucleotides, about 27 nucleotides, about 28 nucleotides, about 29 nucleotides, about 30 nucleotides, about 31 nucleotides, about 32 nucleotides, about 33 nucleotides, about 34 nucleotides, about 35 nucleotides, about 36 nucleotides, about 37 nucleotides, about 38 nucleotides, about 39 nucleotides, about 40 nucleotides, about 41 nucleotides, about 42 nucleotides, about 43 nucleotides, about 44 nucleotides, about 45 nucleotides, about 46 nucleotides, about 47 nucleotides, about 48 nucleotides, about 49 nucleotides, about 50 nucleotides, about 60 nucleotides, about 70 nucleotides, about 80 nucleotides, about 90 nucleotides, about 100 nucleotides, about 125 nucleotides, about 150 nucleotides, about 175 nucleotides, about 200 nucleotides, about 250 nucleotides, about 300 nucleotides, about 350 nucleotides, about 400 nucleotides, about 450 nucleotides, about 500 nucleotides, about 600 nucleotides, about 700 nucleotides, about 800 nucleotides, about 900, about 1,000 nucleotides, about 1,500 nucleotides, about 2,000 nucleotides, about 2,500 nucleotides, about 3,000 nucleotides, about 3,500 nucleotides, about 4,000 nucleotides, about 4,500 nucleotides, about 5,000 nucleotides, about 6,000 nucleotides, about7,000 nucleotides, about 8,000 nucleotides, about 9,000 nucleotides, about 10,000 nucleotides, and any number or range in between. In one aspect, the intergenic region between two polynucleotides includes about 10-100 nucleotides, about 10-200 nucleotides, about 10-300 nucleotides, about 10-400 nucleotides, or about 10-500 nucleotides. In another aspect, the intergenic region between two polynucleotides includes about 1-10 nucleotides, about 1-20 nucleotides, about 1-30 nucleotides, about 1-40 nucleotides, or about 1- 50 nucleotides. In yet another aspect, the region includes about 44 nucleotides.

[0076] In one aspect, the intergenic region between two polynucleotides includes a viral sequence. The intergenic region between two polynucleotides can include a sequence from any virus, such as alphaviruses and rubiviruses, for example. In one aspect, the intergenic region between two polynucleotides comprises an alphavirus sequence, such as a sequence from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis Virus (WEEV), Highland J Virus (HJV), Fort Morgan Virus (FMV), Ndumu Virus (NDUV), Salmonid Alphavirus (SAV), Buggy Creek Virus (BCRV), or any combination thereof. In another aspect, the intergenic region between two polynucleotides comprises a sequence from Venezuelan Equine Encephalitis Virus (VEEV). In some embodiments, the intergenic region comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO: 153. In some embodiments, the intergenic region between two polynucleotides comprises a sequence having at least 90% identity to the RNA encoded by SEQ ID NO: 153. In some embodiments, the intergenic region between two polynucleotides comprises a sequence having at least 95% identity to the RNA encoded by SEQ ID NO: 153. In some embodiments, the intergenic region between two polynucleotides comprises the RNA sequence encoded by SEQ ID NO: 153. Natural and Modified Nucleotides

[0077] A self-replicating RNA of the disclosure can comprise one or more chemically modified nucleotides. Examples of nucleic acid monomers include non-natural, modified, and chemically-modified nucleotides, including any such nucleotides known in the art. Nucleotides can be artificially modified at either the base portion or the sugar portion. In nature, most polynucleotides comprise nucleotides that are “unmodified” or “natural” nucleotides, which include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). These bases are typically fixed to a ribose or deoxy ribose at the 1’ position. The use of RNA polynucleotides comprising chemically modified nucleotides have been shown to improve RNA expression, expression rates, half-life and / or expressed protein concentrations. RNA polynucleotides comprising chemically modified nucleotides have also been useful in optimizing protein localization thereby avoiding deleterious bio-responses such as immune responses and / or degradation pathways.

[0078] Examples of modified or chemically-modified nucleotides include 5-hydroxycytidines, 5-alkylcytidines, 5-hydroxyalkylcytidines, 5-carboxycytidines, 5-formylcytidines, 5- alkoxycytidines, 5-alkynylcytidines, 5-halocytidines, 2-thiocytidines, N4-alkylcytidines, N4- aminocytidines, N4-acetylcytidines, and N4,N4-dialkylcytidines.

[0079] Examples of modified or chemically-modified nucleotides include 5-hydroxycytidine, 5-methylcytidine, 5-hydroxymethylcytidine, 5-carboxycytidine, 5-formylcytidine, 5- methoxycytidine, 5-propynylcytidine, 5-bromocytidine, 5-iodocytidine, 2-thiocytidine; N4- methylcytidine, N4-aminocytidine, N4-acetylcytidine, and N4,N4-dimethylcytidine.

[0080] Examples of modified or chemically-modified nucleotides include 5-hydroxyuridines, 5-alkyluridines, 5-hydroxyalkyluridines, 5-carboxyuridines, 5-carboxyalkylesteruridines, 5- formyluridines, 5-alkoxyuridines, 5-alkynyluridines, 5-halouridines, 2-thiouridines, and 6- alkyluridines.

[0081] Examples of modified or chemically-modified nucleotides include 5-hydroxyuridine, 5- methyluridine, 5-hydroxymethyluridine, 5-carboxyuridine, 5-carboxymethylesteruridine, 5- formyluridine, 5-methoxyuridine (also referred to herein as “5MeOU”), 5-propynyluridine, 5- bromouridine, 5-fluorouridine, 5-iodouridine, 2-thiouridine, and 6-methyluridine.

[0082] Examples of modified or chemically-modified nucleotides include 5- methoxycarbonylmethyl-2-thiouridine, 5-methylaminomethyl-2-thiouridine, 5- carbamoylmethyluridine, 5-carbamoylmethyl-2’-O-methyluridine, 1-methyl-3-(3-amino-3- carboxypropy)pseudouridine, 5-methylaminomethyl-2-selenouridine, 5-carboxymethyluridine, 5- methyldihydrouridine, 5-taurinomethyluridine, 5-taurinomethyl-2-thiouridine, 5- (isopentenylaminomethyl)uridine, 2’-O-methylpseudouridine, 2-thio-2’O-methyluridine, and 3,2’-O-dimethyluridine.

[0083] Examples of modified or chemically-modified nucleotides include N6-methyladenosine, 2-aminoadenosine, 3-methyladenosine, 8-azaadenosine, 7-deazaadenosine, 8-oxoadenosine, 8-bromoadenosine, 2-methylthio-N6-methyladenosine, N6-isopentenyladenosine, 2-methylthio- N6-isopentenyladenosine, N6-(cis-hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis- hydroxyisopentenyl)adenosine, N6-glycinylcarbamoyladenosine, N6-threonylcarbamoyl- adenosine, N6-methyl-N6-threonylcarbamoyl-adenosine, 2-methylthio-N6-threonylcarbamoyl- adenosine, N6,N6-dimethyladenosine, N6-hydroxynorvalylcarbamoyladenosine, 2-methylthio- N6-hydroxynorvalylcarbamoyl-adenosine, N6-acetyl-adenosine, 7-methyl-adenine, 2- methylthio-adenine, 2-methoxy-adenine, alpha-thio-adenosine, 2'-O-methyl-adenosine, N6,2'-O- dimethyl-adenosine, N6,N6,2'-O-trimethyl-adenosine, 1,2'-O-dimethyl-adenosine, 2'-O- ribosyladenosine, 2-amino-N6-methyl-purine, 1-thio-adenosine, 2'-F-ara-adenosine, 2'-F- adenosine, 2'-OH-ara-adenosine, and N6-(19-amino-pentaoxanonadecyl)-adenosine.

[0084] Examples of modified or chemically-modified nucleotides include Nl-alkylguanosines, N2-alkylguanosines, thienoguanosines, 7-deazaguanosines, 8-oxoguanosines, 8- bromoguanosines, O6-alkylguanosines, xanthosines, inosines, and Nl-alkylinosines.

[0085] Examples of modified or chemically-modified nucleotides include Nl-methylguanosine, N2-methylguanosine, thienoguanosine, 7-deazaguanosine, 8-oxoguanosine, 8-bromoguanosine, O6-methylguanosine, xanthosine, inosine, and Nl-methylinosine.

[0086] Examples of modified or chemically-modified nucleotides include pseudouridines. Examples of pseudouridines include Nl-alkylpseudouridines, Nl-cycloalkylpseudouridines, N1- hydroxypseudouridines, N1-hydroxyalkylpseudouridines, Nl-phenylpseudouridines, Nl- phenylalkylpseudouridines, Nl-aminoalkylpseudouridines, N3-alkylpseudouridines, N6- alkylpseudouridines, N6-alkoxypseudouridines, N6-hydroxypseudouridines, N6- hydroxyalkylpseudouridines, N6-morpholinopseudouridines, N6-phenylpseudouridines, and N6- halopseudouridines. Examples of pseudouridines include Nl-alkyl-N6-alkylpseudouridines, Nl- alkyl-N6-alkoxypseudouridines, Nl-alkyl-N6-hydroxypseudouridines, Nl-alkyl-N6- hydroxyalkylpseudouridines, Nl-alkyl-N6-morpholinopseudouridines, Nl-alkyl-N6- phenylpseudouridines, and Nl-alkyl-N6-halopseudouridines. In these examples, the alkyl, cycloalkyl, and phenyl substituents may be unsubstituted, or further substituted with alkyl, halo, haloalkyl, amino, or nitro substituents.

[0087] Examples of pseudouridines include Nl-methylpseudouridine (also referred to herein as “N1MPU”), Nl-ethylpseudouridine, Nl-propylpseudouridine, Nl-cyclopropylpseudouridine, Nl- phenylpseudouridine, Nl-aminomethylpseudouridine, N3-methylpseudouridine, N1- hydroxypseudouridine, and N1-hydroxymethylpseudouridine.

[0088] Examples of nucleic acid monomers include modified and chemically-modified nucleotides, including any such nucleotides known in the art.

[0089] Examples of modified and chemically-modified nucleotide monomers include any such nucleotides known in the art, for example, 2'-O-methyl ribonucleotides, 2'-O-methyl purine nucleotides, 2'-deoxy-2'-fluoro ribonucleotides, 2'-deoxy-2'-fluoro pyrimidine nucleotides, 2'- deoxy ribonucleotides, 2'-deoxy purine nucleotides, universal base nucleotides, 5-C-methyl- nucleotides, and inverted deoxyabasic monomer residues.

[0090] Examples of modified and chemically-modified nucleotide monomers include 3'-end stabilized nucleotides, 3'-glyceryl nucleotides, 3'-inverted abasic nucleotides, and 3'-inverted thymidine.

[0091] Examples of modified and chemically-modified nucleotide monomers include locked nucleic acid nucleotides (LNA), 2'-O,4'-C-methylene-(D-ribofuranosyl) nucleotides, 2'- methoxyethoxy (MOE) nucleotides, 2'-methyl-thio-ethyl, 2'-deoxy-2'-fluoro nucleotides, and 2'- O-methyl nucleotides. In an exemplary embodiment, the modified monomer is a locked nucleic acid nucleotide (LNA).

[0092] Examples of modified and chemically-modified nucleotide monomers include 2′,4′- constrained 2′-O-methoxyethyl (cMOE) and 2′-O-Ethyl (cEt) modified DNAs.

[0093] Examples of modified and chemically-modified nucleotide monomers include 2'-amino nucleotides, 2'-O-amino nucleotides, 2'-C-allyl nucleotides, and 2'-O-allyl nucleotides.

[0094] Examples of modified and chemically-modified nucleotide monomers include N6- methyladenosine nucleotides.

[0095] Examples of modified and chemically-modified nucleotide monomers include nucleotide monomers with modified bases 5-(3-amino)propyluridine, 5-(2-mercapto)ethyluridine, 5-bromouridine; 8-bromoguanosine, or 7-deazaadenosine.

[0096] Examples of modified and chemically-modified nucleotide monomers include 2’-O- aminopropyl substituted nucleotides.

[0097] Examples of modified and chemically-modified nucleotide monomers include replacing the 2'-OH group of a nucleotide with a 2'-R, a 2'-OR, a 2'-halogen, a 2'-SR, or a 2'-amino, where R can be H, alkyl, alkenyl, or alkynyl.

[0098] Exemplary base modifications described above can be combined with additional modifications of nucleoside or nucleotide structure, including sugar modifications and linkage modifications. Certain modified or chemically-modified nucleotide monomers may be found in nature.

[0099] Preferred nucleotide modifications include N1-methylpseudouridine and 5- methoxyuridine.Viral Replication Proteins and Polynucleotides Encoding Them

[0100] Provided herein, in some embodiments, are RNA molecules encoding one or more viral replication proteins. As used herein, the term “replication protein” or “viral replication protein” refers to any protein or any protein subunit of a protein complex that functions in replication of a viral genome. Generally, viral replication proteins are non-structural proteins. Viral replication proteins encoded by nucleic acid molecules provided herein can function in the replication of any viral genome. The viral genome can be a single-stranded positive-sense RNA genome, a single-stranded negative-sense RNA genome, a double-stranded RNA genome, a single-stranded positive-sense DNA genome, a single-stranded negative-sense DNA genome, or a double-stranded DNA genome. Viral genomes can include a single nucleic acid molecule or more than one nucleic acid molecule. Nucleic acid molecules provided herein can encode one or more viral replication proteins from any virus or virus family, including animal viruses and plant viruses, for example. Viral replication proteins encoded by polynucleotides included in nucleic acid molecules provided herein can be expressed from self-replicating RNA.

[0101] In some embodiments, RNA molecules provided herein can encode one or more togavirus replication proteins. In some embodiments, the one or more viral replication proteins encoded by RNA molecules provided herein are alphavirus proteins. In some embodiments, the one or more viral replication proteins encoded by RNA molecules provided herein are rubivirus proteins. RNA molecules provided herein can encode any alphavirus replication protein and any rubivirus replication protein. Exemplary replication proteins from alphaviruses include proteins from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis Virus (WEEV), Highland J Virus (HJV), Fort Morgan Virus (FMV), Ndumu Virus (NDUV), Salmonid Alphavirus (SAV), Buggy Creek Virus (BCRV), and any combination thereof. Exemplary rubivirus replication proteins include proteins from rubella virus.

[0102] Viral replication proteins encoded by RNA molecules provided herein can be expressed as one or more polyproteins or as separate or single proteins. Generally, polyproteins are precursor proteins that are cleaved to generate individual or separate proteins. Accordingly, proteins derived from a precursor polyprotein can be expressed from a single open reading frame (ORF). As used herein, the term “ORF” refers to a nucleotide sequence that begins with a startcodon, generally ATG, and that ends with a stop codon, such as TAA, TAG, or TGA, for example. It will be appreciated that T is present in DNA, while U is present in RNA. Accordingly, a start codon of ATG in DNA corresponds to AUG in RNA, and the stop codons TAA, TAG, and TGA in DNA correspond to UAA, UAG, and UGA in RNA. It will further be appreciated that for any sequence provided in the present disclosure, T is present in DNA, while U is present in RNA. Accordingly, for any sequence provided herein, T present in DNA is substituted with U for an RNA molecule, and U present in RNA is substituted with T for a DNA molecule.

[0103] The protease cleaving a polyprotein can be a viral protease or a cellular protease. In some embodiments, the RNA molecules provided herein encodes one or more viral replication proteins comprising an alphavirus nsP1 protein, an alphavirus nsP2 protein, an alphavirus nsP3 protein, an alphavirus nsP4 protein, or any combination thereof. In some embodiments, the RNA molecules provided herein encode one or more viral replication proteins comprising an alphavirus nsP1 protein, an alphavirus nsP2 protein, an alphavirus nsP3 protein, or any combination thereof, and an alphavirus nsP4 protein. In some embodiments, the polyprotein is a VEEV polyprotein. In some embodiments, the alphavirus nsP1, nsP2, nsP3, and nsP4 proteins are VEEV proteins.

[0104] In one aspect, the RNA molecules provided herein lack a stop codon between sequences encoding an nsP3 protein and an nsP4 protein. Accordingly, in some aspects, polynucleotides of RNA molecules provided herein encode a P1234 polyprotein comprising nsP1, nsP2, nsP3, and nsP4. The RNA molecules provided herein can also include a stop codon between sequences encoding an nsP3 and an nsP4 protein. Accordingly, in some aspects, polynucleotides of nucleic acid molecules provided herein encode a P123 polyprotein comprising nsP1, nsP2, and nsP3 and a P1234 polyprotein comprising nsP1, nsP2, nsP3, and nsP4 as a result of stop codon readthrough, for example. In some embodiments, the nsP1, nsP2, and nsP4 proteins are VEEV proteins, and the nsP3 protein is a chikungunya virus (CHIKV) nsP3 protein.

[0105] In some embodiments, the one or more viral replication proteins include a mutant nsP2 protein and / or a mutant nsP3 protein. Any of a variety of suitable mutations, and combinations thereof, can be included in the nsP2 and / or nsP3 protein. In some embodiments, one or more mutations included in viral replication proteins increases replication and / or gene expression compared to the absence of mutations.

[0106] In some embodiments, the RNA molecules provided herein encode one or more viral replication proteins. In some embodiments, the sequence encoding one or more viral replication proteins comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO:4. Insome embodiments, the sequence encoding one or more viral replication proteins comprises the RNA sequence encoded by SEQ ID NO: 4. 5’ Untranslated Region (5’ UTR)

[0107] Nucleic acid molecules provided herein can further comprise untranslated regions (UTRs). Untranslated regions, including 5’ UTRs and 3’ UTRs, for example, can affect RNA stability and / or efficiency of RNA translation, such as translation of cellular and viral mRNAs, for example.5’ UTRs and 3’ UTRs can also affect stability and translation of viral genomic RNAs and self-replicating RNAs, including virally derived self-replicating RNAs or replicons. Exemplary viral genomic RNAs whose stability and / or efficiency of translation can be affected by 5’ UTRs and 3’ UTRs include the genome nucleic acid of positive-sense RNA viruses. Both genome nucleic acid of positive-sense RNA viruses and self-replicating RNAs, including virally derived self-replicating RNAs or replicons, can be translated upon infection or introduction into a cell.

[0108] In some aspects, nucleic acid molecules provided herein further include a 5’ untranslated region (5’ UTR). Any 5’ UTR sequence can be included in nucleic acid molecules provided herein. In some embodiments, nucleic acid molecules provided herein include a viral 5’ UTR. In one aspect, nucleic acid molecules provided herein include a non-viral 5’ UTR. Any non- viral 5’ UTR can be included in nucleic acid molecules provided herein, such as 5’ UTRs of transcripts expressed in any cell or organ, including muscle, skin, subcutaneous tissue, liver, spleen, lymph nodes, antigen-presenting cells, and others. In another aspect, nucleic acid molecules provided herein include a 5’ UTR comprising viral and non-viral sequences. Accordingly, a 5’ UTR included in nucleic acid molecules provided herein can comprise a combination of viral and non-viral 5’ UTR sequences. In some aspects, the 5’ UTR included in nucleic acid molecules provided herein is located upstream of or 5’ of a polynucleotide that encodes one or more viral replication proteins. In some aspects, the 5’ UTR is located 5’ of or upstream of a polynucleotide of nucleic acid molecules provided herein that encodes one or more viral replication proteins, which is in turn located 5’ of or upstream of one or more further polynucleotides of nucleic acid molecules provided herein (e.g., one or more of a polynuceotide encoding an NA or an HA polypeptide).

[0109] In one aspect, the 5’ UTR of nucleic acid molecules provided herein comprises an alphavirus 5’ UTR. A 5’ UTR from any alphavirus can be included in nucleic acid molecules provided herein, including 5’ UTR sequences from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV),Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis Virus (WEEV), Highland J Virus (HJV), Fort Morgan Virus (FMV), Ndumu Virus (NDUV), Salmonid Alphavirus (SAV), or Buggy Creek Virus (BCRV). In some embodiments, the alphavirus 5’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 5’ UTR sequence. In another aspect, the 5’ UTR comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to the RNA sequence encoded by SEQ ID NO: 5, for example. In some embodiments, the 5’ UTR comprises the RNA sequence encoded by SEQ ID NO: 5.

[0110] In some embodiments, the 5’ UTR comprises a sequence selected from the 5’ UTRs of human IL-6, alanine aminotransferase 1, human apolipoprotein E, human fibrinogen alpha chain, human transthyretin, human haptoglobin, human alpha-1-antichymotrypsin, human antithrombin, human alpha-1-antitrypsin, human albumin, human beta globin, human complement C3, human complement C5, SynK (thylakoid potassium channel protein derived from the cyanobacteria, Synechocystis sp.), mouse beta globin, mouse albumin, and a tobacco etch virus, or fragments of any of the foregoing. Preferably, the 5’ UTR is derived from a tobacco etch virus (TEV). In one aspect, the 5’ UTR includes a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to sequence of SEQ ID NO: 26. In another aspect, the 5’ UTR includes the sequence of SEQ ID NO: 26 or the RNA sequence encoded by SEQ ID NO: 5.

[0111] An mRNA or any other RNA described herein can comprise any 5’ UTR sequence provided herein. For example, an RNA described herein can comprise a 5’ UTR sequence that is derived from a gene expressed by Arabidopsis thaliana. In some aspects, the 5’ UTR sequence of a gene expressed by Arabidopsis thaliana is AT1G58420. Examples of 5 UTRs and 3’ UTRs are described in US20190002906A1, the contents of which are herein incorporated by reference. Exemplary 5’ UTR sequences include sequences of SEQ ID NOs: 26-55, as shown in Table 1.Table 1. Exemplary 5’ UTR Sequences

[0112] Additional exemplary 5’ UTR sequences of SEQ ID NOs: 56-102 are shown in Table 2. Table 2. Exemplary 5’ UTR Sequences3’ Untranslated Region (3’ UTR)

[0113] In some aspects, nucleic acid molecules provided herein further include a 3’ untranslated region (3’ UTR). Any 3’ UTR sequence can be included in nucleic acid molecules provided herein. In one aspect, nucleic acid molecules provided herein include a viral 3’ UTR. In another aspect, nucleic acid molecules provided herein include a non-viral 3’ UTR. Any non-viral 3’ UTR can be included in nucleic acid molecules provided herein, such as 3’ UTRs of transcripts expressed in any cell or organ, including muscle, skin, subcutaneous tissue, liver, spleen, lymph nodes, antigen-presenting cells, and others. In some aspects, nucleic acid molecules provided herein include a 3’ UTR comprising viral and non-viral sequences. Accordingly, a 3’ UTR included in nucleic acid molecules provided herein can comprise a combination of viral and non- viral 3’ UTR sequences. In one aspect, the 3’ UTR is located 3’ of or downstream of a polynucleotide of nucleic acid molecules provided herein that comprises a first transgene encoding a first antigenic protein or a fragment thereof (e.g., an NA or HA polypeptide). In some aspects, the 3’ UTR is located 3’ of or downstream of the polynucleotide of nucleic acid molecules provided herein that comprises a first transgene encoding a first antigenic protein or a fragment thereof, which in turn is located 3’ of or downstream of one or more additional polynucleotides of nucleic acid molecules provided herein (e.g., a polynucleotide encoding another antigenic protein or fragment thereof, and / or a polynucleotide encoding one or more viral replication proteins).

