Multivalent covid-19 vaccines based on adenoviral vectors

Abstract

The present invention relates to the construction of Adenovirus-based vectors und to their use for inducing a broad, robust and durable cellular and humoral immune response in a subject.

Description

[0001] Multivalent COVID-19 vaccines based on Adenoviral vectors

[0002] The present invention relates to the construction of Adenovirus-based vectors und to their use for inducing a broad, robust and durable cellular and humoral immune response in a subject.

[0003] Corona Virus Disease 2019 (COVID-19) is a serious infectious disease caused by a member of the corona virus family, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Since its outbreak in Wuhan China in 2019, the disease has spread worldwide, leading to an ongoing pandemic. Numerous attempts to treat the disease have so far not had sufficient success. Despite medical interventions, the mortality rate is significant, particularly in elderly, immune compromised individuals. While work is underway to develop drugs that inhibit the virus, the primary treatment is symptomatic. Management involves the treatment of symptoms, supportive care, isolation, and experimental measures. Several COVID-19 vaccines have been approved and distributed in various countries. Among them, there are vaccines are based on mRNA and adenoviral platforms to express the spike protein of the ancestral SARS-CoV-2 and elicit neutralizing antibody responses against the Wuhan strain.

[0004] However, since the original appearance in Wuhan, several virus variants of concern have emerged that have multiple mutations, especially in the spike protein. Of particular importance are mutations within the receptor-binding domain (RBD) that reduce their neutralization by antibodies present in convalescent or vaccine-induced sera. Several first-generation vaccines have demonstrated reduced effectiveness in protecting from COVID-19 caused by these emerging variants of concern. So far, no vaccines adapted to SARS-CoV-2 variants have been authorized. An alternative strategy is to develop recombinant viral vectored multivalent vaccines. Besides the spike protein, such vaccines may express additional conserved SARS-CoV-2 antigens to broaden T cell immunity. Since antigenic changes in conserved, internal viral proteins that are the primary focus of T cell responses are improbable in SARS-CoV-2 viruses including variants of concern, such multivalent vaccines do not require frequent updating while they can boost the spike-specific immunity induced by first-generation vaccines. Thus, these vaccines are expected to be effective against both ancestral and variants of SARS-CoV-2. However, there is still a need to provide improved vaccine compositions and methods that render a therapeutic effect, reduce or prevent viral entry into a cell, reduce direct and indirect toxicity of the virus to the patient, and produce an immune response that is effective to clear the virus from the patient. Advantageously, the vaccines should be able to provide protection against emerging new virus variants.

[0005] The present invention provides a solution to this problem by disclosing a replication defective adenoviral vector comprising

[0006] (i) a nucleic acid encoding at least one SARS-CoV-2 spike protein or a derivative thereof and

[0007] (ii) a nucleic acid encoding at least one SARS-CoV-2 nucleocapsid protein or a derivative thereof, wherein the adenoviral vector displays a polypeptide comprising a receptor-binding domain (RBD) of a SARS-CoV-2 spike protein or a derivative thereof via protein IX (pIX) on its capsid.

[0008] SARS-CoV-2 is a virus of the species severe acute respiratory syndrome-related coronavirus (SARS-CoV). It is a positive-sense single-stranded RNA (+ssRNA) virus, with a single linear RNA segment. Like other coronaviruses, SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins; the N protein holds the RNA genome, and the S, E, and M proteins together create the viral envelope. Coronavirus S proteins are glycoproteins, and type I membrane proteins (membranes containing a single transmembrane domain oriented on the extracellular side). They are divided into two functional parts (S1 and S2). The spike protein is the protein responsible for allowing the virus to attach to and fuse with the membrane of a host cell. The N protein forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.

[0009] Adenoviruses are among the most commonly used vectors for the delivery of genetic material into human cells. They have been used as vaccine delivery vehicles and to express recombinant proteins in cell lines and tissues. Adenoviral vectors characteristically induce strong cellular responses against their encoded transgenes, compared to recombinant, adjuvanted proteins that induce strong antibody responses. Those antibody responses alone may, however not suffice to provide protection against complex pathogens where a synergistic T cell response has proven to be beneficial.

[0010] The adenoviral vector of the present invention encodes spike proteins because of the potential to induce antibodies to against the RBD to neutralize the ability of the virus to bind host cells. More specifically, the SARS-CoV-2 spike protein is presented in two ways, firstly in the form of a nucleic acid encoding at least one SARS-CoV-2 spike protein or a derivative thereof, and secondly in the form of a polypeptide comprising a receptor-binding domain (RBD) of a SARS-CoV-2 spike protein or a derivative thereof displayed on the adenovirus capsid via protein IX (pIX). Due to this special characteristic, the adenoviral vector of the present invention combines the benefits of genetic and protein-based vaccination within one vaccine construct. Transgeneexpression and produci bi lity of the vector are not impeded by the pIX-display. The minor capsid protein IX (pIX) tolerates fusion of relatively large, functional proteins to its surface-exposed C-terminus without drastically decreasing its function. Compared to immunization with soluble protein, fusion of the RBD of the SARS-CoV-2 spike protein or a derivative thereof to pIX may ensure presentation of the antigen in its native conformation and in a highly repetitive nature inherent to viral capsids, both of which were shown to deliver strong activation signals to the recognizing B-cells.

[0011] The RBD of the SARS-CoV-2 spike protein or a derivative thereof can be attached with or without a linker. For example, a flexible glycine linker or a spacer can be used. Accessibility of the RBD of the SARS-Cov-2 spike protein or a derivative thereof on the surface of the adenoviral vector particle may be improved by the pIX- fusion via a linker and / or a spacer in comparison to direct fusion. The linker may be acting as a molecular hinge, making the antigen more flexible in its interaction with the antigen-binding domains of the B-cell receptor. A spacer molecule may ensure display of the antigen over its full length at an optimal distance from the surface of the adenovirus capsid by lifting the antigen up towards the surface.

