WO2003091401A2 - Multi plasmid system for the production of influenza virus - Google Patents

Abstract

Vectors and methods for the production of influenza viruses suitable as recombinant influenza vaccines in cell culture are provided. Bi-directional expression vectors for use in a multi-plasmid influenza virus expression system are provided.

Description

MULTI PLASMID SYSTEM FOR THE PRODUCTION OF INFLUENZA

VIRUS

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to and benefit of United States Provisional Applications Number 60/375,675, filed April 26, 2002; Number 60/394,983, filed July 9, 2002; Number 60/410,576, filed September 12, 2002; Number 60/419,802, filed October 18, 2002; Number 60/420,708, filed October 23, 2002; Number 60/457,699 (Attorney Docket Number 26-000250US); filed March 24, 2003, and Attorney Docket Number 26- 000260US entitled "Multi-Plasmid System for the Production of Influenza Virus," filed April 10, 2003, the disclosures of each of which are incorporated herein in their entirety for all purposes.

BACKGROUND OF THE INVENTION

[0002] Influenza viruses are made up of an internal ribonucleoprotein core containing a segmented single-stranded RNA genome and an outer lipoprotein envelope lined by a matrix protein. Influenza A and B viruses each contain eight segments of single stranded RNA with negative polarity. The influenza A genome encodes at least eleven polypeptides. Segments 1-3 encode the three polypeptides, making up the viral RNA- dependent RNA polymerase. Segment 1 encodes the polymerase complex protein PB2. The remaining polymerase proteins PBl and PA are encoded by segment 2 and segment 3, respectively. In addition, segment 1 of some influenza A strains encodes a small protein, PB1-F2, produced from an alternative reading frame within the PBl coding region. Segment 4 encodes the hemagglutinin (HA) surface glycoprotein involved in cell attachment and entry during infection. Segment 5 encodes the nucleocapsid nucleoprotein (NP) polypeptide, the major structural component associated with viral RNA. Segment 6 encodes a neuraminidase (NA) envelope glycoprotein. Segment 7 encodes two matrix proteins, designated Ml and M2, which are translated from differentially spliced mRNAs. Segment 8 encodes NS1 and NS2 (NEP), two nonstructural proteins, which are translated from alternatively spliced mRNA variants.

[0003] The eight genome segments of influenza B encode 11 proteins. The three largest genes code for components of the RNA polymerase, PBl, PB2 and PA. Segment 4 encodes the HA protein. Segment 5 encodes NP. Segment 6 encodes the NA protein and the NB protein. Both proteins, NB and NA, are translated from overlapping reading frames of a biscistronic mRNA. Segment 7 of influenza B also encodes two proteins: Ml and BM2. The smallest segment encodes two products: NS1 is translated from the full length RNA, while NS2 is translated from a spliced mRNA variant. [0004] Vaccines capable of producing a protective immune response specific for influenza viruses have been produced for over 50 years. Vaccines can be characterized as whole virus vaccines, split virus vaccines, surface antigen vaccines and live attenuated virus vaccines. While appropriate formulations of any of these vaccine types is able to produce a systemic immune response, live attenuated virus vaccines are also able to stimulate local mucosal immunity in the respiratory tract.