[0114] In one aspect, the 3’ UTR of nucleic acid molecules provided herein comprises an alphavirus 3’ UTR. A 3’ UTR from any alphavirus can be included in nucleic acid molecules provided herein, including 3’ UTR sequences from Venezuelan Equine Encephalitis Virus (VEEV), Eastern Equine Encephalitis Virus (EEEV), Everglades Virus (EVEV), Mucambo Virus (MUCV), Semliki Forest Virus (SFV), Pixuna Virus (PIXV), Middleburg Virus (MIDV), Chikungunya Virus (CHIKV), O'Nyong-Nyong Virus (ONNV), Ross River Virus (RRV), Barmah Forest Virus (BFV), Getah Virus (GETV), Sagiyama Virus (SAGV), Bebaru Virus (BEBV), Mayaro Virus (MAYV), Una Virus (UNAV), Sindbis Virus (SINV), Aura Virus (AURAV), Whataroa Virus (WHAV), Babanki Virus (BABV), Kyzylagach Virus (KYZV), Western Equine Encephalitis Virus (WEEV), Highland J Virus (HJV), Fort Morgan Virus (FMV), Ndumu Virus (NDUV), Salmonid Alphavirus (SAV), or Buggy Creek Virus (BCRV). In some embodiments, the alphavirus 3’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 3’ UTR sequence. In some embodiments, the 3’ UTR comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, identity to the RNA sequence encoded by SEQ ID NO: 7. In some embodiments, the 3’ UTR comprises the RNA sequence encoded by SEQ ID NO: 7. In some embodiments, the 3’ UTR comprises a poly-A tail of about 20-300 nucleotides. In some embodiments, the poly-A tail comprises about 20-300 consecutive A nucleotides. In some embodiments, the poly-A tail comprises about 20, about 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120, about 130, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, about 220, about 230, about 240, about 250, about 260, about 270, about 280, about 290, about 300, and any number or range in between, nucleotides. In some embodiments, the nucleotides of the poly-A tail are A nucleotides. In some embodiments, the 3’ UTR includes a poly-C tail.

[0115] In some embodiments, the 3’ UTR comprises a sequence selected from the 3’ UTRs of alanine aminotransferase 1, human apolipoprotein E, human fibrinogen alpha chain, human haptoglobin, human antithrombin, human alpha globin, human beta globin, human complement C3, human growth factor, human hepcidin, MALAT-1, mouse beta globin, mouse albumin, and Xenopus beta globin, or fragments of any of the foregoing. In some embodiments, the 3’ UTR is derived from Xenopus beta globin. Any 3’ UTR provided herein can include a poly-A tail. A 3’ UTR provided herein can be included in any RNA molecule provided herein, including self-replicating RNA and mRNA molecules. Exemplary 3’ UTR sequences include SEQ ID NOs: 103-109, as shown in Table 3.Table 3.3’ UTR sequences

[0116] Additional exemplary 3’ UTR sequences of SEQ ID NOs: 110-147 are shown in Table 4.Table 4. Exemplary 3’ UTR SequencesTriple Stop Codon

[0117] In some embodiments, RNA molecules provided herein, including self-replicating RNA and mRNA, may comprise a sequence immediately downstream of a coding region (i.e., ORF) that creates a triple stop codon. A triple stop codon is a sequence of three consecutive stop codons. The triple stop codon can ensure total insulation of an expression cassette and may be incorporated to enhance the efficiency of translation. In some embodiments, RNA molecules of the disclosure may comprise a triple combination of any of the sequences UAG, UGA, or UAA immediately downstream of an ORF described herein. The triple combination can be three of the same codons, three different codons, or any other permutation of the three stop codons. Translation Enhancers and Kozak Sequences

[0118] For translation initiation, proper interactions between ribosomes and mRNAs must be established to determine the exact position of the translation initiation region. However, ribosomes also must dissociate from the translation initiation region to slide toward the downstream sequence during mRNA translation. Translation enhancers upstream from initiation sequences of mRNAs enhance the yields of protein biosynthesis. Several studies have investigated the effects of translation enhancers. In some embodiments, an RNA molecule described herein, such as a self-replicating RNA or an mRNA, comprises a translation enhancer sequence. These translation enhancer sequences enhance the translation efficiency of a self-replicating RNA or mRNA of the disclosure and thereby provide increased production of the protein encoded by the RNA. The translation enhancer region may be located in the 5’ or 3’ UTR of a self-replicating RNA or an mRNA sequence. Examples of translation enhancer regions include naturally- occurring enhancer regions from the TEV 5’ UTR and the Xenopus beta-globin 3’ UTR.Exemplary 5’ UTR enhancer sequences include but are not limited to those derived from mRNAs encoding human heat shock proteins (HSP) including HSP70-P2, HSP70-M1 HSP72-M2, HSP17.9 and HSP70-P1. Exemplary translation enhancer sequences used in accordance with the embodiments of the present disclosure are represented by SEQ ID NOs: 148-152, as shown in Table 5. Table 5.5’ UTR Enhancers

[0119] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises one or more Kozak sequences. As is understood in the art, a Kozak sequence is a short consensus sequence centered around the translational initiation site of eukaryotic mRNAs that allows for efficient initiation of translation of the self-replicating RNA or mRNA. See, for example, Kozak, Marilyn (1988) Mol. and Cell Biol, 8:2737-2744; Kozak, Marilyn (1991) J. Biol. Chem, 266: 19867-19870; Kozak, Marilyn (1990) Proc Natl. Acad. Sci. USA, 87:8301-8305; and Kozak, Marilyn (1989) J. Cell Biol, 108:229-241. It ensures that a protein is correctly translated from the genetic message, mediating ribosome assembly and translation initiation. The ribosomal translation machinery recognizes the AUG initiation codon in the context of the Kozak sequence. A Kozak sequence may be inserted upstream of the coding sequence for the protein of interest, downstream of a 5’ UTR or inserted upstream of the coding sequence for the protein of interest and downstream of a 5’ UTR. In some embodiments, a self-replicating RNA or mRNA described herein comprises a Kozak sequence having the sequence GCCACC. A self-replicating RNA or mRNA described herein can comprise a partial Kozak sequence “p” having the nucleotide sequence GCCA. Antigenic Proteins

[0120] In some embodiments, nucleic acid molecules provided herein (e.g., RNA molecules, and polynucleotides encoding the same) can encode an antigenic protein (e.g., an avian influenza virus protein) or a fragment thereof. In some embodiments, the RNA moleculesprovided herein encode an entire HA polypeptide or an antigenic fragment thereof. In some embodiments, the RNA molecules provided herein encode an entire NA polypeptide or an antigenic fragment thereof. The RNA molecules provided herein may encode a homolog of any antigenic protein provided herein. Any antigenic protein can be encoded by nucleic acid molecules provided herein. In one aspect, the antigenic protein is an avian influenza virus protein. RNA molecules provided herein can be expressed from a subgenomic RNA derived from a self- replicating RNA or from an mRNA.

[0121] In some aspects, the antigenic protein, when administered to a mammalian subject, raises an immune response to a pathogen (e.g., an avian influenza virus). In other aspects, the antigenic protein is expressed on the outer surface of the pathogen; while in further aspects, the antigen may be a non-surface antigen, e.g., useful as a T-cell epitope. The immune response may comprise an antibody response (usually including IgG) and / or a cell mediated immune response. The polypeptide immunogen will typically elicit an immune response that recognizes the corresponding pathogen polypeptide, but in some embodiments, the polypeptide may act as a mimotope to elicit an immune response that recognizes a saccharide. The immunogen can be a surface polypeptide, e.g., an adhesin, a hemagglutinin, an envelope glycoprotein, a spike glycoprotein, etc.

[0122] In one aspect, one or more antigenic proteins encoded by nucleic acid molecules provided herein are avian influenza virus proteins or fragments thereof. In some embodiments, a nucleic acid molecule provided herein encodes one or both of a hemagglutinin (HA) polypeptide and a neuraminidase (NA) polypeptide of an avian influenza virus (or variant / mutant thereof). In some embodiments, the avian influenza virus proteins comprise a hemagglutinin (HA) polypeptide and a neuraminidase (NA) polypeptide of the same strain of avian influenza virus (or variant / mutant thereof). In some embodiments, the avian influenza virus is an H5N1 influenza virus. In some embodiments, the H5N1 influenza virus is a strain of A / Indonesia / 5 / 2005.

[0123] In some embodiments, the HA polypeptide comprises an antigenic polypeptide of HA. In some embodiments, the HA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises a sequence having at least 90% identity to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises a sequence having at least 95% identity to SEQ ID NO: 11. In some embodiments, the HA polypeptide is encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by any one of SEQ ID NOs: 3 or 13-19. In some embodiments, the HA polypeptide is encoded by a sequence having at least 90% identity to the RNA encoded by any one of SEQ ID NOs: 3 or 13-19. In some embodiments, the HA polypeptide is encoded by a sequence having at least 95% identity to theRNA encoded by any one of SEQ ID NOs: 3 or 13-19. In some embodiments, the HA polypeptide is encoded by the RNA encoded by any one of SEQ ID NOs: 3 or 13-19. In some embodiments, the HA polypeptide is encoded by the RNA encoded by SEQ ID NO: 3. In some embodiments, the HA polypeptide comprises one or more of R224C, K228C, K404I, 342-345del, N27D, N39D, N100D, N170D, N181D, N209D, N302D, or N500D, relative to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises R224C and K228C, relative to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises R224C, K228C, and K404I, relative to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises N27D, N39D, N100D, N170D, N181D, N209D, and N302D, relative to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises N170D and N181D, relative to SEQ ID NO: 11. In some embodiments, the HA polypeptide comprises N27D, N39D, N170D, N181D, N302D, and N500D, relative to SEQ ID NO: 11. The designation “342-345del” relative to SEQ ID NO: 11 indicates that the amino acids at positions 342-345 of SEQ ID NO: 11 (or positions corresponding thereto) have been deleted. In some embodiments, the HA polypeptide comprises the sequence of SEQ ID NO: 11.

[0124] In some embodiments, the NA polypeptide comprises an antigenic polypeptide of NA. In some embodiments, the NA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO: 10. In some embodiments, the NA polypeptide comprises a sequence having at least 90% identity to SEQ ID NO: 10. In some embodiments, the NA polypeptide comprises a sequence having at least 95% identity to SEQ ID NO: 10. In some embodiments, the NA polypeptide is encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by any one of SEQ ID NOs: 2 or 20-25. In some embodiments, the NA polypeptide is encoded by a sequence having at least 90% identity to the RNA encoded by any one of SEQ ID NOs: 2 or 20-25. In some embodiments, the NA polypeptide is encoded by a sequence having at least 95% identity to the RNA encoded by any one of SEQ ID NOs: 2 or 20-25. In some embodiments, the NA polypeptide is encoded by the RNA encoded by any one of SEQ ID NOs: 2 or 20-25. In some embodiments, the NA polypeptide is encoded by the RNA encoded by SEQ ID NO: 2. In some embodiments, the NA polypeptide comprises one or more of 48InsPCNQSIITYENNTWVNQTYVN (SEQ ID NO: 12), N68S, V79P, H80L, I86V, T111Q, N126S, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, N215S, Q388M, R399V, relative to SEQ ID NO: 10. In some embodiments, the NA polypeptide comprises V79P, H80L, C141V, E145S, S152A, V157I, S176T, V185I, Q388M, and R399V, relative to SEQ ID NO: 10. In some embodiments, the NA polypeptide comprises: V79P, C141V, E145S, S152A, V157I, S176T, V185I, relative to SEQ ID NO: 10. In some embodiments, the NA polypeptide comprises V79P, H80L, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, Q388M, and R399V, relative to SEQ ID NO: 10. In some embodiments, the NApolypeptide comprises V79P, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, and V185I, relative to SEQ ID NO. 10. In some embodiments, the NA polypeptide comprises N68S, N126S, N215S, relative to SEQ ID NO: 10. The designation “48InsPCNQSIITYENNTWVNQTYVN (SEQ ID NO: 12)” relative to SEQ ID NO: 10 indicates an insertion of SEQ ID NO: 12 between amino acid positions 47 and 48 of SEQ ID NO: 10 (or positions corresponding thereto). In some embodiments, the NA polypeptide comprises the sequence of SEQ ID NO: 10.

[0125] In some aspects, the polynucleotides of nucleic acid molecules provided herein encode a reporter or a marker, including selectable markers. Reporters and markers can include fluorescent proteins, such as green fluorescent protein (GFP), red fluorescent protein (RFP), yellow fluorescent protein (YFP), luciferase enzymes, such as firefly and Renilla luciferases, and antibiotic selection markers, for example.

[0126] In some aspects, the nucleic acid molecules provided herein comprise at least two transgenes (e.g., at least two transgenes in addition to one or more viral replication proteins). Any number of transgenes can be included in nucleic acid molecules provided herein, such as one, two, three, four, five, six, seven, eight, nine, ten, or more transgenes. In one aspect, a polynucleotide of nucleic acid molecules provided herein encode an antigenic protein or a fragment thereof or an immunomodulatory protein. In one aspect, the nucleic acid molecule further comprises an internal ribosomal entry site (IRES), a sequence encoding a 2A peptide, or a combination thereof, located between transgenes. As used herein, the term “2A peptide” refers to a small (generally 18-22 amino acids) sequence that allows for efficient, stoichiometric production of discrete protein products within a single reading frame through a ribosomal skipping event within the 2A peptide sequence. As used herein, the term “internal ribosomal entry site” or “IRES” refers to a nucleotide sequence that allows for the initiation of protein translation of a messenger RNA (mRNA) sequence in the absence of an AUG start codon or without using an AUG start codon. An IRES can be found anywhere in an mRNA sequence, such as at or near the beginning, at or near the middle, or at or near the end of the mRNA sequence, for example. In another aspect, the nucleic acid molecules provided herein comprise one or more subgenomic promoter (e.g., upstream of each HA or NA encoded by the nucleic acid molecule). A subgenomic promoter located between transgenes can be a further subgenomic promoter, such as a second, third, fourth, etc. subgenomic promoter located between second and third, third and fourth, fourth and fifth, etc. transgenes, for example.

[0127] Any number of transgenes included in nucleic acid molecules provided herein can be expressed via any combination of 2A peptide and IRES sequences. For example, a second transgene located 3’ of a first transgene can be expressed via a 2A peptide sequence or via anIRES sequence. As another example, a second transgene located 3’ of a first transgene and a third transgene located 3’ of the second transgene can be expressed via 2A peptide sequences located between the first and second transgenes and the second and third transgenes, via an IRES sequence located between the first and second transgenes and the second and third transgenes, via a 2A peptide sequence located between the first and second transgenes and an IRES located between the second and third transgenes, or via an IRES sequence located between the first and second transgenes and a 2A peptide sequence located between the second and third transgenes. Similar configurations and combinations of 2A peptide and IRES sequences located between transgenes are contemplated for any number of transgenes included in polynucleotides of nucleic acid molecules provided herein. In addition to expression via 2A peptide and IRES sequences, two or more transgenes included in nucleic acid molecules provided herein can also be expressed from separate subgenomic RNAs.

[0128] Polynucleotides of nucleic acid molecules provided herein can encode an immunomodulatory protein or a functional fragment or functional variant thereof. Any immunomodulatory protein or a functional fragment or functional variant thereof can be encoded by polynucleotides.

[0129] As used herein, the terms “functional variant” or “functional fragment” refer to a molecule, including a nucleic acid or protein, for example, that comprises a nucleotide and / or amino acid sequence that is altered by one or more nucleotides and / or amino acids compared to the nucleotide and / or amino acid sequences of the parent or reference molecule. For a protein, a functional variant is still able to function in a manner that is similar to the parent molecule. In other words, the modifications in the amino acid and / or nucleotide sequence of the parent molecule do not significantly affect or alter the functional characteristics of the molecule encoded by the nucleotide sequence or containing the amino acid sequence. The functional variant may have conservative sequence modifications including nucleotide and amino acid substitutions, additions and deletions. These modifications can be introduced by standard techniques known in the art, such as site-directed mutagenesis and random PCR-mediated mutagenesis. Functional variants can also include, but are not limited to, derivatives that are substantially similar in primary structural sequence, but which contain, e.g., in vitro or in vivo modifications, chemical and / or biochemical, that are not found in the parent molecule. Such modifications include, inter alia, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross- links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation,glycosylation, GPI-anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA-mediated addition of amino acids to proteins such as arginylation, ubiquitination, and the like.

[0130] In one aspect, a transgene included in nucleic acid molecules provided herein encodes a cytokine, a chemokine, or an interleukin. Transgenes encoding a cytokine, a chemokine, or an interleukin can be included in nucleic acid molecules provided herein in addition to transgenes encoding HA, NA, both HA and NA, any other antigenic protein, or any combination thereof. Exemplary cytokines include interferons, TNF-α, TGF-β, G-CSF, and GM-CSF. Exemplary chemokines include CCL3, CCL26, and CXCL7. Exemplary interleukins include IL-I, IL-2, IL- 3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12, IL-15, IL-18, IL-21, and IL-23. Any transgene or combination of transgenes encoding any cytokine, chemokine, interleukin, or combinations thereof, can be included in nucleic acid molecules provided herein. RNA and DNA Molecules RNA Molecules – Exemplary Features

[0131] Nucleic acid molecules provided herein can be DNA molecules or RNA molecules. It will be appreciated that T present in DNA is substituted with U in RNA, and vice versa. In one aspect, nucleic acid molecules provided herein are RNA molecules, wherein a first polynucleotide is located 5’ of a second polynucleotide (which second polynucleotide may optionally be located 5’ of a third polynucleotide, and so on). Sequences presented herein as RNA sequences may be encoded by a corresponding DNA sequence, in which U is replaced with T. Similarly, sequences presented herein as DNA sequences may be converted to the corresponding RNA sequence encoded thereby by replacing T with U. In general, the RNA sequence “encoded” by a DNA sequence refers herein to an RNA with the same 5’ to 3’ orientation and order of bases (except for U replacing T), and not the reverse complement. Both the DNA and RNA versions of a given sequence are contemplated herein, unless context clearly indicates otherwise. In some cases, a DNA sequence may include elements not found in an RNA encoded thereby (e.g., a promoter sequence). In some cases, an RNA sequence may include elements not found in a DNA construct encoding the RNA (e.g., a poly-A tail when added post-transcriptionally).

[0132] RNA molecules provided herein can be self-replicating RNAs. In one aspect, RNA molecules provided herein include a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, and any number or range in between, or 100% identity tothe RNA sequence encoded by SEQ ID NO:1. RNA molecules provided herein can also be mRNAs. It will be appreciated that T of sequences provided herein will be substituted with U in an RNA molecule.

[0133] An RNA molecule provided herein can be generated by in vitro transcription (IVT) of DNA molecules provided herein. In one aspect, RNA molecules provided herein are self- replicating RNA molecules. In another aspect, RNA molecules provided herein are mRNA molecules. In yet another aspect, RNA molecules provided herein further comprise a 5’ cap. Any 5’ cap can be included in RNA molecules provided herein, including 5’ caps having a Cap 1 structure, a Cap 1 (m6A) structure, a Cap 2 structure, or a Cap 0 structure. A population or plurality of RNA molecules provided herein can have the same 5’ cap or can have different 5’ caps. For example, a population or plurality of RNA molecules can have 5’ caps having a Cap 1 structure, a Cap 1 (m6A) structure, a Cap 2 structure, a Cap 0 structure, or any combination thereof.

[0134] In one aspect, RNA molecules provided herein include a 5’ cap having Cap 1 structure. In yet another aspect, RNA molecules provided herein are self-replicating RNA molecules comprising a 5’ cap having a Cap 1 structure. In a further aspect, RNA molecules provided herein comprise a cap having a Cap 1 structure, wherein a m7G is linked via a 5’-5’ triphosphate to the 5’ end of the 5’ UTR. In yet a further aspect, RNA molecules provided herein comprise a cap having a Cap 1 structure, wherein a m7G is linked via a 5’-5’ triphosphate to the 5’ end of the 5’ UTR comprising the RNA sequence encoded by SEQ ID NO:5. Any method of capping can be used, including, but not limited to using a Vaccinia Capping enzyme (New England Biolabs, Ipswich, Mass.) and co-transcriptional capping or capping at or shortly after initiation of in vitro transcription (IVT), by for example, including a capping agent as part of an in vitro transcription (IVT) reaction. (Nuc. Acids Symp. (2009) 53:129).

[0135] Only those RNA molecules, such mRNAs and self-replicating RNAs that can function as mRNAs, that carry the Cap structure are active in Cap dependent translation; “decapitation” of mRNA results in an almost complete loss of their template activity for protein synthesis (Nature, 255:33-37, (1975); J. Biol. Chem., vol.253:5228-5231, (1978); and Proc. Natl. Acad. Sci. USA, 72:1189-1193, (1975)).

[0136] Another element of eukaryotic mRNA is the presence of 2′-O-methyl nucleoside residues at transcript position 1 (Cap 1), and in some cases, at transcript positions 1 and 2 (Cap 2). The 2′-O-methylation of mRNA provides higher efficacy of mRNA translation in vivo (Proc. Natl. Acad. Sci. USA, 77:3952-3956 (1980)) and further improves nuclease stability of the 5′- capped mRNA. The mRNA with Cap 1 (and Cap 2) is a distinctive mark that allows cells to recognize the bona fide mRNA 5′ end, and in some instances, to discriminate against transcripts emanating from infectious genetic elements (Nucleic Acid Research 43: 482-492 (2015)).

[0137] Some examples of 5' cap structures and methods for preparing mRNAs comprising the same are given in WO2015 / 051169A2, WO / 2015 / 061491, US 2018 / 0273576, and US Patent Nos. 8,093,367, 8,304,529, and U.S.10,487,105. In some embodiments, the 5’ cap is m7GpppAmpG, which is known in the art. In some embodiments, the 5’ cap is m7GpppG or m7GpppGm, which are known in the art. Structural formulas for embodiments of 5’ cap structures are provided below.

[0138] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a 5’ cap having the structure of Formula (Cap I). (Cap I) wherein B1is a natural or modified nucleobase; R1and R2are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phophorothioate, and boranophosphate wherein each L is linked by diester bonds; n is 0 or 1. and mRNA represents an mRNA of the present disclosure linked at its 5’ end. In some embodiments B1is G, m7G, or A. In some embodiments, n is 0. In some embodiments n is 1. In some embodiments, B1is A or m6A and R1is OCH3; wherein G is guanine, m7G is 7-methylguanine, A is adenine, and m6A is N6-methyladenine.