[0012] Another characteristic feature of the adenoviral vector of the present invention is that in addition to the spike protein, an additional antigen is provided against which responses can be elicited. The adenoviral vector comprises a nucleic acid encoding at least one SARS-CoV-2 nucleocapsid protein or a derivative thereof. Thereby, the risk of the emergence of new strains of the virus with mutations in spike is addressed. The nucleocapsid protein is a highly conserved but is known to have variant regions in the emerging virus variants of concern. The terms “nucleocapsid protein,” “nucleoprotein,” and “nucleocapsid” are used interchangeably throughout this disclosure. Nucleocapsid associates with viral RNA within the virus and has a role in viral RNA replication, virus particle assembly, and release. The SARS-CoV-2 nucleocapsid was found to be a highly antigenic protein and patients infected with SARS-CoV-2 show antibody responses to the nucleocapsid. In addition, the nucleocapsid was found to particularly induce T-cell immunity. The T-cell based responses are critical given the finding that neutralizing antibody titers decline in COVID-19 patients after about 3 months. T cells are an important part of long-term immunity.

[0013] The at least one SARS-CoV-2 spike protein of (i) can be selected from spike proteins of any known SARS-CoV-2 viruses derived from the Wuhan variant and derivatives thereof. The spike protein of the original Wuhan coronavirus is preferably not included. In other words, the at least one spike protein of (i) relates preferably to any SARS-CoV- 2 spike protein excluding the Wuhan coronavirus spike protein.

[0014] As used herein and in accordance with NCBI taxonomy database, the terms “original Wuhan coronavirus”, “Wuhan variant”, “2019-nCoV”, “COVID-19”, “COVID-19 virus”, “Wuhan seafood market pneumonia virus” can be used interchangeably herein.

[0015] Five SARS-CoV-2 variants have been designated as variants of concern by the World Health Organization: the Alpha, Beta, Gamma, Delta, and Omicron variants. Thus, according to a preferred embodiment, the at least one SARS-CoV-2 spike protein of (i) comprises the spike protein of at least one of these variants of concern or derivatives thereof. Also included are the spike proteins of any subtypes of the above variants of concern, such as the Delta Plus variant and Omicron subvariants B.1.1.529 and BA.2.

[0016] According to a particularly preferred embodiment, the at least one SARS-CoV-2 spike protein of (i) comprises the spike protein of SARS-CoV-2 Omicron variant or a derivative thereof, SARS-CoV-2 Delta Plus variant or a derivative thereof, or any combinations thereof.

[0017] However, it is understood that the at least one SARS-CoV-2 spike protein of (i) can also be selected from spike proteins of other emerging SARS-CoV-2 variants, such as lineages B.1.1.207, B.1.1.317, B.1.616, B.1.618, B.1.640.2, AZ.5, C.1.2, B.1.429, B.1.427, C.37 (Lambda variant), B.1.621 (Mu variant), CAL.20C (Epsilon variant), B.1.617.1 (Kappa variant), B.1.526 (lota variant), P.2 (Zeta variant), P.3 (Theta variant), B.1.525 (Eta variant), B.1.630, and B.1.640, as well as derivatives thereof and combinations of spike proteins from two or more different variants.

[0018] The respective sequences of the spike proteins can be taken from common data bases.

[0019] The term "derivatives" of the respective SARS-CoV-2 spike proteins is understood herein to mean proteins that deviate from the respective spike proteins in their sequence without losing the desired functionality. In addition, deviations in the sequence, for example in the form of substitutions, deletions or additions, are possible. For example, a derivative may have a shortened sequence compared to the complete spike protein, while preferably retaining the RBD. For example, the identity of the sequence of a derivative to the sequence of the complete spike protein may be at least 50%, at least 75%, at least 85%, at least 90%, at least 95% or at least 99%, over the entire length of the sequence.

[0020] The at least one nucleocapsid protein of (ii) can be selected from nucleocapsid proteins of any known SARS-CoV-2 viruses derived from the Wuhan variant and derivatives thereof, in particular those described above for the spike protein of (i). For example, it can be a nucleocapsid protein from a SARS-CoV-2 virus variant of concern such as the Alpha, Beta, Gamma, Delta, and Omicron variants or any subtypes thereof, e.g. the Delta Plus variant and Omicron subvariants B.1.1.529 and BA.2. The nucleocapsid protein of the original Wuhan virus is preferably not included. In other words, the at least one nucleocapsid protein of (ii) relates preferably to any SARS-CoV-2 nucleocapsid protein excluding the Wuhan coronavirus nucleocapsid protein.

[0021] According to a particularly preferred embodiment, the at least one SARS-CoV-2 nucleocapsid protein of (ii) comprises the nucleocapsid protein of SARS-CoV-2 Omicron variant or a derivative thereof, SARS-CoV-2 Delta Plus variant or a derivative thereof, or combinations thereof.

[0022] The respective sequences of the nucleocapsid proteins can be taken from common data bases.

[0023] The term "derivatives" of the respective SARS-CoV-2 nucleocapsid proteins is understood herein to mean proteins that deviate from the respective nucleocapsid proteins in their sequence without losing the desired functionality. In addition, deviations in the sequence, for example in the form of substitutions, deletions or additions, are possible. For example, a derivative may have a shortened sequence compared to the complete nucleocapsid protein. For example, the identity of the sequence of a derivative to the sequence of the complete nucleocapsid protein may be at least 50%, at least 75%, at least 85%, at least 90%, at least 95% or at least 99%, over the entire length of the sequence.

[0024] The RBD displayed on the capsid can be selected from RBDs of any known spike proteins of SARS-CoV-2 viruses derived from the Wuhan variant and derivatives thereof, in particular those described above for the spike protein of (i). For example, it can be a RBD of the spike protein from a SARS-CoV-2 virus variant of concern such as the Alpha, Beta, Gamma, Delta, and Omicron variants or any subtypes thereof, e.g. the Delta Plus variant and Omicron subvariants B.1.1.529 and BA.2. The respective sequences of the RBD can be taken from common data bases. The RBD of the spike protein of the original Wuhan virus is preferably not included. In other words, the RBD displayed on the capsid can be selected from RBDs of any known spike proteins of SARS-CoV-2 viruses excluding the Wuhan coronavirus spike protein.