[0005] FluMist™ is a live, attenuated vaccine that protects children and adults from influenza illness (Belshe et al. (1998) The efficacy of live attenuated, cold-adapted, trivalent, intranasal influenza virus vaccine in children N Engl J Med 338:1405-12; Nichol et al. (1999) Effectiveness of live, attenuated intranasal influenza virus vaccine in healthy, working adults: a randomized controlled trial JAMA 282: 137-44). FluMist™ vaccine strains contain HA and NA gene segments derived from the currently circulating wild-type strains along with six gene segments, PBl, PB2, PA, NP, M and NS, from a common master donor virus (MDV). The MDV for influenza A strains of FluMist (MDV- A), was created by serial passage of the wt A/ Ann Arbor/6/60 (A/AA/6/60) strain in primary chicken kidney tissue culture at successively lower temperatures (Maassab (1967) Adaptation and growth characteristics of influenza virus at 25 degrees C Nature 213:612- 4). MDV-A replicates efficiently at 25°C (ca, cold adapted), but its growth is restricted at 38 and 39 °C (ts, temperature sensitive). Additionally, this virus does not replicate in the lungs of infected ferrets (att, attenuation). The ts phenotype is believed to contribute to the attenuation of the vaccine in humans by restricting its replication in all but the coolest regions of the respiratory tract. The stability of this property has been demonstrated in animal models and clinical studies. In contrast to the ts phenotype of influenza strains created by chemical mutagenesis, the ts property of MDV-A did not revert following passage through infected hamsters or in shed isolates from children (for a recent review, see Murphy & Coelingh (2002) Principles underlying the development and use of live attenuated cold-adapted influenza A and B virus vaccines Viral Immunol 15:295-323). [0006] Clinical studies in over 20,000 adults and children involving 12 separate

6:2 reassortant strains have shown that these vaccines are attenuated, safe and efficacious (Belshe et al. (1998) The efficacy of live attenuated, cold-adapted, trivalent, intranasal influenza virus vaccine in children N Engl J Med 338:1405-12; Boyce et al. (2000) Safety and immunogenicity ofadjuvanted and unadjuvanted subunit influenza vaccines administered intranasally to healthy adults Vaccine 19:217-26; Edwards et al. (1994) A randomized controlled trial of cold adapted and inactivated vaccines for the prevention of influenza A disease J Infect Pis 169:68-76 ; Nichol et al. (1999) Effectiveness of live, attenuated intranasal influenza virus vaccine in healthy, working adults: a randomized controlled trial JAMA 282: 137-44). Reassortants carrying the six internal genes of MDV- A and the two HA and NA gene segments of the wt virus (6:2 reassortant) consistently maintain ca, ts and att phenotypes (Maassab et al. (1982) Evaluation of a cold- recombinant influenza virus vaccine in ferrets J Infect Pis 146:780-900).

[0007] To date, all commercially available influenza vaccines in the United States have been propagated in embryonated hen's eggs. Although influenza virus grows well in hen's eggs, production of vaccine is dependent on the availability of eggs. Supplies of eggs must be organized, and strains for vaccine production selected months in advance of the next flue season, limiting the flexibility of this approach, and often resulting in delays and shortages in production and distribution. [0008] Systems for producing influenza viruses in cell culture have also been developed in recent years (See, e.g., Furminger. Vaccine Production, in Nicholson et al. (eds) Textbook of Influenza pp. 324-332; Merten et al. (1996) Production of influenza virus in cell cultures for vaccine preparation, in Cohen & Shafferman (eds) Novel Strategies in Design and Production of Vaccines pp. 141-151). Typically, these methods involve the infection of suitable immortalized host cells with a selected strain of virus.

While eliminating many of the difficulties related to vaccine production in hen's eggs, not all pathogenic strains of influenza grow well and can be produced according to established tissue culture methods. In addition, many strains with desirable characteristics, e.g., attenuation, temperature sensitivity and cold adaptation, suitable for production of live attenuated vaccines, have not been successfully grown in tissue culture using established methods. [0009] Production of influenza viruses from recombinant DNA would significantly increase the flexibility and utility of tissue culture methods for influenza vaccine production. Recently, systems for producing influenza A viruses from recombinant plasmids incorporating cDNAs encoding the viral genome have been reported (See, e.g., Neumann et al. (1999) Generation of influenza A virus entirely from cloned cDNAs. Proc Natl Acad Sci USA 96:9345-9350; Fodor et al. (1999) Rescue of influenza A virus from recombinant DNA. J. Virol 73:9679-9682; Hoffmann et al. (2000) A DNA transfection system for generation of influenza A virus from eight plasmids Proc Natl Acad Sci USA 97:6108-6113; WO 01/83794). These systems offer the potential to produce recombinant viruses, and reassortant viruses expressing the immunogenic HA and NA proteins from any selected strain. However, unlike influenza A virus, no reports have been published describing plasmid-only systems for influenza B virus.