[0139] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a 5’ cap having the structure of Formula (Cap II). (Cap II) wherein B1and B2are each independently a natural or modified nucleobase; R1, R2, and R3are each independently selected from a halogen, OH, and OCH3;each L is independently selected from the group consisting of phosphate, phophorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1. In some embodiments B1is G, m7G, or A. In some embodiments, n is 0. In some embodiments, n is 1. In some embodiments, B1is A or m6A and R1is OCH3; wherein G is guanine, m7G is 7-methylguanine, A is adenine, and m6A is N6-methyladenine.

[0140] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a 5’ cap having the structure of Formula (Cap III). (Cap III)

[0141] wherein B1, B2, and B3 are each independently a natural or modified nucleobase; R1, R2, R3, and R4 are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1.In some embodiments, at least one of R1, R2, R3, and R4 is OH. In some embodiments B1 is G, m7G, or A. In some embodiments, B1 is A or m6A and R1 is OCH3; wherein G is guanine, m7G is 7-methylguanine, A is adenine, and m6A is N6-methyladenine. In some embodiments, n is 1.

[0142] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7GpppG 5’ cap analog having the structure of Formula (Cap IV). (Cap IV) wherein, R1, R2, and R3are each independently selected from a halogen, OH, and OCH3;each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; n is 0 or 1. In some embodiments, at least one of R1, R2, and R3is OH. In some embodiments, the 5’ cap is m7GpppG wherein R1, R2, and R3are each OH, n is 1, and each L is a phosphate. In some embodiments, n is 1. In some embodiments, the 5’ cap is m7GpppGm, wherein R1and R2are each OH, R3is OCH3, each L is a phosphate, and n is 1.

[0143] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7G 5’ cap analog having the structure of Formula (Cap V). (Cap V) wherein, R1, R2, and R3are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1. In some embodiments, at least one of R1, R2, and R3is OH. In some embodiments, n is 1.

[0144] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7GpN, 5’ cap analog, wherein N is a natural or modified nucleotide, the 5’ cap analog having the structure of Formula (Cap VI). (Cap VI) wherein B3is a natural or modified nucleobase; R1, R2, R3, and R4are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 3. In some embodiments, at least one of R1, R2, R3, and R4is OH. In some embodiments B1is G, m7G, or A. In some embodiments, B1is A or m6A and R1is OCH3; wherein G is guanine, m7G is 7-methylguanine, A is adenine, and m6A is N6-methyladenine. In some embodiments, n is 1.

[0145] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7GpG 5’ cap analog having the structure of Formula (Cap VII). (Cap VII) wherein, R1, R2, R3, and R4are each independently selected from a halogen, OH, and OCH3;each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1. In some embodiments, at least one of R1, R2, R3, and R4is OH. In some embodiments, n is 1.

[0146] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7Gpppm7Gpm7G 5’ cap analog having the structure of Formula (Cap VIII). (Cap VIII) wherein, R1, R2, R3, and R4are each independently selected from a halogen, OH, and OCH3;each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; n is 0 or 1. In some embodiments, at least one of R1, R2, R3, and R4is OH. In some embodiments, n is 1.

[0147] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7GpppA 5’ cap analog having the structure of Formula (Cap IX).(Cap IX) wherein, R1, R2, and R3are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1. In some embodiments, at least one of R1, R2, and R3is OH. In some embodiments, n is 1.

[0148] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7GpppApN 5’ cap analog, wherein N is a natural or modified nucleotide, and the 5’ cap has the structure of Formula (Cap X). (Cap X) wherein B3is a natural or modified nucleobase; R1, R2, R3, and R4are each independently selected from a halogen, OH, and OCH3;each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1. In some embodiments, at least one of R1, R2, R3, and R4is OH. In some embodiments B3is G, m7G, A or m6A; wherein G is guanine, m7G is 7-methylguanine, A is adenine, and m6A is N6-methyladenine. In some embodiments, n is 1.

[0149] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7GpppAmpG 5’ cap analog having the structure of Formula (Cap XI).(Cap XI) wherein, R1, R2, and R4are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1. In some embodiments, at least one of R1, R2, and R4is OH. In some embodiments, the compound of Formula Cap XI is m7GpppAmpG, wherein R1, R2, and R4are each OH, n is 1, and each L is a phosphate linkage. In some embodiments, n is 1.

[0150] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7GpppApm7G 5’ cap analog having the structure of Formula (Cap XII). (Cap XII) wherein, R1, R2, R3, and R4are each independently selected from a halogen, OH, and OCH3;each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or1. In some embodiments,at least one of R1, R2, R3, and R4is OH. In some embodiments, n is 1.

[0151] In some embodiments, a self-replicating RNA or mRNA of the disclosure comprises a m7GpppApm7G 5’ cap analog having the structure of Formula (Cap XIII).(Cap XIII) wherein, R1, R2, and R4are each independently selected from a halogen, OH, and OCH3; each L is independently selected from the group consisting of phosphate, phosphorothioate, and boranophosphate wherein each L is linked by diester bonds; mRNA represents an mRNA of the present disclosure linked at its 5’ end; and n is 0 or 1. In some embodiments, at least one of R1, R2, and R4is OH. In some embodiments, n is 1. Poly-Adenine (Poly-A) Tail

[0152] Polyadenylation is the addition of a poly(A) tail, a chain of adenine nucleotides usually about 100-120 monomers in length, to a mRNA or an RNA that can function as an mRNA. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation and begins as the transcription of a gene terminates. The 3′-most segment of a newly made pre-mRNA is first cleaved off by a set of proteins; these proteins then synthesize the poly(A) tail at the 3′ end. The poly(A) tail is important for the nuclear export, translation, and stability of mRNA. The tail is shortened over time, and, when it is short enough, the mRNA is enzymatically degraded. However, in a few cell types, mRNAs with short poly(A) tails are stored for later activation by re-polyadenylation in the cytosol. In some embodiments, the poly-A tail is transcribed from a template polynucleotide (e.g, the template incoding the entire saRNA), or is added post-transcriptionally. In some embodiments, an RNA molecule of the present disclosure comprises a poly-A tail encoded by the sequence of SEQ ID NO: 8 or 9. In some embodiments, the poly-A tail is less than 100 nucleotides in length (SEQ ID NO: 157) (e.g., 20-99 nucleotides in length). In some embodiments, the poly-A tail is less than 90, 80, 75, 70, 65, 60, 55, or 50 nucleotides in length (SEQ ID NO: 158).

[0153] In some embodiments, an RNA molecule of the disclosure comprises a 3’ tail region, which can serve to protect the RNA from exonuclease degradation. The tail region may be a 3’poly(A) and / or 3’poly(C) region. Preferably, the tail region is a 3’ poly(A) tail. Any self- replicating RNA and any mRNA, and any 3’ UTR of any self-replicating RNA or mRNA provided herein can include a poly(A) tail. As used herein a “3’ poly(A) tail” is a polymer of sequentialadenine nucleotides that can range in size from, for example: 10 to 250 sequential adenine nucleotides (SEQ ID NO: 159); 60-125 sequential adenine nucleotides (SEQ ID NO: 160), 90- 125 sequential adenine nucleotides (SEQ ID NO: 161), 95-125 sequential adenine nucleotides (SEQ ID NO: 162), 95-121 sequential adenine nucleotides (SEQ ID NO: 163), 100 to 121 sequential adenine nucleotides (SEQ ID NO: 164), 110-121 sequential adenine nucleotides (SEQ ID NO: 165); 112-121 sequential adenine nucleotides (SEQ ID NO: 166); 114-121 adenine sequential nucleotides (SEQ ID NO: 167); or 115 to 121 sequential adenine nucleotides (SEQ ID NO: 168). In some aspects, a 3’ poly(a) tail as described herein includes about 10, about 20, about 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120, about 130, about 140, about 150, about 160, about 170, about 180, about 190, about 200, about 210, about 220, about 230, 240, 250, 260, 270, 280, 290, 300, and any number or range in between, sequential adenine nucleotides. Preferably, a 3’ poly(A) tail as described herein comprises 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, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, or 150 sequential adenine nucleotides (SEQ ID NO: 169). In some embodiments, the 3’ poly(A) tail as described herein comprises 90 sequential adenine nucleotides (SEQ ID NO: 8). In some embodiments, the 3’ poly(A) tail as described herein comprises 106 sequential adenine nucleotides (SEQ ID NO: 170). In some embodiments, the 3’ poly(A) tail as described herein comprises 117 sequential adenine nucleotides (SEQ ID NO: 171). In some embodiments, the 3’ poly(A) tail as described herein comprises 141 sequential adenine nucleotides (SEQ ID NO: 172).3’ Poly(A) tails can be added using a variety of methods known in the art, e.g., using poly(A) polymerase to add tails to synthetic or in vitro transcribed RNA. Other methods include the use of a transcription vector to encode poly(A) tails or the use of a ligase (e.g., via splint ligation using a T4 RNA ligase and / or T4 DNA ligase), wherein poly(A) may be ligated to the 3' end of a sense RNA. In some embodiments, a combination of any of the above methods is utilized. An illustrative example of a sequence encoding an RNA in accordance with embodiments herein, and including a poly(A) tail, is provided as SEQ ID NO: 154. DNA Molecules

[0154] In one aspect, provided herein are DNA molecules encoding the RNA molecules disclosed herein. In another aspect, DNA molecules provided herein further comprise a promoter. As used herein, the term “promoter” refers to a regulatory sequence that initiates transcription. A promoter can be operably linked to one or more polynucleotides of DNA molecules providedherein, with the one or more polynucleotides of DNA molecules corresponding to encoded one or more polynucleotides of RNA molecules provided herein. Generally, promoters included in DNA molecules provided herein include promoters for in vitro transcription (IVT). Any suitable promoter for in vitro transcription can be included in DNA molecules provided herein, such as a T7 promoter, a T3 promoter, an SP6 promoter, and others. In one aspect, DNA molecules provided herein comprise a T7 promoter. In another aspect, the promoter is located 5’ of the 5’ UTR included in DNA molecules provided herein. In yet another aspect, the promoter is a T7 promoter located 5’ of the 5’ UTR included in DNA molecules provided herein. In yet another aspect, the promoter overlaps with the 5’ UTR. A promoter and a 5’ UTR can overlap by about one nucleotide, about two nucleotides, about three nucleotides, about four nucleotides, about five nucleotides, about six nucleotides, about seven nucleotides, about eight nucleotides, about nine nucleotides, about ten nucleotides, about 11 nucleotides, about 12 nucleotides, about 13 nucleotides, about 14 nucleotides, about 15 nucleotides, about 16 nucleotides, about 17 nucleotides, about 18 nucleotides, about 19 nucleotides, about 20 nucleotides, about 21 nucleotides, about 22 nucleotides, about 23 nucleotides, about 24 nucleotides, about 25 nucleotides, about 26 nucleotides, about 27 nucleotides, about 28 nucleotides, about 29 nucleotides, about 30 nucleotides, about 31 nucleotides, about 32 nucleotides, about 33 nucleotides, about 34 nucleotides, about 35 nucleotides, about 36 nucleotides, about 37 nucleotides, about 38 nucleotides, about 39 nucleotides, about 40 nucleotides, about 41 nucleotides, about 42 nucleotides, about 43 nucleotides, about 44 nucleotides, about 45 nucleotides, about 46 nucleotides, about 47 nucleotides, about 48 nucleotides, about 49 nucleotides, about 50 nucleotides, or more nucleotides.

[0155] In some aspects, DNA molecules provided herein include a promoter for in vivo transcription. Generally, the promoter for in vivo transcription is an RNA polymerase II (RNA pol II) promoter. Any RNA pol II promoter can be included in DNA molecules provided herein, including constitutive promoters, inducible promoters, and tissue-specific promoters. Exemplary constitutive promoters include a cytomegalovirus (CMV) promoter, an EF1α promoter, an SV40 promoter, a PGK1 promoter, a Ubc promoter, a human beta actin promoter, a CAG promoter, and others. Any tissue-specific promoter can be included in DNA molecules provided herein. In one aspect, the RNA pol II promoter is a muscle-specific promoter, skin-specific promoter, subcutaneous tissue-specific promoter, liver-specific promoter, spleen-specific promoter, lymph node-specific promoter, or a promoter with any other tissue specificity. DNA molecules provided herein can also include an enhancer. Any enhancer that increases transcription can be included in DNA molecules provided herein.Design and Synthesis of RNA and DNA Molecules

[0156] RNA molecules provided herein can include any combination of the RNA sequences provided herein, including, for example, any 5’ UTR sequences, any sequences encoding a polyprotein that includes nsP1, nsP2, nsP3, and nsP4, any sequences encoding any transgene disclosed herein (e.g., antigenic avian influenza polypeptides or fragments thereof), and any 3’ UTR sequences provided herein. In some aspects, RNA molecules provided herein are self- replicating RNA molecules. Self-replicating RNA molecules can encode one or more viral replication proteins that include nsP1, nsP2, nsP3, and nsP4, for example. In some aspects, RNA molecules provided herein are mRNA molecules. Generally, mRNA molecules do not include sequences encoding a polyprotein for replication of the RNA.

[0157] In some aspects, RNA molecules provided herein include modified nucleotides. For example, 0% to 100%, 1% to 100%, 25% to 100%, 50% to 100% and 75% to 100% of the uracil nucleotides of the RNA molecules can be modified. In some aspects, 1% to 100% of the uracil nucleotides are N1-methylpseudouridine or 5-methoxyuridine. In some embodiments,100% of the uracil nucleotides are N1-methylpseudouridine. In some embodiments, 100% of the uracil nucleotides are 5-methoxyuridine.

[0158] An RNA molecule, such as a self-replicating RNA or mRNA, of the disclosure may be obtained by any suitable means. Methods for the manufacture of RNA molecules are known in the art and would be readily apparent to a person of ordinary skill. An RNA molecule of the disclosure may be prepared according to any available technique including, but not limited to chemical synthesis, in vitro transcription (IVT) or enzymatic or chemical cleavage of a longer precursor, etc.

[0159] In some embodiments, an RNA molecule, such as a self-replicating RNA or mRNA, of the disclosure is produced from a primary complementary DNA (cDNA) construct. The cDNA constructs can be produced on an RNA template by the action of a reverse transcriptase (e.g., RNA-dependent DNA-polymerase). The process of design and synthesis of the primary cDNA constructs described herein generally includes the steps of gene construction, RNA production (either with or without modifications) and purification. In the IVT method, a target polynucleotide sequence encoding an RNA molecule of the disclosure is first selected for incorporation into a vector which will be amplified to produce a cDNA template. Optionally, the target polynucleotide sequence and / or any flanking sequences may be codon optimized. The cDNA template is then used to produce an RNA molecule of the disclosure through in vitro transcription (IVT). After production, the RNA molecule of the disclosure may undergo purification and clean-up processes. The steps of which are provided in more detail below.

[0160] The step of gene construction may include, but is not limited to gene synthesis, vector amplification, plasmid purification, plasmid linearization and clean-up, and cDNA template synthesis and clean-up. Once a protein of interest is selected for production, a primary construct is designed. Within the primary construct, a first region of linked nucleosides encoding the polypeptide of interest may be constructed using an open reading frame (ORF) of a selected nucleic acid (DNA or RNA) transcript. The ORF may comprise the wild type ORF, an isoform, variant or a fragment thereof. As used herein, an “open reading frame” or “ORF” is meant to refer to a nucleic acid sequence (DNA or RNA) which can encode a polypeptide of interest. ORFs often begin with the start codon, ATG and end with a nonsense or termination codon or signal.

[0161] The cDNA templates may be transcribed to produce an RNA molecule of the disclosure using an in vitro transcription (IVT) system. The system typically comprises a transcription buffer, nucleotide triphosphates (NTPs), an RNase inhibitor and a polymerase. The NTPs may be selected from, but are not limited to, those described herein including natural and unnatural (modified) NTPs. The polymerase may be selected from, but is not limited to, T7 RNA polymerase, T3 RNA polymerase and mutant polymerases such as, but not limited to, polymerases able to incorporate modified nucleic acids.

[0162] The primary cDNA template or transcribed RNA sequence may also undergo capping and / or tailing reactions. A capping reaction may be performed by methods known in the art to add a 5′ cap to the 5′ end of the primary construct. Methods for capping include, but are not limited to, using a Vaccinia Capping enzyme (New England Biolabs, Ipswich, Mass.) or capping at initiation of in vitro transcription, by for example, including a capping agent as part of the IVT reaction. (Nuc. Acids Symp. (2009) 53:129). A poly(A) tailing reaction may be performed by methods known in the art, such as, but not limited to, 2′ O-methyltransferase and by methods as described herein. If the primary construct generated from cDNA does not include a poly-T, it may be beneficial to perform the poly(A)-tailing reaction before the primary construct is cleaned.

[0163] Codon optimized cDNA constructs encoding the non-structural proteins and the transgene for a self-replicating RNA are particularly suitable for generating self-replicating RNA sequences described herein. For example, such cDNA constructs may be used as the basis to transcribe, in vitro, a polyribonucleotide encoding a protein of interest as part of a self-replicating RNA. Codon optimized cDNA constructs can also be used to generate mRNAs provided herein.

[0164] The present disclosure also provides expression vectors comprising a nucleotide sequence encoding a self-replicating RNA or mRNA that is preferably operably linked to at least one regulatory sequence. Regulatory sequences are art-recognized and are selected to direct expression of the encoded polypeptide.

[0165] Accordingly, the term regulatory sequence includes promoters, enhancers, and other expression control elements. The design of the expression vector may depend on such factors as the choice of the host cell to be transformed and / or the type of protein desired to be expressed.

[0166] The present disclosure also provides polynucleotides (e.g., DNA, RNA, cDNA, mRNA, etc.) directed to a self-replicating RNA or mRNA of the disclosure that may be operably linked to one or more regulatory nucleotide sequences in an expression construct, such as a vector or plasmid. In certain embodiments, such constructs are DNA constructs. Regulatory nucleotide sequences will generally be appropriate for a host cell used for expression. Numerous types of appropriate expression vectors and suitable regulatory sequences are known in the art for a variety of host cells.

[0167] Typically, said one or more regulatory nucleotide sequences may include, but are not limited to, promoter sequences, leader or signal sequences, ribosomal binding sites, transcriptional start and termination sequences, translational start and termination sequences, and enhancer or activator sequences. Constitutive or inducible promoters as known in the art are contemplated by the embodiments of the present disclosure. The promoters may be either naturally occurring promoters, or hybrid promoters that combine elements of more than one promoter.

[0168] An expression construct may be present in a cell on an episome, such as a plasmid, or the expression construct may be inserted in a chromosome. In some embodiments, the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selectable marker genes are well known in the art and will vary with the host cell used.

[0169] The present disclosure also provides a host cell transfected with a self-replicating RNA, mRNA, or DNA described herein. The self-replicating RNA, mRNA, or DNA can encode any protein of interest, for example an antigen or any other viral glycoprotein, such as the influenza virus hemagglutinin and neuraminidase. The host cell may be any prokaryotic or eukaryotic cell. For example, a polypeptide encoded by a self-replicating RNA or mRNA may be expressed in bacterial cells such as E. coli, insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells. Other suitable host cells are known to those skilled in the art.

[0170] A host cell transfected with an expression vector comprising a self-replicating RNA or mRNA of the disclosure can be cultured under appropriate conditions to allow expression of the self-replicating RNA or mRNA and translation of the polypeptide to occur. Once expressed, a self-replicating RNA generally undergoes self-amplification and translation. The polypeptide may be secreted and isolated from a mixture of cells and medium containing the polypeptides. Alternatively, the polypeptides may be retained in the cytoplasm or in a membrane fraction and the cells harvested, lysed and the protein isolated. A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art.

[0171] The expressed proteins described herein can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins, including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for particular epitopes of the polypeptide. Compositions and Pharmaceutical Compositions

[0172] Provided herein, in some embodiments, are compositions comprising any of the RNA or DNA molecules provided herein. Compositions provided herein can include a lipid. In one aspect, the lipid is an ionizable cationic lipid. Any ionizable cationic lipid can be included in compositions comprising nucleic acid molecules provided herein.

[0173] The compositions, molecules and polynucleotides of the present disclosure may be used to immunize or vaccinate a subject against a viral infection, such as an avian influenza virus. In some embodiments, the compositions, molecules and polynucleotides of the present disclosure may be used to vaccinate or immunize a subject against one or more strains of influenza (e.g., one or more strains of influenza A subtype H5N1).

[0174] Also provided herein, in some embodiments, are pharmaceutical compositions comprising any of the RNA and DNA molecules provided herein and a lipid formulation. Any lipid can be included in lipid formulations of pharmaceutical compositions provided herein. In one aspect, lipid formulations of pharmaceutical compositions provided herein include an ionizable cationic lipid. Exemplary ionizable cationic lipids of compositions and pharmaceutical compositions provided herein include the following in Table 6: Table 6. Exemplary Ionizable Cationic LipidsCompound-86 Compound-87Compound-88Compound-89andCompound-90.

[0175] In one aspect, the ionizable cationic lipid of compositions provided herein has a structure of(Compound-77), or a pharmaceutically acceptable salt thereof.

[0176] In another aspect, the ionizable cationic lipid of compositions provided herein has a structure of(Compound-90), or a pharmaceutically acceptable salt thereof. Lipid Formulations / LNPs

[0177] Therapies based on the intracellular delivery of nucleic acids to target cells face both extracellular and intracellular barriers. Indeed, naked nucleic acid materials cannot be easily systemically administered due to their toxicity, low stability in serum, rapid renal clearance, reduced uptake by target cells, phagocyte uptake and their ability in activating the immune response, all features that preclude their clinical development. When exogenous nucleic acid material (e.g., mRNA) enters the human biological system, it is recognized by the reticuloendothelial system (RES) as foreign pathogens and cleared from blood circulation before having the chance to encounter target cells within or outside the vascular system. It has been reported that the half-life of naked nucleic acid in the blood stream is around several minutes (Kawabata K, Takakura Y, Hashida MPharm Res. 1995 Jun; 12(6):825-30). Chemical modification and a proper delivery method can reduce uptake by the RES and protect nucleic acidsfrom degradation by ubiquitous nucleases, which increase stability and efficacy of nucleic acid- based therapies. In addition, RNAs or DNAs are anionic hydrophilic polymers that are not favorable for uptake by cells, which are also anionic at the surface. The success of nucleic acid- based therapies thus depends largely on the development of vehicles or vectors that can efficiently and effectively deliver genetic material to target cells and obtain sufficient levels of expression in vivo with minimal toxicity.