[0025] According to a particularly preferred embodiment, the RBD displayed on the capsid is the RBD of SARS-CoV-2 Delta Plus variant or a derivative thereof.

[0026] Adenoviruses have been isolated from a large number of different species, and more than 100 different human serotypes have been reported. The overall organization of the Adenoviral genome is conserved among serotypes, such that specific functions are similarly positioned. Most adults have been exposed to the Adenovirus serotypes most commonly used in therapy. While vectors based on human Adenovirus 5 (HAdV5) are most frequently used, their immunogenicity is impaired by high levels of pre-existing immunity. Alternative Adenovirus serotypes such as HAdV35, HAdV26 and ChAdV3 are highly immunogenic while less sero-prevalent and unaffected by pre-existing immunity to HAdV5, making them suitable as vaccine vectors. The adenoviral vector of the present invention can be derived from adenoviruses of different species, preferably human or chimpanzee. The serotype of the adenovirus can for example be 5, 26, 35 or 3, in particular human Adenovirus serotype 5, 26 or 35 and chimpanzee Adenovirus serotype 3. The adenoviral vector of the present invention is replication deficient. According to a preferred embodiment, it has deletions at least in the E1 , and / or E3 gene regions and optionally one or more additional regions such as the E2b region. The sequences of wild type Adenovirus genome and the respective E1 and E3 regions are described in common databases. For example, the wild type Adenovirus 5 genome is described in Gen Bank Accession No. AY339865.1.

[0027] The term “deleted”, or “deletion”, as used herein in context with deletions in the E1 , or E3 gene regions, refers to a specific DNA sequence that is mutated in such a way so as to prevent expression and / or function of at least one E1 , or E3 gene product. Thus, in certain embodiments, “deleted” is used in relation to a specific DNA sequence that is deleted (removed) from the Ad genome. E1 / E3 deleted or “containing a deletion within the E1 / E3 region” refers to a deletion of at least one base pair within the respective region of the Ad genome. Thus, in certain embodiments, more than one base pair is deleted and in further embodiments, at least 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, or 150 base pairs are deleted. In another embodiment, the deletion is of more than 150, 160, 170, 180, 190, 200, 250, or 300 base pairs within the E1 , and / or E3 region of the Ad genome, respectively. A deletion may be a deletion that prevents expression and / or function of at least one gene product and therefore, encompasses deletions within exons of encoding portions of E1 E3-specific proteins as well as deletions within promoter and leader sequences. In a further embodiment, “deleted” refers to one or more point mutations in the DNA sequence of this region of an Ad genome such that one or more encoded proteins is non-functional. Such mutations include residues that are replaced with a different residue leading to a change in the amino acid sequence that result in a nonfunctional protein.

[0028] Referring to human Adenovirus 5 serotype, a deletion in the E1 gene region may be a deletion of positions 454-3513 compared to the wild type Adenovirus 5 genome (GenBank: AY339865.1). A deletion in the E3 gene region may be a deletion of positions 28592- 30465 compared to the wild type Adenovirus 5 genome (GenBank: AY339865.1).

[0029] The nucleic acid sequence of a particularly preferred adenoviral vector of the present invention is shown in SEQ ID NO:1 .

[0030] The adenoviral vector of the present invention is optimized for immunogenicity. It is capable to provide robust, durable cell-mediated and humoral immunity against SARS- CoV-2 infection. Thus, in one embodiment, the present disclosure provides an adenoviral vector for use in the prevention or treatment of a COVID-19 disease.

[0031] According to a preferred embodiment, the inventive adenoviral vector comprises a further a nucleic acid encoding at least one protein or derivative thereof of a microorganism, which is different from SARS-CoV-2. Preferably, such microorgansim is responsible for an infectious disease. “Derivative” in the sense of the invention means any portion of a wild-type, mutated or engineered protein which can elicit an immune response resulting in immunogenicity. Microorganisms can be any bacteria, protozoa or viruses.

[0032] When provided prophylactically, the compositions of the present disclosure are administered in advance of the development of, or the detection of the development of, a coronavirus disease, with the goal of preventing, inhibiting or delaying the development of the coronavirus disease; and / or generally preventing or inhibiting progression of the coronavirus disease in an individual. Therefore, prophylactic compositions can be administered to individuals that appear to be coronavirus disease free (healthy, or normal, individuals), or to individuals who have not yet been detected of coronavirus. Individuals who are at high risk for developing a coronavirus disease, may be treated prophylactically with a composition of the present disclosure.

[0033] When provided therapeutically, the compositions of the present invention are administered to an individual who is diagnosed with a coronavirus disease, with the goal of ameliorating or curing the coronavirus disease; increasing survival of the individual; preventing, inhibiting, reversing or delaying development of coronavirus disease in the individual.

[0034] Routes and frequency of administration of the therapeutic compositions described herein, as well as dosage, may vary from individual to individual, and may be readily established using standard techniques.

[0035] The administration of the adenoviral vector can be through a variety of suitable paths for delivery. One preferred route contemplated herein is by injection, such as intramuscular injection, intravenous injection or subcutaneous injection. In some embodiments, intramuscular or subcutaneous injection is preferred. Intramuscular administration is particularly favorable to optimize immunogenicity with the direct delivery of the adenoviral vector to the blood supply in the muscle to induce systemic immunity.

[0036] Another possible route is by administration to the respiratory tract. For protective immunity against mucosal pathogens, (i.e. , SARS coronaviruses) immune activation in mucosal tissues instead of the more common approach of tolerance to maintain mucosal homeostasis allows for enhanced mucosal immune responses and better local protection. Thus, in one aspect of the invention, the adenoviral vector may be administered to the respiratory tract of a subject, in particular to the mucosa of the respiratory tract to induce mucosal immunity in addition to cell-mediated and humoral immunity. This type of vaccination induces both mucosal immunity as well as systemic immunity.

[0037] Further, the adenoviral vector can be administered to a patient by more than one route of administration, e.g. to induce both local and systemic immune responses.

