Recombinant multivalent influenza viruses

Abstract

The invention provides a composition useful to prepare influenza vaccine viruses, e.g., in the absence of helper virus, which includes internal viral segments from an influenza virus vaccine strain or isolate, e.g., one that is safe in humans, for instance, one that does not result in significant disease, and encodes a heterologous antigen.

Claims

1. A composition for intranasal delivery comprising an amount of an isolated, single cycle, multivalent recombinant influenza virus having at least seven viral segments selected from influenza virus PA, PB1, PB2, NP, NS, M, HA or NA viral segments, or having at least six viral segments selected from PA, PB1, PB2, NP, NS, M, or HEF viral segments, wherein the NS viral segment comprises coding sequences for an antigenic coronavirus protein, or an antigenic portion thereof, flanked by protease recognition sites, wherein the coding sequences include a receptor binding domain of the coronavirus S protein, wherein the M viral segment comprises a mutant M gene that expresses a functional M1 protein and a mutant M2 protein with a deletion of the cytoplasmic tail and either lacking a transmembrane domain or having a mutated transmembrane domain, wherein the amount is effective to induce a mucosal immune response.

2. The composition of claim 1 wherein the antigenic coronavirus protein comprises S1 sequences.

3. The composition of claim 1 wherein antigenic coronavirus protein comprises a soluble protein.

4. The composition of claim 1 wherein the antigenic coronavirus protein sequences or the portion thereof have at least 80% amino acid sequence identity to one of SEQ ID Nos. 25-28 and 50-52.

5. The composition of claim 1 wherein the virus comprises eight or nine viral segments.

6. The composition of claim 1 wherein the virus is an influenza A or B virus.

7. The composition of claim 1 wherein the virus is bivalent or trivalent.

8. The composition of claim 1 wherein the M2 lacks the transmembrane domain.

9. The composition of claim 1 wherein at least one of PA, PB1, or PB2 viral segments has a C to U promoter mutation.

10. The composition of claim 1 wherein the PB2 segment has one or more of a C4U promoter mutation, 202L/323L or 504V; the PB1 segment has one or more of C4U, 40L, 112G, 180W or 247H; the PA segment has one or more of C4U, 142N, 225C or 401K; the NP segment has 74K or 116L; or the NS segment has 30P in NS1 or 118K in NS1, wherein the numbering is relative to a PB2 encoded by SEQ ID NO:3, a PB1 encoded by SEQ ID NO:2, a PA encoded by SEQ ID NO:1, a NP encoded by SEQ ID NO:4 or a NS1 encoded by SEQ ID NO:6.

11. A vaccine comprising the virus of claim 1.

12. The vaccine of claim 11 wherein the recombinant virus comprises influenza A HA.

13. A method to immunize a vertebrate, comprising: administering to the vertebrate the vaccine of claim 11.

14. The method of claim 13 wherein the vertebrate is a human.

15. The composition of claim 1 wherein the NS viral segment encodes protease recognition sites comprising T2A (EGRGSLLTCGDVEENPGP; SEQ ID NO:53), P2A (ATNFSLLKQAGDVEENPGP; SEQ ID NO:54), E2A (QCTNYALLKLAGDVESNPGP; SEQ ID NO: 55) or F2A (VKQTLNFDLLKAGDVESNPGP; SEQ ID NO:56).

16. The composition of claim 1 wherein the protease recognition sequences are autocatalytically cleaved.

Description

BRIEF DESCRIPTION OF THE FIGURES

(1) FIGS. 1A-1E. Nucleotide sequence for PR8(Cambridge) genes (SEQ ID NOs:10-15).

(2) FIG. 2: Overview of library passages and the identification of high-yield candidates.

(3) FIG. 3. Number of clones with random mutations having specified HA titers.

(4) FIG. 4. Titers of clones having selected mutations.

(5) FIGS. 5A-5D. Growth curves of UW-PR8 viruses possessing previously identified mutations in PB2 (A), PB1 (B), PA (C), and NP, M or NS1 (D).

(6) FIG. 6. Summary of mutations that confer high replicative property in MDCK cells.

(7) FIGS. 7A-7B. A) Virus stocks were tested for HA titers (in 2.sup.n) and virus titers (in PFU/mL). B) Growth curves in MDCK cells.

(8) FIGS. 8A-8C. A) HA titer of wild type (UW-PR8) and clone #4. B) Viral protein for wild type (UW-PR8) and #4. C) SDS-PAGE analysis of viral proteins of wild type and #4.

(9) FIGS. 9A-9B. A) Comparison of titers of wild type virus (UW-PR8) and high replicative virus with mutations in M1. B) Growth kinetics of wild type virus (UW-PR8) and high replicative virus with mutations in M1.

(10) FIGS. 10A-10M. A) Codon usage table for canines. B) Relative adaptiveness of wild type (UW-PR8) and rare codon optimized PB2 viruses. C) Relative adaptiveness of wild type (UW-PR8) and all codon optimized PB2 viruses. D) Growth kinetics of PB2 codon optimized viruses. E) Growth kinetics of viruses with codon optimized PB2, PB1, PA, or NP viral segment or combinations of segments. F) Sequence of PB2, PB1, PA and NP viral segments of UW-PR8 and sequence of canine codon-usage optimized PB2, PB1, PA and NP viral segments of UW-PR8 (SEQ ID NOs: 3, 13, 2, 12, 1, 11, 4).

(11) FIGS. 11A-11C. A) Nucleotide position 4 of each gene of PR8 and Indo/NC/09. B) All 3C4U mutant. C) Growth kinetics of a recombinant UW-PR8 virus encoding C at position 4 of the PB2, PB1, and PA genes (black), and a mutant encoding U at position 4 of all eight segments (red).

(12) FIG. 12A-12C. Nucleotide and amino acid sequences for H7 and N9 which are exemplary sequences for use with the internal viral segment sequences disclosed herein useful to provide high titer influenza viruses for vaccines (SEQ ID NOs: 20-24 and 29-31).

(13) FIGS. 13A-13B. A) Schematic of chimeric HA and NA genes to increase virus titer. B) Growth kinetics of chimeric viruses.

(14) FIGS. 14A-14B. A) Growth kinetics of viruses with combinations of mutations. B) PFU and HA titers of viruses with combinations of mutations.

(15) FIG. 15. Screening in eggs.

(16) FIG. 16. HA titers of 216 clones isolated from Vero cells.

(17) FIG. 17. Recombinant viruses generated with different PR8 backbone mutations.

(18) FIG. 18A-18B. Overview of generation of viruses with enhanced growth in MDCK cells and Vero cells.

(19) FIGS. 19A-19D. Exemplary high yield substitutions (relative to PR8 (UW)).

(20) FIG. 20. Growth kinetics and HA titers of reassortant viruses possessing one or several vRNAs of PR8-HY virus.

(21) FIG. 21. Viral polymerase activity in mini-replicon assays in 293T, MDCK, Vero, and DF1 cells. The PB2, PB1, PA, and NP proteins were derived from UW-PR8 wild-type (WT) virus or from the high-yield PR8-HY (HY) variant.

(22) FIG. 22. Exemplary method to prepare bivalent viruses.

(23) FIG. 23. Exemplary SARS-CoV-2 spike (S) protein sequences (SEQ ID Nos. 25-28 and 50-52). The S1 portion of S is generally from residues 1 to 681 and the receptor binding domain in S1 is within residues 330 to 521 (see, e.g., Wrapp et al., Science, 67:1260 (2020), the disclosure of which is incorporated by reference herein).

DETAILED DESCRIPTION

Definitions

(24) As used herein, the term isolated refers to in vitro preparation and/or isolation of a nucleic acid molecule, e.g., vector or plasmid, peptide or polypeptide (protein), or virus of the invention, so that it is not associated with in vivo substances, or is substantially purified from in vitro substances. An isolated virus preparation is generally obtained by in vitro culture and propagation, and/or via passage in eggs, and is substantially free from other infectious agents.

(25) As used herein, substantially purified means the object species is the predominant species, e.g., on a molar basis it is more abundant than any other individual species in a composition, and preferably is at least about 80% of the species present, and optionally 90% or greater. e.g., 95%, 98%, 99% or more, of the species present in the composition.

(26) As used herein, substantially free means below the level of detection for a particular infectious agent using standard detection methods for that agent.

(27) A recombinant virus is one which has been manipulated in vitro, e.g., using recombinant DNA techniques, to introduce changes to the viral genome. Reassortant viruses can be prepared by recombinant or nonrecombinant techniques.

(28) As used herein, the term recombinant nucleic acid or recombinant DNA sequence or segment refers to a nucleic acid, e.g., to DNA, that has been derived or isolated from a source, that may be subsequently chemically altered in vitro, so that its sequence is not naturally occurring, or corresponds to naturally occurring sequences that are not positioned as they would be positioned in the native genome. An example of DNA derived from a source, would be a DNA sequence that is identified as a useful fragment, and which is then chemically synthesized in essentially pure form. An example of such DNA isolated from a source would be a useful DNA sequence that is excised or removed from said source by chemical means, e.g., by the use of restriction endonucleases, so that it can be further manipulated, e.g., amplified, for use in the invention, by the methodology of genetic engineering.

(29) As used herein, a heterologous influenza virus gene or viral segment is from an influenza virus source that is different than a majority of the other influenza viral genes or viral segments in a recombinant, e.g., reassortant, influenza virus.

(30) The terms isolated polypeptide, isolated peptide or isolated protein include a polypeptide, peptide or protein encoded by cDNA or recombinant RNA including one of synthetic origin, or some combination thereof.

(31) The term recombinant protein orrecombinant polypeptide as used herein refers to a protein molecule expressed from a recombinant DNA molecule. In contrast, the term native protein is used herein to indicate a protein isolated from a naturally occurring (i.e., a nonrecombinant) source. Molecular biological techniques may be used to produce a recombinant form of a protein with identical properties as compared to the native form of the protein.

(32) Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm.

(33) Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Alignments using these programs can be performed using the default parameters. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). The algorithm may involve first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached.

(34) In addition to calculating percent sequence identity, the BLAST algorithm may also perform a statistical analysis of the similarity between two sequences. One measure of similarity provided by the BLAST algorithm may be the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid sequence to the reference nucleic acid sequence is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

(35) The BLASTN program (for nucleotide sequences) may use as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=4, and a comparison of both strands. For amino acid sequences, the BLASTP program may use as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix. See http://www.ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection.

(36) For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

(37) Influenza Virus Structure and Propagation

(38) Influenza A viruses possess a genome of eight single-stranded negative-sense viral RNAs (vRNAs) that encode at least ten proteins. The influenza virus life cycle begins with binding of the hemagglutinin (HA) to sialic acid-containing receptors on the surface of the host cell, followed by receptor-mediated endocytosis. The low pH in late endosomes triggers a conformational shift in the HA, thereby exposing the N-terminus of the HA2 subunit (the so-called fusion peptide). The fusion peptide initiates the fusion of the viral and endosomal membrane, and the matrix protein (M1) and RNP complexes are released into the cytoplasm. RNPs consist of the nucleoprotein (NP), which encapsidates vRNA, and the viral polymerase complex, which is formed by the PA, PB1, and PB2 proteins. RNPs are transported into the nucleus, where transcription and replication take place. The RNA polymerase complex catalyzes three different reactions: synthesis of an mRNA with a 5 cap and 3 polyA structure, of a full-length complementary RNA (cRNA), and of genomic vRNA using the cRNA as a template. Newly synthesized vRNAs, NP, and polymerase proteins are then assembled into RNPs, exported from the nucleus, and transported to the plasma membrane, where budding of progeny virus particles occurs. The neuraminidase (NA) protein plays a crucial role late in infection by removing sialic acid from sialyloligosaccharides, thus releasing newly assembled virions from the cell surface and preventing the self aggregation of virus particles. Although virus assembly involves protein-protein and protein-vRNA interactions, the nature of these interactions is largely unknown.

(39) Although influenza B and C viruses are structurally and functionally similar to influenza A virus, there are some differences. For example, influenza B virus does not have a M2 protein with ion channel activity but has BM2 and has a viral segment with both NA and NB sequences. Influenza C virus and Influenza D virus have only seven viral segments.

(40) Cell Lines that can be Used in the Present Invention

(41) Any cell, e.g., any avian or mammalian cell, such as a human, e.g., 293T or PER.C6@ cells, or canine, e.g., MDCK, e.g., humanized MDCK cells (see U.S. application Ser. No. 16/785,449, filed on Feb. 7, 2020, which is incorporated herein by reference) or M2 expressing cell line (see Itwasuki et al., J. Virol., 80:5233 (2006), the disclosure of which is incorporated by reference herein), bovine, equine, feline, swine, ovine, rodent, for instance mink, e.g., MvLu1 cells, or hamster, e.g., CHO cells, or non-human primate, e.g., Vero cells, including mutant cells, which supports efficient replication of influenza virus can be employed to isolate and/or propagate influenza viruses. Isolated viruses can be used to prepare a reassortant virus. In one embodiment, host cells for vaccine production are continuous mammalian or avian cell lines or cell strains. A complete characterization of the cells to be used, may be conducted so that appropriate tests for purity of the final product can be included. Data that can be used for the characterization of a cell includes (a) information on its origin, derivation, and passage history; (b) information on its growth and morphological characteristics; (c) results of tests of adventitious agents; (d) distinguishing features, such as biochemical, immunological, and cytogenetic patterns which allow the cells to be clearly recognized among other cell lines; and (e) results of tests for tumorigenicity. In one embodiment, the passage level, or population doubling, of the host cell used is as low as possible.

(42) In one embodiment, the cells are WHO certified, or certifiable, continuous cell lines. The requirements for certifying such cell lines include characterization with respect to at least one of genealogy, growth characteristics, immunological markers, virus susceptibility tumorigenicity and storage conditions, as well as by testing in animals, eggs, and cell culture. Such characterization is used to confirm that the cells are free from detectable adventitious agents. In some countries, karyology may also be required. In addition, tumorigenicity may be tested in cells that are at the same passage level as those used for vaccine production. The virus may be purified by a process that has been shown to give consistent results, before vaccine production (see, e.g., World Health Organization, 1982).

(43) Virus produced by the host cell may be highly purified prior to vaccine or gene therapy formulation. Generally, the purification procedures result in extensive removal of cellular DNA and other cellular components, and adventitious agents. Procedures that extensively degrade or denature DNA may also be used.

(44) Influenza Vaccines

(45) A vaccine of the invention includes an isolated recombinant influenza virus of the invention, and optionally one or more other isolated viruses including other isolated influenza viruses, one or more immunogenic proteins or glycoproteins of one or more isolated influenza viruses or one or more other pathogens, e.g., an immunogenic protein from one or more bacteria, non-influenza viruses, yeast or fungi, or isolated nucleic acid encoding one or more viral proteins (e.g., DNA vaccines) including one or more immunogenic proteins of the isolated influenza virus of the invention. In one embodiment, the influenza viruses of the invention may be vaccine vectors for influenza virus or other pathogens.

(46) A complete virion vaccine may be concentrated by ultrafiltration and then purified by zonal centrifugation or by chromatography. Viruses other than the virus of the invention, such as those included in a multivalent vaccine, may be inactivated before or after purification using formalin or beta-propiolactone, for instance.

(47) A subunit vaccine comprises purified glycoproteins. Such a vaccine may be prepared as follows: using viral suspensions fragmented by treatment with detergent, the surface antigens are purified, by ultracentrifugation for example. The subunit vaccines thus contain mainly HA protein, and also NA. The detergent used may be cationic detergent for example, such as hexadecyl trimethyl ammonium bromide (Bachmeyer, 1975), an anionic detergent such as ammonium deoxycholate (Laver & Webster, 1976); or a nonionic detergent such as that commercialized under the name TRITON X100. The hemagglutinin may also be isolated after treatment of the virions with a protease such as bromelin, and then purified. The subunit vaccine may be combined with a virus of the invention in a multivalent vaccine.