[0010] Additionally, none of the currently available plasmid only systems are suitable for generating attenuated, temperature sensitive, cold adapted strains suitable for live attenuated vaccine production. The present invention provides an eight plasmid system for the generation of influenza B virus entirely from cloned cDNA, and methods for the production of attenuated live influenza A and B virus suitable for vaccine formulations, such as live virus vaccine formulations useful for intranasal administration, as well as numerous other benefits that will become apparent upon review of the specification.

SUMMARY OF THE INVENTION

[0011] The present invention relates to a multi-vector system for the production of influenza viruses in cell culture, and to methods for producing recombinant and reassortant influenza viruses, including, e.g., attenuated (att) , cold adapted (ca) and/or temperature sensitive (ts) influenza viruses, suitable as vaccines, including live attenuated influenza vaccines, such as those suitable for administration in an intranasal vaccine formulation.

[0012] In a first aspect the invention provides vectors and methods for producing recombinant influenza B virus in cell culture, e.g., in the absence of helper virus (i.e., a helper virus free cell culture system). The methods of the invention involve introducing a plurality of vectors, each of which incorporates a portion of an influenza B virus into a population of host cells capable of supporting viral replication. The host cells are cultured under conditions permissive for viral growth, and influenza viruses are recovered. In some embodiments, the influenza B viruses are attenuated viruses, cold adapted viruses and/or temperature sensitive viruses. For example, in an embodiment, the vector-derived recombinant influenza B viruses are attenuated, cold adapted, temperature sensitive viruses, such as are suitable for administration as a live attenuated vaccine, e.g., in a intranasal vaccine formulation. In an exemplary embodiment, the viruses are produced by introducing a plurality of vectors incorporating all or part of an influenza B/Ann Arbor/1/66 virus genome, e.g., a ca B/Ann Arbor/1/66 virus genome.

[0013] For example, in some embodiments, the influenza B viruses are artificially engineered influenza viruses incorporating one or more amino acid substitutions which influence the characteristic biological properties of influenza strain ca B/Ann Arbor/1/66.

Such influenza viruses include mutations resulting in amino acid substitutions at one or more of positions PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴, such as: PBl³⁹¹ (K391E),

PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G). Any mutation (at one or more of these positions) which individually or in combination results in increased temperature sensitivity, cold adaptation or attenuation relative to wild type viruses is a suitable mutation in the context of the present invention.

[0014] In some embodiments, a plurality of vectors incorporating at least the 6 internal genome segments of a one influenza B strain along with one or more genome segments encoding immunogenic influenza surface antigens of a different influenza strain are introduced into a population of host cells. For example, at least the 6 internal genome segments of a selected attenuated, cold adapted and/or temperature sensitive influenza B strain, e.g., a ca, att, ts strain of B/Ann Arbor/1/66 or an artificially engineered influenza B strain including an amino acid substitution at one or more of the positions specified above, are introduced into a population of host cells along with one or more segments encoding immunogenic antigens derived from another virus strain. Typically the immunogenic surface antigens include either or both of the hemagglutinin (HA) and/or neuraminidase (NA) antigens. In embodiments where a single segment encoding an immunogenic surface antigen is introduced, the 7 complementary segments of the selected virus are also introduced into the host cells. [0015] In certain embodiments, a plurality of plasmid vectors incorporating influenza B virus genome segments are introduced into a population of host cells. For example, 8 plasmids, each of which incorporates a different genome segment are utilized to introduce a complete influenza B genome into the host cells. Alternatively, a greater number of plasmids, incorporating smaller genomic subsequences can be employed.