[0038] In a preferred aspect, administration of the adenoviral vector of the invention is capable to generate long-term T and B cell memory.

[0039] The invention further provides a vaccine composition comprising the adenoviral vector disclosed herein. The vaccine composition can be formulated in a pharmaceutically acceptable excipient suitable for administration to a subject. According to a preferred embodiment the vaccine may comprise further active agents, i.e. in particular further immunogenicity conferring agents. Such further immunogenicity conferring agents may be directed against the same target, the same virus, the same subtype or any other subtype or even any other virus.

[0040] The vaccine composition may be adapted for the preferred way of administration described above. Thus, in one embodiment, the present disclosure provides a vaccine composition adapted for injection, in particular for intramuscular or subcutaneous injection.

[0041] In another embodiment, the present disclosure provides a vaccine composition adapted for administration to the respiratory tract of a subject, in particular to the mucosa of the respiratory tract to induce mucosal immunity in addition to cell-mediated and humoral immunity. Accordingly, the vaccine composition can be adapted for oral, intranasal, or sublingual administration.

[0042] In a preferred aspect, the vaccine disclosed herein generates long-term T and B cell memory.

[0043] Also disclosed herein are methods for preventing and / or treating coronavirus diseases, and especially COVID-19. Preferably, the method includes using an adenoviral vector as defined above that encodes the nucleocapsid protein and the spike protein of the coronavirus and displays a polypeptide comprising a receptor-binding domain (RBD) of a SARS-CoV-2 spike protein or a derivative thereof via protein IX (pIX) on its capsid. The described method is able to induce a broader cellular immunity against SARS-CoV- 2. The adenoviral vector can be administered to a subject individual in an immunogenic composition. The virus vaccine, thus administered, would induce the cellular expression of SARS-CoV-2 nucleocapsid and spike protein and a direct immune response against SARS-CoV-2 spike protein RBD on the virus surface. With that in place, the individual would have an immune response against it, and be vaccinated. Notably, as the spike protein and in particular the nucleocapsid protein are relatively conserved polypeptides, immune responses can be elicited for a variety of members of the coronavirus family.

[0044] The vaccine compositions described herein can be used as a universal booster vaccine to any anti-SARS-CoV-2 vaccine directed against the SARS-CoV-2 spike (S) and / or nucleocapsid (N) proteins. According to this aspect, the present invention provides a method of boosting an antigen-specific immune response in a mammal comprising administering to said mammal a sufficient amount of the adenoviral vector or the vaccine composition disclosed herein. This booster can work even in patients who were immunized with any SARS-CoV-2 spike or nucleoprotein encoding vaccine other than those described herein and broaden the immunogenicity of these patients.

[0045] In certain embodiments, the boost described herein is administered at least 7 days after the initial prime vaccination, for example at least 8 days, at least 9 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 16 days, at least 17 days, at least 18 days, at least 19 days, at least 20 days, at least 21 days, at least 28 days, at least 35 days, or at least 42 days. Preferably, the boost is administered after at least 2 months, at least 3 months, at least 4 months, or later. Booster administration after about 3 month is in particular preferred. The boost as described herein can effectively improve both antibody production against SARS- CoV-2 and cell-mediated immunity against SARS-CoV-2. The efficacy of the booster vaccine can be measured by any standard quantification of immune response.

[0046] Further booster vaccine administration, such as a second or third booster administration, are possible.

[0047] In particular embodiments, the boost described herein is administered by injection, preferably by intramuscular or subcutaneous injection. In alternative embodiments, the boost described herein is administered to the respiratory tract of a subject, e.g. to the mucosa of the respiratory tract, in particular via intranasal or oral administration. According to an especially preferred embodiment, the boost is administered by injection, preferably by intramuscular or subcutaneous injection, after about three month.

[0048] According to a further aspect, the present invention relates to a platform, i.e. a widely applicable technology, for providing multivalent vaccines comprising at least one adenoviral vector according as herein described. A vaccine platform can be understood as a “plug-and-play” physical framework that can be used when developing vaccines for emerging infectious diseases. According to a preferred embodiment, the inventive adenoviral vector comprises a further a nucleic acid encoding at least one protein or derivative thereof of a microorganism responsible for an infectious disease.

[0049] The invention is further described by the following figures and examples, which are not intended to limit the scope of the invention.

[0050] Figures

[0051] Fig. 1 Designed two vectors in order to generate novel Ad5 vector:

[0052] A Plasmid map for Vector-1 pAd5-CMV-Om_S-T2A-Om / DP_N-SV40pA-plX-DP_RBD,

[0053] DNA 39814 bases

[0054] B Plasmid map for Vector-2 pAd5-CM V-Om_S-T2A-Om_DP_delta121 N-SV40pA-plX-DP_RBD,

[0055] DNA 39451 bases

[0056] Fig. 2 PCR confirmation of the Vector-1 plasmid DNA and viral DNA by agarose gel electrophoresis. “P” stands for plasmid DNA. “V” stands for viral DNA. Fig. 3 PCR confirmation of the Vector-2 plasmid DNA and viral DNA by agarose gel electrophoresis.

[0057] P: plasmid DNA

[0058] V: viral DNA V1 : extracted from the non-purified adenovirus

[0059] V2: extracted from the CsCI ultra-purified adenovirus

[0060] Fig. 4 Restriction Digestion and confirmation of Vector integrity

[0061] Fig. 5 SDS PAGE analysis of Purified virus stock

[0062] Purified Virus of Vector-1 was used for SDS PAGE analysis and compared with ChAdOx-1 Vector and showed similar band pattern representing Adenovirus structural proteins.

[0063] M: marker, A: ChAdOxI , C: Vector-1 , D: Vector-2

[0064] Band at 70 kDa indicates presence of RBD on the virus surface.