(48) A split vaccine comprises virions which have been subjected to treatment with agents that dissolve lipids. A split vaccine can be prepared as follows: an aqueous suspension of the purified virus obtained as above, inactivated or not, is treated, under stirring, by lipid solvents such as ethyl ether or chloroform, associated with detergents. The dissolution of the viral envelope lipids results in fragmentation of the viral particles. The aqueous phase is recuperated containing the split vaccine, constituted mainly of hemagglutinin and neuraminidase with their original lipid environment removed, and the core or its degradation products. Then the residual infectious particles are inactivated if this has not already been done. The split vaccine may be combined with a virus of the invention in a multivalent vaccine.

(49) Inactivated Vaccines. Inactivated influenza virus vaccines are provided by inactivating replicated virus using known methods, such as, but not limited to, formalin or -propiolactone treatment. Inactivated vaccine types that can be used in the invention can include whole-virus (WV) vaccines or subvirion (SV) (split) vaccines. The WV vaccine contains intact, inactivated virus, while the SV vaccine contains purified virus disrupted with detergents that solubilize the lipid-containing viral envelope, followed by chemical inactivation of residual virus.

(50) In addition, vaccines that can be used include those containing the isolated HA and NA surface proteins, which are referred to as surface antigen or subunit vaccines.

(51) Live Attenuated Virus Vaccines. Live, attenuated influenza virus vaccines, can be used for preventing or treating influenza virus infection. In one embodiment, attenuation may be achieved in a single step by transfer of attenuated genes from an attenuated donor virus to a replicated isolate or reassorted virus according to known methods. Since resistance to influenza A virus is mediated primarily by the development of an immune response to the HA and/or NA glycoproteins, the genes coding for these surface antigens come from the reassorted viruses or clinical isolates. The attenuated genes may be derived from an attenuated parent. In this approach, genes that confer attenuation generally do not code for the HA and NA glycoproteins.

(52) Viruses (donor influenza viruses) are available that are capable of reproducibly attenuating influenza viruses, e.g., a cold adapted (ca) donor virus can be used for attenuated vaccine production. Live, attenuated reassortant virus vaccines can be generated by mating the ca donor virus with a virulent replicated virus. Reassortant progeny are then selected at 25 C. (restrictive for replication of virulent virus), in the presence of an appropriate antiserum, which inhibits replication of the viruses bearing the surface antigens of the attenuated ca donor virus. Useful reassortants are: (a) infectious, (b) attenuated for seronegative non-adult mammals and immunologically primed adult mammals, (c) immunogenic and (d) genetically stable. The immunogenicity of the ca reassortants parallels their level of replication. Thus, the acquisition of the six transferable genes of the ca donor virus by new wild-type viruses has reproducibly attenuated these viruses for use in vaccinating susceptible mammals both adults and non-adult.

(53) Other attenuating mutations can be introduced into influenza virus genes by site-directed mutagenesis to rescue infectious viruses bearing these mutant genes. Attenuating mutations can be introduced into non-coding regions of the genome, as well as into coding regions. Such attenuating mutations can also be introduced into genes other than the HA or NA, e.g., the PB2 polymerase gene. Thus, new donor viruses can also be generated bearing attenuating mutations introduced by site-directed mutagenesis, and such new donor viruses can be used in the production of live attenuated reassortants vaccine candidates in a manner analogous to that described above for the ca donor virus. Similarly, other known and suitable attenuated donor strains can be reassorted with influenza virus to obtain attenuated vaccines suitable for use in the vaccination of mammals.

(54) In one embodiment, such attenuated viruses maintain the genes from the virus that encode antigenic determinants substantially similar to those of the original clinical isolates. This is because the purpose of the attenuated vaccine is to provide substantially the same antigenicity as the original clinical isolate of the virus, while at the same time lacking pathogenicity to the degree that the vaccine causes minimal chance of inducing a serious disease condition in the vaccinated mammal.

(55) The viruses in a multivalent vaccine can thus be attenuated, single cycle (live) or inactivated, formulated and administered, according to known methods, as a vaccine to induce an immune response in an animal, e.g., a mammal. Methods are well-known in the art for determining whether such attenuated, live single cycle or inactivated vaccines have maintained similar antigenicity to that of the clinical isolate or high growth strain derived therefrom. Such known methods include the use of antisera or antibodies to eliminate viruses expressing antigenic determinants of the donor virus; chemical selection (e.g., amantadine or rimantidine); HA and NA activity and inhibition; and nucleic acid screening (such as probe hybridization or PCR) to confirm that donor genes encoding the antigenic determinants (e.g., HA or NA genes) are not present in attenuated viruses.

(56) Pharmaceutical Compositions

(57) Pharmaceutical compositions of the present invention, suitable for inoculation, e.g., nasal, parenteral or oral administration, comprise one or more influenza virus isolates, e.g., one or more attenuated, live single cycle or inactivated influenza viruses, a subunit thereof, isolated protein(s) thereof, and/or isolated nucleic acid encoding one or more proteins thereof, optionally further comprising sterile aqueous or non-aqueous solutions, suspensions, and emulsions. The compositions can further comprise auxiliary agents or excipients, as known in the art. The composition of the invention is generally presented in the form of individual doses (unit doses).

(58) Conventional vaccines generally contain about 0.1 to 200 g, e.g., 30 to 100 g, of HA from each of the strains entering into their composition. The vaccine forming the main constituent of the vaccine composition of the invention may comprise a single influenza virus, or a combination of influenza viruses, for example, at least two or three influenza viruses, including one or more reassortant(s).

(59) Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and/or emulsions, which may contain auxiliary agents or excipients known in the art. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Carriers or occlusive dressings can be used to increase skin permeability and enhance antigen absorption. Liquid dosage forms for oral administration may generally comprise a liposome solution containing the liquid dosage form. Suitable forms for suspending liposomes include emulsions, suspensions, solutions, syrups, and elixirs containing inert diluents commonly used in the art, such as purified water. Besides the inert diluents, such compositions can also include adjuvants, wetting agents, emulsifying and suspending agents, or sweetening, flavoring, or perfuming agents.

(60) When a composition of the present invention is used for administration to an individual, it can further comprise salts, buffers, adjuvants, or other substances which are desirable for improving the efficacy of the composition. For vaccines, adjuvants, substances which can augment a specific immune response, can be used. Normally, the adjuvant and the composition are mixed prior to presentation to the immune system, or presented separately, but into the same site of the organism being immunized.

(61) Heterogeneity in a vaccine may be provided by mixing replicated influenza viruses for at least two influenza virus strains, such as 2-20 strains or any range or value therein. Vaccines can be provided for variations in a single strain of an influenza virus, using techniques known in the art.

(62) A pharmaceutical composition according to the present invention may further or additionally comprise at least one chemotherapeutic compound, for example, for gene therapy, immunosuppressants, anti-inflammatory agents or immune enhancers, and for vaccines, chemotherapeutics including, but not limited to, gamma globulin, amantadine, guanidine, hydroxybenzimidazole, interferon-, interferon-, interferon-, tumor necrosis factor-alpha, thiosemicarbarzones, methisazone, rifampin, ribavirin, a pyrimidine analog, a purine analog, foscamet, phosphonoacetic acid, acyclovir, dideoxynucleosides, a protease inhibitor, or ganciclovir.

(63) The composition can also contain variable but small quantities of endotoxin-free formaldehyde, and preservatives, which have been found safe and not contributing to undesirable effects in the organism to which the composition is administered.

(64) Pharmaceutical Purposes

(65) The administration of the composition (or the antisera that it elicits) may be for either a prophylactic or therapeutic purpose. When provided prophylactically, the compositions of the invention which are vaccines are provided before any symptom or clinical sign of a pathogen infection becomes manifest. The prophylactic administration of the composition serves to prevent or attenuate any subsequent infection. When provided prophylactically, the gene therapy compositions of the invention, are provided before any symptom or clinical sign of a disease becomes manifest. The prophylactic administration of the composition serves to prevent or attenuate one or more symptoms or clinical signs associated with the disease.

(66) When provided therapeutically, a viral vaccine is provided upon the detection of a symptom or clinical sign of actual infection. The therapeutic administration of the compound(s) serves to attenuate any actual infection. When provided therapeutically, a gene therapy composition is provided upon the detection of a symptom or clinical sign of the disease. The therapeutic administration of the compound(s) serves to attenuate a symptom or clinical sign of that disease.

(67) Thus, a vaccine composition of the present invention may be provided either before the onset of infection (so as to prevent or attenuate an anticipated infection) or after the initiation of an actual infection. Similarly, for gene therapy, the composition may be provided before any symptom or clinical sign of a disorder or disease is manifested or after one or more symptoms are detected.

(68) A composition is said to be pharmacologically acceptable if its administration can be tolerated by a recipient mammal. Such an agent is said to be administered in a therapeutically effective amount if the amount administered is physiologically significant. A composition of the present invention is physiologically significant if its presence results in a detectable change in the physiology of a recipient patient, e.g., enhances at least one primary or secondary humoral or cellular immune response against at least one strain of an infectious influenza virus.

(69) The protection provided need not be absolute, i.e., the influenza infection need not be totally prevented or eradicated, if there is a statistically significant improvement compared with a control population or set of mammals. Protection may be limited to mitigating the severity or rapidity of onset of symptoms or clinical signs of the influenza virus infection.

(70) Pharmaceutical Administration

(71) A composition of the present invention may confer resistance to one or more pathogens, e.g., one or more influenza virus strains, by either passive immunization or active immunization. In active immunization, an attenuated or single cycle live vaccine composition is administered prophylactically to a host (e.g., a mammal), and the host's immune response to the administration protects against infection and/or disease. For passive immunization, the elicited antisera can be recovered and administered to a recipient suspected of having an infection caused by at least one influenza virus strain. A gene therapy composition of the present invention may yield prophylactic or therapeutic levels of the desired gene product by active immunization.

(72) In one embodiment, the vaccine is provided to a mammalian female (at or prior to pregnancy or parturition), under conditions of time and amount sufficient to cause the production of an immune response which serves to protect both the female and the fetus or newborn (via passive incorporation of the antibodies across the placenta or in the mother's milk).

(73) The present invention thus includes methods for preventing or attenuating a disorder or disease, e.g., an infection by at least one strain of pathogen. As used herein, a vaccine is said to prevent or attenuate a disease if its administration results either in the total or partial attenuation (i.e., suppression) of a clinical sign or condition of the disease, or in the total or partial immunity of the individual to the disease. As used herein, a gene therapy composition is said to prevent or attenuate a disease if its administration results either in the total or partial attenuation (i.e., suppression) of a clinical sign or condition of the disease, or in the total or partial immunity of the individual to the disease.

(74) A composition having at least one influenza virus of the present invention, including one which is single cycle, attenuated or inactivated and one or more other isolated viruses, one or more isolated viral proteins thereof, one or more isolated nucleic acid molecules encoding one or more viral proteins thereof, or a combination thereof, may be administered by any means that achieve the intended purposes.

(75) For example, administration of such a composition may be by various parenteral routes such as subcutaneous, intravenous, intradermal, intramuscular, intraperitoneal, intranasal, oral or transdermal routes. Parenteral administration can be accomplished by bolus injection or by gradual perfusion over time.

(76) A typical regimen for preventing, suppressing, or treating an influenza virus related pathology, comprises administration of an effective amount of a vaccine composition as described herein, administered as a single treatment, or repeated as enhancing or booster dosages, over a period up to and including between one week and about 24 months, or any range or value therein.

(77) According to the present invention, an effective amount of a composition is one that is sufficient to achieve a desired effect. It is understood that the effective dosage may be dependent upon the species, age, sex, health, and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment, and the nature of the effect wanted. The ranges of effective doses provided below are not intended to limit the invention and represent dose ranges.

(78) The dosage of a live, attenuated or killed virus vaccine for an animal such as a mammalian adult organism may be from about 10.sup.210.sup.18, e.g., 10.sup.3-10.sup.12, plaque forming units (PFU)/kg, or any range or value therein. The dose of inactivated vaccine may range from about 0.1 to 1000, e.g., 30 to 100 g, of HA protein. However, the dosage should be a safe and effective amount as determined by conventional methods, using existing vaccines as a starting point.

(79) The dosage of immunoreactive HA in each dose of replicated virus vaccine may be standardized to contain a suitable amount, e.g., 30 to 100 g or any range or value therein, or the amount recommended by government agencies or recognized professional organizations. The quantity of NA can also be standardized, however, this glycoprotein may be labile during purification and storage.

(80) The dosage of immunoreactive HA in each dose of replicated virus vaccine can be standardized to contain a suitable amount, e.g., 1-50 g or any range or value therein, or the amount recommended by the U.S. Public Health Service (PHS), which is usually 15 g per component for older children (greater than or equal to 3 years of age), and 7.5 g per component for children less than 3 years of age. The quantity of NA can also be standardized, however, this glycoprotein can be labile during the processor purification and storage (Kendal et al., 1980; Kerr et al., 1975). Each 0.5-ml dose of vaccine may contains approximately 1-50 billion virus particles, and preferably 10 billion particles.

(81) In one embodiment, the vaccine generally contains about 0.1 to 200 g, e.g., 30 to 100 g, 0.1 to 2 g, 0.5 to 5 g, 1 to 10 g, 10 g to 20 g, 15 g to 30 g, or 10 to 30 g, of HA from each of the strains entering into their composition. The vaccine forming the main constituent of the vaccine composition of the invention may comprise a single influenza virus, or a combination of influenza viruses, for example, at least two or three influenza viruses, including one or more reassortant(s).

(82) In one embodiment, the dosage of a live, attenuated or killed virus vaccine for an animal such as a mammalian adult organism may be from about 10.sup.20-10.sup.20, e.g., 10.sup.3-10.sup.12, 10.sup.2-10.sup.10, 10.sup.5-10.sup.10, 10.sup.5-10.sup.15, 10.sup.2-10.sup.10, or 10.sup.15-10.sup.20 plaque forming units (PFU)/kg, or any range or value therein. The dose of one viral isolate vaccine, e.g., in an inactivated vaccine, may range from about 0.1 to 1000, e.g., 0.1 to 10 g, 1 to 20 g, 30 to 100 g, 10 to 50 g, 50 to 200 g, or 150 to 300 g, of HA protein. However, the dosage should be a safe and effective amount as determined by conventional methods, using existing vaccines as a starting point.

(83) In one embodiment, the dosage of immunoreactive HA in each dose of replicated virus vaccine may be standardized to contain a suitable amount, e.g., 0.1 g to 1 g, 0.5 g to 5 g, 1 g to 10 g, 10 g to 20 g, 15 g to 30 g, or 30 g to 100 g or any range or value therein, or the amount recommended by government agencies or recognized professional organizations. The quantity of NA can also be standardized, however, this glycoprotein may be labile during purification and storage.

(84) The dosage of immunoreactive HA in each dose of replicated virus vaccine can be standardized to contain a suitable amount, e.g., 1-50 g or any range or value therein, or the amount recommended by the U.S. Public Health Service (PHS), which is usually 15 g, per component for older children >3 years of age, and 7.5 g per component for children <3 years of age. The quantity of NA can also be standardized, however, this glycoprotein can be labile during the processor purification and storage (Kendal et al., 1980: Kerr et al., 1975). Each 0.5-ml dose of vaccine may contain approximately 0.1 to 0.5 billion viral particles, 0.5 to 2 billion viral particles, 1 to 50 billion virus particles, 1 to 10 billion viral particles, 20 to 40 billion viral particles, 1 to 5 billion viral particles, or 40 to 80 billion viral particles.