[0178] Moreover, upon internalization into a target cell, nucleic acid delivery vectors are challenged by intracellular barriers, including endosome entrapment, lysosomal degradation, nucleic acid unpacking from vectors, translocation across the nuclear membrane (for DNA), release at the cytoplasm (for RNA), and so on. Successful nucleic acid-based therapy thus depends upon the ability of the vector to deliver the nucleic acids to the target sites inside of the cells in order to obtain sufficient levels of a desired activity such as expression of a gene.

[0179] While several gene therapies have been able to successfully utilize a viral delivery vector (e.g., AAV), lipid-based formulations have been increasingly recognized as one of the most promising delivery systems for RNA and other nucleic acid compounds due to their biocompatibility and their ease of large-scale production. One of the most significant advances in lipid-based nucleic acid therapies happened in August 2018 when Patisiran (ALN-TTR02) was the first siRNA therapeutic approved by the Food and Drug Administration (FDA) and by the European Commission (EC). ALN-TTR02 is an siRNA formulation based upon the so-called Stable Nucleic Acid Lipid Particle (SNALP) transfecting technology. Despite the success of Patisiran, the delivery of nucleic acid therapeutics, including mRNA, via lipid formulations is still under ongoing development.

[0180] Some art-recognized lipid-formulated delivery vehicles for nucleic acid therapeutics include, according to various embodiments, polymer based carriers, such as polyethyleneimine (PEI), lipid nanoparticles and liposomes, nanoliposomes, ceramide-containing nanoliposomes, multivesicular liposomes, proteoliposomes, both natural and synthetically-derived exosomes, natural, synthetic and semi-synthetic lamellar bodies, nanoparticulates, micelles, and emulsions. These lipid formulations can vary in their structure and composition, and as can be expected in a rapidly evolving field, several different terms have been used in the art to describe a single type of delivery vehicle. At the same time, the terms for lipid formulations have varied as to their intended meaning throughout the scientific literature, and this inconsistent use has caused confusion as to the exact meaning of several terms for lipid formulations. Among the several potential lipid formulations, liposomes, cationic liposomes, and lipid nanoparticles are specifically described in detail and defined herein for the purposes of the present disclosure.

[0181] In some embodiments, the compositions disclosed herein comprise a nitrogen to phosphate ratio (N:P) of about 3:1 to about 10:1. In some embodiments, the N:P ratio is about 3:1 to about 9:1. In some embodiments, the N:P ratio is about 3:1 to about 8:1 (e.g., about 5:1 to about 7:1). In some embodiments, the N:P ratio is about 9:1 or less. In some embodiments, the N:P ratio is about 7:1 or less. In some embodiments, the N:P ratio is about 6:1 or less. In some embodiments, the N:P ratio is about 5:1 or less.

[0182] In one aspect, the present disclosure provides a composition comprising (i) a polynucleotide having a length of about 5,000 to about 20,000 nucleotides, and (ii) an ionizable cationic lipid, wherein the composition comprises a nitrogen to phosphate ratio (N:P) of about 5:1 to about 7:1. In some embodiments, the nitrogen to phosphate ratio (N:P) is about 7:1. In some embodiments, the polynucleotide is a polynucleotide disclosed herein, which may have a length of at least 5,000 nucleotides (e.g., about 6,000, 7,000, 8,000, 9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000, 20,000, or more). In some embodiments, the polynucleotide has a length of about 7,500 nucleotide or more. In some embodiments, the polynucleotide has a length of about 10,000 nucleotide or more. In some embodiments, the polynucleotide has a length of about 15,000 nucleotide or more. In some embodiments, the ionizable cationic lipid is an ionizable cationic lipid disclosed herein (e.g., Compound-77 or Compound-90). In some embodiments, the N:P ratio is about 3:1 to about 8:1 (e.g., about 5:1 to about 7:1). In some embodiments, the N:P ratio is about 7:1 or less. In some embodiments, the N:P ratio is about 6:1 or less. In some embodiments, the N:P ratio is about 5:1 or less. Liposomes

[0183] Conventional liposomes are vesicles that consist of at least one bilayer and an internal aqueous compartment. Bilayer membranes of liposomes are typically formed by amphiphilic molecules, such as lipids of synthetic or natural origin that comprise spatially separated hydrophilic and hydrophobic domains (Lasic, Trends Biotechnol., 16: 307-321, 1998). Bilayer membranes of the liposomes can also be formed by amphiphilic polymers and surfactants (e.g., polymerosomes, niosomes, etc.). They generally present as spherical vesicles and can range in size from 20 nm to a few microns. Liposomal formulations can be prepared as a colloidal dispersion or they can be lyophilized to reduce stability risks and to improve the shelf-life for liposome-based drugs. Methods of preparing liposomal compositions are known in the art and would be within the skill of an ordinary artisan.

[0184] Liposomes that have only one bilayer are referred to as being unilamellar, and those having more than one bilayer are referred to as multilamellar. The most common types of liposomes are small unilamellar vesicles (SUV), large unilamellar vesicle (LUV), and multilamellar vesicles (MLV). In contrast to liposomes, lysosomes, micelles, and reversedmicelles are composed of monolayers of lipids. Generally, a liposome is thought of as having a single interior compartment, however some formulations can be multivesicular liposomes (MVL), which consist of numerous discontinuous internal aqueous compartments separated by several nonconcentric lipid bilayers.

[0185] Liposomes have long been perceived as drug delivery vehicles because of their superior biocompatibility, given that liposomes are basically analogs of biological membranes, and can be prepared from both natural and synthetic phospholipids (Int J Nanomedicine. 2014; 9:1833-1843). In their use as drug delivery vehicles, because a liposome has an aqueous solution core surrounded by a hydrophobic membrane, hydrophilic solutes dissolved in the core cannot readily pass through the bilayer, and hydrophobic compounds will associate with the bilayer. Thus, a liposome can be loaded with hydrophobic and / or hydrophilic molecules. When a liposome is used to carry a nucleic acid such as RNA, the nucleic acid will be contained within the liposomal compartment in an aqueous phase. Cationic Liposomes

[0186] Liposomes can be composed of cationic, anionic, and / or neutral lipids. As an important subclass of liposomes, cationic liposomes are liposomes that are made in whole or part from positively charged lipids, or more specifically a lipid that comprises both a cationic group and a lipophilic portion. In addition to the general characteristics profiled above for liposomes, the positively charged moieties of cationic lipids used in cationic liposomes provide several advantages and some unique structural features. For example, the lipophilic portion of the cationic lipid is hydrophobic and thus will direct itself away from the aqueous interior of the liposome and associate with other nonpolar and hydrophobic species. Conversely, the cationic moiety will associate with aqueous media and more importantly with polar molecules and species with which it can complex in the aqueous interior of the cationic liposome. For these reasons, cationic liposomes are increasingly being researched for use in gene therapy due to their favorability towards negatively charged nucleic acids via electrostatic interactions, resulting in complexes that offer biocompatibility, low toxicity, and the possibility of the large-scale production required for in vivo clinical applications. Cationic lipids suitable for use in cationic liposomes are listed herein below. Lipid Nanoparticles

[0187] In contrast to liposomes and cationic liposomes, lipid nanoparticles (LNP) have a structure that includes a single monolayer or bilayer of lipids that encapsulates a compound in a solid phase. Thus, unlike liposomes, lipid nanoparticles do not have an aqueous phase or other liquid phase in its interior, but rather the lipids from the bilayer or monolayer shell are directly complexed to the internal compound thereby encapsulating it in a solid core. Lipid nanoparticlesare typically spherical vesicles having a relatively uniform dispersion of shape and size. While sources vary on what size qualifies a lipid particle as being a nanoparticle, there is some overlap in agreement that a lipid nanoparticle can have a diameter in the range of from 10 nm to 1000 nm. However, more commonly they are considered to be smaller than 120 nm or even 100 nm.

[0188] For lipid nanoparticle nucleic acid delivery systems, the lipid shell is formulated to include an ionizable cationic lipid which can complex to and associate with the negatively charged backbone of the nucleic acid core. Ionizable cationic lipids with apparent pKa values below about 7 have the benefit of providing a cationic lipid for complexing with the nucleic acid’s negatively charged backbone and loading into the lipid nanoparticle at pH values below the pKa of the ionizable lipid where it is positively charged. Then, at physiological pH values, the lipid nanoparticle can adopt a relatively neutral exterior allowing for a significant increase in the circulation half-lives of the particles following i.v. administration. In the context of nucleic acid delivery, lipid nanoparticles offer many advantages over other lipid-based nucleic acid delivery systems including high nucleic acid encapsulation efficiency, potent transfection, improved penetration into tissues to deliver therapeutics, and low levels of cytotoxicity and immunogenicity.

[0189] Prior to the development of lipid nanoparticle delivery systems for nucleic acids, cationic lipids were widely studied as synthetic materials for delivery of nucleic acid medicines. In these early efforts, after mixing together at physiological pH, nucleic acids were condensed by cationic lipids to form lipid-nucleic acid complexes known as lipoplexes. However, lipoplexes proved to be unstable and characterized by broad size distributions ranging from the submicron scale to a few microns. Lipoplexes, such as the Lipofectamine® reagent, have found considerable utility for in vitro transfection. However, these first-generation lipoplexes have not proven useful in vivo. The large particle size and positive charge (Imparted by the cationic lipid) result in rapid plasma clearance, hemolytic and other toxicities, as well as immune system activation.In some aspects, nucleic acid molecules provided herein and lipids or lipid formulations provided herein form a lipid nanoparticle (LNP).

[0190] In other aspects, nucleic acid molecules provided herein are incorporated into a lipid formulation (i.e., a lipid-based delivery vehicle).

[0191] In the context of the present disclosure, a lipid-based delivery vehicle typically serves to transport a desired RNA to a target cell or tissue. The lipid-based delivery vehicle can be any suitable lipid-based delivery vehicle known in the art. In some aspects, the lipid-based delivery vehicle is a liposome, a cationic liposome, or a lipid nanoparticle containing a self-replicating RNA or mRNA of the disclosure. In some aspects, the lipid-based delivery vehicle comprises a nanoparticle or a bilayer of lipid molecules and a self-replicating RNA or mRNA of the disclosure. In some aspects, the lipid bilayer further comprises a neutral lipid or a polymer. In some aspects,the lipid formulation comprises a liquid medium. In some aspects, the formulation further encapsulates a nucleic acid. In some aspects, the lipid formulation further comprises a nucleic acid and a neutral lipid or a polymer. In some aspects, the lipid formulation encapsulates the nucleic acid.

[0192] The description provides lipid formulations comprising one or more RNA molecules encapsulated within the lipid formulation. In some aspects, the lipid formulation comprises liposomes. In some aspects, the lipid formulation comprises cationic liposomes. In some aspects, the lipid formulation comprises lipid nanoparticles.

[0193] In some aspects, the self-replicating RNA or mRNA is fully encapsulated within the lipid portion of the lipid formulation such that the RNA in the lipid formulation is resistant in aqueous solution to nuclease degradation. In other aspects, the lipid formulations described herein are substantially non-toxic to animals such as humans and other mammals.

[0194] The lipid formulations of the disclosure also typically have a total lipid:RNA ratio (mass / mass ratio) of from about 1:1 to about 100:1, from about 1:1 to about 50:1, from about 2:1 to about 45:1, from about 3:1 to about 40:1, from about 5:1 to about 45:1, or from about 10:1 to about 40:1, or from about 15:1 to about 40:1, or from about 20:1 to about 40:1; or from about 25:1 to about 45:1; or from about 30:1 to about 45:1; or from about 32:1 to about 42:1; or from about 34:1 to about 42:1. In some aspects, the total lipid:RNA ratio (mass / mass ratio) is from about 30:1 to about 45:1. The ratio may be any value or subvalue within the recited ranges, including endpoints.

[0195] The lipid formulations of the present disclosure typically have a mean diameter of from about 30 nm to about 150 nm, from about 40 nm to about 150 nm, from about 50 nm to about 150 nm, from about 60 nm to about 130 nm, from about 70 nm to about 110 nm, from about 70 nm to about 100 nm, from about 80 nm to about 100 nm, from about 90 nm to about 100 nm, from about 70 to about 90 nm, from about 80 nm to about 90 nm, from about 70 nm to about 80 nm, or about 30 nm, about 35 nm, about 40 nm, about 45 nm, about 50 nm, about 55 nm, about 60 nm, about 65 nm, about 70 nm, about 75 nm, about 80 nm, about 85 nm, about 90 nm, about 95 nm, about 100 nm, about 105 nm, about 110 nm, about 115 nm, about 120 nm, about 125 nm, about 130 nm, about 135 nm, about 140 nm, about 145 nm, or about 150 nm, and are substantially non-toxic. The diameter may be any value or subvalue within the recited ranges, including endpoints. In addition, nucleic acids, when present in the lipid nanoparticles of the present disclosure, generally are resistant in aqueous solution to degradation with a nuclease.

[0196] In some embodiments, the lipid nanoparticle has a size of less than about 500 nm, less than about 400 nm, less than about 300 nm, less than about 200 nm, less than about 100 nm, less than about 95 nm, less than about 90 nm, less than about 85 nm, less than about 80 nm, less thanabout 75 nm, less than about 70 nm, less than about 65 nm, less than about 60 nm, less than about 55 nm, or less than about 50 nm. In specific embodiments, the lipid nanoparticle has a size of about 55 nm to about 90 nm.

[0197] In some aspects, the lipid formulations comprise a self-replicating RNA or mRNA, a cationic lipid (e.g., one or more cationic lipids or salts thereof described herein), a phospholipid, and a conjugated lipid that inhibits aggregation of the particles (e.g., one or more PEG-lipid conjugates). The lipid formulations can also include cholesterol. In one aspect, the cationic lipid is an ionizable cationic lipid.

[0198] In the nucleic acid-lipid formulations, the RNA may be fully encapsulated within the lipid portion of the formulation, thereby protecting the nucleic acid from nuclease degradation. In some aspects, a lipid formulation comprising an RNA is fully encapsulated within the lipid portion of the lipid formulation, thereby protecting the nucleic acid from nuclease degradation. In certain aspects, the RNA in the lipid formulation is not substantially degraded after exposure of the particle to a nuclease at 37°C for at least 20, 30, 45, or 60 minutes. In certain other aspects, the RNA in the lipid formulation is not substantially degraded after incubation of the formulation in serum at 37°C for at least 30, 45, or 60 minutes or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36 hours. In some aspects, the RNA is complexed with the lipid portion of the formulation. One of the benefits of the formulations of the present disclosure is that the nucleic acid-lipid compositions are substantially non-toxic to animals such as humans and other mammals.

[0199] In the context of nucleic acids, full encapsulation may be determined by performing a membrane-impermeable fluorescent dye exclusion assay, which uses a dye that has enhanced fluorescence when associated with nucleic acid. Encapsulation is determined by adding the dye to a lipid formulation, measuring the resulting fluorescence, and comparing it to the fluorescence observed upon addition of a small amount of nonionic detergent. Detergent-mediated disruption of the lipid layer releases the encapsulated nucleic acid, allowing it to interact with the membrane- impermeable dye. Nucleic acid encapsulation may be calculated as E = (I0 - I) / I0, where / and I0 refers to the fluorescence intensities before and after the addition of detergent.

[0200] In some aspects, the present disclosure provides a nucleic acid-lipid composition comprising a plurality of nucleic acid-liposomes, nucleic acid-cationic liposomes, or nucleic acid- lipid nanoparticles. In some aspects, the nucleic acid-lipid composition comprises a plurality of RNA-liposomes. In some aspects, the nucleic acid-lipid composition comprises a plurality of RNA-cationic liposomes. In some aspects, the nucleic acid-lipid composition comprises a plurality of RNA-lipid nanoparticles.

[0201] In some aspects, the lipid formulations comprise RNA that is fully encapsulated within the lipid portion of the formulation, such that from about 30% to about 100%, from about 40% to about 100%, from about 50% to about 100%, from about 60% to about 100%, from about 70% to about 100%, from about 80% to about 100%, from about 90% to about 100%, from about 30% to about 95%, from about 40% to about 95%, from about 50% to about 95%, from about 60% to about 95%, from about 70% to about 95%, from about 80% to about 95%, from about 85% to about 95%, from about 90% to about 95%, from about 30% to about 90%, from about 40% to about 90%, from about 50% to about 90%, from about 60% to about 90%, from about 70% to about 90%, from about 80% to about 90%, or at least about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% (or any fraction thereof or range therein) of the particles have the RNA encapsulated therein. The amount may be any value or subvalue within the recited ranges, including endpoints. The RNA included in any RNA-lipid composition or RNA-lipid formulation provided herein can be a self-replicating RNA or an mRNA.

[0202] Depending on the intended use of the lipid formulation, the proportions of the components can be varied, and the delivery efficiency of a particular formulation can be measured using assays known in the art.

[0203] In some aspects, nucleic acid molecules provided herein are lipid formulated. The lipid formulation is preferably selected from, but not limited to, liposomes, cationic liposomes, and lipid nanoparticles. In one aspect, a lipid formulation is a cationic liposome or a lipid nanoparticle (LNP) comprising: (a) an RNA of the present disclosure, (b) a cationic lipid, (c) an aggregation reducing agent (such as polyethylene glycol (PEG) lipid or PEG- modified lipid), (d) optionally a non-cationic lipid (such as a neutral lipid), and (e) optionally, a sterol.

[0204] In another aspect, the cationic lipid is an ionizable cationic lipid. Any ionizable cationic lipid can be included in lipid formulations, including exemplary cationic lipids provided herein.

[0205] In some aspects, compositions that include lipids and / or lipid formulations provided herein include an RNA molecule encoded by the sequence of SEQ ID NO:1. In some aspects, compositions provided herein include lipid nanoparticles (LNPs). In some aspects, compositions provided herein include lyophilized LNPs.

[0206] Provided herein, in some embodiments, are lipid nanoparticle compositions comprising a lipid formulation comprising i. about 45 mol% to about 55 mol% of an ionizable cationic lipid having the structure of Compound-77: Compound- 77; ii. about 8 mol% to about 12 mol% DSPC; iii. about 35 mol% to about 42 mol% cholesterol; and iv. about 1.25 mol% to about 1.75 mol% PEG2000-DMG; and b. an RNA molecule having at least 80% identity to the RNA sequence encoded by SEQ ID NO:1; wherein the lipid formulation encapsulates the RNA molecule and the lipid nanoparticle has a size of about 60 to about 90 nm. In some aspects, lipid nanoparticle compositions provided herein are lyophilized.

[0207] Also provided herein, in some embodiments, are lipid nanoparticle compositions comprising a lipid formulation comprising i. about 45 mol% to about 55 mol% of an ionizable cationic lipid having the structure of Compound-90: Compound- 90; ii. about 8 mol% to about 12 mol% DSPC; iii. about 35 mol% to about 42 mol% cholesterol; and iv. about 1.25 mol% to about 1.75 mol% PEG2000-DMG; and b. an RNA molecule having at least 80% identity to the RNA sequence encoded by SEQ ID NO:1; wherein the lipid formulationencapsulates the RNA molecule and the lipid nanoparticle has a size of about 60 to about 90 nm. In some aspects, lipid nanoparticle compositions provided herein are lyophilized. Cationic Lipids

[0208] In one aspect, the lipid nanoparticle formulation comprises (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid. In another aspect, the cationic lipid is an ionizable cationic lipid. In yet another aspect, the lipid nanoparticle formulation comprises (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid, in a molar ratio of about 40-70% ionizable cationic lipid: about 2-15% helper lipid: about 20-45% sterol; about 0.5-5% PEG-lipid. In a further aspect, the cationic lipid is an ionizable cationic lipid.

[0209] In one aspect, the lipid nanoparticle formulation consists of (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid. In another aspect, the cationic lipid is an ionizable cationic lipid. In yet another aspect, the lipid nanoparticle formulation consists of (i) at least one cationic lipid; (ii) a helper lipid; (iii) a sterol (e.g., cholesterol); and (iv) a PEG-lipid, in a molar ratio of about 40-70% ionizable cationic lipid: about 2-15% helper lipid: about 20-45% sterol; about 0.5-5% PEG-lipid. In a further aspect, the cationic lipid is an ionizable cationic lipid.

[0210] In the presently disclosed lipid formulations, the cationic lipid may be, for example, N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), N,N-distearyl-N,N- dimethylammonium bromide (DDAB), 1,2-dioleoyltrimethylammoniumpropane chloride (DOTAP) (also known as N-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride and l,2-Dioleyloxy-3-trimethylaminopropane chloride salt), N-(l-(2,3-dioleyloxy)propyl)-N,N,N- trimethylammonium chloride (DOTMA), N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA), l,2-DiLinoleyloxy-N,N-dimethylaminopropane (DLinDMA), l,2-Dilinolenyloxy-N,N- dimethylaminopropane (DLenDMA), l,2-di-y-linolenyloxy-N,N-dimethylaminopropane (γ- DLenDMA), 1,2-Dilinoleylcarbamoyloxy-3-dimethylaminopropane (DLin-C-DAP), l,2- Dilinoleyoxy-3-(dimethylamino)acetoxypropane (DLin-DAC), l,2-Dilinoleyoxy-3- morpholinopropane (DLin-MA), l,2-Dilinoleoyl-3-dimethylaminopropane (DLinDAP), l,2- Dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA), l-Linoleoyl-2-linoleyloxy-3- dimethylaminopropane (DLin-2-DMAP), l,2-Dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.Cl), l,2-Dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.Cl), l,2- Dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ), or 3-(N,N-Dilinoleylamino)-l,2- propanediol (DLinAP), 3-(N,N-Dioleylamino)-l,2-propanediol (DOAP), l,2-Dilinoleyloxo-3-(2- N,N- dimethylamino)ethoxypropane (DLin-EG-DMA), 2,2-Dilinoleyl-4-dimethylaminomethyl- [l,3]-dioxolane (DLin-K-DMA) or analogs thereof, (3aR,5s,6aS)-N,N-dimethyl-2,2-di((9Z,12Z)-octadeca-9,12-dienyl)tetrahydro-3aH-cyclopenta[d][l,3]dioxol-5-amine, (6Z,9Z,28Z,31Z)- heptatriaconta-6,9,28,31-tetraen-19-yl4-(dimethylamino)butanoate (MC3), l,l'-(2-(4-(2-((2- (bis(2-hydroxydodecyl)amino)ethyl)(2-hydroxydodecyl)amino)ethyl)piperazin-l- yl)ethylazanediyl)didodecan-2-ol (C12-200), 2,2-dilinoleyl-4-(2-dimethylaminoethyl)-[l,3]- dioxolane (DLin-K-C2-DMA), 2,2-dilinoleyl-4-dimethylaminomethyl-[l,3]-dioxolane (DLin-K- DMA), (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28 31-tetraen-19-yl 4-(dimethylamino) butanoate (DLin-M-C3-DMA), 3-((6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,3 l-tetraen-19-yloxy)-N,N- dimethylpropan-l-amine (MC3 Ether), 4-((6Z,9Z,28Z,31 Z)-heptatriaconta-6,9,28,31-tetraen-19- yloxy)-N,N-dimethylbutan-l-amine (MC4 Ether), or any combination thereof. Other cationic lipids include, but are not limited to, N,N-distearyl-N,N-dimethylammonium bromide (DDAB), 3P-(N-(N',N'-dimethylaminoethane)- carbamoyl)cholesterol (DC-Choi), N-(l-(2,3- dioleyloxy)propyl)-N-2-(sperminecarboxamido)ethyl)-N,N-dimethylammonium trifluoracetate (DOSPA), dioctadecylamidoglycyl carboxyspermine (DOGS), l,2-dileoyl-sn-3- phosphoethanolamine (DOPE), l,2-dioleoyl-3-dimethylammonium propane (DODAP), N-(l,2- dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammonium bromide (DMRIE), and 2,2- Dilinoleyl-4-dimethylaminoethyl-[l,3]-dioxolane (XTC). Additionally, commercial preparations of cationic lipids can be used, such as, e.g., LIPOFECTIN (including DOTMA and DOPE, available from GIBCO / BRL), and Lipofectamine (comprising DOSPA and DOPE, available from GIBCO / BRL).