[0065] Fig. 6 Silver staining of in process Vector-1 samples at different purification steps

[0066] M: marker, A: ChAdOx, B: Flow Through, C: Post Load Wash, D: Wash, E: Elution, F: Elution After Peak, G: Elution After Diafiltration, H: Salt Strip, I: Salt Strip After Diafiltration

[0067] Fig. 7 NTA analysis of Vector-1

[0068] Fig. 8 TEM analysis of Vector-1 virus particles

[0069] Fig. 9 Western Blot Analysis of Vector-1 samples with anti-SARS-CoV-2 Spike RBD antibody

[0070] M: marker, A: ChAdOx Vector, B: Sample 1 , C: Sample 2, D: Sample 3

[0071] Western blot analysis confirmed surface expression of P-IX RBD on purified Vector- 1 Fig. 10 Cesium chloride density gradient ultracentrifugation of Vector-1 showing separation of completely formed and partially formed virus particles

[0072] Fig. 11 Analytical Ultracentrifuge (AUC) of Vector-1 sample

[0073] AUC analysis showed purification efficiency and majority of Virus particles are with Full capsid having sedimentation coefficient 597S and mass 83.4 MDa

[0074] Table of sequences Examples

[0075] Production of Recombinant Adenovirus from Plasmid

[0076] Preparing Bacterial Culture

[0077] Follow the procedure below to prepare 200 ml bacterial culture.

[0078] 1. Streak the E. coli onto a freshly prepared LB agar plate containing the appropriate selective antibiotics and incubate at 37°C overnight.

[0079] 2. Prepare a starter culture by inoculating a single colony into 4-6 ml of LB medium containing the appropriate selective antibiotics and incubate at 37°C at a rotation speed of -225-250 rpm for -8 hours.

[0080] 3. Use the starter culture to inoculate an overnight culture. Dilute the starter culture 1 :500 to 1 : 1000 into a larger volume of selective medium in a flask with a volume of at least 3-4 times greater than the volume of medium. Put flasks in a shaking incubator, and incubate at 37°C with vigorous shaking (-250-300 rpm) to saturation (12-16 hours).

[0081] Preparing Endotoxin-Free Recombinant Adenoviral pDNA

[0082] For a successful adenovirus packaging, high yield and high-quality plasmid DNA (pDNA) is required to achieve optimal DNA transfection.

[0083] The type of plasmid, especially the size and the origin of replication have a crucial influence on pDNA yield. In general, the larger the plasmid is, the lower is the expected pDNA yield due to a lower copy number. Even the SARS-CoV-2 Spike protein adenoviral expression vectors that we constructed using a pUC origin of replication based high-copy construct can behave like a low-copy construct because of the insert of 36 kb Ad5 viral genome. The E. coli host strain mostly influences the quality of the plasmid DNA. pDNA isolation from E. coli can exist in different topological forms: covalently closed circular or supercoiled, open circular and linear along with catenanes or multimers. Among all the isoforms, the supercoiled pDNA has intact strands (no breakage) and corresponds to the active form for plasmid applications. Whereas strains like DH5a or XL1 -Blue usually produce high level of supercoiled pDNA, other strains like for example HB101 with high levels of endonuclease activity might yield lower quality plasmid giving poor results in downstream applications.

[0084] Endotoxins are released during the lysis step of plasmid preparations and are often copurified with plasmid DNA. Endotoxins, also known as lipopolysaccharides (LPS), are cell membrane components of E. coli host strains. LPS consists of a hydrophobic lipid A moiety, a complex array of sugar residues and negatively charged phosphate groups. Their presence sharply reduces transfection efficiency by competing with negatively charged pDNA for “free” transfection reagent and significantly influences the viability of the transfected cells.

[0085] Follow the procedure below to prepare and qualify isolated adenoviral pDNA.

[0086] 1. Isolate at least 50-100 pg of purified adenoviral pDNA with NucleoBond Xtra Midi kit.

[0087] 2. Measure pDNA concentration using NanoDrop.

[0088] 3. Quality control of Plasmid DNA by restriction enzyme digestion, PCR, Sanger sequencing of inserts sequence.

[0089] Preparing Pac l-Digested Recombinant Adenoviral pDNA

[0090] Before adenoviral packaging, the left and right ITRs must be exposed to allow proper viral replication and packaging. Each adenoviral expression vector contains Pac I restriction sites flanking the ITRs. Digestion of the vector with Pac I allows exposure of the left and right viral ITRs and removal of the bacterial sequences (i.e. origin of plasmid replication and ampicillin resistance gene).

[0091] Follow the procedure below to prepare and qualify Pac l-digested adenoviral pDNA. 1. Digest at least 15 g of purified adenoviral pDNA with Pac I (New England Biolabs, Catalog no. R0547S). Follow the manufacturer’s instructions.

[0092] 2. Purify the digested plasmid DNA using phenol / chloroform extraction followed by ethanol precipitation.

[0093] A. Precipitate the DNA by adding 1 / 1 Oth volume of 3 M sodium acetate, pH 5.2, and two volumes of ethanol. Incubate at -20°C for at least 30 minutes.

[0094] B. Pellet the DNA in a microcentrifuge for 15 minutes at top speed. Carefully remove the supernatant.

[0095] C. Rinse the pellet by adding 500 pl of 70% ethanol and centrifuging for 15 minutes at top speed.

[0096] D. Carefully remove the supernatant.

[0097] E. Air dry for 5-10 mins.

[0098] F. Dissolve DNA pellet

[0099] 3. Dissolve the Pac l-digested pDNA in sterile water or TE Buffer, pH 8.0 to a final concentration of 0.3-1.0 pg / pl.

[0100] 4. DNA qualification by agarose gel analysis

[0101] 5. DNA qualification by measuring OD260 / 280 and OD260 / 230.

[0102] 6. DNA identification by sequencing the insert sequence.

[0103] Producing Recombinant Adenovirus in 293-Derived Cell Line

[0104] The major components for producing recombinant adenovirus include:

[0105] • An E1 and E3-deleted adenoviral expression vector containing the gene of interest under the control of a promoter of choice. The vector also contains the elements required to allow packaging of the expression construct into virions (e.g. 5' and 3' ITRs, encapsidation signal, adenoviral late genes).

[0106] • An E1 expressing cell line is used to facilitate initial production, amplification, and titering of replication-incompetent adenovirus. The 293-derived cell lines contain a stably integrated copy of E1 that supplies the E1 proteins (E1a and E1 b) in trans required to generate adenovirus.