(85) Exemplary Embodiments for High Growth PR8 or Cambridge Variants

(86) In one embodiment, the invention provides an isolated recombinant influenza virus having PA, PB1, PB2, NP, NS, and M viral segments from a first influenza vaccine virus isolate, a heterologous influenza virus NA viral segment, and a heterologous HA viral segment, wherein two or more of the PA, PB1, PB2, NP, NS, and M viral segments have selected amino acid residues at positions 30, 31, 105, 142, 149, 225, 356, 357, 401, and/or 550 in PA; positions 40, 54, 59, 62, 63, 75, 76, 78, 79, 80, 112, 180, 247, 327, 507, 624, 644, 667, 694, 695, 697, 699, 700, 701, 702, 705, 713, and/or 714 in PB1; positions 57, 58, 59, 61, 66, 202, 323, 368, 391, 504, 591, 677, 678, and/or 679, in PB2; positions 74, 112, 116, 224, 293, 371, 377, 417, 422 or 442 in NP; positions 90, 97 and/or 100 in M1; or positions 30, 49, 55, 118, 140, 161 and/or 223 in NS1. In one embodiment, the isolated virus has 142N, 225C, 358R, or 550L in PA; has one or more of 112G, 247H, 507V, or 644A in PB1; has one or more of 202L, 323L or 504V in PB2; has one or more of 74K, 112L, 116L, 417D, or 442A in NP; 97A and/or 100H in M1; and/or 55E and/or 140Q in NS1, or combinations thereof, e.g., has at least one of 202L and/or 323L in PB2, 247H in PB1 or 74K in NP and optionally at least one of 142N in PA1, 55K in NS1 or 97A and/or 100H in M1 or has at least one of 202L and/or 323L in PB2, 247H in PB1 or 74K in NP and at least one of 142N in PA1, 55K in NS1 or 97A and/or 100H in M1. In one embodiment, the virus has at least one of 202L and/or 323L in PB2, 247H in PB1 or 74K in NP and optionally at least one of 142N in PA1, 55K in NS1 or 97A and/or 100H in M1. In one embodiment, the virus has at least one of 202L and/or 323L in PB2, 247H in PB1 or 74K in NP and at least one of 142N in PA1, 55K in NS1 or 97A and/or 100H in M1. In one embodiment, the isolated virus has 202L and/or 323L in PB2, and optionally has 247H in PB1 and optionally 74K in NP. In one embodiment, the isolated virus has 247H in PB1 and optionally 74K in NP. In one embodiment, the isolated virus has 401, 40L, 112G, 180W, 247H, 507V, or 644A in PB1 and optionally has 202L and/or 323L in PB2, and optionally has 74K, 112L, 116L, 377N, 417D, or 422L in NP, and optionally has 30P, 118K, 161T or 140Q in NS1, and optionally has 142N, 225C, 356R, 401K, or 550L in PA. In one embodiment, the isolated virus has 401, 40L, 112G, 180W, 247H, 507V, or 644A in PB1. In one embodiment, the isolated virus has 202L and/or 323L in PB2. In one embodiment, the isolated virus has 74K, 112L, 116L, 377N, 417D, or 422L in NP. In one embodiment, the isolated virus has 30P, 118K, 161T or 140Q in NS1. In one embodiment, the isolated virus has 142N, 225C, 356R, 401K, or 550L in PA. In one embodiment, the selected amino acid residues at specified positions in the PA is/are at position(s) 97, 105, 142, 149, 225, 356, 357, 401, 404, and/or 421. In one embodiment, the selected amino acid residues at specified positions in the PB1 is/are at position(s) 12, 40, 54, 59, 62, 63, 66, 75, 76, 78, 79, 80, 180, 247, 507, 624, 644, 694, 695, 697, 699, 700, 701, 705, 713, 714, and/or 762. In one embodiment, the selected amino acid residues at specified positions in the PB2 is/are at position(s) 57, 58, 59, 61, 68, 202, 243, 323, 504, 677, 678, and/or 679. In one embodiment, the selected amino acid residues at specified positions in the NP is/are at position(s) 74, 112, 116, 224, 293, 417, and/or 442. In one embodiment, the selected amino acid residues at specified positions in the M1 is/are at position(s) 90, 97, and/or 100. In one embodiment, the selected amino acid residues at specified positions in the NS1 is/are at position(s) 49, 30, 55, 161, and/or 223. In one embodiment, the selected amino acid residues at specified positions in the PA is/are at position(s) 97, 105, 142, 149, 225, 356, 357, 401, 404, and/or 421; and optionally the selected amino acid residues at specified positions in the PB1 is/are at position(s) 12, 40, 54, 59, 62, 63, 66, 75, 76, 78, 79, 80, 180, 247, 507, 624, 644, 694, 695, 697, 699, 700, 701, 705, 713, 714, and/or 762, in any combination with the selected residues for PA; and optionally the selected amino acid residues at specified positions in the PB2 is/are at position(s) 57, 58, 59, 61, 66, 202, 243, 323, 504, 677, 678, and/or 679 in any combination with the selected residues for PA and/or PB1; and optionally the selected amino acid residues at specified positions in the NP is/are at position(s) 74, 112, 116, 224, 293, 417, and/or 442 any combination with the selected residues for PA, PB1 and/or PB2; and optionally the selected amino acid residues at specified positions in the M1 is/are at position(s) 90, 97, and/or 100 any combination with the selected residues for PA, PB1, PB2, and/or NP; and optionally the selected amino acid residues at specified positions in the NS1 is/are at position(s) 49, 30, 55, 161, and/or 223, or in any combination with the selected residues for PA, PB1, PB2, NP, and/or M1.

(87) For any of the exemplary viruses disclosed above, in one embodiment, the PA, PB1, PB2, NP, NS, and M viral segments comprise sequences for at least one of the following: a PB1 having the amino acid sequence encoded by SEQ ID NO:2 or PB1 with at least 95% amino acid sequence identity to the PB1 encoded by SEQ ID NO:2; a PB2 having the amino acid sequence encoded by SEQ ID NO:3 or PB2 with at least 95% amino acid sequence identity to the PB2 encoded by SEQ ID NO:3; a PA having the amino acid sequence encoded by SEQ ID NO:1 or PA with at least 95% amino acid sequence identity to the PA encoded by SEQ ID NO:1; a NP having the amino acid sequence encoded by SEQ ID NO:4 or NP with at least 95% amino acid sequence identity to the NP encoded by SEQ ID NO:4; a M having the amino acid sequence encoded by SEQ ID NO:5 or M with at least 95% amino acid sequence identity to the M encoded by SEQ ID NO:5; or a NS having the amino acid sequence encoded by SEQ ID NO:6 or NS with at least 95% amino acid sequence identity to the NS encoded by SEQ ID NO:6, or the PA, PB1, PB2, NP, NS, and M viral segments comprise sequences for at least one of the following: a PB1 having the amino acid sequence encoded by SEQ ID NO:10 or PB1 with at least 95% amino acid sequence identity to the PB1 encoded by SEQ ID NO:10; a PB2 having the amino acid sequence encoded by SEQ ID NO:11 or PB2 with at least 95% amino acid sequence identity to the PB2 encoded by SEQ ID NO:11; a PA having the amino acid sequence encoded by SEQ ID NO:12 or PA with at least 95% amino acid sequence identity to the PA encoded by SEQ ID NO:12; a NP having the amino acid sequence encoded by SEQ ID NO:13 or NP with at least 95% amino acid sequence identity to the NP encoded by SEQ ID NO:13; a M having the amino acid sequence encoded by SEQ ID NO:14 or M with at least 95% amino acid sequence identity to the M encoded by SEQ ID NO:14; or a NS having the amino acid sequence encoded by SEQ ID NO:15 or NS with at least 95% amino acid sequence identity to the NS encoded by SEQ ID NO:15.

(88) For any of the exemplary viruses disclosed above, in one embodiment, at least one of the PA, PB1, PB2, NP, NS, and M viral segments has a C to U promoter mutation.

(89) Any of the isolated viruses disclosed herein may be employed in a vaccine.

(90) In one embodiment, the invention provides a plurality of influenza virus vectors for preparing a reassortant. In one embodiment, the plurality includes a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus PA DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus PB1 DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus PB2 DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus HA DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus NP DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus NA DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus M DNA linked to a transcription termination sequence, and a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus NS cDNA linked to a transcription termination sequence, wherein the PB1, PB2, PA, NP, NS, and M DNAs in the vectors for vRNA or cRNA production are from one or more influenza vaccine virus isolates, wherein the NA DNA in the vector for vRNA production of NA has sequences for a heterologous NA, and wherein the HA DNA in the vector for vRNA or cRNA production of HA has sequences for a heterologous HA, 30, 31, 105, 142, 149, 225, 356, 357, 401, and/or 550 in PA; 40, 54, 59, 62, 63, 75, 76, 78, 79, 80, 112, 180, 247, 327, 507, 624, 644, 667, 694, 695, 697, 699, 700, 701, 702, 705, 713, or 714 and/or 247 in PB1; 57, 58, 59, 61, 66, 202, 323, 368, 391, 504, 591, 677, 678, or 679, 202 and/or 323 in PB2; 74, 112, 116, 224, 293, 371, 377, 417, 422 and/or 442 in NP; 90, 97 and/or 100 in M1; or 30, 49, 55, 118, 140, 161 and/or 223 in NS; and a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus PA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus PB1, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus PB2, and a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus NP, and optionally a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus HA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus NA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus M1, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus M2, or a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus NS2. In one embodiment, the PB1, PB2, PA, NP, NS, and M DNAs in the vectors for vRNA or cRNA production have a sequence corresponding to one that encodes a polypeptide having at least 95% amino acid sequence identity to a corresponding polypeptide encoded by SEQ ID NOs:1-6 or 10-15. In one embodiment, the promoter for vRNA or cRNA vectors is a RNA polymerase I promoter, a RNA polymerase II promoter, a RNA polymerase Ill promoter, a T3 promoter or a T7 promoter. In one embodiment, the NA is N9. In one embodiment, the HA is H7. In one embodiment, the PA, PB1, PB2, NP, NS, and/or M viral segments has/have a promoter C to a mutation.

(91) In one embodiment, the invention provides a method to prepare influenza virus. The method includes contacting a cell with: a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus PA DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus PB1 DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus PB2 DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus HA DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus NP DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus NA DNA linked to a transcription termination sequence, a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus M DNA linked to a transcription termination sequence, and a vector for vRNA or cRNA production comprising a promoter operably linked to an influenza virus NS DNA linked to a transcription termination sequence, wherein the PB1, PB2, PA, NP, NS, and M DNAs in the vectors for vRNA or cRNA production are from one or more influenza vaccine virus isolates, wherein the NA DNA in the vector for vRNA or cRNA production of NA has sequences for a heterologous NA, and wherein the HA DNA in the vector for vRNA or cRNA production of HA has sequences for a heterologous HA, 30, 31, 105, 142, 149, 225, 356, 357, 401, and/or 550 in PA; 40, 54, 59, 62, 63, 75, 76, 78, 79, 80, 112, 180, 247, 327, 507, 624, 644, 667, 694, 695, 697, 699, 700, 701, 702, 705, 713, and/or 714 and/or 247 in PB1; 57, 58, 59, 61, 66, 202, 323, 368, 391, 504, 591, 677, 678, and/or 679, 202 and/or 323 in PB2; 74, 112, 116, 224, 293, 371, 377, 417, 422 and/or 442 in NP; 90, 97 and/or 100 in M1; or 30, 49, 55, 118, 140, 161 or 223 in NS; and a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus PA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus PB1, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus PB2, and a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus NP, and optionally a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus HA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus NA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus M1, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus M2, or a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus NS2; in an amount effective to yield infectious influenza virus. In one embodiment, the cell is an avian cell or a mammalian cell, e.g., a Vero cell, a human cell or a MDCK cell. In one embodiment, the PB1, PB2. PA, NP. NS, and M DNAs in the vectors for vRNA productions have a sequence that corresponds to one that encodes a polypeptide having at least 95% amino acid sequence identity to a corresponding polypeptide encoded by SEQ ID NOs:1-6 or 10-15. In one embodiment, the method includes isolating the virus. In one embodiment, at least one of PA, PB1, or PB2 viral segments has a C to U promoter mutation.

(92) Further provided is a vector for vRNA, cRNA or mRNA expression of influenza virus PA having at least 95% amino acid sequence identity to a polypeptide encoded by SEQ ID NO:1 and having a threonine at position 30, a lysine at position 31, cysteine at position 105 or a lysine at position 401; a vector for vRNA, cRNA or mRNA expression of influenza virus PB1 having at least 95% amino acid sequence identity to a polypeptide encoded by SEQ ID NO:2 and having a leucine at position 40, an alanine or isoleucine at position 54, glycine at position 112, histidine at position 247, valine at position 507, alanine at position 644, or cysteine at position 713; a vector for vRNA, cRNA or mRNA expression of PB2 having at least 95% amino acid sequence identity to a polypeptide encoded by SEQ ID NO:3 and a leucine at position 202 and/or 323; a vector for vRNA, cRNA or mRNA expression of influenza virus NP having at least 95% amino acid sequence identity to a polypeptide encoded by SEQ ID NO:4 and having a lysine at position 74, leucine at position 116, isoleucine at position 224, lysine at position 293, asparagine at position 377, or aspartic acid at position 417; a vector for vRNA, cRNA or mRNA expression of influenza virus NS1 having at least 95% amino acid sequence identity to a NS1 polypeptide encoded by SEQ ID NO:6 and having a proline at position 30, alanine at position 49, lysine at position 118, glutamine at position 140, threonine at position 161, or glutamic acid at position 223; and a vector for vRNA, cRNA or mRNA expression of influenza virus M1 having at least 95% amino acid sequence identity to a M1 polypeptide encoded by SEQ ID NO:5 and having a serine at position 90.

(93) Exemplary M Viral Segments

(94) Wild-type influenza A virus M2 protein consists of three structural domains: a 24-amino-acid extracellular domain, a 19-amino-acid transmembrane domain, and a 54-amino-acid cytoplasmic tail domain. The M2 transmembrane domain has ion channel activity, which functions at an early stage of the viral life cycle between the steps of virus penetration and uncoating. The M2 cytoplasmic tail domain may also have an important role in viral assembly and morphogenesis. M1 protein and M2 protein share N-terminal sequences. The M2 protein is encoded by a spliced transcript and RNAs encoding the M1 protein and the M2 protein share 3 sequences, although the coding sequences for M1 and M2 in those 3 sequences are in different reading frames. The C-terminal residues of M1 and C-terminal portion of the extracellular domain of M2 are encoded by the overlapping 3 coding sequences.

(95) A functional M1 protein provides for export of viral nucleic acid from the host cell nucleus, a viral coat, and/or virus assembly and budding. Thus, the M1 protein in the recombinant influenza viruses of the invention has substantially the same function (e.g., at least 10%, 20%, 50% or greater) as a wild-type M1 protein. Thus, any alteration in the M1 coding region in a mutant M viral segment in a recombinant influenza virus does not substantially alter the replication of that virus, e.g., in vitro, for instance, viral titers are not reduced more than about 1 to 2 logs in a host cell that supplies M2 in trans.

(96) In one embodiment, an isolated recombinant influenza virus comprises a mutant M2 protein having a deletion of one or more residues of the cytoplasmic tail of M2, which virus replicates in vitro, e.g., producing titers that are substantially the same or at most 10, 100 or 1,000 fold less than a corresponding wild-type influenza virus, but wherein the replication of the recombinant virus in vivo is limited to a single cycle (e.g., no progeny viruses are produced). In one embodiment, the deletion includes 2 or more residues and up to 21 residues of the cytoplasmic tail of M2. In one embodiment, the M viral segment for the mutant M2 has one to two stop codons near the splice donor or splice acceptor site for the M2 transcript. In one embodiment, the coding region for the transmembrane and/or cytoplasmic domain of M2 is also deleted.