[0016] Typically, the plasmid vectors of the invention are bi-directional expression vectors. A bi-directional expression vector of the invention typically includes a first promoter and a second promoter, wherein the first and second promoters are operably linked to alternative strands of the same double stranded cONA encoding the viral nucleic acid including a segment of the influenza virus genome. Optionally, the bi-directional expression vector includes a polyadenylation signal and/or a terminator sequence. For example, the polyadenylation signal and/or the terminator sequence can be located flanking a segment of the influenza virus genome internal to the two promoters. One favorable polyadenylation signal in the context of the invention is the SV40 polyadenylation signal. An exemplary plasmid vector of the invention is the plasmid ρAP3000, illustrated in Figure 1.

[0017] The vectors are introduced into host cells capable of supporting the replication of influenza virus from the vector promoters. Favorable examples of host cells include Vero cells, Per.C6 cells, BHK cells, PCK cells, MPCK cells, MPBK cells, 293 cells (e.g., 293T cells), and COS cells. In combination with the pAO3000 plasmid vectors described herein, Vero cells, 293 cells, and COS cells are particularly suitable. In some embodiments, co-cultures of a mixture of at least two of these cell lines, e.g., a combination of COS and MOCK cells or a combination of 293T and MDCK cells, constitute the population of host cells. [0018] The host cells including the influenza B vectors are then grown in culture under conditions permissive for replication and assembly of viruses. Typically, host cells incorporating the influenza B plasmids of the invention are cultured at a temperature below 37 °C, preferably at a temperature equal to, or less than, 35 °C. Typically, the cells are cultured at a temperature between 32 °C and 35 °C. In some embodiments, the cells are cultured at a temperature between about 32 °C and 34 °C, e.g., at about 33 °C.

Following culture for a suitable period of time to permit replication of the virus to high titer, recombinant and/or reassortant viruses are recovered. Optionally, the recovered viruses can be inactivated.

[0019] The invention also provides broadly applicable methods of producing recombinant influenza viruses in cell culture by introducing a plurality of vectors incorporating an influenza virus genome into a population of host cells capable of supporting replication of influenza virus, culturing the cells at a temperature less than or equal to 35 °C, and recovering influenza viruses.

[0020] In certain embodiments, a plurality of plasmid vectors incorporating influenza virus genome segments are introduced into a population of host cells. In certain embodiments, 8 plasmids, each of which incorporates a different genome segment are utilized to introduce a complete influenza genome into the host cells. Typically, the plasmid vectors of the invention are bi-directional expression vectors. An exemplary plasmid vector of the invention is the plasmid pAD3000, illustrated in Figure 1.

[0021] In some embodiments, the influenza viruses correspond to an influenza B virus. In some embodiments, the influenza viruses correspond to an influenza A virus. In certain embodiments, the methods include recovering recombinant and/or reassortant influenza viruses capable of eliciting an immune response upon administration, e.g., intranasal administration, to a subject. In some embodiments, the viruses are inactivated prior to administration, in other embodiments, live-attenuated viruses are administered. Recombinant and reassortant influenza A and influenza B viruses produced according to the methods of the invention are also a feature of the invention.

[0022] In certain embodiments, the viruses include an attenuated influenza virus, a cold adapted influenza virus, a temperature sensitive influenza virus, or a virus with any combination of these desirable properties. In one embodiment, the influenza virus incorporates an influenza B/Ann Arbor/1/66 strain virus, e.g., a cold adapted, temperature sensitive, attenuated strain of B/Ann Arbor/1/66. In another embodiment, the influenza virus incorporates an influenza A/ Ann Arbor/6/60 strain virus, e.g., a cold adapted, temperature sensitive, attenuated strain of A/ Ann Arbor/6/60. In another embodiment of the invention, the viruses are artificially engineered influenza viruses incorporating one or more substituted amino acid which influences the characteristic biological properties of, e.g., ca A/ Ann Arbor/6/60 or ca B/Ann Arbor/1/66. Such substituted amino acids favorably correspond to unique amino acids of ca A/ Ann Arbor/6/60 or ca B/Ann Arbor/1/66, e.g., in an A strain virus: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G); and, in a B strain virus: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V). Similarly, other amino acid substitutions at any of these positions resulting in temperature sensitivity, cold adaptation and/or attenuation are encompassed by the viruses and methods of the invention.