[0107] • DNA transfection reagent.

[0108] Follow the procedure below to transfect 293-derived cells using jetPRIME® transfection reagent. 1. The day before transfection, trypsinize and count cells, subculture at 5 x 10A5 cells per well in a 6- well plate. Plate cells in 2 ml of normal growth medium containing serum.

[0109] 2. On the day of transfection, remove the culture medium from the 293-derived cells and replace with 1.5 ml of normal growth medium containing serum.

[0110] 3. Prepare DNA-jetPRIME® transfection reagent complexes for each transfection sample by performing the following:

[0111] • Dilute 3 pg of Pac l-digested adenoviral pDNA in 300 pl of jetPRIME® buffer. Mix by vortexing gently.

[0112] • Vortex jetPRIME® reagent gently for 5 sec and spin down briefly before use.

[0113] • Add 6 pl jetPRIME® reagent in the diluted pDNA solution. Mix thoroughly and gently by vortexing 1-2 sec, spin down briefly.

[0114] • Incubate for 10 minutes at room temperature to allow the DNA- transfection reagent complexes to form.

[0115] 4. Add 300 pl DNA-transfection reagent complexes dropwise to each well, and distribute evenly.

[0116] 5. Mix gently by rocking the plate back and forth. Incubate the cells overnight at 37°C in a CO2 incubator.

[0117] 6. The next day, remove the medium containing the DNA-transfection reagent complexes and replace with complete culture medium (i.e. DMEM containing 10% FBS).

[0118] 7. Replace culture medium with fresh, complete culture medium every 2-3 days until visible regions of cytopathic effect (CPE) are observed (typically 5-10 days post-transfection).

[0119] 8. Replenish culture medium and allow infections to proceed until approximately 80% CPE is observed (typically 10-15 days post-transfection).

[0120] 9. Harvest adenovirus-containing cells by aspirating cells off the plate with a 1 ml filtered pipette tip. Transfer cells and media to a sterile, 15 ml, capped tube.

[0121] 10. Place the tube containing harvested cells and media at -80°C for at least 30 minutes. Remove tube and place in a 37°C water bath for 15 minutes to thaw. Repeat the freezing and thawing steps twice. 11. Centrifuge the cell lysate in a table-top centrifuge at 4000 rpm for 10 minutes at 4°C to pellet the cell debris.

[0122] 12. Transfer the supernatant containing viral particles to cryovials in 100 pl aliquots. Store the viral stocks at -80°C.

[0123] Amplifying P0 Adenoviral Stocks in A T175 Flask

[0124] Follow the procedure below to amplify P0 adenoviral stock using 293-derived cells. Make sure that the 293-derived cells are healthy at the time of plating.

[0125] 1 . The day before infection, trypsinize and count cells, plate them at 9 x 10A6 cells in a T175 flask. Plate cells in 25 ml of normal growth medium containing serum.

[0126] 2. On the day of infection, verify that the cells are at 80-90% confluency before proceeding. Add the desired amount of P0 adenoviral stocks (e.g. 3x100 pl) to the cells. Swirl the plate gently to mix.

[0127] 3. Incubate the cells at 37°C in a CO2 incubator and allow infection to proceed until 80-90% of the cells have rounded up and some are floating or lightly attached to the tissue culture dish (typically 2- 4 days post-infection). This indicates that cells are loaded with adenoviral particles.

[0128] 4. Harvest adenovirus-containing cells by aspirating cells off the plate with a 10 ml tissue culture pipette. Transfer cells and media to a sterile, 50 ml, capped tube.

[0129] 5. Centrifuge the cells in a table-top centrifuge at 4000 rpm for 10 minutes at 4°C. Discard the supernatant.

[0130] 6. Resuspend the cell pellet with 1.5 ml sterile HBSS buffer. Transfer cells to a sterile, 15 ml, capped tube.

[0131] 7. Place the tube containing the cells at -80°C for 30 minutes. Remove tube and place in a 37°C water bath for 15 minutes to thaw. Repeat the freezing and thawing steps twice.

[0132] 8. Centrifuge the cell lysate in a table-top centrifuge at 4000 rpm for 10 minutes at 4°C to pellet the cell debris.

[0133] 9. Transfer the supernatant containing viral particles to cryovials in 100 pl aliquots. Store the viral stocks at -80°C.

[0134] Amplifying P1 Adenoviral Stocks in a 5-Layer Cell Factory Follow the procedure below to amplify P1 adenoviral stocks using 293-derived cells.

[0135] Make sure that the 293-derived cells are healthy at the time of plating.

[0136] 1 . The day before infection, trypsinize and count the 293-derived cells, plate them at 1 x 10A8 cells in a 5-layer cell factory. Plate cells in 700 ml of normal growth medium containing serum.

[0137] 2. On the day of infection, verify that the cells are at 80-90% confluency before proceeding. Add the desired amount of P1 adenoviral stocks (e.g. 3x100 pl) to the cells. Swirl the plate gently to mix.

[0138] 3. Incubate the cells at 37°C in a CO2 incubator and allow infection to proceed until 80-90% of the cells have rounded up and some are floating or lightly attached to the tissue culture dish (typically 2- 4 days post-infection). This indicates that cells are loaded with adenoviral particles.

[0139] 4. Harvest adenovirus-containing cells by aspirating the trypsinized cells off the surface of cell factory with a 25 ml tissue culture pipette. T ransfer cells and media to 4 sterile, 250 ml, capped bottles.

[0140] 5. Centrifuge the cells in a centrifuge at 4000 rpm for 20 minutes at 4°C. Discard the supernatant.

[0141] 6. Resuspend the cell pellet with 10 ml sterile HBSS buffer. Transfer cells to 2 sterile, 15 ml, capped tubes.

[0142] 7. Place the tubes containing the cells at -80°C for 30 minutes. Remove tube and place in a 37°C water bath for 15 minutes to thaw. Repeat the freezing and thawing steps twice.