(97) In one embodiment, the deletion of M2 includes 21 or more residues and up to 54 residues, i.e., the entire cytoplasmic tail, of the cytoplasmic tail of M2. In one embodiment, the mutant M2 protein may also comprise at least one amino acid substitution relative to a corresponding wild-type M2 protein. The substitution(s) in the M2 protein may be in the extracellular domain, the transmembrane (TM) domain, or the cytoplasmic domain, or any combination thereof. For example, substitutions in the TM domain may be at residues 25 to 43 of M2, e.g., positions 27, 30, 31, 34, 38, and/or 41 of the TM domain of M2. In another embodiment, the mutant M2 protein may also comprise a deletion in at least a portion of the extracellular domain and/or the TM domain, e.g., a deletion of residues 29 to 31, relative to a corresponding wild-type M2 protein. In yet another embodiment, the mutant M2 protein further comprises a heterologous protein, e.g., the cytoplasmic domain of a heterologous protein (a non-influenza viral protein), which may have a detectable phenotype, fused to the cytoplasmic tail or extracellular domain of M2, forming a chimeric protein. In one embodiment, a cytoplasmic domain of a heterologous protein is fused to the remaining residues of the cytoplasmic tail of the deleted M2 protein. In one embodiment, the presence of one or more substitutions, deletions, or insertions of heterologous sequences, or any combination thereof, does not substantially alter the properties of the recombinant influenza virus, e.g., the presence of one or more substitutions, deletions, or insertions of heterologous sequences does not result in virus titers in vitro that are more than about 1.5 to 2 logs lower, but allows for a single cycle of replication in vivo (e.g., no progeny viruses are produced) for a recombinant influenza virus comprising a mutant M2 protein having a deletion of one or more residues of the cytoplasmic tail of M2.

(98) In one embodiment, the deletion in the cytoplasmic domain of M2 includes 2, 3, 4, 5 or more, e.g., 11, 12, 13, 14, or 15 residues, but less than 22 residues, of the C-terminus of the cytoplasmic tail of M2. In one embodiment, the deletion is 2 up to 10 residues, including any integer in between. In one embodiment, the deletion is from 1 up to less than 8 residues, including any integer in between. In one embodiment, the deletion is from 5 up to 21 residues, including any integer in between. In one embodiment, the deletion is from 5 up to less than 28 residues, including any integer in between. In one embodiment, the deletion is from 9 up to 15 residues, including any integer in between. In one embodiment, the deletion is from 9 up to 23 residues, including any integer in between.

(99) In one embodiment, the deletion in the cytoplasmic domain of M2 includes 22, 23, 24, 25 or more. e.g., 41, 42, 43, 44, or 45 residues, but less than 54 residues, of the C-terminus of the cytoplasmic tail of M2.

(100) In one embodiment, the deletion is from 22 up to 35 residues, including any integer in between. In one embodiment, the deletion is from 29 up to 35 residues, including any integer in between. In one embodiment, the deletion is from 35 up to 45 residues, including any integer in between. In one embodiment, the deletion is from 9 to less than 28 residues, including any integer in between.

(101) In one embodiment, an isolated recombinant influenza virus is provided comprising a mutant M viral segment that is mutated so that upon viral replication, the mutant M gene expresses a functional M1 protein and a mutant M2 protein with a deletion of the cytoplasmic tail and a deletion of at least a portion of the transmembrane domain, e.g., internal or C-terminal deletions, and/or includes one or more substitutions in the transmembrane domain. In one embodiment, the mutant M2 protein has a deletion that includes the entire cytoplasmic tail and transmembrane domain of M2, and has one or more residues of the extracellular domain, e.g., has the first 9 to 15 residues of the extracellular domain. The replication of the recombinant virus is, in one embodiment, a single cycle in vivo relative to a corresponding virus without a mutant M viral segment. The recombinant influenza virus replicates in vitro in the presence of M2 supplied in trans, e.g., producing titers that are substantially the same or at most 10, 100 or 1,000 fold less than a corresponding wild-type influenza virus.

(102) In one embodiment, a live single cycle or attenuated influenza virus elicits both systemic and mucosal immunity at the primary portal of infection. In one embodiment, the live, single cycle or attenuated influenza virus has reduced replication in lung compared to wild-type influenza virus, e.g., the live, single cycle or attenuated influenza virus has titers in lung that are at least one to two logs less, and in one embodiment, replication in nasal turbinates is not detectable. The live, single cycle or attenuated virus may be employed in a vaccine or immunogenic composition, and so is useful to immunize a vertebrate, e.g., an avian or a mammal, or induce an immune response in a vertebrate, respectively.

(103) In one embodiment, the mutations in the M2 gene result in a mutant M2 protein with a deletion of the entire cytoplasmic tail and deletion or substitution of one or more residues in the transmembrane (TM) domain of M2 and may also comprise at least one amino acid substitution in the extracellular domain, or a combination thereof, relative to a corresponding wild-type M2 protein encoded by a M viral segment. For example, substitutions in the TM domain may include those at residues 25 to 43 of M2, e.g., positions 27, 30, 31, 34, 38, and/or 41 of the TM domain of M2. Substitutions and/or deletions in the TM domain may result in a truncated M2 protein that is not embedded in the viral envelope. For example, a deletion of 10 residues at the C-terminus of the transmembrane domain may result in a truncated M2 protein that is not embedded in the viral envelope. In another embodiment, the mutant M2 protein may also comprise a deletion in at least a portion of the extracellular domain in addition to deletion of the cytoplasmic domain and a deletion in the TM domain. In one embodiment, the mutant M2 protein has a deletion of the entire cytoplasmic tail and the TM domain and at least one residue of the extracellular domain, e.g., 1 to 15 residues, or any integer in between, of the C-terminal portion of the extracellular domain. In yet another embodiment, the mutant M2 protein having at least a portion of the extracellular domain further comprises a heterologous protein, e.g., the cytoplasmic and/or TM domain of a heterologous protein (a non-influenza viral protein), which may have a detectable phenotype, that is fused to the C-terminus of at least the extracellular domain of M2, forming a chimeric protein. In one embodiment, the presence of one or more substitutions, deletions, or insertions of heterologous sequences, or any combination thereof, in the M2 gene does not substantially alter the properties of the recombinant influenza virus, e.g., the presence of one or more substitutions, deletions, or insertions of heterologous sequences does not result in virus titers in vitro that are more than about 1.5 to 2 logs lower, and/or but allows for a single cycle (e.g., no progeny viruses are produced) of replication in vivo for the recombinant influenza virus with a mutant M2 protein gene having a deletion of the cytoplasmic tail and TM domain of M2.

(104) In one embodiment, the deletion in the TM domain of M2 includes 1, 2, 3, 4, 5 or more, e.g., 11, 12, 13, 14, or 15 residues, up to 19 residues. In one embodiment, the deletion is from 2 up to 9 residues, including any integer in between. In one embodiment, the deletion is from 15 up to 19 residues, including any integer in between. In one embodiment, the deletion is from 10 up to 19 residues, including any integer in between. In one embodiment, the deletion is the result of at least one substitution of a codon for an amino acid to a stop codon. In one embodiment, the deletion is the result of deletion of at least one codon for an amino acid. In one embodiment, the TM domain of M2 has one or more substitutions, e.g., includes 1, 2, 3, 4, 5 or more, e.g., 11, 12, 13, 14, or 15 substitutions, up to 19 residues of the TM domain. In one embodiment, the one or more amino acid deletions and/or substitutions in the TM domain in a mutant M2 protein that also lacks the cytoplasmic tail of M2, provides for a mutant M2 protein that lacks M2 activity and/or when expressed in a virus yields a live, single cycle virus.

(105) In one embodiment, a deletion in the extracellular (ectodomain) domain of M2 may include 1, 2, 3, 4 or more, e.g., 5, 10, 15, or 20 residues, up to 24 residues of the extracellular domain. In one embodiment, the deletion in the extracellular domain is from 1 up to 15 residues, including any integer in between. In one embodiment, the deletion is the result of at least one substitution of a codon for an amino acid to a stop codon. In one embodiment, the deletion is the result of deletion of at least codon for an amino acid. In one embodiment, the extracellular domain of M2 may also include one or more substitutions. In one embodiment, the mutations in the M2 gene of a M viral segment that result in deletion(s) or substitution(s) in the extracellular domain of M2 do not substantially alter the function of the protein encoded by the M1 gene.

(106) In one embodiment, fewer than 20%, e.g., 10% or 5%, of the residues in the TM domain or extracellular domain are substituted. In one embodiment, fewer than 60%, e.g., 50%, 40%, 30%, 20%, 10%, or 5% of the residues in the extracellular domain are deleted. In one embodiment, more than 20%, e.g., 30%, 40%, 50%, 80% or more, of the residues in the TM domain are deleted.

(107) Exemplary PR8 Viral Segment Variants

Example A

(108) Methods

(109) Cells and Viruses

(110) 293T human embryonic kidney cells are maintained in Dulbecco's modified Eagle's minimal essential medium (DMEM) with 10% fetal calf serum and antibiotics. Madin-Darby canine kidney (MDCK) cells are grown in MEM with 5% newbom calf serum and antibiotics. African green monkey Vero WCB cells, which had been established after biosafety tests for use in human vaccine production (Sugawara et al., 2002), are maintained in serum-free VP-SFM medium (GIBCO-BRL) with antibiotics. Cells are maintained at 37 C. in 5% CO.sub.2. A WHO-recommended vaccine seed virus is NIBRG-14.

(111) Construction of Plasmids and Reverse Genetics

(112) To generate reassortants of influenza A viruses, a plasmid-based reverse genetics (Neumann et al., 1999) is used. The full-length cDNAs were cloned into a plasmid under control of the human polymerase I promoter and the mouse RNA polymerase I terminator (Poll plasmids).

(113) A previously produced series of Poll constructs, derived from A/WSN/33 (H5N1; WSN) or PR8 strains is used, for reverse genetics (Horimoto et al., 2006; Neumann et al., 1999). The World Health Organization (WHO) recommends A/Puerto Rico/8/34 (H1N1; PR8) as a donor virus, because of its safety in humans (Wood & Robertson, 2004; Webby & Webster, 2003).

(114) Plasmids expressing WSN or PR8 NP, PA, PB1, or PB2 under control of the chicken actin, e.g., beta-actin, promoter are used for all reverse genetics experiments (Horimoto et al., 2006; Neumann et al., 1999). Briefly, Poll plasmids and protein expression plasmids are mixed with a transfection reagent, Trans-IT 293T (Panvera), incubated at room temperature for 15 minutes, and then added to 293T cells. Transfected cells are incubated in Opti-MEM I (GIBCO-BRL) for 48 hours. For reverse genetics in Vero WCB cells, an electroporator (Amaxa) is used to transfect the plasmid mixtures according to the manufacturer's instructions. Sixteen hours after transfection, freshly prepared Vero WCB cells were added onto the transfected cells and TPCK-trypsin (1 g/mL) is added to the culture 6 hours later. Transfected cells are incubated in serum-free VP-SFM for a total of 4 days. Supernatants containing infectious viruses are harvested, and may be biologically cloned by limiting dilution.

(115) A recombinant virus having the HA and NA genes from A/Hong Kong/213/2003 (H5N1) and the remainder of the type A influenza virus genes from PR8(UW) was prepared. The titer of the recombinant virus was 10.sup.10.87 EID.sub.50/mL, and the HA titer was 1:1600

(116) TABLE-US-00001 TABLE 1 Virus possessing PR8 genes together with the following HA and NA HA titer (HAU/mL) in each dilition genes 10-2 10-3 10-4 10-5 10-6 10-7 10-8 WSN-HA NA 160 40 40 320 40 640 <1 HK-HAavir NA 400 800 400 400 400 800 <1

(117) The sequences of PR8 (UVV) genes are as follows: Exemplary viral sequences for a master vaccine strain (PR8UW)

(118) HA

(119) TABLE-US-00002 (SEQIDNO:32) AGCAAAAGCAGGGGAAAATAAAAACAACCAAAATGAAGGCAAACCTACT GGTCCTGTTATGTGCACTTGCAGCTGCAGATGCAGACACAATATGTATA GGCTACCATGCGAACAATTCAACCGACACTGTTGACACAGTACTCGAGA AGAATGTGACAGTGACACACTCTGTTAACCTGCTCGAAGACAGCCACAA CGGAAAACTATGTAGATTAAAAGGAATAGCCCCACTACAATTGGGGAAA TGTAACATCGCCGGATGGCTCTTGGGAAACCCAGAATGCGACCCACTGC TTCCAGTGAGATCATGGTCCTACATTGTAGAAACACCAAACTCTGAGAA TGGAATATGTTATCCAGGAGATTTCATCGACTATGAGGAGCTGAGGGAG CAATTGAGCTCAGTGTCATCATTCGAAAGATTCGAAATATTTCCCAAAG AAAGCTCATGGCCCAACCACAACACAAACGGAGTAACGGCAGCATGCTC CCATGAGGGGAAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGAG AAGGAGGGCTCATACCCAAAGCTGAAAAATTCTTATGTGAACAAAAAAG GGAAAGAAGTCCTTGTACTGTGGGGTATTCATCACCCGCCTAACAGTAA GGAACAACAGAATCTCTATCAGAATGAAAATGCTTATGTCTCTGTAGTG ACTTCAAATTATAACAGGAGATTTACCCCGGAAATAGCAGAAAGACCCA AAGTAAGAGATCAAGCTGGGAGGATGAACTATTACTGGACCTTGCTAAA ACCCGGAGACACAATAATATTTGAGGCAAATGGAAATCTAATAGCACCA ATGTATGCTTTCGCACTGAGTAGAGGCTTTGGGTCCGGCATCATCACCT CAAACGCATCAATGCATGAGTGTAACACGAAGTGTCAAACACCCCTGGG AGCTATAAACAGCAGTCTCCCTTACCAGAATATACACCCAGTCACAATA GGAGAGTGCCCAAAATACGTCAGGAGTGCCAAATTGAGGATGGTTACAG GACTAAGGAACATTCCGTCCATTCAATCCAGAGGTCTATTTGGAGCCAT TGCCGGTTTTATTGAAGGGGGATGGACTGGAATGATAGATGGATGGTAT GGTTATCATCATCAGAATGAACAGGGATCAGGCTATGCAGCGGATCAAA AAAGCACACAAAATGCCATTAACGGGATTACAAACAAGGTGAACACTGT TATCGAGAAAATGAACATTCAATTCACAGCTGTGGGTAAAGAATTCAAC AAATTAGAAAAAAGGATGGAAAATTTAAATAAAAAAGTTGATGATGGAT TTCTGGACATTTGGACATATAATGCAGAATTGTTAGTTCTACTGGAAAA TGAAAGGACTCTGGATTTCCATGACTCAAATGTGAAGAATCTGTATGAG AAAGTAAAAAGCCAATTAAAGAATAATGCCAAAGAAATCGGAAATGGAT GTTTTGAGTTCTACCACAAGTGTGACAATGAATGCATGGAAAGTGTAAG AAATGGGACTTATGATTATCCCAAATATTCAGAAGAGTCAAAGTTGAAC AGGGAAAAGGTAGATGGAGTGAAATTGGAATCAATGGGGATCTATCAGA TTCTGGCGATCTACTCAACTGTCGCCAGTTCACTGGTGCTTTTGGTCTC CCTGGGGGCAATCAGTTTCTGGATGTGTTCTAATGGATCTTTGCAGTGC AGAATATGCATCTGAGATTAGAATTTCAGAGATATGAGGAAAAACACCC TTGTTTCTACT
NA