[0211] Other suitable cationic lipids are disclosed in International Publication Nos. WO 09 / 086558, WO 09 / 127060, WO 10 / 048536, WO 10 / 054406, WO 10 / 088537, WO 10 / 129709, and WO 2011 / 153493; U.S. Patent Publication Nos. 2011 / 0256175, 2012 / 0128760, and 2012 / 0027803; U.S. Patent Nos. 8,158,601; and Love et al., PNAS, 107(5), 1864-69, 2010, the contents of which are herein incorporated by reference.

[0212] The RNA-lipid formulations of the present disclosure can comprise a helper lipid, which can be referred to as a neutral helper lipid, non-cationic lipid, non-cationic helper lipid, anionic lipid, anionic helper lipid, or a neutral lipid. It has been found that lipid formulations, particularly cationic liposomes and lipid nanoparticles have increased cellular uptake if helper lipids are present in the formulation. (Curr. Drug Metab.2014; 15(9):882-92). For example, some studies have indicated that neutral and zwitterionic lipids such as 1,2-dioleoylsn-glycero-3- phosphatidylcholine (DOPC), Di-Oleoyl-Phosphatidyl-Ethanoalamine (DOPE) and 1,2- DiStearoyl-sn-glycero-3-PhosphoCholine (DSPC), being more fusogenic (i.e., facilitating fusion) than cationic lipids, can affect the polymorphic features of lipid-nucleic acid complexes, promoting the transition from a lamellar to a hexagonal phase, and thus inducing fusion and a disruption of the cellular membrane. (Nanomedicine (Lond).2014 Jan; 9(1):105-20). In addition,the use of helper lipids can help to reduce any potential detrimental effects from using many prevalent cationic lipids such as toxicity and immunogenicity.

[0213] Non-limiting examples of non-cationic lipids suitable for lipid formulations of the present disclosure include phospholipids such as lecithin, phosphatidylethanolamine, lysolecithin, lysophosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, egg sphingomyelin (ESM), cephalin, cardiolipin, phosphatidic acid, cerebrosides, dicetylphosphate, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoylphosphatidylethanolamine (DOPE), palmitoyloleoyl-phosphatidylcholine (POPC), palmitoyloleoyl-phosphatidylethanolamine (POPE), palmitoyloleyol-phosphatidylglycerol (POPG), dioleoylphosphatidylethanolamine 4-(N- maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal), dipalmitoyl- phosphatidylethanolamine (DPPE), dimyristoyl- phosphatidylethanolamine (DMPE), distearoyl- phosphatidylethanolamine (DSPE), monomethyl-phosphatidylethanolamine, dimethyl- phosphatidylethanolamine, dielaidoyl- phosphatidylethanolamine (DEPE), stearoyloleoyl- phosphatidylethanolamine (SOPE), lysophosphatidylcholine, dilinoleoylphosphatidylcholine, and mixtures thereof. Other diacylphosphatidylcholine and diacylphosphatidylethanolamine phospholipids can also be used. The acyl groups in these lipids are preferably acyl groups derived from fatty acids having C10-C24 carbon chains, e.g., lauroyl, myristoyl, palmitoyl, stearoyl, or oleoyl.

[0214] Additional examples of non-cationic lipids include sterols such as cholesterol and derivatives thereof. As a helper lipid, cholesterol increases the spacing of the charges of the lipid layer interfacing with the nucleic acid making the charge distribution match that of the nucleic acid more closely. (J. R. Soc. Interface.2012 Mar 7; 9(68): 548–561). Non-limiting examples of cholesterol derivatives include polar analogues such as 5α-cholestanol, 5α-coprostanol, cholesteryl-(2'-hydroxy)-ethyl ether, cholesteryl-(4'- hydroxy)-butyl ether, and 6-ketocholestanol; non-polar analogues such as 5α-cholestane, cholestenone, 5α-cholestanone, 5α-cholestanone, and cholesteryl decanoate; and mixtures thereof. In some aspects, the cholesterol derivative is a polar analogue such as cholesteryl-(4'-hydroxy)-butyl ether.

[0215] In some aspects, the helper lipid present in the lipid formulation comprises or consists of a mixture of one or more phospholipids and cholesterol or a derivative thereof. In other aspects, the neutral lipid present in the lipid formulation comprises or consists of one or more phospholipids, e.g., a cholesterol-free lipid formulation. In yet other aspects, the neutral lipid present in the lipid formulation comprises or consists of cholesterol or a derivative thereof, e.g., a phospholipid-free lipid formulation.

[0216] Other examples of helper lipids include nonphosphorous containing lipids such as, e.g., stearylamine, dodecylamine, hexadecylamine, acetyl palmitate, glycerol ricinoleate, hexadecyl stearate, isopropyl myristate, amphoteric acrylic polymers, triethanolamine-lauryl sulfate, alkyl- aryl sulfate polyethyloxylated fatty acid amides, dioctadecyldimethyl ammonium bromide, ceramide, and sphingomyelin.

[0217] Other suitable cationic lipids include those having alternative fatty acid groups and other dialkylamino groups, including those, in which the alkyl substituents are different (e.g., N- ethyl- N-methylamino-, and N-propyl-N-ethylamino-). These lipids are part of a subcategory of cationic lipids referred to as amino lipids. In some embodiments of the lipid formulations described herein, the cationic lipid is an amino lipid. In general, amino lipids having less saturated acyl chains are more easily sized, particularly when the complexes must be sized below about 0.3 microns, for purposes of filter sterilization. Amino lipids containing unsaturated fatty acids with carbon chain lengths in the range of C14 to C22 may be used. Other scaffolds can also be used to separate the amino group and the fatty acid or fatty alkyl portion of the amino lipid.

[0218] In some embodiments, the lipid formulation comprises the cationic lipid with Formula I according to the patent application US20200163878A1. In this context, the disclosure of US20200163878A1 is also incorporated herein by reference.

[0219] In some embodiments, amino or cationic lipids of the present disclosure are ionizable and have at least one protonatable or deprotonatable group, such that the lipid is positively charged at a pH at or below physiological pH (e.g., pH 7.4), and neutral at a second pH, preferably at or above physiological pH. Of course, it will be understood that the addition or removal of protons as a function of pH is an equilibrium process, and that the reference to a charged or a neutral lipid refers to the nature of the predominant species and does not require that all of the lipid be present in the charged or neutral form. Lipids that have more than one protonatable or deprotonatable group, or which are zwitterionic, are not excluded from use in the disclosure. In certain embodiments, the protonatable lipids have a pKa of the protonatable group in the range of about 4 to about 11. In some embodiments, the ionizable cationic lipid has a pKa of about 5 to about 7. In some embodiments, the pKa of an ionizable cationic lipid is about 6 to about 7.

[0220] In some embodiments, the lipid formulation comprises an ionizable cationic lipid of Formula I:(I) or a pharmaceutically acceptable salt or solvate thereof, wherein R5 and R6 are each independently selected from the group consisting of a linear or branched C1-C31 alkyl, C2-C31 alkenyl or C2-C31 alkynyl and cholesteryl; L5 and L6 are each independently selected from the group consisting of a linear C1-C20 alkyl and C2-C20 alkenyl; X5 is -C(O)O-, whereby -C(O)O- R6 is formed or -OC(O)- whereby -OC(O)-R6 is formed; X6 is -C(O)O- whereby -C(O)O-R5 is formed or -OC(O)- whereby -OC(O)-R5 is formed; X7 is S or O; L7 is absent or lower alkyl; R4 is a linear or branched C1-C6 alkyl; and R7 and R8 are each independently selected from the group consisting of a hydrogen and a linear or branched C1-C6 alkyl.

[0221] In some embodiments, X7 is S.

[0222] In some embodiments, X5 is -C(O)O-, whereby -C(O)O-R6 is formed and X6 is - C(O)O- whereby -C(O)O-R5 is formed.

[0223] In some embodiments, R7 and R8 are each independently selected from the group consisting of methyl, ethyl and isopropyl.

[0224] In some embodiments, L5 and L6 are each independently a C1-C10 alkyl. In some embodiments, L5 is C1-C3 alkyl, and L6 is C1-C5 alkyl. In some embodiments, L6 is C1-C2 alkyl. In some embodiments, L5 and L6 are each a linear C7 alkyl. In some embodiments, L5 and L6 are each a linear C9 alkyl.

[0225] In some embodiments, R5 and R6 are each independently an alkenyl. In some embodiments, R6 is alkenyl. In some embodiments, R6 is C2-C9 alkenyl. In some embodiments, the alkenyl comprises a single double bond. In some embodiments, R5 and R6 are each alkyl. In some embodiments, R5 is a branched alkyl. In some embodiments, R5 and R6 are each independently selected from the group consisting of a C9 alkyl, C9 alkenyl and C9 alkynyl. In some embodiments, R5 and R6 are each independently selected from the group consisting of a C11 alkyl, C11 alkenyl and C11 alkynyl. In some embodiments, R5 and R6 are each independently selected from the group consisting of a C7 alkyl, C7 alkenyl and C7 alkynyl. In some embodiments, R5 is –CH((CH2)pCH3)2 or –CH((CH2)pCH3)((CH2)p-1CH3), wherein p is 4-8. In some embodiments, p is 5 and L5 is a C1-C3 alkyl. In some embodiments, p is 6 and L5is a C3 alkyl. In some embodiments, p is 7. In some embodiments, p is 8 and L5 is a C1-C3 alkyl. In some embodiments, R5 consists of –CH((CH2)pCH3)((CH2)p-1CH3), wherein p is 7 or 8.

[0226] In some embodiments, R4 is ethylene or propylene. In some embodiments, R4 is n- propylene or isobutylene.

[0227] In some embodiments, L7 is absent, R4 is ethylene, X7 is S and R7 and R8 are each methyl. In some embodiments, L7 is absent, R4 is n-propylene, X7 is S and R7 and R8 are each methyl. In some embodiments, L7 is absent, R4 is ethylene, X7 is S and R7 and R8 are each ethyl.

[0228] In some embodiments, X7 is S, X5 is -C(O)O-, whereby -C(O)O-R6 is formed, X6 is -C(O)O- whereby -C(O)O-R5 is formed, L5 and L6 are each independently a linear C3-C7 alkyl, L7 is absent, R5 is –CH((CH2)pCH3)2, and R6 is C7-C12 alkenyl. In some further embodiments, p is 6 and R6 is C9 alkenyl.

[0229] In embodiments, any one or more lipids recited herein may be expressly excluded.

[0230] In some aspects, the helper lipid comprises from about 2 mol% to about 20 mol%, from about 3 mol% to about 18 mol%, from about 4 mol% to about 16 mol%, about 5 mol% to about 14 mol%, from about 6 mol% to about 12 mol%, from about 5 mol% to about 10 mol%, from about 5 mol% to about 9 mol%, or about 2 mol%, about 3 mol%, about 4 mol%, about 5 mol%, about 6 mol%, about 7 mol%, about 8 mol%, about 9 mol%, about 10 mol%, about 11 mol%, or about 12 mol% (or any fraction thereof or the range therein) of the total lipid present in the lipid formulation.

[0231] The lipid portion, or the cholesterol or cholesterol derivative in the lipid formulation may comprise up to about 40 mol%, about 45 mol%, about 50 mol%, about 55 mol%, or about 60 mol% of the total lipid present in the lipid formulation. In some aspects, the cholesterol or cholesterol derivative comprises about 15 mol% to about 45 mol%, about 20 mol% to about 40 mol%, about 25 mol% to about 35 mol%, or about 28 mol% to about 35 mol%; or about 25 mol%, about 26 mol%, about 27 mol%, about 28 mol%, about 29 mol%, about 30 mol%, about 31 mol%, about 32 mol%, about 33 mol%, about 34 mol%, about 35 mol%, about 36 mol%, or about 37 mol% of the total lipid present in the lipid formulation.

[0232] In specific embodiments, the lipid portion of the lipid formulation is about 35 mol% to about 42 mol% cholesterol.

[0233] In some aspects, the phospholipid component in the mixture may comprise from about 2 mol% to about 20 mol%, from about 3 mol% to about 18 mol%, from about 4 mol % to about 16 mol %, about 5 mol % to about 14 mol %, from about 6 mol % to about 12 mol%, from about 5 mol% to about 10 mol%, from about 5 mol% to about 9 mol%, or about 2 mol%, about 3 mol%, about 4 mol%, about 5 mol%, about 6 mol%, about 7 mol%, about 8 mol%, about 9 mol%, about10 mol%, about 11 mol%, or about 12 mol% (or any fraction thereof or the range therein) of the total lipid present in the lipid formulation.

[0234] In certain embodiments, the lipid portion of the lipid formulation comprises about, but is not necessarily limited to, 40 mol% to about 60 mol% of the ionizable cationic lipid, about 4 mol% to about 16 mol% DSPC, about 30 mol% to about 47 mol% cholesterol, and about 0.5 mol% to about 3 mol% PEG2000-DMG.

[0235] In certain embodiments, the lipid portion of the lipid formulation may comprise, but is not necessarily limited to, about 42 mol% to about 58 mol% of the ionizable cationic lipid, about 6 mol% to about 14 mol% DSPC, about 32 mol% to about 44 mol% cholesterol, and about 1 mol% to about 2 mol% PEG2000-DMG.

[0236] In certain embodiments, the lipid portion of the lipid formulation may comprise, but is not necessarily limited to, about 45 mol% to about 55 mol% of the ionizable cationic lipid, about 8 mol% to about 12 mol% DSPC, about 35 mol% to about 42 mol% cholesterol, and about 1.25 mol% to about 1.75 mol% PEG2000-DMG.

[0237] The percentage of helper lipid present in the lipid formulation is a target amount, and the actual amount of helper lipid present in the formulation may vary, for example, by ± 5 mol%.

[0238] A lipid formulation that includes a cationic lipid compound or ionizable cationic lipid compound may be on a molar basis about 30-70% cationic lipid compound, about 25-40 % cholesterol, about 2-15% helper lipid, and about 0.5-5% of a polyethylene glycol (PEG) lipid, wherein the percent is of the total lipid present in the formulation. In some aspects, the composition is about 40-65% cationic lipid compound, about 25- 35% cholesterol, about 3-9% helper lipid, and about 0.5-3% of a PEG-lipid, wherein the percent is of the total lipid present in the formulation.

[0239] The formulation may be a lipid particle formulation, for example containing 8-30% nucleic acid compound, 5-30% helper lipid, and 0-20% cholesterol; 4-25% cationic lipid, 4-25% helper lipid, 2- 25% cholesterol, 10- 35% cholesterol-PEG, and 5% cholesterol-amine; or 2-30% cationic lipid, 2-30% helper lipid, 1-15% cholesterol, 2-35% cholesterol-PEG, and 1-20% cholesterol-amine; or up to 90% cationic lipid and 2-10% helper lipids, or even 100% cationic lipid. Lipid Conjugates

[0240] The lipid formulations described herein may further comprise a lipid conjugate. The conjugated lipid is useful in that it prevents the aggregation of particles. Suitable conjugated lipids include, but are not limited to, PEG-lipid conjugates, cationic-polymer-lipid conjugates, and mixtures thereof. Furthermore, lipid delivery vehicles can be used for specific targeting byattaching ligands (e.g., antibodies, peptides, and carbohydrates) to its surface or to the terminal end of the attached PEG chains (Front Pharmacol.2015 Dec 1; 6:286).

[0241] In some aspects, the lipid conjugate is a PEG-lipid. The inclusion of polyethylene glycol (PEG) in a lipid formulation as a coating or surface ligand, a technique referred to as PEGylation, helps to protect nanoparticles from the immune system and their escape from RES uptake (Nanomedicine (Lond). 2011 Jun; 6(4):715-28). PEGylation has been used to stabilize lipid formulations and their payloads through physical, chemical, and biological mechanisms. Detergent-like PEG lipids (e.g., PEG-DSPE) can enter the lipid formulation to form a hydrated layer and steric barrier on the surface. Based on the degree of PEGylation, the surface layer can be generally divided into two types, brush-like and mushroom-like layers. For PEG-DSPE- stabilized formulations, PEG will take on the mushroom conformation at a low degree of PEGylation (usually less than 5 mol%) and will shift to brush conformation as the content of PEG- DSPE is increased past a certain level (Journal of Nanomaterials. 2011;2011:12). PEGylation leads to a significant increase in the circulation half-life of lipid formulations (Annu. Rev. Biomed. Eng.2011 Aug 15; 13():507-30; J. Control Release.2010 Aug 3; 145(3):178-81).

[0242] Examples of PEG-lipids include, but are not limited to, PEG coupled to dialkyloxypropyls (PEG-DAA), PEG coupled to diacylglycerol (PEG-DAG), methoxypolyethyleneglycol (PEG-DMG or PEG2000-DMG), PEG coupled to phospholipids such as phosphatidylethanolamine (PEG-PE), PEG conjugated to ceramides, PEG conjugated to cholesterol or a derivative thereof, and mixtures thereof.

[0243] PEG is a linear, water-soluble polymer of ethylene PEG repeating units with two terminal hydroxyl groups. PEGs are classified by their molecular weights and include the following: monomethoxypolyethylene glycol (MePEG-OH), monomethoxypolyethylene glycol- succinate (MePEG-S), monomethoxypolyethylene glycol-succinimidyl succinate (MePEG-S- NHS), monomethoxypolyethylene glycol-amine (MePEG-NH2), monomethoxypolyethylene glycol-tresylate (MePEG-TRES), monomethoxypolyethylene glycol-imidazolyl-carbonyl (MePEG-IM), as well as such compounds containing a terminal hydroxyl group instead of a terminal methoxy group (e.g., HO-PEG-S, HO-PEG-S-NHS, HO-PEG-NH2).

[0244] The PEG moiety of the PEG-lipid conjugates described herein may comprise an average molecular weight ranging from about 550 daltons to about 10,000 daltons. In certain aspects, the PEG moiety has an average molecular weight of from about 750 daltons to about 5,000 daltons (e.g., from about 1,000 daltons to about 5,000 daltons, from about 1,500 daltons to about 3,000 daltons, from about 750 daltons to about 3,000 daltons, from about 750 daltons to about 2,000 daltons). In some aspects, the PEG moiety has an average molecular weight of about2,000 daltons or about 750 daltons. The average molecular weight may be any value or subvalue within the recited ranges, including endpoints.

[0245] In certain aspects, the PEG can be optionally substituted by an alkyl, alkoxy, acyl, or aryl group. The PEG can be conjugated directly to the lipid or may be linked to the lipid via a linker moiety. Any linker moiety suitable for coupling the PEG to a lipid can be used including, e.g., non-ester-containing linker moieties and ester-containing linker moieties. In one aspect, the linker moiety is a non-ester-containing linker moiety. Exemplary non-ester-containing linker moieties include, but are not limited to, amido (-C(O)NH-), amino (-NR-), carbonyl (-C(O)-), carbamate (-NHC(O)O-), urea (-NHC(O)NH-), disulfide (-S-S-), ether (-O-), succinyl (- (O)CCH2CH2C(O)-), succinamidyl (-NHC(O)CH2CH2C(O)NH-), ether, as well as combinations thereof (such as a linker containing both a carbamate linker moiety and an amido linker moiety). In one aspect, a carbamate linker is used to couple the PEG to the lipid.

[0246] In some aspects, an ester-containing linker moiety is used to couple the PEG to the lipid. Exemplary ester-containing linker moieties include, e.g., carbonate (-OC(O)O-), succinoyl, phosphate esters (-O-(O)POH-O-), sulfonate esters, and combinations thereof.

[0247] Phosphatidylethanolamines having a variety of acyl chain groups of varying chain lengths and degrees of saturation can be conjugated to PEG to form the lipid conjugate. Such phosphatidylethanolamines are commercially available or can be isolated or synthesized using conventional techniques known to those of skill in the art. Phosphatidylethanolamines containing saturated or unsaturated fatty acids with carbon chain lengths in the range of C10to C20are preferred. Phosphatidylethanolamines with mono- or di-unsaturated fatty acids and mixtures of saturated and unsaturated fatty acids can also be used. Suitable phosphatidylethanolamines include, but are not limited to, dimyristoyl- phosphatidylethanolamine (DMPE), dipalmitoyl- phosphatidylethanolamine (DPPE), dioleoyl-phosphatidylethanolamine (DOPE), and distearoyl- phosphatidylethanolamine (DSPE).

[0248] In some aspects, the PEG-DAA conjugate is a PEG-didecyloxypropyl (C10) conjugate, a PEG-dilauryloxypropyl (C12) conjugate, a PEG-dimyristyloxypropyl (C14) conjugate, a PEG-dipalmityloxypropyl (C16) conjugate, or a PEG-distearyloxypropyl (C18) conjugate. In some aspects, the PEG has an average molecular weight of about 750 or about 2,000 daltons. In some aspects, the terminal hydroxyl group of the PEG is substituted with a methyl group.

[0249] In addition to the foregoing, other hydrophilic polymers can be used in place of PEG. Examples of suitable polymers that can be used in place of PEG include, but are not limited to, polyvinylpyrrolidone, polymethyloxazoline, polyethyloxazoline, polyhydroxypropyl,methacrylamide, polymethacrylamide, and polydimethylacrylamide, polylactic acid, polyglycolic acid, and derivatized celluloses such as hydroxymethylcellulose or hydroxyethylcellulose.