[0143] 8. Centrifuge the cell lysate in a table-top centrifuge at 4000 rpm for 10 minutes at 4°C to pellet the cell debris.

[0144] 9. Transfer 10 ml of the supernatant containing viral particles to an ultracentrifuge tube filled with CsCI gradient solutions.

[0145] 10. Proceed to Purification of Recombinant Adenovirus by CsCI Density Gradient Ultracentrifugation protocol.

[0146] 11. After desalting and buffer exchange, transfer the CsCI ultrapurified viral particles to cryovials in 100 pl aliquots. Store the viral stocks at -80°C. Plasmid Quality check before Transfection:

[0147] Testing of Virus stock:

[0148] PCR Confirmation of Plasmid DNA and Virus Stock integrity:

[0149] PCR target genes and primer sequences

[0150] Purified plasmids and Adenovirus samples for Vector-1 and Vector-2 were checked for specially designed target gene panel. These target regions will give idea about vector integrity, identification of transgene, Adenovirus backbone, promoter identification and confirmation of replication deficient adenovirus as per vector map (Fig. 1A and 1 B). PCR results are confirming both produced plasmids and vectors are as per design and having complete integrity (Fig. 2 and Fig. 3).

[0151] E1A gene identification:

[0152] Vector is derived by recombineering the Ad5 genome that involves the deletion of E1 gene. These genes are essential in viral replication inside the cognate host cells. Genomic DNA of these vectors were accessed for the presence of E1A gene using PCR. These viral genomes are incapable of expression E1A gene from the original Ad5. (Fig. 2 and Fig. 3)

[0153] Sanger Sequencing of Vectors:

[0154] Sanger sequencing were performed for Vector-1 and Vector-2 and confirms the targeted regions containing both transgenes, pIX-RBD and Adenovirus backbone.

[0155] Restriction enzyme digestion and confirmation of Vector integrity

[0156] Restriction digestion of adenoviral vector constructs is a fast, cost-efficient method for providing indirect sequence information. Simultaneously, multiple vector constructs can be analyzed for the presence or absence of an insert, orientation of the insert, plasmid size, and some site-specific sequence data. Here overall genome organization mapped with RE digestion. Since the restriction enzymes have a very high specificity in target site recognition, this strategy is useful to identify whether any major genomic rearrangements have taken place. In this study we mapped Vector-1 and Vector-2 for the presence of sites for the restriction enzymes listed below: RE digestion pattern is as per expectation and confirming there are no genomic rearrangements and complete vector integrity. (Fig. 4)

[0157] Size Heterogenicity (Viral Particle Size by NanoSight)

[0158] Size heterogeneity was performed using Nanoparticle Tracking (NTA) analysis; viral particle hydrodynamic size was confirmed by nanoparticle tracking analysis (NTA) analysis. NanoSight instrument was used for NTA, to measure particle size distribution in sub-micron range (30 to 1000 nm). The technique uses a Laser beam to illuminate the particles in the sample. The scattered light from the particles is detected and recorded by a camera at 90° angle through a 20X objective lens. The camera operates at 30 frames per second and captures the video of particles moving under Brownian motion. Multiple particles are tracked individually and simultaneously, and the Stokes- Einstein equation is used to calculate the hydrodynamic size for each of the particles in the population. Vector-1 samples were diluted with PBS before testing to reach a particle concentration suitable for NanoSight working range (1.0E+8 to 2.5E+9 particles / ml). The hydrodynamic diameter for predominant particles is approximately 90-100 nm. (Fig. 7)

[0159] Transmission Electron Microscopy

[0160] Electron microscopy allows for the direct visualization of viral particles. Vector were placed on a 400-mesh glow-discharged carbon grid by first inverting the grid and placing it on top of a 10 pL droplet of Vector-1 , deposited on parafilm, for 30 seconds. Excess sample was blotted off by gently touching the edge of the grid against Whatman filter paper. The grid was then washed twice on two 20 pL droplets of ddH2O. The samplecontaining grid was then stained by placing on top of a 20 pL droplet of 1.5% uranyl acetate for 10 seconds.

[0161] Excess stain was blotted off by gently touching the edge of the grid against Whatman filter paper. The size and shape of the assembled viral particles was confirmed by negatively stained transmission electron microscopy (TEM). The viral particle images show the expected icosahedral shape with a diameter of approximately 90 nm. TEM also showed morphology difference between the empty and full capsid. Full particle was observed as bright spheres and empty particle were spheres with darker spot. Manually counting of these particles showed more than >95% particles are Full capsids. (Fig. 8)

[0162] Western Blot analysis of purified Virus Samples

[0163] Western blot analysis of purified Vector-1 was carried out. After running gradient SDS- PAGE and protein visualization (Fig. 5), protein bands from other gel were transferred on nitrocellulose membrane. The blots were blocked with BSA in PBS containing 0.5% Tween-20 (PBST) for 2 h at 37 °C and further incubated with SARS-CoV-2 RBD-specific antibody overnight at 4 °C. Then blots were incubated with horseradish peroxidase (HRP)-conjugated goat anti-mouse IgG for 1 h at room temperature and then visualized with substrate reagents (Fig. 9).

[0164] Cesium chloride density gradient Ultracentrifugation of Vector-1

[0165] Cesium chloride (CsCI) density gradient along with ultracentrifugation is the gold standard method for small scale separation of completely formed and partially formed adenovirus particles.

[0166] 1. Prepare three different concentrations (1.25 g / cm3; 1.35g / cm3; 1.45 of cesium chloride in 0.01 M Tris buffer, pH 7.5.

[0167] 2. Cell lysis: Add lysis buffer to the infected cell and lysis for 2 hrs along with Benzonase treatment.

[0168] 3. After lysis, centrifuge the lysate for 5 min at 1500 rpm and collect the supernatant.

[0169] 4. For 30 ml tube add 21 ml of cesium chloride solutions and 8-9 ml of cell lysate. Start with addition of 7 ml CsC1 1 .25 g / cm3 with a syringe to the bottom of the tube. Then add 7 ml of CsC1 1.35 g / cm3 with a syringe to the bottom of the tube and slowly add layers. Add CsCI 1.45 g / cm3 to the very bottom of the tube.