(120) TABLE-US-00003 (SEQIDNO:33) AGCAAAAGCAGGGGTTTAAAATGAATCCAAATCAGAAAATAATAACCAT TGGATCAATCTGTCTGGTAGTCGGACTAATTAGCCTAATATTGCAAATA GGGAATATAATCTCAATATGGATTAGCCATTCAATTCAAACTGGAAGTC AAAACCATACTGGAATATGCAACCAAAACATCATTACCTATAAAAATAG CACCTGGGTAAAGGACACAACTTCAGTGATATTAACCGGCAATTCATCT CTTTGTCCCATCCGTGGGTGGGCTATATACAGCAAAGACAATAGCATAA GAATTGGTTCCAAAGGAGACGTTTTTGTCATAAGAGAGCCCTTTATTTC ATGTTCTCACTTGGAATGCAGGACCTTTTTTCTGACCCAAGGTGCCTTA CTGAATGACAAGCATTCAAGTGGGACTGTTAAGGACAGAAGCCCTTATA GGGCCTTAATGAGCTGCCCTGTCGGTGAAGCTCCGTCCCCGTACAATTC AAGATTTGAATCGGTTGCTTGGTCAGCAAGTGCATGTCATGATGGCATG GGCTGGCTAACAATCGGAATTTCAGGTCCAGATAATGGAGCAGTGGCTG TATTAAAATACAACGGCATAATAACTGAAACCATAAAAAGTTGGAGGAA GAAAATATTGAGGACACAAGAGTCTGAATGTGCCTGTGTAAATGGTTCA TGTTTTACTATAATGACTGATGGCCCGAGTGATGGGCTGGCCTCGTACA AAATTTTCAAGATCGAAAAGGGGAAGGTTACTAAATCAATAGAGTTGAA TGCACCTAATTCTCACTATGAGGAATGTTCCTGTTACCCTGATACCGGC AAAGTGATGTGTGTGTGCAGAGACAATTGGCATGGTTCGAACCGGCCAT GGGTGTCTTTCGATCAAAACCTGGATTATCAAATAGGATACATCTGCAG TGGGGTTTTCGGTGACAACCCGCGTCCCGAAGATGGAACAGGCAGCTGT GGTCCAGTGTATGTTGATGGAGCAAACGGAGTAAAGGGATTTTCATATA GGTATGGTAATGGTGTTTGGATAGGAAGGACCAAAAGTCACAGTTCCAG ACATGGGTTTGAGATGATTTGGGATCCTAATGGATGGACAGAGACTGAT AGTAAGTTCTCTGTGAGGCAAGATGTTGTGGCAATGACTGATTGGTCAG GGTATAGCGGAAGTTTCGTTCAACATCCTGAGCTGACAGGGCTAGACTG TATGAGGCCGTGCTTCTGGGTTGAATTAATCAGGGGACGACCTAAAGAA AAAACAATCTGGACTAGTGCGAGCAGCATTTCTTTTTGTGGCGTGAATA GTGATACTGTAGATTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCAG CATTGACAAGTAGTCTGTTCAAAAAACTCCTTGTTTCTACT
PA

(121) TABLE-US-00004 (SEQIDNO:34) AGCGAAAGCAGGTACTGATCCAAAATGGAAGATTTTGTGC GACAATGCTTCAATCCGATGATTGTCGAGCTTGCGGAAAA AACAATGAAAGAGTATGGGGAGGACCTGAAAATCGAAACA AACAAATTTGCAGCAATATGCACTCACTTGGAAGTATGCT TCATGTATTCAGATTTTCACTTCATCAATGAGCAAGGCGA GTCAATAATCGTAGAACTTGGTGATCCAAATGCACTTTTG AAGCACAGATTTGAAATAATCGAGGGAAGAGATCGCACAA TGGCCTGGACAGTAGTAAACAGTATTTGCAACACTACAGG GGCTGAGAAACCAAAGTTTCTACCAGATTTGTATGATTAC AAGGAGAATAGATTCATCGAAATTGGAGTAACAAGGAGAG AAGTTCACATATACTATCTGGAAAAGGCCAATAAAATTAA ATCTGAGAAAACACACATCCACATTTTCTCGTTCACTGGG GAAGAAATGGCCACAAAGGCAGACTACACTCTCGATGAAG AAAGCAGGGCTAGGATCAAAACCAGACTATTCACCATAAG ACAAGAAATGGCCAGCAGAGGCCTCTGGGATTCCTTTCGT CAGTCCGAGAGAGGAGAAGAGACAATTGAAGAAAGGTTTG AAATCACAGGAACAATGCGCAAGCTTGCCGACCAAAGTCT CCCGCCGAACTTCTCCAGCCTTGAAAATTTTAGAGCCTAT GTGGATGGATTCGAACCGAACGGCTACATTGAGGGCAAGC TGTCTCAAATGTCCAAAGAAGTAAATGCTAGAATTGAACC TTTTTTGAAAACAACACCACGACCACTTAGACTTCCGAAT GGGCCTCCCTGTTCTCAGCGGTCCAAATTCCTGCTGATGG ATGCCTTAAAATTAAGCATTGAGGACCCAAGTCATGAAGG AGAGGGAATACCGCTATATGATGCAATCAAATGCATGAGA ACATTCTTTGGATGGAAGGAACCCAATGTTGTTAAACCAC ACGAAAAGGGAATAAATCCAAATTATCTTCTGTCATGGAA GCAAGTACTGGCAGAACTGCAGGACATTGAGAATGAGGAG AAAATTCCAAAGACTAAAAATATGAAGAAAACAAGTCAGC TAAAGTGGGCACTTGGTGAGAACATGGCACCAGAAAAGGT AGACTTTGACGACTGTAAAGATGTAGGTGATTTGAAGCAA TATGATAGTGATGAACCAGAATTGAGGTCGCTTGCAAGTT GGATTCAGAATGAGTTTAACAAGGCATGCGAACTGACAGA TTCAAGCTGGATAGAGCTCGATGAGATTGGAGAAGATGTG GCTCCAATTGAACACATTGCAAGCATGAGAAGGAATTATT TCACATCAGAGGTGTCTCACTGCAGAGCCACAGAATACAT AATGAAGGGAGTGTACATCAATACTGCCTTGCTTAATGCA TCTTGTGCAGCAATGGATGATTTCCAATTAATTCCAATGA TAAGCAAGTGTAGAACTAAGGAGGGAAGGCGAAAGACCAA CTTGTATGGTTTCATCATAAAAGGAAGATCCCACTTAAGG AATGACACCGACGTGGTAAACTTTGTGAGCATGGAGTTTT CTCTCACTGACCCAAGACTTGAACCACATAAATGGGAGAA GTACTGTGTTCTTGAGATAGGAGATATGCTTATAAGAAGT GCCATAGGCCAGGTTTCAAGGCCCATGTTCTTGTATGTGA GAACAAATGGAACCTCAAAAATTAAAATGAAATGGGGAAT GGAGATGAGGCGTTGCCTCCTCCAGTCACTTCAACAAATT GAGAGTATGATTGAAGCTGAGTCCTCTGTCAAAGAGAAAG ACATGACCAAAGAGTTCTTTGAGAACAAATCAGAAACATG GCCCATTGGAGAGTCCCCCAAAGGAGTGGAGGAAAGTTCC ATTGGGAAGGTCTGCAGGACTTTATTAGCAAAGTCGGTAT TCAACAGCTTGTATGCATCTCCACAACTAGAAGGATTTTC AGCTGAATCAAGAAAACTGCTTCTTATCGTTCAGGCTCTT AGGGACAACCTGGAACCTGGGACCTTTGATCTTGGGGGGC TATATGAAGCAATTGAGGAGTGCCTGATTAATGATCCCTG GGTTTTGCTTAATGCTTCTTGGTTCAACTCCTTCCTTACA CATGCATTGAGTTAGTTGTGGCAGTGCTACTATTTGCTAT CCATACTGTCCAAAAAAGTACCTTGTTTCTACT
PB1

(122) TABLE-US-00005 (SEQIDNO:35) AGCGAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACCTTACTTT TCTTAAAAGTGCCAGCACAAAATGCTATAAGCACAACTTTCCCTTATAC TGGAGACCCTCCTTACAGCCATGGGACAGGAACAGGATACACCATGGAT ACTGTCAACAGGACACATCAGTACTCAGAAAAGGGAAGATGGACAACAA ACACCGAAACTGGAGCACCGCAACTCAACCCGATTGATGGGCCACTGCC AGAAGACAATGAACCAAGTGGTTATGCCCAAACAGATTGTGTATTGGAG GCGATGGCTTTCCTTGAGGAATCCCATCCTGGTATTTTTGAAAACTCGT GTATTGAAACGATGGAGGTTGTTCAGCAAACACGAGTAGACAAGCTGAC ACAAGGCCGACAGACCTATGACTGGACTCTAAATAGAAACCAACCTGCT GCAACAGCATTGGCCAACACAATAGAAGTGTTCAGATCAAATGGCCTCA CGGCCAATGAGTCTGGAAGGCTCATAGACTTCCTTAAGGATGTAATGGA GTCAATGAACAAAGAAGAAATGGGGATCACAACTCATTTTCAGAGAAAG AGACGGGTGAGAGACAATATGACTAAGAAAATGATAACACAGAGAACAA TGGGTAAAAAGAAGCAGAGATTGAACAAAAGGAGTTATCTAATTAGAGC ATTGACCCTGAACACAATGACCAAAGATGCTGAGAGAGGGAAGCTAAAA CGGAGAGCAATTGCAACCCCAGGGATGCAAATAAGGGGGTTTGTATACT TTGTTGAGACACTGGCAAGGAGTATATGTGAGAAACTTGAACAATCAGG GTTGCCAGTTGGAGGCAATGAGAAGAAAGCAAAGTTGGCAAATGTTGTA AGGAAGATGATGACCAATTCTCAGGACACCGAACTTTCTTTCACCATCA CTGGAGATAACACCAAATGGAACGAAAATCAGAATCCTCGGATGTTTTT GGCCATGATCACATATATGACCAGAAATCAGCCCGAATGGTTCAGAAAT GTTCTAAGTATTGCTCCAATAATGTTCTCAAACAAAATGGCGAGACTGG GAAAAGGGTATATGTTTGAGAGCAAGAGTATGAAACTTAGAACTCAAAT ACCTGCAGAAATGCTAGCAAGCATCGATTTGAAATATTICAATGATTCA ACAAGAAAGAAGATTGAAAAAATCCGACCGCTCTTAATAGAGGGGACTG CATCATTGAGCCCTGGAATGATGATGGGCATGTTCAATATGTTAAGCAC TGTATTAGGCGTCTCCATCCTGAATCTTGGACAAAAGAGATACACCAAG ACTACTTACTGGTGGGATGGTCTTCAATCCTCTGACGATTTTGCTCTGA TTGTGAATGCACCCAATCATGAAGGGATTCAAGCCGGAGTCGACAGGTT TTATCGAACCTGTAAGCTACTTGGAATCAATATGAGCAAGAAAAAGTCT TACATAAACAGAACAGGTACATTTGAATTCACAAGTTTTTTCTATCGTT ATGGGTTTGTTGCCAATTTCAGCATGGAGCTTCCCAGTTTTGGGGTGTC TGGGATCAACGAGTCAGCGGACATGAGTATTGGAGTTACTGTCATCAAA AACAATATGATAAACAATGATCTTGGTCCAGCAACAGCTCAAATGGCCC TTCAGTTGTTCATCAAAGATTACAGGTACACGTACCGATGCCATATAGG TGACACACAAATACAAACCCGAAGATCATTTGAAATAAAGAAACTGTGG GAGCAAACCCGTTCCAAAGCTGGACTGCTGGTCTCCGACGGAGGCCCAA ATTTATACAACATTAGAAATCTCCACATTCCTGAAGTCTGCCTAAAATG GGAATTGATGGATGAGGATTACCAGGGGCGTTTATGCAACCCACTGAAC CCATTTGTCAGCCATAAAGAAATTGAATCAATGAACAATGCAGTGATGA TGCCAGCACATGGTCCAGCCAAAAACATGGAGTATGATGCTGTTGCAAC AACACACTCCTGGATCCCCAAAAGAAATCGATCCATCTTGAATACAAGT CAAAGAGGAGTACTTGAGGATGAACAAATGTACCAAAGGTGCTGCAATT TATTTGAAAAATTCTTCCCCAGCAGTTCATACAGAAGACCAGTCGGGAT ATCCAGTATGGTGGAGGCTATGGTTTCCAGAGCCCGAATTGATGCACGG ATTGATTTCGAATCTGGAAGGATAAAGAAAGAAGAGTTCACTGAGATCA TGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAAAAATAGTGAAT TTAGCTTGTCCTTCATGAAAAAATGCCTTGTTTCTACT
PB2

(123) TABLE-US-00006 (SEQIDNO:36) AGCGAAAGCAGGTCAATTATATTCAATATGGAAAGAATAA AAGAACTACGAAATCTAATGTCGCAGTCTCGCACCCGCGA GATACTCACAAAAACCACCGTGGACCATATGGCCATAATC AAGAAGTACACATCAGGAAGACAGGAGAAGAACCCAGCAC TTAGGATGAAATGGATGATGGCAATGAAATATCCAATTAC AGCAGACAAGAGGATAACGGAAATGATTCCTGAGAGAAAT GAGCAAGGACAAACTTTATGGAGTAAAATGAATGATGCCG GATCAGACCGAGTGATGGTATCACCTCTGGCTGTGACATG GTGGAATAGGAATGGACCAATAACAAATACAGTTCATTAT CCAAAAATCTACAAAACTTATTTTGAAAGAGTCGAAAGGC TAAAGCATGGAACCTTTGGCCCTGTCCATTTTAGAAACCA AGTCAAAATACGTCGGAGAGTTGACATAAATCCTGGTCAT GCAGATCTCAGTGCCAAGGAGGCACAGGATGTAATCATGG AAGTTGTTTTCCCTAACGAAGTGGGAGCCAGGATACTAAC ATCGGAATCGCAACTAACGATAACCAAAGAGAAGAAAGAA GAACTCCAGGATTGCAAAATTTCTCCTTTGATGGTTGCAT ACATGTTGGAGAGAGAACTGGTCCGCAAAACGAGATTCCT CCCAGTGGCTGGTGGAACAAGCAGTGTGTACATTGAAGTG TTGCATTTGACTCAAGGAACATGCTGGGAACAGATGTATA CTCCAGGAGGGGAAGTGAGGAATGATGATGTTGATCAAAG CTTGATTATTGCTGCTAGGAACATAGTGAGAAGAGCTGCA GTATCAGCAGATCCACTAGCATCTTTATTGGAGATGTGCC ACAGCACACAGATTGGTGGAATTAGGATGGTAGACATCCT TAGGCAGAACCCAACAGAAGAGCAAGCCGTGGATATATGC AAGGCTGCAATGGGACTGAGAATTAGCTCATCCTTCAGTT TTGGTGGATTCACATTTAAGAGAACAAGCGGATCATCAGT CAAGAGAGAGGAAGAGGTGCTTACGGGCAATCTTCAAACA TTGAAGATAAGAGTGCATGAGGGATATGAAGAGTTCACAA TGGTTGGGAGAAGAGCAACAGCCATACTCAGAAAAGCAAC CAGGAGATTGATTCAGCTGATAGTGAGTGGGAGAGACGAA CAGTCGATTGCCGAAGCAATAATTGTGGCCATGGTATTTT CACAAGAGGATTGTATGATAAAAGCAGTCAGAGGTGATCT GAATTTCGTCAATAGGGCGAATCAACGATTGAATCCTATG CATCAACTTTTAAGACATTTTCAGAAGGATGCGAAAGTGC TTTTTCAAAATTGGGGAGTTGAACCTATCGACAATGTGAT GGGAATGATTGGGATATTGCCCGACATGACTCCAAGCATC GAGATGTCAATGAGAGGAGTGAGAATCAGCAAAATGGGTG TAGATGAGTACTCCAGCACGGAGAGGGTAGTGGTGAGCAT TGACCGTTTTTTGAGAATCCGGGACCAACGAGGAAATGTA CTACTGTCTCCCGAGGAGGTCAGTGAAACACAGGGAACAG AGAAACTGACAATAACTTACTCATCGTCAATGATGTGGGA GATTAATGGTCCTGAATCAGTGTTGGTCAATACCTATCAA TGGATCATCAGAAACTGGGAAACTGTTAAAATTCAGTGGT CCCAGAACCCTACAATGCTATACAATAAAATGGAATTTGA ACCATTTCAGTCTTTAGTACCTAAGGCCATTAGAGGCCAA TACAGTGGGTTTGTAAGAACTCTGTTCCAACAAATGAGGG ATGTGCTTGGGACATTTGATACCGCACAGATAATAAAACT TCTTCCCTTCGCAGCCGCTCCACCAAAGCAAAGTAGAATG CAGTTCTCCTCATTTACTGTGAATGTGAGGGGATCAGGAA TGAGAATACTTGTAAGGGGCAATTCTCCTGTATTCAACTA TAACAAGGCCACGAAGAGACTCACAGTTCTCGGAAAGGAT GCTGGCACTTTAACTGAAGACCCAGATGAAGGCACAGCTG GAGTGGAGTCCGCTGTTCTGAGGGGATTCCTCATTCTGGG CAAAGAAGACAAGAGATATGGGCCAGCACTAAGCATCAAT GAACTGAGCAACCTTGCGAAAGGAGAGAAGGCTAATGTGC TAATTGGGCAAGGAGACGTGGTGTTGGTAATGAAACGGAA ACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACC AAAAGAATTCGGATGGCCATCAATTAGTGTCGAATAGTTT AAAAACGACCTTGTTTCTACT
NP