[0250] In some aspects, the lipid conjugate (e.g., PEG-lipid) comprises from about 0.1 mol% to about 2 mol%, from about 0.5 mol% to about 2 mol%, from about 1 mol% to about 2 mol%, from about 0.6 mol% to about 1.9 mol%, from about 0.7 mol% to about 1.8 mol%, from about 0.8 mol% to about 1.7 mol%, from about 0.9 mol% to about 1.6 mol%, from about 0.9 mol% to about 1.8 mol%, from about 1 mol% to about 1.8 mol%, from about 1 mol% to about 1.7 mol%, from about 1.2 mol% to about 1.8 mol%, from about 1.2 mol% to about 1.7 mol%, from about 1.3 mol% to about 1.6 mol%, or from about 1.4 mol% to about 1.6 mol% (or any fraction thereof or range therein) of the total lipid present in the lipid formulation. In other embodiments, the lipid conjugate (e.g., PEG-lipid) comprises about 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1.0%, 1.2%, 1.3%, 1.4%, 1.5%, 1.6%, 1.7%, 1.8%, 1.9%, 2.0%, 2.5%, 3.0%, 3.5%, 4.0%, 4.5%, or 5%, (or any fraction thereof or range therein) of the total lipid present in the lipid formulation. The amount may be any value or subvalue within the recited ranges, including endpoints.

[0251] The percentage of lipid conjugate (e.g., PEG-lipid) present in the lipid formulations of the disclosure is a target amount, and the actual amount of lipid conjugate present in the formulation may vary, for example, by ± 0.5 mol%. One of ordinary skill in the art will appreciate that the concentration of the lipid conjugate can be varied depending on the lipid conjugate employed and the rate at which the lipid formulation is to become fusogenic.

[0252] In some embodiments, the lipid formulation for any of the compositions described herein comprises a lipoplex, a liposome, a lipid nanoparticle, a polymer-based particle, an exosome, a lamellar body, a micelle, or an emulsion. Mechanism of Action for Cellular Uptake of Lipid Formulations

[0253] In some aspects, lipid formulations for the intracellular delivery of nucleic acids, particularly liposomes, cationic liposomes, and lipid nanoparticles, are designed for cellular uptake by penetrating target cells through exploitation of the target cells’ endocytic mechanisms where the contents of the lipid delivery vehicle are delivered to the cytosol of the target cell. (Nucleic Acid Therapeutics, 28(3):146-157, 2018). Prior to endocytosis, functionalized ligands such as PEG-lipid at the surface of the lipid delivery vehicle are shed from the surface, which triggers internalization into the target cell. During endocytosis, some part of the plasma membrane of the cell surrounds the vector and engulfs it into a vesicle that then pinches off from the cell membrane, enters the cytosol and ultimately enters and moves through the endolysosomal pathway. For ionizable cationic lipid-containing delivery vehicles, the increased acidity as the endosome ages results in a vehicle with a strong positive charge on the surface. Interactions between the delivery vehicle and the endosomal membrane then result in a membrane fusion eventthat leads to cytosolic delivery of the payload. For RNA payloads, the cell’s own internal translation processes will then translate the RNA into the encoded protein. The encoded protein can further undergo postranslational processing, including transportation to a targeted organelle or location within the cell or excretion from the cell.

[0254] By controlling the composition and concentration of the lipid conjugate, one can control the rate at which the lipid conjugate exchanges out of the lipid formulation and, in turn, the rate at which the lipid formulation becomes fusogenic. In addition, other variables including, e.g., pH, temperature, or ionic strength, can be used to vary and / or control the rate at which the lipid formulation becomes fusogenic. Other methods which can be used to control the rate at which the lipid formulation becomes fusogenic will become apparent to those of skill in the art upon reading this disclosure. Also, by controlling the composition and concentration of the lipid conjugate, one can control the liposomal or lipid particle size. Lipid Formulation Manufacture

[0255] There are many different methods for the preparation of lipid formulations comprising a nucleic acid. (Curr. Drug Metabol.2014, 15, 882–892; Chem. Phys. Lipids 2014, 177, 8–18; Int. J. Pharm. Stud. Res. 2012, 3, 14–20). The techniques of thin film hydration, double emulsion, reverse phase evaporation, microfluidic preparation, dual assymetric centrifugation, ethanol injection, detergent dialysis, spontaneous vesicle formation by ethanol dilution, and encapsulation in preformed liposomes are briefly described herein. Thin Film Hydration

[0256] In Thin Film Hydration (TFH) or the Bangham method, the lipids are dissolved in an organic solvent, then evaporated through the use of a rotary evaporator leading to a thin lipid layer formation. After the layer hydration by an aqueous buffer solution containing the compound to be loaded, Multilamellar Vesicles (MLVs) are formed, which can be reduced in size to produce Small or Large Unilamellar vesicles (LUV and SUV) by extrusion through membranes or by the sonication of the starting MLV. Double Emulsion

[0257] Lipid formulations can also be prepared through the Double Emulsion technique, which involves lipids dissolution in a water / organic solvent mixture. The organic solution, containing water droplets, is mixed with an excess of aqueous medium, leading to a water-in-oil- in-water (W / O / W) double emulsion formation. After mechanical vigorous shaking, part of the water droplets collapse, giving Large Unilamellar Vesicles (LUVs). Reverse Phase Evaporation

[0258] The Reverse Phase Evaporation (REV) method also allows one to achieve LUVs loaded with nucleic acid. In this technique a two-phase system is formed by phospholipidsdissolution in organic solvents and aqueous buffer. The resulting suspension is then sonicated briefly until the mixture becomes a clear one-phase dispersion. The lipid formulation is achieved after the organic solvent evaporation under reduced pressure. This technique has been used to encapsulate different large and small hydrophilic molecules including nucleic acids. Microfluidic Preparation

[0259] The Microfluidic method, unlike other bulk techniques, gives the possibility of controlling the lipid hydration process. The method can be classified in continuous-flow microfluidic and droplet-based microfluidic, according to the way in which the flow is manipulated. In the microfluidic hydrodynamic focusing (MHF) method, which operates in a continuous flow mode, lipids are dissolved in isopropyl alcohol which is hydrodynamically focused in a microchannel cross junction between two aqueous buffer streams. Vesicles size can be controlled by modulating the flow rates, thus controlling the lipids solution / buffer dilution process. The method can be used for producing oligonucleotide (ON) lipid formulations by using a microfluidic device consisting of three-inlet and one-outlet ports. Dual Asymmetric Centrifugation

[0260] Dual Asymmetric Centrifugation (DAC) differs from more common centrifugation as it uses an additional rotation around its own vertical axis. An efficient homogenization is achieved due to the two overlaying movements generated: the sample is pushed outwards, as in a normal centrifuge, and then it is pushed towards the center of the vial due to the additional rotation. By mixing lipids and an NaCl-solution a viscous vesicular phospholipid gel (VPC) is achieved, which is then diluted to obtain a lipid formulation dispersion. The lipid formulation size can be regulated by optimizing DAC speed, lipid concentration and homogenization time. Ethanol Injection

[0261] The Ethanol Injection (EI) method can be used for nucleic acid encapsulation. This method provides the rapid injection of an ethanolic solution, in which lipids are dissolved, into an aqueous medium containing nucleic acids to be encapsulated, through the use of a needle. Vesicles are spontaneously formed when the phospholipids are dispersed throughout the medium. Detergent Dialysis

[0262] The Detergent dialysis method can be used to encapsulate nucleic acids. Briefly lipid and plasmid are solubilized in a detergent solution of appropriate ionic strength, after removing the detergent by dialysis, a stabilized lipid formulation is formed. Unencapsulated nucleic acid is then removed by ion-exchange chromatography and empty vesicles by sucrose density gradient centrifugation. The technique is highly sensitive to the cationic lipid content and to the salt concentration of the dialysis buffer, and the method is also difficult to scale.Spontaneous Vesicle Formation by Ethanol Dilution

[0263] Stable lipid formulations can also be produced through the Spontaneous Vesicle Formation by Ethanol Dilution method in which a stepwise or dropwise ethanol dilution provides the instantaneous formation of vesicles loaded with nucleic acid by the controlled addition of lipid dissolved in ethanol to a rapidly mixing aqueous buffer containing the nucleic acid. Encapsulation in Preformed Liposomes

[0264] The entrapment of nucleic acids can also be obtained starting with preformed liposomes through two different methods: (1) A simple mixing of cationic liposomes with nucleic acids which gives electrostatic complexes called “lipoplexes”, where they can be successfully used to transfect cell cultures, but are characterized by their low encapsulation efficiency and poor performance in vivo; and (2) a liposomal destabilization, slowly adding absolute ethanol to a suspension of cationic vesicles up to a concentration of 40% v / v followed by the dropwise addition of nucleic acids achieving loaded vesicles; however, the two main steps characterizing the encapsulation process are too sensitive, and the particles have to be downsized. Excipients

[0265] The pharmaceutical compositions disclosed herein can be formulated using one or more excipients to: (1) increase stability; (2) increase cell transfection; (3) permit a sustained or delayed release (e.g., from a depot formulation of the polynucleotide, primary construct, or RNA); (4) alter the biodistribution (e.g., target the polynucleotide, primary construct, or RNA to specific tissues or cell types); (5) increase the translation of encoded protein in vivo; and / or (6) alter the release profile of encoded protein in vivo.

[0266] The pharmaceutical compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology. In general, such preparatory methods include the step of associating the active ingredient (i.e., nucleic acid) with an excipient and / or one or more other accessory ingredients. A pharmaceutical composition in accordance with the present disclosure may be prepared, packaged, and / or sold in bulk, as a single unit dose, and / or as a plurality of single unit doses.

[0267] Pharmaceutical compositions may additionally comprise a pharmaceutically acceptable excipient, which, as used herein, includes, but is not limited to, any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, and the like, as suited to the particular dosage form desired.

[0268] In addition to traditional excipients such as any and all solvents, dispersion media, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonicagents, thickening or emulsifying agents, preservatives, excipients of the present disclosure can include, without limitation, liposomes, lipid nanoparticles, polymers, lipoplexes, core-shell nanoparticles, peptides, proteins, cells transfected with primary DNA construct, or RNA (e.g., for transplantation into a subject), hyaluronidase, nanoparticle mimics and combinations thereof.

[0269] Accordingly, the pharmaceutical compositions described herein can include one or more excipients, each in an amount that together increases the stability of the nucleic acid in the lipid formulation, increases cell transfection by the nucleic acid, increases the expression of the encoded protein, and / or alters the release profile of encoded proteins. Further, the RNA of the present disclosure may be formulated using self-assembled nucleic acid nanoparticles.

[0270] Various excipients for formulating pharmaceutical compositions and techniques for preparing the composition are known in the art (see Remington: The Science and Practice of Pharmacy, 21st Edition, A. R. Gennaro, Lippincott, Williams & Wilkins, Baltimore, Md., 2006; incorporated herein by reference in its entirety). The use of a conventional excipient medium may be contemplated within the scope of the embodiments of the present disclosure, except insofar as any conventional excipient medium may be incompatible with a substance or its derivatives, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutical composition.

[0271] The pharmaceutical compositions of this disclosure may further contain as pharmaceutically acceptable carriers substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, and wetting agents, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, and mixtures thereof. For solid compositions, conventional nontoxic pharmaceutically acceptable carriers can be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like.

[0272] In certain embodiments of the disclosure, the RNA-lipid formulation may be administered in a time release formulation, for example in a composition which includes a slow- release polymer. The active agent can be prepared with carriers that will protect against rapid release, for example a controlled release vehicle such as a polymer, microencapsulated delivery system, or a bioadhesive gel. Prolonged delivery of the RNA, in various compositions of the disclosure can be brought about by including in the composition agents that delay absorption, for example, aluminum monostearate hydrogels and gelatin.Methods of Inducing Immune Responses

[0273] Provided herein, in some embodiments, are methods of inducing an immune response in a subject. Any type of immune response can be induced using the methods provided herein, including adaptive and innate immune responses. In one aspect, immune responses induced using the methods provided herein include an antibody response, a cellular immune response, or both an antibody response and a cellular immune response.

[0274] Methods of inducing an immune response provided herein include administering to a subject an effective amount of any composition, RNA or DNA molecule, i.e., nucleic acid molecule, provided herein. In one aspect, methods of inducing an immune response include administering to a subject an effective amount of any composition comprising an RNA molecule and a lipid provided herein. In another aspect, methods of inducing an immune response include administering to a subject an effective amount of any pharmaceutical composition comprising an RNA molecule and a lipid formulation provided herein. In some aspects, RNA molecules, compositions, and pharmaceutical composition provided here are vaccines that can elicit a protective or a therapeutic immune response, for example.

[0275] As used herein, the term “subject” refers to any individual or patient on which the methods disclosed herein are performed. The term “subject” can be used interchangeably with the term “individual” or “patient.” The subject can be a human, although the subject may be an animal, as will be appreciated by those in the art. Thus, other animals, including mammals such as rodents (including mice, rats, hamsters and guinea pigs), cats, dogs, rabbits, farm animals including cows, horses, goats, sheep, pigs, etc., and primates (including monkeys, chimpanzees, orangutans and gorillas) are included within the definition of subject. As used herein, the term “effective amount” or “therapeutically effective amount” refers to that amount of an RNA molecule, composition, or pharmaceutical composition described herein that is sufficient to effect the intended application, including but not limited to inducing an immune response and / or disease treatment, as defined herein. The therapeutically effective amount may vary depending upon the intended application (e.g., inducing an immune response, treatment, application in vivo), or the subject or patient and disease condition being treated, e.g., the weight and age of the subject, the species, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art. The term also applies to a dose that will induce a particular response in a target cell. The specific dose will vary depending on the particular RNA molecule, composition, or pharmaceutical composition chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.

[0276] Exemplary doses of nucleic molecules that can be administered include about 0.01 μg, about 0.02 μg, about 0.03 μg, about 0.04 μg, about 0.05 μg, about 0.06 μg, about 0.07 μg, about 0.08 μg, about 0.09 μg, about 0.1 μg, about 0.2 μg, about 0.3 μg, about 0.4 μg, about 0.5 μg, about 0.6 μg, about 0.7 μg, about 0.8 μg, about 0.9 μg, about 1.0 μg, about 1.5 μg, about 2.0 μg, about 2.5 μg, about 3.0 μg, about 3.5 μg, about 4.0 μg, about 4.5 μg, about 5.0 μg, about 5.5 μg, about 6.0 μg, about 6.5 μg, about 7.0 μg, about 7.5 μg, about 8.0 μg, about 8.5 μg, about 9.0 μg, about 9.5 μg, about 10 μg, about 11 μg, about 12 μg, about 13 μ, about 14 μg, about 15 μg, about 16 μg, about 17 μg, about 18 μg, about 19 μg, about 20 μg, about 21 μg, about 22 μg, about 23 μg, about 24 μg, about 25 μg, about 26 μg, about 27 μg, about 28 μg, about 29 μg, about 30 μg, about 35 μg, about 40 μg, about 45 μg, about 50 μg, about 55 μg, about 60 μg, about 65 μg, about 70 μg, about 75 μg, about 80 μg, about 85 μg, about 90 μg, about 95 μg, about 100 μg, about 125 μg, about 150 μg, about 175 μg, about 200 μg, about 250 μg, about 300 μg, about 350 μg, about 400 μg, about 450 μg, about 500 μg, about 600 μg, about 700 μg, about 800 μg, about 900 μg, about 1,000 μg, or more, and any number or range in between. In one aspect, the nucleic acid molecules are RNA molecules. In another aspect, the nucleic acid molecules are DNA molecules. In yet another aspect, nucleic acid molecules include one RNA molecule or one DNA molecule. In a further aspect, nucleic acid molecules include two, three, four, five, six, seven, eight, or more different RNA molecules or DNA molecules. Nucleic acid molecules can have a unit dosage comprising about 0.01 μg to about 1,000 μg or more nucleic acid in a single dose.

[0277] In some aspects, compositions provided herein that can be administered include about 0.01 μg, about 0.02 μg, about 0.03 μg, about 0.04 μg, about 0.05 μg, about 0.06 μg, about 0.07 μg, about 0.08 μg, about 0.09 μg, about 0.1 μg, about 0.2 μg, about 0.3 μg, about 0.4 μg, about 0.5 μg, about 0.6 μg, about 0.7 μg, about 0.8 μg, about 0.9 μg, about 1.0 μg, about 1.5 μg, about 2.0 μg, about 2.5 μg, about 3.0 μg, about 3.5 μg, about 4.0 μg, about 4.5 μg, about 5.0 μg, about 5.5 μg, about 6.0 μg, about 6.5 μg, about 7.0 μg, about 7.5 μg, about 8.0 μg, about 8.5 μg, about 9.0 μg, about 9.5 μg, about 10 μg, about 11 μg, about 12 μg, about 13 μg, about 14 μg, about 15 μg, about 16 μg, about 17 μg, about 18 μg, about 19 μg, about 20 μg, about 21 μg, about 22 μg, about 23 μg, about 24 μg, about 25 μg, about 26 μg, about 27 μg, about 28 μg, about 29 μg, about 30 μg, about 35 μg, about 40 μg, about 45 μg, about 50 μg, about 55 μg, about 60 μg, about 65 μg, about 70 μg, about 75 μg, about 80 μg, about 85 μg, about 90 μg, about 95 μg, about 100 μg, about 125 μg, about 150 μg, about 175 μg, about 200 μg, about 250 μg, about 300 μg, about 350 μg, about 400 μg, about 450 μg, about 500 μg, about 600 μg, about 700 μg, about 800 μg, about 900 μg, about 1,000 μg, or more, and any number or range in between, nucleic acid and lipid. Inother aspects, pharmaceutical compositions provided herein that can be administered include about 0.01 μg, about 0.02 μg, about 0.03 μg, about 0.04 μg, about 0.05 μg, about 0.06 μg, about 0.07 μg, about 0.08 μg, about 0.09 μg, about 0.1 μg, about 0.2 μg, about 0.3 μg, about 0.4 μg, about 0.5 μg, about 0.6 μg, about 0.7 μg, about 0.8 μg, about 0.9 μg, about 1.0 μg, about 1.5 μg, about 2.0 μg, about 2.5 μg, about 3.0 μg, about 3.5 μg, about 4.0 μg, about 4.5 μg, about 5.0 μg, about 5.5 μg, about 6.0 μg, about 6.5 μg, about 7.0 μg, about 7.5 μg, about 8.0 μg, about 8.5 μg, about 9.0 μg, about 9.5 μg, about 10 μg, about 11 μg, about 12 μg, about 13 μg, about 14 μg, about 15 μg, about 16 μg, about 17 μg, about 18 μg, about 19 μg, about 20 μg, about 21 μg, about 22 μg, about 23 μg, about 24 μg, about 25 μg, about 26 μg, about 27 μg, about 28 μg, about 29 μg, about 30 μg, about 35 μg, about 40 μg, about 45 μg, about 50 μg, about 55 μg, about 60 μg, about 65 μg, about 70 μg, about 75 μg, about 80 μg, about 85 μg, about 90 μg, about 95 μg, about 100 μg, about 125 μg, about 150 μg, about 175 μg, about 200 μg, about 250 μg, about 300 μg, about 350 μg, about 400 μg, about 450 μg, about 500 μg, about 600 μg, about 700 μg, about 800 μg, about 900 μg, about 1,000 μg, or more, and any number or range in between, nucleic acid and lipid formulation. In some aspects, compositions or pharmaceutical compositions include one RNA molecule or one DNA molecule. In further aspects, compositions or pharmaceutical compositions include include two, three, four, five, six, seven, eight, or more different RNA molecules or DNA molecules.

[0278] In one aspect, compositions provided herein can have a unit dosage comprising about 0.01 μg to about 1,000 μg or more nucleic acid and lipid in a single dose. In another aspect, pharmaceutical compositions provided herein can have a unit dosage comprising about 0.01 μg to about 1,000 μg or more nucleic acid and lipid formulation in a single dose. A vaccine unit dosage can correspond to the unit dosage of nucleic acid molecules, compositions, or pharmaceutical compositions provided herein and that can be administered to a subject. In one aspect, vaccine compositions of the instant disclosure have a unit dosage comprising about 0.01 μg to about 1,000 μg or more nucleic acid and lipid formulation in a single dose. In another aspect, vaccine compositions of the instant disclosure have a unit dosage comprising about 0.01 μg to about 50 μg nucleic acid and lipid formulation in a single dose. In yet another aspect, vaccine compositions of the instant disclosure have a unit dosage comprising about 0.2 μg to about 20 μg nucleic acid and lipid formulation in a single dose.

[0279] A dosage form of the composition of this disclosure can be solid, which can be reconstituted in a liquid prior to administration. The solid can be administered as a powder. The solid can be in the form of a capsule, tablet, or gel. In some embodiments, the pharmaceutical composition comprises a nucleic acid lipid formulation that has been lyophilized. In someembodiments, the lyophilized composition may comprise one or more lyoprotectants, such as, including but not necessarily limited to, glucose, trehalose, sucrose, maltose, lactose, mannitol, inositol, hydroxypropyl-β-cyclodextrin, and / or polyethylene glycol. In some embodiments, the lyophilized composition comprises a poloxamer, potassium sorbate, sucrose, or any combination thereof. In specific embodiments, the poloxamer is poloxamer 188. In some embodiments, the lyophilized compositions described herein may comprise about 0.01 to about 1.0% w / w of a poloxamer. In some embodiments, the lyophilized compositions described herein may comprise about 1.0 to about 5.0% w / w of potassium sorbate. The percentages may be any value or subvalue within the recited ranges, including endpoints.