[0170] 5. Check for absence of bubbles so that the density boundaries do not mix. Carefully overlay 8-9 ml cell lysate on the top of the gradient.

[0171] 6. Balance the centrifuge and run at 28000 rpm for 90 minutes at 4°C.

[0172] 7. After centrifugation, observe for two layers of completely formed (full capsid) and partially formed (empty capsid) adenovirus particles.

[0173] 8. Lower buffy coat layer containing complete virus particles were used for further process and characterization (Fig. 10). Analytical Ultracentrifuge (AUC) of Vector-1 sample

[0174] Analytical Ultracentrifuge is a versatile and powerful method for the quantitative analysis of purified macromolecules or supramolecular assemblies in a solution. AUC allows to distinguish full particles, partially filled particles and empty viral particles, and therefore facilitates purification efficiency and aggregate analysis. It also used to characterize the homogeneity, under product formulation conditions, of preparations of adenovirus vectors used for gene therapy or vaccines. Adenovirus samples were purified and in process samples were analyzed by SDS-PAGE analysis followed by Silver staining.

[0175] Silver staining gel confirms the purification efficiency (Fig. 6). These purified final eluted samples used for AUC analysis and showed majority of Virus particles are with Full capsid having sedimentation coefficient 597S and mass 83.4 MDa. (Fig. 11)

Claims

Claims1 . A replication defective adenoviral vector comprising(i) a nucleic acid encoding at least one SARS-CoV-2 spike protein or a derivative thereof and(ii) a nucleic acid encoding at least one SARS-CoV-2 nucleocapsid protein or a derivative thereof, wherein the adenoviral vector displays a polypeptide comprising a receptorbinding domain (RBD) of a SARS-CoV-2 spike protein or a derivative thereof via protein IX (pIX) on its capsid.

2. The adenoviral vector according to claim 1 , wherein the at least one SARS-CoV- 2 spike protein of (i) is selected from spike proteins of any known SARS-CoV viruses derived from the Wuhan variant and derivatives thereof, in particular spike proteins of SARS-CoV-2 variants of concern, such as Alpha, Beta, Gamma, Delta and Omicron variants, more particularly wherein the at least one SARS-CoV-2 spike protein of (i) comprises the spike protein of SARS-CoV-2 omicron variant or a derivative thereof, SARS-CoV-2 Delta plus variant or a derivative thereof, or combinations thereof.

3. The adenoviral vector according to claim 2, wherein the at least one SARS-CoV- 2 spike protein of (i) is encoded by a nucleic acid sequence comprising nucleotides 1131 to 4931 as shown in SEQ ID NO:1.

4. The adenoviral vector according to any one of claims 1 -3, wherein the at least one nucleocapsid protein of (ii) is selected from nucleocapsid proteins of any known SARS-CoV viruses derived from the Wuhan variant and derivatives thereof, in particular nucleocapsid proteins of SARS-CoV-2 variants of concern, such as Alpha, Beta, Gamma, Delta and Omicron variants, more particularly wherein the at least one nucleocapsid protein of (ii) comprises the nucleocapsid protein of SARS-CoV-2 Omicron variant or a derivative thereof, SARS-CoV-2 delta plus variant or a derivative thereof, or combinations thereof.

5. The adenoviral vector according to claim 4, wherein the nucleocapsid protein of(iii) is encoded by a nucleic acid sequence comprising nucleotides 4995 to 6242 of SEQ ID NO:1.

6. The adenoviral vector according to any one of claims 1-5, wherein the RBD displayed on the capsid is selected from RBDs of any known SARS-CoV viruses derived from the Wuhan variant and derivatives thereof, in particular RBDs of SARS-CoV-2 variants of concern, such as Alpha, Beta, Gamma, Delta and Omicron variants, more particularly wherein the RBD displayed on the capsid is the RBD of SARS-CoV-2 delta plus variant or a derivative thereof.

7. The adenoviral vector according to claim 6, wherein the RBD displayed on the capsid comprises a protein encoded by a nucleic acid sequence comprising nucleotides 7031 to 7699 of SEQ ID NO:1.

8. The adenoviral vector according to any one of claims 1-7, wherein the adenovirus is derived from human or chimpanzee serotype 5, 26, 35 or 3, in particular human Adenovirus 5 serotype.

9. The adenoviral vector according to any one of claims 1-8, comprising deletions of the E1 and E3 regions.

10. The adenoviral vector according to any one of claims 1 -9 comprising a further a nucleic acid encoding at least one protein or derivative thereof of a microorganism, which is different from SARS-CoV-2 and which is preferably responsible for an infectious disease.

11. The adenoviral vector according to any one of claims 1 -10, for use in preventing or treating a COVID-19 disease.

12. The adenoviral vector for use according to claim 11 , wherein the vector is administered by injection, in particular by intramuscular or subcutaneous injection, and / or wherein the vector is administered to the respiratory tract of a subject, preferably to the mucosa of the respiratory tract, in particular via intranasal or oral administration.

13. A vaccine composition comprising the adenoviral vector according to any one of claims 1-12, and optionally one or more further active agents, i.e. in particular further immunogenicity-conferring agents.

14. The vaccine composition according to claim 13, adapted(i) for administration by injection, in particular adapted for intramuscular or subcutaneous injection, and / or(ii) for administration to the respiratory tract of a subject, preferably to the mucosa of the respiratory tract, in particular for intranasal or oral administration.

15. A method of boosting an antigen-specific immune response in a subject comprising administering to said subject a sufficient amount of the adenoviral vector according to any one of claims 1-10 or the vaccine composition according to claim 13 or 14.

16. The method according to claim 15, wherein the vector or vaccine composition is administered by injection, in particular by intramuscular or subcutaneous injection, and / or wherein the vector or vaccine composition is administered to the respiratory tract of a subject, preferably to the mucosa of the respiratory tract, in particular via intranasal or oral administration.

17. Platform for providing multivalent vaccines comprising an adenoviral vector according to any one of claims 1 -10, in particular claim 10.

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