[0023] Optionally, reassortant viruses are produced by introducing vectors including the six internal genes of a viral strain selected for its favorable properties regarding vaccine production, in combination with the genome segments encoding the surface antigens (HA and NA) of a selected, e.g., pathogenic strain. For example, the HA segment is favorably selected from a pathogenically relevant HI, H3 or B strain, as is routinely performed for vaccine production. Similarly, the HA segment can be selected from an emerging pathogenic strain such as an H2 strain (e.g., H2N2), an H5 strain (e.g., H5N1) or an H7 strain (e.g., H7N7). Alternatively, the seven complementary gene segments of the first strain are introduced in combination with either the HA or NA encoding segment. In certain embodiments, the internal gene segments are derived from the influenza B/Ann Arbor/1/66 or the A/ Ann Arbor/6/60 strain.

[0024] Additionally, the invention provides methods for producing novel influenza viruses with desirable properties relevant to vaccine production, e.g., temperature sensitive, attenuated, and/or cold adapted, influenza viruses, as well as influenza vaccines including such novel influenza viruses. In certain embodiments, novel influenza A strain virus is produced by introducing mutations that result amino acid substitutions at one or more specified positions demonstrated herein to be important for the temperature sensitive phenotype, e.g., PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴. For example, mutations are introduced at nucleotide positions PBl¹¹⁹⁵, PBl¹⁷⁶⁶, PBl²⁰⁰⁵, PB2⁸²¹ and NP¹⁴⁶, or other nucleotide positions resulting in an amino acid substitution at the specified amino acid position. Any mutation (at one or more of these positions) which individually or in combination results in increased temperature sensitivity, cold adaptation or attenuation relative to wild type viruses is a suitable mutation in the context of the present invention. For example, mutations selected from among PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G) are favorably introduced into the genome of a wild type influenza A strain, e.g., PR8, to produce a temperature sensitive variant suitable for administration as a live attenuated vaccine. To increase stability of the desired phenotype, a plurality of mutations are typically introduced. Following introduction of the selected mutation(s) into the influenza genome, the mutated influenza genome is replicated under conditions in which virus is produced. For example, the mutated influenza virus genome can be replicated in hens' eggs. Alternatively, the influenza virus genome can be replicated in cell culture. In the latter case, the virus is optionally further amplified in hens' eggs to increase the titer. Temperature sensitive, and optionally, attenuated and/or cold adapted viruses produced according to the methods of the invention are also a feature of the invention, as are vaccines including such viruses. Similarly, novel recombinant viral nucleic acids incorporating one or more mutations at positions PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴, e.g., mutations selected from among PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G), and polypeptides with such amino acid substitutions are a feature of the invention. [0025] Likewise, the methods presented herein are adapted to producing novel influenza B strains with temperature sensitive, and optionally attenuated and/or cold adapted phenotypes by introducing one or more specified mutations into an influenza B genome. For example, one or more mutations resulting in an amino acid substitution at a position selected from among PB2⁶³⁰; PA⁴³¹; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³ are introduced into an influenza B strain genome to produce a temperature sensitive influenza B virus. Exemplary amino acid substitutions include the following: : PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V). As indicated above, vaccines incorporating such viruses as well as nucleic acids and polypeptides incorporating these mutations and amino acid substitutions are all features of the invention.

[0026] Accordingly, influenza viruses incorporating the mutations of the invention are a feature of the invention regardless of the method in which they are produced. That is, the invention encompasses influenza strains including the mutations of the invention, e.g., any influenza A virus with an amino acid substitution relative to wild type at one or more positions selected from among: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ or any influenza B virus with an amino acid substitution relative to wild type at one or more positions selected from among: PB2⁶³⁰; PA⁴³¹; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³, with the proviso that the strains ca A Ann Arbor/6/60 and B/Ann Arbor/1/66 are not considered a feature of the present invention. In certain preferred embodiments, the influenza A viruses include a plurality of mutations selected from among PBl (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G); and the influenza B viruses include a plurality of mutations selected from among PB2⁶³ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V), respectively.