[0280] In some embodiments, the lyophilized composition may comprise about 0.01 to about 1.0 % w / w of the nucleic acid molecule. In some embodiments, the composition may comprise about 1.0 to about 5.0 % w / w lipids. In some embodiments, the composition may comprise about 0.5 to about 2.5 % w / w of TRIS buffer. In some embodiments, the composition may comprise about 0.75 to about 2.75 % w / w of NaCl. In some embodiments, the composition may comprise about 5 to about 95 % w / w of a sugar, about 10 to about 95 % w / w of a sugar, about 15 to about 95 % w / w of a sugar, about 20 to about 95 % w / w of a sugar, about 25 to about 95 % w / w of a sugar, about 30 to about 95 % w / w of a sugar, about 35 to about 95 % w / w of a sugar, about 40 to about 95 % w / w of a sugar, about 45 to about 95 % w / w of a sugar, about 50 to about 95 % w / w of a sugar, about 55 to about 95 % w / w of a sugar, about 60 to about 95 % w / w of a sugar, about 65 to about 95 % w / w of a sugar, about 70 to about 95 % w / w of a sugar, about 75 to about 95 % w / w of a sugar, about 80 to about 95 % w / w of a sugar, or about 85 to about 95 % w / w of a sugar. In some embodiments, the composition may comprise about 1 to about 50 % w / w of a sugar, about 5 to about 50 % w / w of a sugar, about 10 to about 50 % w / w of a sugar, about 15 to about 50 % w / w of a sugar, about 20 to about 50 % w / w of a sugar, about 25 to about 50 % w / w of a sugar, about 30 to about 50 % w / w of a sugar, about 35 to about 50 % w / w of a sugar, about 40 to about 50 % w / w of a sugar, or about 45 to about 50 % w / w of a sugar. In some embodiments, the composition may comprise about 1 to about 20 % w / w of a sugar, about 2 to about 20 % w / w of a sugar, about 3 to about 20 % w / w of a sugar, about 4 to about 20 % w / w of a sugar, about 5 to about 20 % w / w of a sugar, about 6 to about 20 % w / w of a sugar, about 7 to about 20 % w / w of a sugar, about 8 to about 20 % w / w of a sugar, about 9 to about 20 % w / w of a sugar, about 10 to about 20 % w / w of a sugar, about 11 to about 20 % w / w of a sugar, about 12 to about 20 % w / w of a sugar, about 13 to about 20 % w / w of a sugar, about 14 to about 20 % w / w of a sugar, about 15 to about 20 % w / w of a sugar, about 16 to about 20 % w / w of a sugar, about 17 to about 20 % w / w of a sugar, about 18 to about 20 % w / w of a sugar, or about 19 to about 20 % w / w of a sugar. In some embodiments, the composition may comprise about 1 to about 18 % w / w of a sugar, about2 to about 18 % w / w of a sugar, about 3 to about 18 % w / w of a sugar, about 4 to about 18 % w / w of a sugar, about 5 to about 18 % w / w of a sugar, about 6 to about 18 % w / w of a sugar, about 7 to about 18 % w / w of a sugar, about 8 to about 18 % w / w of a sugar, about 9 to about 18 % w / w of a sugar, about 10 to about 18 % w / w of a sugar, about 11 to about 18 % w / w of a sugar, about 12 to about 18 % w / w of a sugar, about 13 to about 18 % w / w of a sugar, about 14 to about 18 % w / w of a sugar, about 15 to about 18 % w / w of a sugar, about 16 to about 18 % w / w of a sugar, or about 17 to about 18 % w / w of a sugar. In some embodiments, the composition may comprise about 1 to about 16 % w / w of a sugar, about 2 to about 16 % w / w of a sugar, about 3 to about 16 % w / w of a sugar, about 4 to about 16 % w / w of a sugar, about 5 to about 16 % w / w of a sugar, about 6 to about 16 % w / w of a sugar, about 7 to about 16 % w / w of a sugar, about 8 to about 16 % w / w of a sugar, about 9 to about 16 % w / w of a sugar, about 10 to about 16 % w / w of a sugar, about 11 to about 16 % w / w of a sugar, about 12 to about 16 % w / w of a sugar, about 13 to about 16% w / w of a sugar, about 14 to about 16 % w / w of a sugar, or about 15 to about 16 % w / w of a sugar. In some embodiments, the composition may comprise about 1 to about 12 % w / w of a sugar, about 2 to about 12 % w / w of a sugar, about 3 to about 12 % w / w of a sugar, about 4 to about 12 % w / w of a sugar, about 5 to about 12 % w / w of a sugar, about 6 to about 12 % w / w of a sugar, about 7 to about 12 % w / w of a sugar, about 8 to about 12 % w / w of a sugar, about 9 to about 12 % w / w of a sugar, about 10 to about 12 % w / w of a sugar, or about 11 to about 12 % w / w of a sugar. The percentages may be any value or subvalue within the recited ranges, including endpoints. Compositions provided herein can be lyophilized, a liquid, a frozen liquid, or a liquid suspension.

[0281] In a preferred embodiment, the dosage form of the pharmaceutical compositions described herein can be a liquid suspension of RNA lipid nanoparticles described herein. In some embodiments, the RNA of RNA lipid nanoparticles is a self-replicating RNA. In some embodiments, the RNA of RNA lipid nanoparticles is an mRNA. In some embodiments, the liquid suspension is in a buffered solution. In some embodiments, the buffered solution comprises a buffer selected from the group consisting of HEPES, MOPS, TES, and TRIS. In some embodiments, the buffer has a pH of about 7.4. In some preferred embodiments, the buffer is HEPES. In some further embodiments, the buffered solution further comprises a cryoprotectant. In some embodiments, the cryoprotectant is selected from a sugar and glycerol or a combination of a sugar and glycerol. In some embodiments, the sugar is a dimeric sugar. In some embodiments, the sugar is sucrose. In some preferred embodiments, the buffer comprises HEPES, sucrose, and glycerol at a pH of 7.4. In certain embodiments, the composition comprises a HEPES, MOPS, TES, or TRIS buffer at a pH of about 7.0 to about 8.5. In some embodiments, the HEPES, MOPS,TES, or TRIS buffer may at a concentration ranging from 7 mg / ml to about 15 mg / ml. The pH or concentration may be any value or subvalue within the recited ranges, including endpoints.

[0282] In some embodiments, the suspension is frozen during storage and thawed prior to administration. In some embodiments, the suspension is frozen at a temperature below about 70 °C. In some embodiments, the suspension is diluted with sterile water during intravenous administration. In some embodiments, intravenous administration comprises diluting the suspension with about 2 volumes to about 6 volumes of sterile water. In some embodiments, the suspension comprises about 0.1 mg to about 3.0 mg RNA / mL, about 15 mg / mL to about 25 mg / mL of an ionizable cationic lipid, about 0.5 mg / mL to about 2.5 mg / mL of a PEG-lipid, about 1.8 mg / mL to about 3.5 mg / mL of a helper lipid, about 4.5 mg / mL to about 7.5 mg / mL of a cholesterol, about 7 mg / mL to about 15 mg / mL of a buffer, about 2.0 mg / mL to about 4.0 mg / mL of NaCl, about 70 mg / mL to about 110 mg / mL of sucrose, and about 50 mg / mL to about 70 mg / mL of glycerol. In some embodiments, a lyophilized RNA-lipid nanoparticle formulation can be resuspended in a buffer as described herein.

[0283] In some embodiments, the compositions of the disclosure are administered to a subject such that a RNA concentration of at least about 0.05 mg / kg, at least about 0.1 mg / kg, at least about 0.5 mg / kg, at least about 1.0 mg / kg, at least about 2.0 mg / kg, at least about 3.0 mg / kg, at least about 4.0 mg / kg, at least about 5.0 mg / kg of body weight is administered in a single dose or as part of single treatment cycle. In some embodiments, the compositions of the disclosure are administered to a subject such that a total amount of at least about 0.1 mg, at least about 0.5 mg, at least about 1.0 mg, at least about 2.0 mg, at least about 3.0 mg, at least about 4.0 mg, at least about 5.0 mg, at least about 6.0 mg, at least about 7.0 mg, at least about 8.0 mg, at least about 9.0 mg, at least about 10 mg, at least about 15 mg, at least about 20 mg, at least about 25 mg, at least about 30 mg, at least about 35 mg, at least about 40 mg, at least about 45 mg, at least about 50 mg, at least about 55 mg, at least about 60 mg, at least about 65 mg, at least about 70 mg, at least about 75 mg, at least about 80 mg, at least about 85 mg, at least about 90 mg, at least about 95 mg, at least about 100 mg, at least about 105 mg, at least about 110 mg, at least about 115 mg, at least about 120 mg, or at least about 125 mg RNA is administered in one or more doses up to a maximum dose of about 300 mg, about 350 mg, about 400 mg, about 450 mg, or about 500 mg RNA.

[0284] Any route of administration can be included in methods provided herein. In some aspects, nucleic acid molecules, i.e., RNA or DNA molecules, compositions, and pharmaceutical compositions provided herein are administered intramuscularly, subcutaneously, intradermally, transdermally, intranasally, orally, sublingually, intravenously, intraperitoneally, topically, by aerosol, or by a pulmonary route, such as by inhalation or by nebulization, for example. In someembodiments, the pharmaceutical compositions described are administered systemically. Suitable routes of administration include, for example, oral, rectal, vaginal, transmucosal, pulmonary including intratracheal or inhaled, or intestinal administration; parenteral delivery, including intradermal, transdermal (topical), intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, or intranasal. In particular embodiments, the intramuscular administration is to a muscle selected from the group consisting of skeletal muscle, smooth muscle and cardiac muscle. In some embodiments, the pharmaceutical composition is administered intravenously.

[0285] Pharmaceutical compositions may be administered to any desired tissue. In some embodiments, the RNA delivered is expressed in a tissue different from the tissue in which the lipid formulation or pharmaceutical composition was administered. In preferred embodiments, RNA is delivered and expressed in the liver.

[0286] In other aspects, nucleic acid molecules, i.e., RNA or DNA molecules, compositions, and pharmaceutical compositions provided herein are administered intramuscularly.

[0287] In some aspects, the subject in which an immune response is induced is a healthy subject. As used herein, the term “healthy subject” refers to a subject not having a condition or disease, including an infectious disease or cancer, for example, or not having a condition or disease against which an immune response is induced. Accordingly, in some aspects, a nucleic acid molecule, composition, or pharmaceutical composition provided herein is administered prophylactically to prevent an infectious disease, for example. A nucleic acid molecule, composition, or pharmaceutical composition provided herein can also be administered therapeutically, i.e., to treat a condition or disease, such as an infection, after the onset of the condition or disease.

[0288] As used herein, the terms “treat,” “treatment,” “therapy,” “therapeutic,” and the like refer to obtaining a desired pharmacologic and / or physiologic effect, including, but not limited to, alleviating, delaying or slowing the progression, reducing the effects or symptoms, preventing onset, inhibiting, ameliorating the onset of a diseases or disorder, obtaining a beneficial or desired result with respect to a disease, disorder, or medical condition, such as a therapeutic benefit and / or a prophylactic benefit. “Treatment,” as used herein, includes any treatment of a disease in a mammal, particularly in a human, and includes: (a) preventing the disease from occurring in a subject, including a subject which is predisposed to the disease or at risk of acquiring the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease. A therapeutic benefit includes eradication or amelioration of the underlying disorder being treated. Also, a therapeutic benefit is achieved with the eradication or amelioration of one or more of thephysiological symptoms associated with the underlying disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder. In some aspects, for prophylactic benefit, treatment or compositions for treatment, including pharmaceutical compositions, are administered to a subject at risk of developing a particular disease, or to a subject reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made. The methods of the present disclosure may be used with any mammal or other animal. In some aspects, treatment results in a decrease or cessation of symptoms. A prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.

[0289] Nucleic acid molecules, i.e., RNA or DNA molecules, compositions, and pharmaceutical compositions provided herein can be administered once or multiple times. Accordingly, nucleic acid molecules, compositions, and pharmaceutical compositions provided herein can be administered one, two, three, four, five, six, seven, eight, nine, ten, or more times. Timing between two or more administrations can be one week, two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, weeks, ten weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, 45 weeks, 46 weeks, 47 weeks, 48 weeks, 49 weeks, 50 weeks, 51 weeks, 52 weeks, or more weeks, and any number or range in between. In some aspects, timing between two or more administrations is one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, 11 months, 12 months, 13 months, 14 months, 15 months, 16 months, 17 months, 18 months, 19 months, 20 months, 21 months, 22 months, 23 months, 24 months, or more months, and any number or range in between. In other aspects, timing between two or more administrations can be one year, two years, three years, four years, five years, six years, seven years, eight years, nine years, ten years, or more years, and any number or range in between, Timing between the first and any subsequent administration can be the same or different. In one aspect, nucleic acid molecules, compositions, or pharmaceutical compositions provided herein are administered once.

[0290] More than one nucleic acid molecule, composition, or pharmaceutical composition can be administered in the methods provided herein. In one aspect, two or more nucleic acid molecules, compositions, or pharmaceutical compositions provided herein are administered simultaneously. In another aspect, two or more nucleic acid molecules, compositions, orpharmaceutical compositions provided herein are administered sequentially. Simultaneous and sequential administrations can include any number and any combination of nucleic acid molecules, compositions, or pharmaceutical compositions provided herein. Multiple nucleic acid molecules, compositions, or pharmaceutical compositions that are administered together or sequentially can include transgenes encoding different antigenic proteins or fragments thereof. In this manner, immune responses against different antigenic targets can be induced. Two, three, four, five, six, seven, eight, nine, ten, or more nucleic acid molecules, compositions, or pharmaceutical compositions including transgenes encoding different antigenic proteins or fragments thereof can be administered simultaneously or sequentially. Any combination of nucleic acid molecules, compositions, and pharmaceutical compositions including any combination of transgenes can be administered simultaneously or sequentially. In some aspects, administration is simultaneous. In other aspects, administration is sequential. Timing between two or more administrations can be one week, two weeks, three weeks, four weeks, five weeks, six weeks, seven weeks, eight weeks, nine weeks, weeks, ten weeks, 11 weeks, 12 weeks, 13 weeks, 14 weeks, 15 weeks, 16 weeks, 17 weeks, 18 weeks, 19 weeks, 20 weeks, 21 weeks, 22 weeks, 23 weeks, 24 weeks, 25 weeks, 26 weeks, 27 weeks, 28 weeks, 29 weeks, 30 weeks, 31 weeks, 32 weeks, 33 weeks, 34 weeks, 35 weeks, 36 weeks, 37 weeks, 38 weeks, 39 weeks, 40 weeks, 41 weeks, 42 weeks, 43 weeks, 44 weeks, 45 weeks, 46 weeks, 47 weeks, 48 weeks, 49 weeks, 50 weeks, 51 weeks, 52 weeks, or more weeks, and any number or range in between. In some aspects, timing between two or more administrations is one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, ten months, 11 months, 12 months, 13 months, 14 months, 15 months, months, 16 months, 17 months, 18 months, 19 months, 20 months, 21 months, 22 months, 23 months, 24 months, or more months, and any number or range in between. In other aspects, timing between two or more administrations can be one year, two years, three years, four years, five years, six years, seven years, eight years, nine years, ten years, or more years, and any number or range in between, Timing between the first and any subsequent administration can be the same or different. Nucleic acid molecules, compositions, and pharmaceutical compositions provided herein can be administered with any other vaccine or treatment.

[0291] Following administration of the composition to the subject, the protein product encoded by the RNA of the disclosure (e.g., an antigen) is detectable in the target tissues for at least about one to seven days or longer. The amount of protein product necessary to achieve a therapeutic effect will vary depending on antibody titer necessary to generate an immunity to pathogen or disease such as influenza in the patient. For example, the protein product may be detectable in the target tissues at a concentration (e.g., a therapeutic concentration) of at least about0.025-1.5 μg / ml (e.g., at least about 0.050 μg / ml, at least about 0.075 μg / ml, at least about 0.1 μg / ml, at least about 0.2 μg / ml, at least about 0.3 μg / ml, at least about 0.4 μg / ml, at least about 0.5 μg / ml, at least about 0.6 μg / ml, at least about 0.7 μg / ml, at least about 0.8 μg / ml, at least about 0.9 μg / ml, at least about 1.0 μg / ml, at least about 1.1 μg / ml, at least about 1.2 μg / ml, at least about 1.3 μg / ml, at least about 1.4 μg / ml, or at least about 1.5 μg / ml), for at least about 1, 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, 35, 40, 45 days or longer following administration of the composition to the subject.

[0292] In some embodiments, the composition described herein may be administered one time. In some embodiments, the composition described herein may be administered two times.

[0293] In some embodiments, the composition may be administered in the form of a booster dose, to a subject who was previously vaccinated against influenza.

[0294] In some embodiments, a pharmaceutical composition of the present disclosure is administered to a subject once per month. In some embodiments, a pharmaceutical composition of the present disclosure is administered to a subject twice per month. In some embodiments, a pharmaceutical composition of the present disclosure is administered to a subject three times per month. In some embodiments, a pharmaceutical composition of the present disclosure is administered to a subject four times per month.

[0295] Alternatively, the compositions of the present disclosure may be administered in a local rather than systemic manner, for example, via injection of the pharmaceutical composition directly into a targeted tissue, preferably in a depot or sustained release formulation. Local delivery can be affected in various ways, depending on the tissue to be targeted. For example, aerosols containing compositions of the present disclosure can be inhaled (for nasal, tracheal, or bronchial delivery); compositions of the present disclosure can be injected into the site of injury, disease manifestation, or pain, for example; compositions can be provided in lozenges for oral, tracheal, or esophageal application; can be supplied in liquid, tablet or capsule form for administration to the stomach or intestines, can be supplied in suppository form for rectal or vaginal application; or can even be delivered to the eye by use of creams, drops, or even injection. Formulations containing compositions of the present disclosure complexed with therapeutic molecules or ligands can even be surgically administered, for example in association with a polymer or other structure or substance that can allow the compositions to diffuse from the site of implantation to surrounding cells. Alternatively, they can be applied surgically without the use of polymers or supports. Combinations

[0296] The RNA, such as a self-replicating RNA or mRNA provided herein, formulations thereof, or encoded proteins described herein may be used in combination with one or more othertherapeutic, prophylactic, diagnostic, or imaging agents. By “in combination with,” it is not intended to imply that the agents must be administered at the same time and / or formulated for delivery together, although these methods of delivery are within the scope of the present disclosure. Compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. In general, each agent will be administered at a dose and / or on a time schedule determined for that agent. Preferably, the methods of treatment of the present disclosure encompass the delivery of pharmaceutical, prophylactic, diagnostic, or imaging compositions in combination with agents that may improve their bioavailability, reduce and / or modify their metabolism, inhibit their excretion, and / or modify their distribution within the body. As a non-limiting example, an RNA molecule of the disclosure may be used in combination with a pharmaceutical agent for immunizing or vaccinating a subject. In general, it is expected that agents utilized in combination with the presently disclosed RNA molecules and formulations thereof be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually. In one embodiment, the combinations, each or together may be administered according to the split dosing regimens as are known in the art. Ranges

[0297] Throughout this disclosure, various aspects can be presented in range format. It should be understood that any description in range format is merely for convenience and brevity and not meant to be limiting. Accordingly, the description of a range should be considered to have specifically disclosed all possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6, etc., as well as individual numbers within that range, for example 1, 2, 2.1, 2.2, 2.5, 3, 4, 4.75, 4.8, 4.85, 4.95, 5, 5.5, 5.75, 5.9, 5.00, and 6. This applies to a range of any breadth. EXAMPLES EXAMPLE 1

[0298] Vaccine Design and Construction

[0299] RNAs were designed for use in a vaccine, each RNA encoding a neuraminidase (NA) and hemagglutinin (HA) antigen from the same strain of avian influenza on a single self- amplifying messenger ribonucleic acid (sa-mRNA; FIG. 1). Coding regions in the sa-mRNA constructs include sequences encoding nonstructural proteins (nsP) 1-4 from Venezuelan equine encephalitis virus (VEEV), and the NA and HA from a strain of H5N1 avian influenza (H5N1A / Indonesia / 5 / 2005). The nsP sequences encode replication proteins that replicate the entire sa- mRNA and drive transcription of NA and HA when delivered to the host cell. Non-coding regions of the sa-mRNA were based on sequences from VEEV (5’ UTR, 3’ UTR, and sgP), or other elements designed to enhance translation or stability of the sa-mRNA (Cap, Kozak, poly[A]). The sa-mRNA was composed of natural nucleotides adenine, thymine, guanine, and cytosine.

[0300] The sa-mRNA was then formulated with four lipid components to form a lipid nanoparticle (LNP) used to deliver the sa-mRNA to cells in the vaccine. Both lyophilized and frozen liquid formats were tested in vivo and resulted in similar immunogenicity. These formulations include different excipients. EXAMPLE 2

[0301] Immunogenicity

[0302] Immunogenicity of sa-mRNA constructs encoding H5N1 A / Indonesia / 5 / 2005 NA and / or HA antigens in different orders was evaluated in mice and ferrets.

[0303] Mice were vaccinated intramuscularly with 5 µg of the sa-mRNA constructs, and post vaccination HA-inhibition titers and NA-inhibition titers were measured at day 28 and 56 post- vaccination respectively. Microneutralization titers were also measured at day 70 post- vaccination. No significant differences were observed in HA-inhibition titers when the antigens were encoded in opposing positions (FIG. 2A). NA-inhibition titers were lower when the NA was encoded in the first position (FIG.2B); however, the differences between bicistronic vaccines did not reach significance at either time point. Lastly, microneutralization titers, which closely correlate with HA expression, were lower when HA was encoded in the first position compared to when HA was encoded in the second position (FIG.2C).

[0304] Immunogenicity was also evaluated in ferrets. Ferrets were vaccinated intramuscularly twice with 5 µg of an sa-mRNA construct as shown in FIG.1 (encoded by a nucleic acid having the sequence set forth in SEQ ID NO: 1, and designated “Construct 1” and having a poly-A tail of 90 nucleotides (SEQ ID NO: 8)) or with 15 µg a trimeric HA protein (rHA) from A / Indonesia / 5 / 2005 plus Addavax adjuvant. Doses were administered 28 days apart. The HA- inhibition, NA-inhibition, and microneutralization titers were then evaluated. Responses in all tests performed were higher in the sa-mRNA group compared to either unvaccinated (PBS) or ferrets vaccinated with the rHA (FIGS.3A-3C).EXAMPLE 3

[0305] Assessment of Vaccine Formulations with Different Lipids

[0306] Mice were vaccinated intramuscularly once with 5 µg of an sa-mRNA construct as shown in FIG.1 (encoded by a nucleic acid having the sequence set forth in SEQ ID NO: 1 and having a poly-A tail of 90 nucleotides (SEQ ID NO: 8)) formulated with either Compound-77 or Compound-90. The HA-inhibition, NA-inhibition, and microneutralization titers were then evaluated. Both formulations induced similar functional antibody responses against the HA and NA antigens encoded in the vaccine (FIG.4). EXAMPLE 4

[0307] Immunogenicity of HA and NA variants

[0308] Amino acid mutations in both HA and NA were evaluated to assess whether higher functional antibody responses could be achieved.

[0309] HA variants of H5N1 A / Indonesia / 5 / 2005 were evaluated for their immunogenicity. The HA variants evaluated included variants with replacement of the natural amino acids at positions 224 and 228 with cysteines, a replacement of a lysine with an isoleucine at position 404, a deletion of RRKK amino acids (SEQ ID NO: 155) at positions 342-345, and replacements of asparagines at positions 27, 39, 100, 170, 181, 209, 302, and / or 500 (in various combinations) with aspartic acids to eliminate potential glycosylation sites (positions numbered relative to SEQ ID NO: 11). Mice were vaccinated intramuscularly once with 5 ug of sa-mRNA encoding WT or mutant HA antigens from A / Indonesia / 5 / 2005 as described, formulated with Compound-77. Significant decreases in HA-inhibition titers were only observed in two groups where glycosylation residues were altered (FIG. 5). Mutant designations in FIG. 5 include “S-S” (R224C; K228C), K404I, “ΔRRKK” (342-345del), “GlyNeg” (N27D, N39D, N100D, N170D, N181D, N209D, N302D), “Head GlyNeg” (N170D, N181D), and “Cnsv GlyNeg” (N27D, N39D, N170D, N181D, N302D, N500D).