(124) TABLE-US-00007 (SEQIDNO:37) AGCAAAAGCAGGGTAGATAATCACTCACTGAGTGACATCA AAATCATGGCGTCTCAAGGCACCAAACGATCTTACGAACA GATGGAGACTGATGGAGAACGCCAGAATGCCACTGAAATC AGAGCATCCGTCGGAAAAATGATTGGTGGAATTGGACGAT TCTACATCCAAATGTGCACCGAACTCAAACTCAGTGATTA TGAGGGACGGTTGATCCAAAACAGCTTAACAATAGAGAGA ATGGTGCTCTCTGCTTTTGACGAAAGGAGAAATAAATACC TTGAAGAACATCCCAGTGCGGGGAAAGATCCTAAGAAAAC TGGAGGACCTATATACAGGAGAGTAAACGGAAAGTGGATG AGAGAACTCATCCTTTATGACAAAGAAGAAATAAGGCGAA TCTGGCGCCAAGCTAATAATGGTGACGATGCAACGGCTGG TCTGACTCACATGATGATCTGGCATTCCAATTTGAATGAT GCAACTTATCAGAGGACAAGAGCTCTTGTTCGCACCGGAA TGGATCCCAGGATGTGCTCTCTGATGCAAGGTTCAACTCT CCCTAGGAGGTCTGGAGCCGCAGGTGCTGCAGTCAAAGGA GTTGGAACAATGGTGATGGAATTGGTCAGAATGATCAAAC GTGGGATCAATGATCGGAACTTCTGGAGGGGTGAGAATGG ACGAAAAACAAGAATTGCTTATGAAAGAATGTGCAACATT CTCAAAGGGAAATTTCAAACTGCTGCACAAAAAGCAATGA TGGATCAAGTGAGAGAGAGCCGGAACCCAGGGAATGCTGA GTTCGAAGATCTCACTTTTCTAGCACGGTCTGCACTCATA TTGAGAGGGTCGGTTGCTCACAAGTCCTGCCTGCCTGCCT GTGTGTATGGACCTGCCGTAGCCAGTGGGTACGACTTTGA AAGGGAGGGATACTCTCTAGTCGGAATAGACCCTTTCAGA CTGCTTCAAAACAGCCAAGTGTACAGCCTAATCAGACCAA ATGAGAATCCAGCACACAAGAGTCAACTGGTGTGGATGGC ATGCCATTCTGCCGCATTTGAAGATCTAAGAGTATTAAGC TTCATCAAAGGGACGAAGGTGCTCCCAAGAGGGAAGCTTT CCACTAGAGGAGTTCAAATTGCTTCCAATGAAAATATGGA GACTATGGAATCAAGTACACTTGAACTGAGAAGCAGGTAC TGGGCCATAAGGACCAGAAGTGGAGGAAACACCAATCAAC AGAGGGCATCTGCGGGCCAAATCAGCATACAACCTACGTT CTCAGTACAGAGAAATCTCCCTTTTGACAGAACAACCATT ATGGCAGCATTCAATGGGAATACAGAGGGGAGAACATCTG ACATGAGGACCGAAATCATAAGGATGATGGAAAGTGCAAG ACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAG CTCTCGGACGAAAAGGCAGCGAGCCCGATCGTGCCTTCCT TTGACATGAGTAATGAAGGATCTTATTTCTTCGGAGACAA TGCAGAGGAGTACGACAATTAAAGAAAAATACCCTTGTTT CTACT
M

(125) TABLE-US-00008 (SEQIDNO:38) AGCAAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACC GAGGTCGAAACGTACGTACTCTCTATCATCCCGTCAGGCC CCCTCAAAGCCGAGATCGCACAGAGACTTGAAGATGTCTT TGCAGGGAAGAACACCGATCTTGAGGTTCTCATGGAATGG CTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGA TTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCG AGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTTAAT GGGAACGGGGATCCAAATAACATGGACAAAGCAGTTAAAC TGTATAGGAAGCTCAAGAGGGAGATAACATTCCATGGGGC CAAAGAAATCTCACTCAGTTATTCTGCTGGTGCACTTGCC AGTTGTATGGGCCTCATATACAACAGGATGGGGGCTGTGA CCACTGAAGTGGCATTTGGCCTGGTATGTGCAACCTGTGA ACAGATTGCTGACTOCCAGCATCGGTCTCATAGGCAAATG GTGACAACAACCAATCCACTAATCAGACATGAGAACAGAA TGGTTTTAGCCAGCACTACAGCTAAGGCTATGGAGCAAAT GGCTGGATCGAGTGAGCAAGCAGCAGAGGCCATGGAGGTT GCTAGTCAGGCTAGACAAATGGTGCAAGCGATGAGAACCA TTGGGACTCATCCTAGCTCCAGTGCTGGTCTGAAAAATGA TCTTCTTGAAAATTTGCAGGCCTATCAGAAACGAATGGGG GTGCAGATGCAACGGTTCAAGTGATCCTCTCACTATTGCC GCAAATATCATTGGGATCTTGCACTTGACATTGTGGATTC TTGATCGTCTTTTTTTCAAATGCATTTACCGTCGCTTTAA ATACGGACTGAAAGGAGGGCCTTCTACGGAAGGAGTGCCA AAGTCTATGAGGGAAGAATATCGAAAGGAACAGCAGAGTG CTGTGGATGCTGACGATGGTCATTTTGTCAGCATAGAGCT GGAGTAAAAAACTACCTTGTTTCTACT
NS

(126) TABLE-US-00009 (SEQIDNO:39) AGCAAAAGCAGGGTGACAAAAACATAATGGATCCAAACAC TGTGTCAAGCTTTCAGGTAGATTGCTTTCTTTGGCATGTC CGCAAACGAGTTGCAGACCAAGAACTAGGCGATGCCCCAT TCCTTGATCGGCTTCGCCGAGATCAGAAATCCCTAAGAGG AAGGGGCAGTACTCTCGGTCTGGACATCAAGACAGCCACA CGTGCTGGAAAGCAGATAGTGGAGCGGATTCTGAAAGAAG AATCCGATGAGGCACTTAAAATGACCATGGCCTCTGTACC TGCGTCGCGTTACCTAACTGACATGACTCTTGAGGAAATG TCAAGGGACTGGTCCATGCTCATACCCAAGCAGAAAGTGG CAGGCCCTCTTTGTATCAGAATGGACCAGGCGATCATGGA TAAGAACATCATACTGAAAGCGAACTTCAGTGTGATTTTT GACCGGCTGGAGACTCTAATATTGCTAAGGGCTTTCACCG AAGAGGGAGCAATTGTTGGCGAAATTTCACCATTGCCTTC TCTTCCAGGACATACTGCTGAGGATGTCAAAAATGCAGTT GGAGTCCTCATCGGAGGACTTGAATGGAATGATAACACAG TTCGAGTCTCTGAAACTCTACAGAGATTCGCTTGGAGAAG CAGTAATGAGAATGGGAGACCTCCACTCACTCCAAAACAG AAACGAGAAATGGCGGGAACAATTAGGTCAGAAGTTTGAA GAAATAAGATGGTTGATTGAAGAAGTGAGACACAAACTGA AGATAACAGAGAATAGTTTTGAGCAAATAACATTTATGCA AGCCTTACATCTATTGCTTGAAGTGGAGCAAGAGATAAGA ACTTTCTCGTTTCAGCTTATTTAGTACTAAAAAACACCCT TGTTTCTACT

(127) High-titer A/PR/8/34 (H1N1, PR8(UW)) virus grows 10 times better than other NAPR/8/34 PR8 strains 45 in eggs (10.sup.10 EID.sub.50/mL; HA titer:1:8.000). Thus, replacement of the HA and NA genes of PR8(UW) with those of a currently circulating strain of influenza virus results in a vaccine strain that can be safely produced, and validates the use of PR8(UW) as a master vaccine strain.

(128) Genes that contribute to different growth properties between PR8(UW) and PR8 (Cambridge), which provides the non-HA and -NA genes of the NIBRG-14 vaccine strain (FIG. 1), were determined. Higher titers in eggs were obtained when the majority of internal genes were from PR8(UW). Highest titers were with the M viral segment of PR8(UW) and the NS gene of PR8 (Cambridge). The NS gene in PR8(UW) has a K (lysine) at residue 55 while the NS gene in PR8(Cam) has a E (glutamic acid). The polymerase subunit (PA, PB1, and PB2) and NP genes of PR8(UW) enhanced the growth of an H5N1 vaccine seed virus in chicken embryonated eggs, and the NS gene of PR8(Cambridge) enhanced the growth of an H5N1 vaccine seed virus in chicken embryonated eggs. A tyrosine (Y) at position 360 in PB2 of PR8(UW) likely contributes to the high growth rate of that virus in MDCK cells.

Example B

(129) To develop an high-yield A/PR/8/34 (H1N1; PR8) virus backbone for growth of vaccine virus in specific host cells, random mutagenesis of the internal genes of PR8(HG) (PRBUW) was conducted. Random mutations were introduced into the UW-PR8 (Example 1) internal genes by error-prone PCR after which plasmid libraries were prepared that possessed the random mutations in an individual UW-PR8 internal gene. Then virus libraries (PR8H5N) were generated that possessed random mutations in an individual UW-PR8 internal gene, along with the other wild type internal genes and the NA and detoxified HA genes of A/chicken/IndonesiaNC/09 (H5N) virus (Table 1), to generate 6+2 recombinant viruses. Consecutive passages of the virus in MDCK cells were employed to select for variants with high-growth properties.

(130) TABLE-US-00010 TABLE 1 Virus libraries generated Internal genes Titer of virus Other library Number Gene library internal genes HA + NA (pfu/ml) Control PR8 wild type NC/09/H5N1 3 10.sup.6 1 PB2 5 UW-PR8 genes NC/09/H5N1 2.1 10.sup.2 2 PB1 5 UW-PR8 genes NC/09/H5N1 1.6 10.sup.5 3 PA 5 UW-PR8 genes NC/09/H5N1 7 10.sup.3 4 NP 5 UW-PR8 genes NC/09/H5N1 1.5 10.sup.3 5 M 5 UW-PR8 genes NC/09/H5N1 1 10.sup.6 6 NS 5 UW-PR8 genes NC/09/H5N1 1.8 10.sup.6 7 PB2 + PB1 + 3UW-PR8 genes NC/09/H5N1 75 PA 8 PB2 + PB1 + 2UW-PR8 genes NC/09/H5N1 33 PA + NP 9 PB2 + NS 4UW-PR8 genes NC/09/H5N1 2 10.sup.2 10 M + NS 4UW-PR8 genes NC/09/H5N1 5.7 10.sup.5
Virus libraries were passaged 12 times in MDCK cells or, after 2 passages, the libraries were mixed and 10 more passages were carried out (FIG. 2).

(131) After 10 to about 12 consecutive passages in MDCK cells, plaque assays were performed and over 1,400 individual plaques were picked. FIG. 3 shows the numbers of clones with various HA titers. Growth enhancing mutations included: PB2: M202L, F323L, I504V, PB1: E1112G, V644A, NP: R74K, N417D, I116L, and NS: S161T. FIG. 4 provides the titers of recombinant viruses generated from selected mutations.

(132) 38 viruses with the highest HA titers from the random mutagenesis libraries were sequenced (Table 2)

(133) TABLE-US-00011 TABLE 2 Sequences of viruses with the highest HA titers HA Clone titer HA (H3 # Library (2.sup.n) PB2 PB1 PA numbering) NP NA M NS WT 7 329 Mix 9 M202L L182V F323L 154 Mix 8.5~9 M202L L182V F323L 347 Mix 9 M202L L182V F323L 94 Mix 8.5 M202L F252I I116L L55S F323L 1045 Mix 9 M202L V644A F252I F323L 965 Mix 8.5~9 M202L F105C V184I P90S F323L 50 Mix 8.5 M202L M148I R293M F323L (HA2) 1005 Mix 9~9.5 M202L V644A R401K M148I T49A F323L (HA2) 134 Mix 8.5 M202L A223E F323L 387 Mix 9 M202L M507V F323L V644A 852 Mix 9~9.5 M202L R54I F323L M243I 981 Mix 8.5~9 M202L Q247H F323L 993 Mix 8.5~9 M202L N224I F323L 1043 Mix 8.5~9 I504V L182V R74K 398 Mix 8.5 I504V L182V R74K, A30P N417D 1007 Mix 8.5 I504V V644A F252I M371V 1042 Mix 8.5~9 I504V E75V F252I R74K D76G E78P P79V S80G V644A E697P F699L F700L P701H S702R Y705T 999 Mix 8.5~9 I504V M148I R74K, (HA2) N417D 1014 Mix 8.5 I504V T59I M148I R74K, A265V G62X (HA2) N417D A63P V644A N694K L695T 1016 Mix 8.5~9 I504V M148I (HA2) 540 PB1 8.5 E112G K162E S161T 548 PB1 8.5~9 E112G K162E S161T L624V 191 PB1 8~8.5 E112G 571 PB1 9~9.5 E112G 572 PB1 8.5 E112G 573 PB1 8.5 E112G 1404 PB1 8.5 I57V E112G T58G S713C A59V K61Q E677D D678E P679M 1408 PB1 8.5 M40I S161T G180W 582 PB1 8.5~9 M40L, S161T G180W 545 PB1 8.5 M40L, K121E G180W (HA2) 543 PB1 8.5 I667T 219 PB1 9 I667T, K162E M714T 344 Mix 8.5~9 M66R L182V 312 Mix 8.5~9 L182V I116L R140Q 320 Mix 8.5 L182V 209 PB1 8.5~9 R54I E136D, Q179L, A194V

(134) In a second approach, potentially growth-enhancing mutations described in the literature were introduced into the background of UW-PR8 virus (see Table 3 for virus stock titers) and tested for replicative ability. FIGS. 5A-D show growth curves for various viruses.

(135) TABLE-US-00012 TABLE 3 UW-PR8 viruses possessing mutation(s) identified in the literature Gene Mutation(s) Virus stock titer (Pfu/ml) WT 2 10.sup.7 PB2 A44S 4.5 10.sup.7 E158G 3.2 10.sup.4 E158G + NP N101G 7.5 10.sup.4 E158A 8.3 0.sup.6 D253N + Q591K 8.3 10.sup.6 D256G 2.8 10.sup.7 R368K 3.1 10.sup.7 E391Q 1.4 10.sup.8 I504V + PA I550L 1.1 10.sup.8 Q591K 4.4 10.sup.7 V613T 1.8 10.sup.7 A661T 2.2 10.sup.7 D701N + S714R + NP N319K 1 10.sup.6 D701N 2.1 10.sup.7 PB1 R327K 1.3 10.sup.7 V336I 2.3 10.sup.7 L473V + L598P 3.9 10.sup.6 PB1F2 F2 N66S 1.6 10.sup.8 F2 K73R 1.1 10.sup.8 F2 V76A 4.4 10.sup.7 F2 R79Q 6.2 10.sup.6 F2 L82S 2.7 10.sup.7 F2 E87Q 1.5 10.sup.6 PA T97I 1.6 10.sup.7 K142N 3.3 10.sup.7 S225C 6.7 10.sup.7 S149P + T357K 3.4 10.sup.8 K356R 8.5 10.sup.7 A404S 5.2 10.sup.7 S421I 2.7 10.sup.7 NP R293K 4.7 10.sup.7 R305K 7.2 10.sup.7 E372D 2.2 10.sup.7 R422K 1.3 10.sup.3 T442A 5 10.sup.7 D455E 2.2 10.sup.7 I109V 3.9 10.sup.7 M V97A + Y100H 1.4 10.sup.7 NS1 K55E 1.6 10.sup.7

(136) In a third approach, candidates from approaches 1 and 2 were combined and HA titers and PFU/mL determined (Table 4).