[0027] In one embodiment, a plurality of plasmid vectors incorporating the influenza virus genome are introduced into host cells. For example, segments of an influenza virus genome can be incorporated into at least 8 plasmid vectors. In one preferred embodiment, segments of an influenza virus genome are incorporated into 8 plasmids. For example, each of 8 plasmids can favorably incorporate a different segment of the influenza virus genome.

[0028] The vectors of the invention can be bi-directional expression vectors. A bi- directional expression vector of the invention typically includes a first promoter and a second promoter, wherein the first and second promoters are operably linked to alternative strands of the same double stranded viral nucleic acid including a segment of the influenza virus genome. Optionally, the bi-directional expression vector includes a polyadenylation signal and/or a terminator sequence. For example, the polyadenylation signal and/or the terminator sequence can be located flanking a segment of the influenza virus genome internal to the two promoters. One favorable polyadenylation signal in the context of the invention is the SV40 polyadenylation signal. An exemplary plasmid vector of the invention is the plasmid pAD3000, illustrated in Figure 1.

[0029] Any host cell capable of supporting the replication of influenza virus from the vector promoters is suitable in the context of the present invention. Favorable examples of host cells include Vero cells, Per.C6 cells, BHK cells, PCK cells, MDCK cells, MDBK cells, 293 cells (e.g., 293T cells), and COS cells. In combination with the pAD3000 plasmid vectors described herein, Vero cells, 293 cells, COS cells are particularly suitable. In some embodiments, co-cultures of a mixture of at least two of these cell lines, e.g., a combination of COS and MDCK cells or a combination of 293T and MDCK cells, constitute the population of host cells. [0030] A feature of the invention is the culture of host cells incorporating the plasmids of the invention at a temperature below 37 °C, preferably at a temperature equal to, or less than, 35 °C. Typically, the cells are cultured at a temperature between 32 °C and 35 °C. In some embodiments, the cells are cultured at a temperature between about 32 °C and 34 °C, e.g., at about 33 °C.

[0031] Another aspect of the invention relates to novel methods for rescuing recombinant or reassortant influenza A or influenza B viruses (i.e., wild type and variant strains of influenza A and or influenza viruses) from Vero cells in culture. A plurality of vectors incorporating an influenza virus genome is electroporated into a population of Vero cells. The cells are grown under conditions permissive for viral replication, e.g., in the case of cold adapted, attenuated, temperature sensitive virus strains, the Vero cells are grown at a temperature below 37 °C, preferably at a temperature equal to, or less than, 35 °C. Typically, the cells are cultured at a temperature between 32 °C and 35 °C. In some embodiments, the cells are cultured at a temperature between about 32 °C and 34 °C, e.g., at about 33 °C. Optionally (e.g., for vaccine production), the Vero cells are grown in serum free medium without any animal-derived products.

[0032] In the methods of the invention described above, viruses are recovered following culture of the host cells incorporating the influenza genome plasmids. In some embodiments, the recovered viruses are recombinant viruses. In some embodiments, the viruses are reassortant influenza viruses having genetic contributions from more than one parental strain of virus. Optionally, the recovered recombinant or reassortant viruses are further amplified by passage in cultured cells or in hens' eggs.

[0033] Optionally, the recovered viruses are inactivated. In some embodiments, the recovered viruses comprise an influenza vaccine. For example, the recovered influenza vaccine can be a reassortant influenza viruses (e.g., 6:2 or 7: 1 reassortant viruses) having an HA and/or NA antigen derived from a selected strain of influenza A or influenza B. In certain favorable embodiments, the reassortant influenza viruses have an attenuated phenotype. Optionally, the reassortant viruses are cold adapted and/or temperature sensitive, e.g., an attenuated, cold adapted or temperature sensitive influenza B virus having one or more amino acid substitutions selected from the substitutions of Table 17. Such influenza viruses are useful, for example, as live attenuated vaccines for the prophylactic production of an immune response specific for a selected, e.g., pathogenic influenza strain. Influenza viruses, e.g., attenuated reassortant viruses, produced according to the methods of the invention are a feature of the invention.