[0310] NA variants of H5N1 A / Indonesia / 5 / 2005 were also evaluated for their immunogenicity. The NA variants evaluated included variants with the following sets of amino acid substitutions: 1) V79P, H80L, C141V, E145S, S152A, V157I, S176T, V185I, Q388M, and R399V (designated “155”); 2) V79P, C141V, E145S, S152A, V157I, S176T, and V185I (designated “155 No B”); 3) V79P, H80L, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, Q388M, and R399V (designated “155 VN04”); 4) V79P, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, and V185I (designated “155 VN04 No B”); 5) an insertion of the following sequence between positions 47 and 48: PCNQSIITYENNTWVNQTYVN (SEQ ID NO: 12) (designated “Large Stalk”); and 6) mutationsof the following asparagines to serines: 68, 126 and 215 (designated “Glyco Neg”); positions numbered relative to SEQ ID NO: 10. Mice were vaccinated intramuscularly once with 5 ug of sa-mRNA encoding WT or mutant NA antigens from A / Indonesia / 5 / 2005 as described, formulated with Compound-77. Decreases in NA-inhibition titers were observed in glycosylation negative groups and groups harboring mutations as part of the VN04 groups. (FIG.6). EXAMPLE 5

[0311] Binding Antibodies to HA and NA

[0312] Binding antibodies against H5N1 A / Indonesia / 5 / 2005 HA and NA were assessed from naïve BALB / c mice immunized with 1 or 5 µg of the sa-mRNA encoding H5N1 A / Indonesia / 5 / 2005 HA and / or NA antigens in different orders.

[0313] No significant differences in HA binding antibodies were observed between the HA only group and the NA-HA group at any time point in the 1 µg dosing groups (FIG.7A; day 28: 103 vs 115, p=0.8750 [not significant; ns]; day 56: 117 vs 144, p=0.5256 [ns]; day 70: 241 vs 246, p=0.9983 [ns]; day 84: 237 vs 267, p=0.8128 [ns]). Neither were differences found in the 5µg dosing groups between HA only and NA-HA (FIG.7B; day 28: 240 vs 187, p=0.5675 [ns]; day 56: 223 vs 165, p=0.2696 [ns]; day 70: 535 vs 402, p=0.5097 [ns]; day 84: 428 vs 355, p=0.7869 [ns]). Differences between groups were considered significant if p values ≤0.05 using 2-way ANOVA and Dunnett’s multiple comparisons test. Significantly higher HA binding antibody titers were observed at days 28 and 70 between HA only group and HA-NA group in the 1 µg dosing groups (FIG.7A; day 28: 103 vs 56, p=0.0025; day 56: 117 vs 86, p=0.1831 [ns]; day 70: 241 vs 175, p=0.0335; day 84: 237 vs 176, p=0.1683 [ns]) but only at day 28 in the 5 µg dosing group groups (FIG.7B; day 28: 240 vs 111, p=0.0258; day 56: 223 vs 129, p=0.0705 [ns]; day 70: 535 vs 281, p=0.0846 [ns]; day 84: 428 vs 289, p=0.3171 [ns]). Taken together, when HA is encoded in the second position (NA-HA group), mice reached titers similar to an HA only vaccine. When HA was encoded in the first position (HA-NA group), mice had consistently lower titers than both the HA only group and the NA-HA group.

[0314] When binding antibody concentrations were assessed against NA, significantly higher antibody levels were observed at days 28 and 70 between mice vaccinated with 1µg of NA only compared to mice vaccinated with 1µg HA-NA vaccine (FIG.8A; day 28: 192 vs 86, p=0.0011; day 56: 270 vs 169, p=0.2554 [ns]; day 70: 610 vs 385, p=0.0372; day 84: 772 vs 451, p=0.1939 [ns]). Antibody concentrations from the NA only group at day 28 and 70 were approximately 2.2 and 1.6 times higher than the HA-NA group, respectively. At the 5µg dose, the NA only group elicited higher antibodies than the HA-NA group, but these differences did not reach significance (FIG.8B; day 28: 310 vs 200, p=0.2946 [ns]; day 56: 426 vs 224, p=0.2234 [ns]; day 70: 1218 vs564, p=0.1678 [ns]; day 84: 1417 vs 673, p=0.2115 [ns]). Responses were lower when the NA antigen was encoded in the first position compared to the response in the second position, similar to observations with HA. When comparing the NA only group to the NA-HA group at a 1µg dose, the NA only group was 4-6 times higher at each time point assessed (FIG.8A; day 28: 192 vs 40, p<0.0001; day 56: 270 vs 51, p=0.0068; day 70: 610 vs 100, p=0.0002; day 84: 772 vs 113, p=0.0062). At the 5µg dose, differences between the NA only and the NA-HA group were significant at all time points except day 56, with the NA only group approximately 3-5 times higher than the NA-HA group (FIG. 8A; day 28: 310 vs 113, p=0.0401; day 56: 426 vs 123, p=0.0515 [ns]; day 70: 1218 vs 311, p=0.0479; day 84: 1417 vs 300, p=0.0496). Altogether, higher binding antibody titers against NA were observed when the NA is encoded in the second position. The NA only vaccine, however, generated the highest NA-specific antibody responses compared to bicistronic constructs at the respective dose levels tested.

[0315] Taken together, when either HA or NA antigen is encoded in the second position of a bicistronic vaccine, the concentration of binding antibodies specific to that antigen is higher than when the same antigen is encoded in the first position. Moreover, bicistronic vaccines encoding either antigen in the second position is similar to when that antigen is encoded in a monocistronic vaccine. EXAMPLE 6

[0316] Ferret Homologous and Heterologous Viral Challenge models

[0317] Ferret homologous and heterologous viral challenge models were developed to assess the efficacy of an exemplary pandemic FLU vaccine (pandFlu). Vaccination with recombinant protein plus adjuvant was compared to vaccination with Construct 1 formulated with ionizable cationic lipid-based LNP. Methods:

[0318] Animals: Male ferrets approximately 3-5 months of age, pre-screened for seasonal influenza strains sourced from Triple F farms were used.

[0319] Vaccines: Construct 1 bi-cistronic HA and NA pandFlu vaccine was formulated with LNP. Recombinant Ind / 05 HA and recombinant Vietnam / 04 HA proteins (rHA) were each mixed with AddaVax™ (squalene-based adjuvant similar to MF59).

[0320] Vaccination: Ferrets were vaccinated intramuscularly with 0.5 mL of vaccine formulations in both of their hind leg muscles (quadriceps / rectus femoris). rHA proteins were mixed with AddaVax™ prior to administration to deliver a more robust immune response than protein alone.

[0321] Infection / Challenge: Viral inoculum with the homologous H5N1 A / Indonesia / 5 / 2005 strain (FIGS. 9A-9I) or the heterologous H5N1 A / Vietnam / 1203 / 2004 strain (FIGS. 10A-10I) was administered intranasally in a dropwise manner to anesthetized ferrets on either Day 49 (FIG. 9A) or 56 (FIG.10A). The homologous challenge included two groups of ferrets vaccinated with Construct 1, formulated with different ionizable cationic lipids.

[0322] Body Temperature: Post-viral challenge, body temperature was measured twice daily through a subcutaneously implanted transponder (TP-1000, BMDS, Seaford, DE.)

[0323] Nasal Wash Collection and Viral Titer (TCID50) Assay: 0.5 ml of sterile PBS containing antibiotics and 0.5% BSA was flushed into each nostril of anesthetized ferrets, and the expelled mixture of fluid was collected for viral titer assay. Nasal wash sample was used to calculate TCID50 to assess and quantify the infectivity of a virus in cells.

[0324] Hemagglutination Inhibition Assay (HAI): Hemagglutination is inhibited when antibodies present in serum prevent attachment of the virus to red blood cells. The HAI titer represents the highest dilution of antibody that prevented hemagglutination.

[0325] Microneutralization Assay (MNT): (MN) assay is a serological test that was used to measure the ability of antibodies to neutralize influenza viruses, hence quantitating the percentage inhibition of infection.

[0326] Enzyme-Linked Lectin Assay (ELLA): The ELLA assay was used to evaluate neuraminidase (NA) antibodies, produced after an influenza infection or vaccination. This assay quantified NA enzyme activity by measuring the amount of galactose that is exposed from glycoproteins when sialic acid is released by NA.. Results:

[0327] All vaccinated ferrets survived infection with H5N1 A / Indonesia / 5 / 2005 while all of the unvaccinated (PBS) ferrets had 100% lethality (FIG. 9B). All vaccinated ferrets survived H5N1 A / Vietnam / 1203 / 2004 challenge, while all unvaccinated ferrets died by 8 days post infection (FIG.10B).

[0328] Pre-challenge baseline weight and post infection weights were recorded, and group average was recorded. For the homologous challenge study with H5N1 A / Indonesia / 5 / 2005, only unvaccinated ferrets lost substantial weight starting at 2 days post viral challenge and presented diarrhea and loss of appetite (FIG. 9C). For the heterologous challenge with H5N1 A / Vietnam / 1203 / 2004, none of the vaccinated groups lost substantial weight during the course ofthe infection, while unvaccinated ferrets lost nearly 10% of their starting weight by Day 3 post infection (FIG.10C).

[0329] Body temperature was measured twice a day and group average of change in temperature was recorded. For the homologous challenge, vaccinated ferrets did not have any disruption in diurnal temperature readings, whereas unvaccinated ferrets were febrile post- challenge (FIG.9D). For the heterologous challenge, unvaccinated ferrets became febrile with a peak in temperature at 3 days post infection, while vaccinated ferrets maintained normal diurnal temperature variation (FIG.10D).

[0330] For the homologous challenge, ferrets vaccinated with Construct 1 showed lower nasal wash viral titers compared to ferrets vaccinated with rHA (FIG. 9E). For the heterologous challenge, ferrets vaccinated with Construct 1 showed the lowest nasal wash viral titers of all groups (FIG. 10E). Viral titers were similar between rHA-vaccinated ferrets and unvaccinated ferrets at 3 days post infection.

[0331] To quantify tissue viral titers, multiple biopsy samples were taken from different lobes of the lungs and other tissues on predetermined termination days as well as from moribund and found dead animals. For the homologous challenge with H5N1 A / Indonesia / 5 / 2005, vaccinated ferrets were nearly devoid of titers in their tissues as opposed to unvaccinated ferrets (FIG.9F). For the heterologous challenge, two of the 3 ferrets in the unvaccinated (PBS) group had viral titers in the lung sample tested, while no virus was found in the lungs of vaccinated animals (FIG. 10F). Exemplary micrograph images of stained lung tissue sections (5 days post-infection) from ferrets vaccinated with Construct 1 compared to lung tissue sections of either unvaccinated ferrets or ferrets vaccinated with recombinant HA, demonstrate that construct 1 vaccination resulted in decreased lung pathology (FIGS.11A-11C).

[0332] The results of hemagglutinin (HA) inhibition assays for the homologous challenge indicated seroconversion in the Construct 1 vaccinated ferrets prior to challenge (FIG. 9G), whereas little seroconversion for HAI for recombinant HA vaccinated ferrets was observed after two doses (prior to viral challenge). For the heterologous challenge, HA inhibition titers against the heterologous challenge strain (A / Vietnam), and the Construct 1 vaccine strain (Indonesia / 05) were measured (FIG.10G). Only Construct 1-vaccinated ferrets showed functional HA inhibition against the heterologous A / Vietnam / 1203 / 2004 prior to challenge, except for a single ferret in the recombinant HA A / Vietnam group on pre-challenge. By the end of the challenge phase, all ferrets showed similar HAI responses.

[0333] In the homologous challenge experiments, results of the ELLA assay for neuraminidase (NA) demonstrated full seroconversion for NA after one dose for Construct 1(FIG.9H), whereas no seroconversion for NA was observed in recombinant HA vaccines. In the heterologous challenge experiments, results of NA inhibition assays showed that vaccination with Construct 1 produced NA inhibition titers that were approximately 3 times higher against the homologous A / Indonesia strain than against the heterologous A / Vietnam strain (FIG.10H).

[0334] For the homologous challenge, results for microneutralization assays demonstrated that sa-mRNA vaccination with Construct 1 generated significantly higher microneutralization (MNT) titers as compared to the Recombinant Ind / 05 HA (with AddaVax™) against homologous Ind / 05 strain (FIG.9I). For the heterologous challenge, higher MNT titers were observed against the homologous Ind / 05 strain in both Construct 1 vaccine groups and rHA Ind / 05-vaccinated groups (FIG. 10I). Construct 1 vaccines showed significantly higher microneutralization than rHA-Ind / 05 against the homologous strain (FIG.10I).

[0335] Taken together, these results demonstrate that illustrative Construct 1 is highly effective as a vaccine against homologous and heterologous H5N1 viral infection, improving immune response, increasing survival, and reducing viral titer, relative to adjuvanted plus recombinant HA comparator vaccines. SEQUENCES SEQ ID NO: 1 (encoding: nsP1-nsP4 (lowercase); NA polypeptide; HA polypeptide)SEQ ID NO: 2 (encoding NA of an H5N1 influenza strain)SEQ ID NO: 3 (encoding HA of an H5N1 influenza strain)SEQ ID NO: 4 (encoding nsP1-nsP4)gg SEQ ID NO: 5 (5’ UTR)SEQ ID NO: 6 (sgP)SEQ ID NO: 7 (3’ UTR)SEQ ID NO: 8 (poly(A) tail)SEQ ID NO: 9 (poly(A) tail)SEQ ID NO: 10 (NA polypeptide)SEQ ID NO: 11 (HA polypeptide)SEQ ID NO: 12 (insert between positions 47 and 48 of SEQ ID NO: 9; designated “48Ins”)SEQ ID NO: 13 (encoding variant HA of an H5N1 influenza strain)SEQ ID NO: 14 (encoding variant HA of an H5N1 influenza strain)SEQ ID NO: 15 (encoding variant HA of an H5N1 influenza strain)SEQ ID NO: 16 (encoding variant HA of an H5N1 influenza strain)SEQ ID NO: 17 (encoding variant HA of an H5N1 influenza strain)SEQ ID NO: 18 (encoding variant HA of an H5N1 influenza strain)SEQ ID NO: 19 (encoding variant HA of an H5N1 influenza strain)SEQ ID NO: 20 (encoding variant NA of an H5N1 influenza strain)SEQ ID NO: 21 (encoding variant NA of an H5N1 influenza strain)SEQ ID NO: 22 (encoding variant NA of an H5N1 influenza strain)SEQ ID NO: 23 (encoding variant NA of an H5N1 influenza strain)SEQ ID NO: 24 (encoding variant NA of an H5N1 influenza strain)SEQ ID NO: 25 (encoding variant NA of an H5N1 influenza strain)SEQ ID NO: 153 (encoding an intergenic sequence)SEQ ID NO: 154 (encoding: nsP1-nsP4 (lowercase); NA polypeptide; HA polypeptide)

[0336] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs.

[0337] Any and all references and citations to other documents, such as patents, patent applications, patent publications, journals, books, papers, web contents, that have been made throughout this disclosure are hereby incorporated herein in their entirety for all purposes.

[0338] Although the invention has been described with reference to the above examples, it will be understood that modifications and variations are encompassed within the spirit and scope of the invention. Accordingly, the invention is limited only by the following claims.

Claims

1. CLAIMS What is claimed is:

1. A composition comprising a self-replicating RNA molecule comprising the following in a 5’ to 3’ direction: (a) a 5’ untranslated region (UTR); (b) a sequence encoding one or more viral replication proteins; (c) a first subgenomic promoter (sgP); (d) a first Kozak sequence; (e) a sequence encoding a first avian influenza virus protein; (f) a second sgP; (g) a second Kozak sequence; (h) a sequence encoding a second avian influenza virus protein; (i) a 3’ UTR; and (j) a poly(A) tail; wherein the first and second avian influenza virus proteins together comprise a hemagglutinin (HA) polypeptide and a neuraminidase (NA) polypeptide of the same strain of avian influenza virus.

2. The composition of claim 1, wherein the avian influenza virus is an H5N1 influenza virus.

3. The composition of claim 2, wherein the H5N1 influenza virus is a strain of A / Indonesia / 5 / 2005.

4. The composition of any one of claims 1-3, wherein the one or more viral replication proteins are alphavirus proteins.

5. The composition of claim 4, wherein the alphavirus proteins are Venezuelan Equine Encephalitis Virus (VEEV) proteins.

6. The composition of claim 4 or 5, wherein the one or more viral replication proteins comprise an alphavirus nonstructural protein 1 (nsP1), an alphavirus nonstructural protein 2 (nsP2), an alphavirus nonstructural protein 3 (nsP3), and an alphavirus nonstructural protein 4 (nsP4).

7. The composition of claim 6, wherein the sequence encoding one or more viral replication proteins comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO:

4.

8. The composition of any one of claims 1-7, wherein the HA polypeptide comprises an antigenic polypeptide of HA.

9. The composition of claim 8, wherein the HA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO:

11.

10. The composition of claim 8, wherein the HA polypeptide is encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by SEQ ID NO:

3.

11. The composition of claim 8, wherein the HA polypeptide is encoded by the RNA sequence encoded by any one of SEQ ID NOs: 3, or 13-19.

12. The composition of any one of claims 1-7, wherein the HA polypeptide comprises one or more of R224C, K228C, K404I, 342-345del, N27D, N39D, N100D, N170D, N181D, N209D, N302D, or N500D, relative to SEQ ID NO:

11.

13. The composition of claim 12, wherein the HA polypeptide comprises: (i) R224C and K228C, relative to SEQ ID NO: 11; (ii) R224C, K228C, and K404I, relative to SEQ ID NO: 11; (iii) N27D, N39D, N100D, N170D, N181D, N209D, and N302D, relative to SEQ ID NO: 11; (iv) N170D and N181D, relative to SEQ ID NO: 11; or (v) N27D, N39D, N170D, N181D, N302D, and N500D, relative to SEQ ID NO:

11.

14. The composition of any one of claims 1-13, wherein the NA polypeptide comprises an antigenic polypeptide of NA.

15. The composition of claim 14, wherein the NA polypeptide comprises a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to SEQ ID NO:

10.

16. The composition of claim 14, wherein the NA polypeptide is encoded by a sequence having at least 80%, at least 90%, at least 95%, or 100% identity to the RNA encoded by SEQ ID NO:

2.

17. The composition of claim 14, wherein the NA polypeptide is encoded by the RNA sequence encoded by any one of SEQ ID NO: 2, or 20-25.

18. The composition of any one of claims 1-13, wherein the NA polypeptide comprises one or more of 48InsPCNQSIITYENNTWVNQTYVN (SEQ ID NO: 12), N68S, V79P, H80L, I86V, T111Q, N126S, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, N215S, Q388M, R399V, relative to SEQ ID NO: 10.

19. The composition of claim 18, wherein the NA polypeptide comprises: (i) V79P, H80L, C141V, E145S, S152A, V157I, S176T, V185I, Q388M, and R399V, relative to SEQ ID NO: 10; (ii) V79P, C141V, E145S, S152A, V157I, S176T, V185I, relative to SEQ ID NO: 10; (iii) V79P, H80L, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, V185I, Q388M, and R399V, relative to SEQ ID NO: 10; (iv) V79P, I86V, T111Q, C141V, V143I, E145S, A146V, S152A, V157I, S176T, and V185I, relative to SEQ ID NO.10; or (v) N68S, N126S, N215S, relative to SEQ ID NO:

10.

20. The composition of any one of claims 1-19, wherein the 5’ UTR comprises a viral 5’ UTR, a non-viral 5’ UTR, or a combination of viral and non-viral 5’ UTR sequences.

21. The composition of claim 20, wherein the 5’ UTR comprises an alphavirus 5’ UTR.

22. The composition of claim 21, wherein the alphavirus 5’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 5’ UTR sequence.

23. The composition of any one of claims 1-19, wherein the 5’ UTR comprises the RNA sequence encoded by SEQ ID NO:

5.

24. The composition of any one of claims 1-23, wherein the 3’ UTR comprises a viral 3’ UTR, a non-viral 3’ UTR, or a combination of viral and non-viral 3’ UTR sequences.

25. The composition of claim 24, wherein the 3’ UTR comprises an alphavirus 3’ UTR sequence.

26. The composition of claim 25, wherein the alphavirus 3’ UTR comprises a Venezuelan Equine Encephalitis Virus (VEEV) 3’ UTR sequence.

27. The composition of any one of claims 1-23, wherein the 3’ UTR comprises the RNA sequence encoded by SEQ ID NO:

7.

28. The composition of any one of claims 1-27, wherein the sgP comprises a sequence having at least 90%, at least 95%, or 100% identity to the RNA sequence encoded by SEQ ID NO:

6.

29. The composition of any one of claims 1-28, wherein the first and second Kozak sequences comprise GCCACC.

30. The composition of claim 1, wherein the RNA molecule comprises a sequence having at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 97.5%, at least 98%, at least 98.5%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or 100% identity to the RNA sequence encoded by SEQ ID NO:

1.

31. The composition of claim 1, wherein the RNA molecule comprises a sequence encoded by any one of SEQ ID NO: 1-9 or 13-25.

32. The composition of claim 1, wherein the RNA molecule comprises a sequence encoded by SEQ ID NO:

1.

33. A composition comprising a DNA molecule encoding the RNA molecule of the composition of any one of claims 1-32.

34. The composition of claim 33, wherein the DNA molecule comprises a promoter.

35. The composition of claim 34, wherein the promoter is a T7 promoter.

36. The composition of any one of claims 1-35, further comprising an ionizable cationic lipid.

37. The composition of claim 36, wherein the ionizable cationic lipid has a structure of Formula I: (I) or a pharmaceutically acceptable salt or solvate thereof, wherein R5and R6are each independently selected from the group consisting of a linear or branched C1-C31alkyl, C2-C31alkenyl or C2-C31 alkynyl and cholesteryl; L5and L6are each independently selected from the group consisting of a linear C1-C20 alkyl and C2-C20 alkenyl; X5is -C(O)O-, whereby -C(O)O-R6is formed or -OC(O)- whereby -OC(O)-R6is formed; X6is -C(O)O- whereby -C(O)O-R5is formed or -OC(O)- whereby -OC(O)-R5is formed; X7is S or O; L7is absent or lower alkyl; R4is a linear or branched C1-C6 alkyl; and R7and R8are each independently selected from the group consisting of a hydrogen and a linear or branched C1-C6alkyl.

38. The composition of claim 37, wherein the ionizable cationic lipid is selected from Table 6.

39. The composition of claim 37, wherein the ionizable cationic lipid is Compound-77: Compound-77.

40. The composition of claim 37, wherein the ionizable cationic lipid is Compound-90: Compound-90.

41. A method of vaccinating a subject against an avian influenza, the method comprising administering to the subject a composition of any one of claims 1-40.

42. The composition of any one of claims 1-40 for use in the preparation of a medicament for vaccinating a subject against an avian influenza.

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