(137) TABLE-US-00013 TABLE 4 High-growth candidates identified in approaches 1 and 2 were tested in various combinations Gene origin Virus stock titer # HA NA PB2 PB1 PA NP M NS HA (2.sup.n) Pfu/ml WT Indo/NC/09 Indo/NC/09 UW- UW- UW- UW- UW- UW- 7 3.00E+07 (detoxified) PR8 PR8 PR8 PR8 PR8 PR8 1 M202L M507V I116L K55E 9~9.5 2.00E+08 F323L V644A 2 M202L R54I N224I K55E 5 1.00E+05 F323L 3 M202L Q247H R401K T49A 9 1.00E+08 F323L 4 M202L M507V K356R T442A V97A K55E 10~10.5 1.60E+08 F323L V644A Y100H 5 I504V M507V I550L R74K K55E 8~8.5 5.70E+07 V644A N417D 6 I504V M507V I550L R74K V97A K55E 9~9.5 4.40E+07 V644A N417D Y100H 7 I505V E112G I550L R74K S161T 9 1.60E+08 8 M202L I667T I116L R140Q <1 <1E3 F323L M714T 9 M202L E112G S161T 8.5 1.30E+08 F323L 10 M66R M40I R74K S161T 8~8.5 2.30E+07 G180W 12 R368K PB1 F2 K356R R422K K55E 5.5 9.00E+02 N66S 13 E391Q R327K S149P R293K 3 1.60E+06 T357K 14 Q591K PB1 F2 S225C R422K K55E 7.5 2.00E+07 K73R 23 V97A 8.5~9 1.50E+07 24 Y100H 9~9.5 2.90E+07 25 NOR 15-19 nt Indo/NC/09 M202L M507V K356R R422K V97A K55E 9.5~10 7.50E+07 mut.sup.1 F323L V644A Y100H 26 Indo/NC/09 Indo/NC/09 A30P 6.5~7 1.00E+07 27 (detoxified) T49A 6.5~7 2.00E+07 28 R140Q 8 4.00E+07 29 S161T 7~7.5 1.40E+07 30 A223E 7.5 1.00E+07 31 I667T 3.5 4.00E+05 M714T 32 NCR 15-19 nt UW-PR8 M202L V644A K356R T442A Y100H K55E 7~7.5 4.30E+06 mut F323L 33 Indo/NC/09 Indo/NC/09 M202L E112G K356R R74K Y100H K55E 9~9.5 7.00E+07 (detoxified) F323L 34 NCR 15-19 nt UW-PR8 I504V M507V V97A K55E 7 2.00E+05 mut V644A Y100H 35 Indo/NC/09 Indo/NC/09 M202L M507V R401K T442A Y100H R140Q 9 3.20E+07 (detoxified) F323L V644A 36 I504V E112G I550L I112L Y100H R140Q 9.5 1.30E+08 37 M202L E112G S149P T442A Y100H K55E 0 0.00E+00 F323L T357K 38 M202L M507V I116L Y100H K55E 10.1 2.30E+08 F323L V644A 39 M202L M507V K356R T442A Y100H K55E 9.8 1.00E+08 F323L V644A 40 I504V M507V I550L T442A Y100H K55E 9.2 6.00E+07 V644A 41 I504V I112G I550L R74K Y100H K55E 9.2 7.50E+07 P17 I504V E112G S225C R74K V97A K55E 9.5~10 5.80E+08 N417D Y100H P26 M202L M40L S225C R422K V97A K55E 10 3.00E+08 F323L G180W Y100H P61 Indo/NC/09 M202L Q247H K142N R74K V97A K55E 10~10.5 2.00E+08 NA P263T.sup.2 F323L Y100H .sup.1Mutation in the HA gene noncoding region; .sup.2A P263T mutation was detected in the NA protein of this virus clone
As shown in Table 4, several recombinant viruses were identified that replicated better than wild type, such as #1, #4, #36, #38, P17, P16, and P61. To identify the growth characteristics of these viruses, growth kinetics in MDCK cells were determined (FIG. 7). For one candidate, virus was purified on sucrose gradients and HA content and viral total protein evaluated. FIG. 8A shows HA titer of wild type (UW-PR8) and #4, FIG. 8B shows viral protein for wild type (UW-PR8) and #4, and FIG. 8BC is a SDS-PAGE analysis of viral proteins of wild type (UW-PR8) and #4. Further analysis demonstrated that viruses possessing the V97ANY100H mutations in M1 yielded higher HA titers than the parental virus, although the virus titer was lower (see FIGS. 9A-B). The V97A/Y100H mutations in M1 may result in particles with a larger surface into which more HA protein can be incorporated. Since inactivated influenza viruses are dosed based on their HA content, variants with high HA content are attractive vaccine candidates.

(138) To identify mutations in the influenza promoter region that provide for enhanced replication, viruses possessing a U at position 4 at the 3 end of all eight vRNA segments were prepared in the UW-PR8 PA, PB1 and PB2 internal genes (the UW-PR8 PB2, PB1, and PA segments possess a C at position 4). The growth curves of the resulting viruses are shown in FIG. 11C.

(139) Viruses possessing combinations of promoter mutations and amino acid changes were prepared and titers determined (Table 5).

(140) TABLE-US-00014 TABLE 5 Virus titers of high-growth candidates. Virus stock titer Gene backbone HA Viruses HA NA PB2 PB1 PA NP M NS (2.sup.n) pfu/ml Control WT WT WT WT WT WT WT WT 7 3.0E+07 1 WT WT 3C4U 3C4U 3C4U R74K V97A K55E 10.5 2.2E+09 2 3 G3A U5C C8U & M202L Q247H K142N Y100H 8.5~9 5.6E+07 5 U3C A8G F323L 3 NCR 15-19 nt mut 9~9.5 1.4E+09 4 3 G3A U5C C8U & 7 7.0E+07 5 U3C A8G & NCR 15-19 nt mut
Codon usage optimization was also conducted. Alteration of codons may increase protein expression but could also alter RNA structure and stability. For example, codon usage optimization of the PB2 gene segment was performed to reflect the codon usage in canine cells (since MOCK cells are of canine origin) (FIG. 10A), while leaving the packaging signals (located at the 5 and 3 ends of the vRNA) unaltered. In one approach, codon optimization was performed for all codons in the internal region of the PB2 gene (FIG. 10C) and in another approach, codon optimization was performed for so-called rare codons (FIG. 10B) (used at significantly lower frequency compared to the codon used most frequently for a given amino acid) (see SEQ ID NO:25 in FIG. 10F). Analyses were carried out using the Graphical Codon Usage Analyser (www.gcua.de). The titers of those viruses are shown in Table 6 (see also FIGS. 10B-C).

(141) TABLE-US-00015 TABLE 6 Titers of viruses encoding codon-optimized PB2 genes. Virus stock titer Gene backbone HA Virus HA NA PB2 PB1 PA NP M NS (2.sup.n) pfu/ml Wild type WT WT WT WT WT WT WT WT 7~7.5 3.5E+07 PB2 codon WT WT Rare codon WT WT WT WT WT 9 2.1E+08 optimization-1 optimized PB2 PB2 codon WT WT All Codon WT WT WT WT WT 3 9.0E+05 optimization-2 optimized PB2
Optimization of rare codons in PB2 resulted in increased titers compared to wild type virus (UW-PR8) (see FIG. 10D). Other gene segments were codon optimized and titers of viruses with those segments or combinations of optimized segments were determined (FIG. 10E).

(142) In another approach to increase virus titer in MDCK cells, chimeric HA and NA genes were prepared (FIG. 13A) and titers of viruses having those genes were determined (FIG. 13B).

(143) Viruses with combinations of the above-mentioned mutations (high growth backbone mutations, promoter mutations, chimeric HA and NA genes and canine codon optimization) were prepared and growth kinetics, PFU and HA titers of those viruses were determined (see FIG. 14).

(144) An exemplary set of backbone mutations are canine codon opti-PB2+C4U+M202L, F323L; PB1: C4U+Q247H; PA: C4U+K142N; NP: Canine codon opti-NP+R74K; M: V97A, Y100H; and NS: K55E.

(145) Any of the mutations described herein, or any combination thereof, may be combined with, for instance, seasonal H1N1 and H3N2, H3N2 Variant, PdmH1N1, H5N1, H7N9 or H9N2, or other clades or candidate vaccine strains. For example, HA and NA genes from A/Califoria/04/2009(pdm H1N1) were combined with the six internal genes of UW-PR/8 to generate 6+2 recombinant viruses. Eleven virus libraries were generated and passaged 10 times in eggs. Three rounds of limiting dilution were performed to screen for high growth mutants (FIG. 15). In one embodiment, a variant with high growth properties in MDCK cells has a PB2 gene segment with a promoter mutation (C4U) and a mutation that results in I504V (relative to the parental virus); a PB1 gene segment with a promoter mutation (C4U) and a mutation that results in E112G; a PA gene segment with a promoter mutation (C4U) and a mutation that results in S225C; a NP gene segment with mutations that result in R74K and N417D; a M gene segment with mutations that result in V97A and Y100H; and a NS gene segment with a mutation that results in K55E, where optionally the sequence of one or more gene segments, e.g., the NP gene segment, is modified to include canine codon optimized codons. In one embodiment, a variant with high growth properties in MDCK cells has a canine codon optimized PB2 gene segment with a promoter mutation (C4U) and mutations that result in M202L and F323L; a PB1 gene segment with a promoter mutation (C4U) and a mutation that results in Q247H; a PA gene segment with a promoter mutation (C4U) and a mutation that results in K142N; a canine codon optimized NP gene segment with a mutation that results in R74K; a M gene segment with mutations that result in V97A Y100H; and a NS gene segment with a mutation that results in K55E.

(146) Similar experiments were conducted in Vero cells, e.g., after about 3 to 5 passages in Vero cells, using clones with high replicative properties in MDCK cells (see FIG. 16). FIG. 17 shows 5 viruses likely to have high replicative properties in Vero cells. In one embodiment, a PR8(UW) variant with high-growth properties in Vero cells has the following mutations that may be used in various combinations to increase the replicative ability of PR8(UW) virus: PB2 segment: C4U (promoter mutation), I504V (amino acid change); PB1 segment: C4U (promoter mutation); M40L (amino acid change), G180W (amino acid change); PA segment: C4U (promoter mutation), R401K (amino acid change); NP segment: I116L (amino acid change); NS segment: A30P (amino acid change in NS1), or R118K (amino acid change in NS1).

(147) In one embodiment, a PR8(UW) variant with high-growth properties has the following residues that may be used in various combinations with each other and/or other residues, e.g., those that enhance virus replication, to increase the replicative ability of reassortants having PR8(UW) based viral segment(s): a HA segment with one or more of 136D, 162E, 179L, 182V, 184I, 252I, 449E, and/or 476I: a NA segment with 55S and/or 265V; a NS segment with NS1 having 118K; F2 with 81G; a PB1 segment with 62A, 261G, 361R, 621R, and/or 654S, and/or viral segment promoters with the growth-enhancing nucleotides described herein. e.g., having one or more of the nucleotide changes G1012C, A1013U, or U1014A in the M viral segment.

Example C

(148) To assess the contribution of individual viral RNA (vRNA) segments to high-yield properties, a series of reassortant viruses was generated that possessed one or several vRNA segments of a high-yield PR8 (PR8-HY) variant in the background of the parental virus [UW-PR8_Indo/05(HA+NA)]. Vero cells were infected in triplicate with the indicated viruses at a MOI of 0.005 and incubated at 37 C. in the presence of trypsin. At the indicated time points, virus titers and HA titers were determined by performing plaque or HA assays, respectively. The results are shown in FIG. 20. These data indicated that several vRNA segments contribute to the properties of PR8-HY virus. In particular, the PB2+PB1+PA+NP vRNAs of PR8-HY virus conferred an appreciable increase in virus and HA titers, evidencing the enhanced replicative ability of this virus.

(149) To further assess which component of the viral replication complex that provides for high-yield properties, wild-type or high-yield PB2, PB1, PA, and NP proteins were tested in various combinations in minireplicon assays in human 293T, canine MDCK, African green monkey Vero, and avian DF1 cells. The results are shown in FIG. 21. Interestingly, the PB2, PB1, PA, and NP proteins of PR8-HY virus attenuated the viral replicative ability in 293T, Vero, and DF1 cells; this effect was primarily conferred by the PB2 protein. In contrast, the combination of PB2+PB1+PA+NP proteins derived from PR8-HY virus conferred a substantial increase in replicated ability in canine MDCK cells, which were used for the selection of PR8-HY virus. The findings suggested host-dependent mechanisms underlying the high yield of PR8-HY virus. For example, the combination of PB1+PA+NP proteins, or a subset thereof, derived from PR8-HY may confer enhanced viral replicative ability in 293T, Vero, and DF1 cells.

Exemplary Embodiments

(150) An isolated, single cycle recombinant influenza virus is provided having at least seven viral segments selected from PA, PB1, PB2, NP, NS, M, HA or NA viral segments, or having at least six viral segments selected from PA, PB1, PB2, NP, NS, M, or HEF viral segments, one of which segments comprises coding sequences for an antigenic coronavirus protein or an antigenic portion thereof. In one embodiment, the antigenic coronavirus protein comprises coronavirus S (spike) sequences. In one embodiment, the antigenic coronavirus protein comprises S1 sequences. In one embodiment, the antigenic coronavirus protein comprises a soluble protein. In one embodiment, the antigenic portion comprises the receptor binding domain. In one embodiment, the antigenic coronavirus protein sequences or the portion thereof have at least 80% amino acid sequence identity to one of SEQ ID Nos. 25-28 and 50-52. In one embodiment, the virus comprises eight viral segments. In one embodiment, the virus comprises nine viral segments. In one embodiment, the virus is an influenza A or B virus. In one embodiment, the virus is an influenza C or D virus. In one embodiment, coding sequences for the antigenic coronavirus protein sequences or the portion thereof replace at least a portion of the coding sequences for one of PA, PB1, PB2, NP, NS1, NS2, M1, M2, HA, or NA. In one embodiment, coding sequences for the antigenic coronavirus protein sequences or the portion thereof are inserted into coding sequences in the viral segment of one of PA, PB1, PB2, NP, NS, M, HA or NA viral segments. In one embodiment, the virus is bivalent or trivalent. In one embodiment, the M viral segment is mutated so that upon viral replication the mutant M gene expresses a functional M1 protein and a mutant M2 protein with a deletion of the cytoplasmic tail and either lacking a transmembrane domain or having a mutated transmembrane domain. In one embodiment, the mutant M2 protein comprises the M2 extracellular domain. In one embodiment, the M2 extracellular domain comprises less than 24 residues. In one embodiment, the M2 extracellular domain comprises at least 9 residues. In one embodiment, the mutation in the transmembrane domain comprises at least one amino acid substitution. In one embodiment, the transmembrane domain is deleted. In one embodiment, the deletion in the transmembrane domain includes residues 29 to 31. In one embodiment, the deletion in the transmembrane domain comprises at least 10 residues. In one embodiment, two or more of the PA, PB1, PB2, NP, NS, and M viral segments have selected amino acid residues at positions 30, 31, 105, 142, 149, 225, 356, 357, 401, and/or 550 in PA; positions 40, 54, 59, 62, 63, 75, 76, 78, 79, 80, 112, 180, 247, 327, 507, 624, 644, 667, 694, 695, 697, 699, 700, 701, 702, 705, 713, and/or 714 in PB1; positions 57, 58, 59, 61, 66, 202, 323, 368, 391, 504, 591, 677, 678, and/or 679, in PB2; positions 74, 112, 116, 224, 293, 371, 377, 417, 422 or 442 in NP; positions 90, 97 and/or 100 in M1; or positions 30, 49, 55, 118, 140, 161 and/or 223 in NS1. In one embodiment, at least of the viral segments has a C to U promoter mutation. In one embodiment, at least one of PA, PB1, or PB2 viral segments has a C to U promoter mutation. In one embodiment, the PB2 segment has a C4U promoter mutation or 504V; the PB1 segment has one or more of C4U, 40L or 180W; the PA segment has C4U or 401K; the NP segment has 116L; or the NS segment has 30P in NS1 or 118K in NS1.