[0034] In another aspect, the invention relates to methods for producing a recombinant influenza virus vaccine involving introducing a plurality of vectors incorporating an influenza virus genome into a population of host cells capable of supporting replication of influenza virus, culturing the host cells at a temperature less than or equal to 35 °C, and recovering an influenza virus capable of eliciting an immune response upon administration to a subject. The vaccines of the invention can be either influenza A or influenza B strain viruses. In some embodiments, the influenza vaccine viruses include an attenuated influenza virus, a cold adapted influenza virus, or a temperature sensitive influenza virus. In certain embodiments, the viruses possess a combination of these desirable properties. In an embodiment, the influenza virus contains an influenza A/ Ann Arbor/6/60 strain virus. In another embodiment, the influenza virus incorporates an influenza B/Ann Arbor/1/66 strain virus. Alternatively, the vaccine includes artificially engineered influenza A or influenza B viruses incorporating at least one substituted amino acid which influences the characteristic biological properties of ca A/ Ann Arbor/6/60 or ca B/Ann Arbor/1/66, such as a unique amino acid of these strains. For example, vaccines encompassed by the invention include artificially engineered recombinant and reassortant influenza A viruses including at least one mutation resulting in an amino acid substitution at a position selected from among PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ and artificially engineered recombinant and reassortant influenza B viruses including at least one mutation resulting in an amino acid substitution at a position selected from among PB2⁶³⁰, PA⁴³¹, PA⁴⁹⁷, NP⁵⁵, NP¹¹⁴, NP⁴¹⁰, NP⁵¹⁰, Ml¹⁵⁹ and Ml¹⁸³. [0035] In some embodiments, the virus includes a reassortant influenza virus (e.g., a 6:2 or 7:1 reassortant) having viral genome segments derived from more than one influenza virus strain. For example, a reassortant influenza virus vaccine favorably includes an HA and/or NA surface antigen derived from a selected strain of influenza A or B, in combination with the internal genome segments of a virus strain selected for its desirable properties with respect to vaccine production. Often, it is desirable to select the strain of influenza from which the HA and/or NA encoding segments are derived based on predictions of local or world-wide prevalence of pathogenic strains (e.g., as described above). In some cases, the virus strain contributing the internal genome segments is an attenuated, cold adapted and/or temperature sensitive influenza strain, e.g., of A/ Ann Arbor/6/60, B/Ann Arbor/1/66, or an artificially engineered influenza strain having one or more amino acid substitutions resulting in the desired phenotype, e.g., influenza A viruses including at least one mutation resulting in an amino acid substitution at a position selected from among PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ and influenza B viruses including at least one mutation resulting in an amino acid substitution at a position selected from among PB2⁶³⁰, PA⁴³¹, PA⁴⁹⁷, NP⁵⁵, NP¹¹⁴, NP⁴¹⁰, NP⁵¹⁰, Ml¹⁵⁹ and Ml¹⁸³. For example, favorable reassortant viruses include artificially engineered influenza A viruses with one or more amino acid substitution selected from among PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G); and influenza B viruses including one or more amino acid substitutions selected from among PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V). [0036] If desired, the influenza vaccine viruses are inactivated upon recovery.

[0037] Influenza virus vaccines, including attenuated live vaccines, produced by the methods of the invention are also a feature of the invention. In certain favorable embodiments the influenza virus vaccines are reassortant virus vaccines.