(151) An isolated, single cycle recombinant influenza virus is provided having PA, PB1, PB2, NP, NS, M, HA or NA viral segments, or having PA, PB1, PB2, NP, NS, M, or HEF viral segments, wherein the NS or PB2 segment comprises coding sequences for an antigenic coronavirus protein or an antigenic portion thereof, and optionally the M viral segment is mutated so that upon viral replication the mutant M gene expresses a functional M1 protein and a mutant M2 protein with a deletion of the cytoplasmic tail and either lacking a transmembrane domain or having a mutated transmembrane domain. In one embodiment, the antigenic coronavirus protein comprises coronavirus S (spike) sequences. In one embodiment, the antigenic coronavirus protein comprises coronavirus S (spike) RBD sequences.

(152) An isolated, single cycle recombinant influenza virus is provided having PA, PB1, PB2, NP, NS, M, HA or NA viral segments, or having PA, PB1, PB2, NP, NS, M, or HEF viral segments, wherein the NS segment comprises coding sequences for an antigenic coronavirus protein or an antigenic portion thereof, and optionally the M viral segment is mutated so that upon viral replication the mutant M gene expresses a functional M1 protein and a mutant M2 protein with a deletion of the cytoplasmic tail and either lacking a transmembrane domain or having a mutated transmembrane domain. In one embodiment, the antigenic coronavirus protein comprises coronavirus S (spike) sequences. In one embodiment, the antigenic coronavirus protein comprises coronavirus S (spike) RBD sequences.

(153) Also provided is an isolated influenza virus having at least seven viral segments selected from PA, PB1, PB2, NP, NS, M, HA or NA viral segments, or having at least six viral segments selected from PA, PB1, PB2, NP, NS, M, or HEF viral segments, one of which segments comprises coding sequences for an antigenic coronavirus protein or an antigenic portion thereof. In one embodiment, the antigenic coronavirus protein comprises S1 sequences. In one embodiment, the antigenic portion comprises the receptor binding domain. In one embodiment, the antigenic coronavirus protein sequences or the portion thereof have at least 80% amino acid sequence identity to one of SEQ ID Nos. 25-28 and 50-52. In one embodiment, the virus comprises eight or nine viral segments. In one embodiment, the virus is an influenza A or B virus. In one embodiment, coding sequences for the antigenic coronavirus protein sequences or the portion thereof replace at least a portion of the coding sequences for one of PA, PB1, PB2, NP, NS1, NS2, M1, M2, HA, or NA. In one embodiment, coding sequences for the antigenic coronavirus protein sequences or the portion thereof are inserted into coding sequences in the viral segment of one of PA, PB1, PB2, NP, NS, M, HA or NA viral segments. In one embodiment, the virus is bivalent or trivalent. In one embodiment, the M viral segment is mutated so that upon viral replication the mutant M gene expresses a functional M1 protein and a mutant M2 protein with a deletion of the cytoplasmic tail and either lacking a transmembrane domain or having a mutated transmembrane domain, wherein the replication of the recombinant virus is abrogated or attenuated in vivo relative to a corresponding influenza virus with a wild-type M viral segment. In one embodiment, the mutant M2 protein comprises the M2 extracellular domain. In one embodiment, the M2 extracellular domain comprises at least 9 or 10 residues. In one embodiment, the mutation in the transmembrane domain comprises a deletion in the transmembrane domain. In one embodiment, two or more of the PA, PB1, PB2, NP, NS, and M viral segments have selected amino acid residues at positions 30, 31, 105, 142, 149, 225, 356, 357, 401, and/or 550 in PA; positions 40, 54, 59, 62, 63, 75, 76, 78, 79, 80, 112, 180, 247, 327, 507, 624, 644, 667, 694, 695, 697, 699, 700, 701, 702, 705, 713, and/or 714 in PB1; positions 57, 58, 59, 61, 66, 202, 323, 368, 391, 504, 591, 677, 678, and/or 679, in PB2; positions 74, 112, 116, 224, 293, 371, 377, 417, 422 or 442 in NP; positions 90, 97 and/or 100 in M1; or positions 30, 49, 55, 118, 140, 161 and/or 223 in NS1. In one embodiment, at least of the viral segments has a C to U promoter mutation. In one embodiment, at least one of PA, PB1, or PB2 viral segments has a C to U promoter mutation. In one embodiment, the PB2 segment has a C4U promoter mutation or 504V; the PB1 segment has one or more of C4U, 40L or 180W; the PA segment has C4U or 401K: the NP segment has 116L; or the NS segment has 30P in NS1 or 118K in NS1.

(154) In one embodiment, a vaccine comprising an effective amount of the virus is provided. In one embodiment, the vaccine is formulated for intranasal delivery. In one embodiment, the virus is bivalent. In one embodiment, the recombinant virus comprises influenza A HA. In one embodiment, the virus comprises H1, H3, H5 or H7 HA. In one embodiment, the vaccine which further comprises a different influenza virus. In one embodiment, the vaccine further comprises at least two different influenza viruses. In one embodiment, the virus is inactivated.

(155) Further provided is a method to immunize a vertebrate, comprising: administering to the vertebrate the vaccine disclosed herein. In one embodiment, the vertebrate is an avian. In one embodiment, the vertebrate is a mammal. In one embodiment, the vertebrate is a human. In one embodiment, the vaccine is intranasally administered. In one embodiment, the vaccine is intramuscularly administered. In one embodiment, more than one dose is administered.

(156) The invention will be described by the following nonlimiting examples.

Example 1

(157) In one embodiment, an eight segment single cycle recombinant influenza A virus is prepared. One of the viral RNA segments (for example, the NS segment) is modified to also express SARS-CoV-2 S (or portions thereof), e.g., a fusion of NS1 and SARS-CoV-2 S protein or a portion thereof. For fusion protein between the flu and SARS proteins, proteases that autocatalytically cleave are employed to generate functional flu and SARS proteins. The addition of heterologous protein sequences does not result in the need for a helper cell to express a protein in trans. However, if influenza virus coding sequences on one or more the viral segments are deleted (either a portion thereof or in their entirety), the corresponding influenza virus protein(s) are supplied in trans. For example, the viral M segment is modified by inserting two stop codons into M2 (downstream of the splice acceptor site), and by deleting the coding region for the transmembrane domain of M2, referred to as M2SR, which undergoes only one round of replication and requires a helper cell line for propagation That is in contrast to live-attenuated viruses which undergo several rounds of slow replication). In one embodiment, one or more of the internal viral segments are from PR8HY. In one embodiment, the HA and NA viral segments are from a heterologous strain. The M2SR having coronavirus sequences (CoroFlu M2SR) is intranasally administrated. In other embodiments, inactivated coronavirus/influenza viruses may be intramuscularly administered.

(158) In one embodiment, a nine-segment virus is generated with eight segments expressing the flu proteins (with M2 modified as described above), and a ninth viral segment in which (part of) the flu coding region is replaced with SARS-CoV-2 S (or portions thereof).

(159) In one embodiment, an attenuated virus is generated, e.g., one having M2 mutations that result in attenuation, e.g., M2del29-31 or M2 cytoplasmic tail deletions (see, e.g., del11 or del 22 etc. in Iwatsuki-Horimoto et al. (2006) and Watanabe et al. (2008).

(160) Other alterations in M2 include two stop codons to prevent expression of the transmembrane domain and cytoplasmic tails and two stop codons and deletion of the coding region of the transmembrane domain (see Watanabe et al. (2009) and Sarawar et al. (2016), which are incorporated by reference herein)

Example 2

(161) An influenza vaccine that includes coronavirus sequences and is limited to a single round of replication in vaccinated individuals, but stimulates mucosal, innate, humoral, and/or cell-mediated immune responses, was prepared. Phase I and Phase IIa clinical studies with the vaccine virus (without coronavirus sequences) have demonstrated its safety (no serious adverse events; no virus shedding) and the ability to elicit neutralizing immune responses to homologous and antigenically mismatched influenza virus strains. Importantly, this vaccine mimics the natural infection process and stimulates mucosal, innate, humoral, and cell-mediated immune responses. Thus, this platform may be employed to generate a single-cycle bivalent influenza vaccine expressing a soluble portion of the spike protein (the major antigen) of a coronavirus, e.g., the new 2019 coronavirus. The immunogenicity and protective efficacy of this vaccine is likely to be superior to that of inactivated vaccines, which stimulate B cell responses, but fail to induce other immune responses.

(162) Generate a Bivalent Coronavirus/Influenza Virus Vaccine Candidate and Test its Protective Efficacy in Animal Models

(163) To generate the novel bivalent coronavirus/influenza virus vaccine based on the M2SR platform (called CoroFlu M2SR, FIG. 22), cells ware transfected with plasmids for influenza virus generation. One plasmid possesses a deletion of the influenza viral M2 coding region. In another plasmid, the coding region for the receptor-binding domain (RBD) of the 2019-nCoV spike (S) protein is inserted between the influenza viral NS1 and NS2 coding regions, separated by foot-and-mouse virus protease 2A autoproteolytic cleavage sites (2A). In cells expressing the M2 protein, CoroFlu M2SR vaccine virus is generated.

(164) In one embodiment, the coronavirus S amino acid sequence, or a portion thereof, has at least 80%, e.g., 90%, 92%, 95%, 97% or 99%, including any integer between 80 and 99, contiguous amino acid sequence identity to a polypeptide having one of SEQ ID Nos. 25-28 and 50-52. In one embodiment, the S polypeptide or a portion thereof has one or more, for instance, 2, 5, 10, 15, 20 or more, conservative amino acids substitutions, e.g., conservative substitutions of up to 10% or 20% of the residues, relative to a polypeptide having one of SEQ ID Nos. 25-28 and 50-52. In one embodiment, a S polypeptide or a portion thereof has one or more, for instance, 2, 5, 10, 15, 20 or more, conservative amino acids substitutions. e.g., conservative substitutions of up to 10% or 20% of 2, 5, 10, 15, 20 or more, of a combination of conservative and non-conservative amino acids substitutions, e.g., conservative substitutions of up to 10% or 20% of the residues, or relative to a polypeptide with one of the sequences disclosed herein. In one embodiment, the coronavirus sequence in the influenza virus has 1, 2, 3, 4 or 5 substitutions relative to one of SEQ ID Nos. 25-28 and 50-52. In one embodiment, the coronavirus S1 sequence in the influenza virus has 1, 2, 3, 4 or 5 substitutions relative to the S1 sequence in one of SEQ ID Nos. 25-28 and 50-52. In one embodiment, the coronavirus RBD sequence in the influenza virus has 1, 2, 3, 4 or 5 substitutions relative to the RBD sequence in one of SEQ ID Nos. 25-28 and 50-52.

(165) For example, the amino acid(s) can be any amino acid within these positions such as any of the amino acids listed in the table below.

(166) TABLE-US-00016 Original Exemplary Alternative Residue Substitutions Substitutions Ala (A) val; leu; ile Val Arg (R) lys; gln; asn Lys Asn (N) gln; his; lys; arg Gln Asp (D) Glu, Asn Glu, Asn Cys (C) Ser Ser Gln (Q) Asn Asn Glu (E) Asp Asp Gly (G) Pro Pro His (H) asn; gln; lys; arg; gln; Arg; Gln Ile (I) leu; val; met; ala; phe Leu norleucine Leu (L) norleucine; ile; val; met; Ile ala; phe Lys (K) arg; gln; asn Arg Met (M) leu; phe; ile Leu Phe (F) leu; val; ile; ala Leu Pro (P) Gly Gly Ser (S) Thr Thr Thr (T) Ser, Ala Ser, Als Trp (W) Tyr Tyr Tyr (Y) trp; phe; thr; ser Phe Val (V) ile; leu; met; phe; ala; Leu norleucine
Conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine and tryptophan; a group of amino acids having basic side chains is lysine, arginine and histidine; and a group of amino acids having sulfur-containing side chain is cysteine and methionine. In one embodiment, conservative amino acid substitution groups are: threonine-valine-leucine-isoleucine-alanine; phenylalanine-tyrosine; lysine-arginine; alanine-valine; glutamic-aspartic; and asparagine-glutamine.

(167) The basic characterization of CoroFlu M2SR includes assessment of virus titers in the Vero M2 production cell line; the virus is passaged 10 consecutive times (followed by sequence analysis) in Vero M2-expressing cells to assess the genomic stability of CoroFlu M2SR.

(168) Animal studies are carried out in Syrian hamsters (in which SARS-CoV replicates efficiently), in ferrets (an animal model that has been used for SARS-CoV research) and in transgenic mice expressing the human angiotensin-converting enzyme-2 (ACE-2) receptor, the SARS-CoV receptor to which 2019-nCoV also binds. Animals are intranasally administered with different amounts of CoroFlu M2SR (e.g., 10.sup.5 to 10.sup.7 PFU). Control animals are administered with M2SR vaccine (expressing the same HA and NA genes as CoroFlu M2SR, but not expressing S/RDB). Another control group is mock-treated. On days 1, 3, 5, and 7 after vaccination, nasal swab samples are collected to confirm the lack of virus shedding. Three weeks post-vaccination, serum samples are collected and tested for antibodies to SARS-Cov2 S/RBD and influenza HA; if the titers are low, animals are boosted.

(169) Animals are vaccinated and challenged with live SARS-Cov2 or influenza virus three weeks after the last immunization. Control groups are mock-vaccinated, followed by live virus challenge with SARS-Cov2 and influenza virus. Groups of animals are euthanized on days 3, 6, and 9 post-infection to titrate the amounts of virus in the nasal turbinates and lungs. Other groups of animals are observed for weight changes and clinical symptoms. Nasal swabs are collected every other day (starting on day 1 post-challenge) to determine the virus load in the challenged animals.

(170) Assess Whether the Vaccine Candidates Cause Antibody-Dependent Enhancement (ADE) of Virulence

(171) ADE (i.e., antibody-dependent enhancement of infectivity and disease severity) is a potential concern with the development of vaccines to a variety of viruses, including coronaviruses (Halsted, 2014; Huisman et al, 2009; Smatti et al., 2018; Wan et al., 2019; Wang et al., 2014; Yip et al., 2014; Takada et al., 2001; Takada et al., 2003; and Takada et al., 2007). Since ADE is most likely caused by non-neutralizing antibodies directed at sub-dominant epitopes, the use of S/RDB (instead of full-length S) may reduce the likelihood of ADE. To test this, animals are vaccinated with CoroFlu M2SR, M2SR, or mock-vaccinated, and sera will be collected three weeks later.

(172) To assess ADE in vitro, the SARS-Cov2 is mixed with different dilutions of serum (obtained from vaccinated or control animals; see previous paragraph) and added to cells to determine virus titers. To assess ADE in vivo, two sets of experiments are carried out: In the first set of experiments, animals are administered different serum dilutions and subsequently infected with the SARS-Cov2. Control groups are treated with serum obtained from mock-vaccinated. In the other set of experiments, animals are vaccinated with CoroFlu M2SR, M2SR, or mock-vaccinated, and three weeks later infected with live SARS-Cov2. At different times post-infection, animals are euthanized to collect organs for virus titration and histopathological analysis, and sera are collected to determine antibody titers. The finding that sera obtained from CoroFlu M2SR-vaccinated animals and vaccination with CoroFlu M2SR do not increase virus titers, disease symptoms, or histopathology compared with the controls establishes the absence of ADE for CoroFlu M2SR vaccine.

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(174) All publications, patents and patent applications are incorporated herein by reference. While in the foregoing specification this invention has been described in relation to certain preferred embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein may be varied considerably without departing from the basic principles of the invention.