[0038] Another aspect of the invention provides plasmids that are bi-directional expression vectors. The bi-directional expression vectors of the invention incorporate a first promoter inserted between a second promoter and a polyadenylation site, e.g., an SV40 polyadenylation site. In an embodiment, the first promoter and the second promoter can be situated in opposite orientations flanking at least one cloning site. An exemplary vector of the invention is the plasmid pAD3000, illustrated in Figure 1. [0039] In some embodiments, at least one segment of an influenza virus genome is inserted into the cloning site, e.g., as a double stranded nucleic acid. For example, a vector of the invention includes a plasmid having a first promoter inserted between a second promoter and an SV40 polyadenylation site, wherein the first promoter and the second promoter are situated in opposite orientations flanking at least one segment of an influenza virus. [0040] Kits including one or more expression vectors of the invention are also a feature of the invention. Typically, the kits also include one or more of: a cell line capable of supporting influenza virus replication, a buffer, a culture medium, an instruction set, a packaging material, and a container. In some embodiments, the kit includes a plurality of expression vectors, each of which includes at least one segment of an influenza virus genome. For example, kits including a plurality of expression vectors each including one of the internal genome segments of a selected virus strain, e.g., selected for its desirable properties with respect to vaccine production or administration, are a feature of the invention. For example, the selected virus strain can be an attenuated, cold adapted and/or temperature sensitive strain, e.g., A/ Ann Arbor/6/60 or B/Ann Arbor/1/66, or an alternative strain with the desired properties, such as an artificially engineered strain having one or more amino acid substitutions as described herein, e.g., in Table 17. In an embodiment, the kit includes a expression vectors incorporating members of a library of nucleic acids encoding variant HA and/or NA antigens. [0041] Productively growing cell cultures including at least one cell incorporating a plurality of vectors including an influenza virus genome, at a temperature less than or equal to 35 °C, is also a feature of the invention. The composition can also include a cell culture medium. In some embodiments, the plurality of vectors includes bi-directional expression vectors, e.g., comprising a first promoter inserted between a second promoter and an SV40 polyadenylation site. For example, the first promoter and the second promoter can be situated in opposite orientations flanking at least one segment of an influenza virus. The cell cultures of the invention are maintained at a temperature less than or equal to 35 °C, such as between about 32 °C and 35 °C, typically between about 32 °C and about 34 °C, for example, at about 33 °C. [0042] The invention also includes a cell culture system including a productively growing cell culture of at least one cell incorporating a plurality of vectors comprising a an influenza virus genome, as described above, and a regulator for maintaining the culture at a temperature less than or equal to 35 °C. For example, the regulator favorably maintains the cell culture at a temperature between about 32 °C and 35 °C, typically between about 32 °C and about 34 °C, e.g., at about 33 °C. [0043] Another feature of the invention are artificially engineered recombinant or reassortant influenza viruses including one or more amino acid substitutions which influence temperature sensitivity, cold adaptation and/or attenuation. For example, artificially engineered influenza A viruses having one or more amino acid substitution at a position selected from among: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ and artificially engineered influenza B viruses having one or more amino acid substitutions at a position selected from among PB2⁶³⁰, PA⁴³¹, PA⁴⁹⁷, NP⁵⁵, NP¹¹⁴, NP⁴¹⁰, NP⁵¹⁰, Ml¹⁵⁹ and Ml¹⁸³ are favorable embodiments of the invention. Exemplary embodiments include influenza A viruses with any one or more of the following amino acid substitutions: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G); and influenza B viruses with any one or more of the following amino acid substitutions: PB2 (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V). In certain embodiments, the viruses include a plurality of mutations, such as one, two, three, four, five, six, seven, eight or nine amino acid substitutions at positions identified above. Accordingly, artificially engineered influenza A viruses having amino acid substitutions at all five positions indicated above, e.g., PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G) and artificially engineered influenza B viruses having amino acid substitutions at eight or all nine of the positions indicated above, e.g., PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹

(H159Q) and Ml¹⁸³ (M183V), are encompassed by the invention. In addition, the viruses can include one or more additional amino acid substitutions not enumerated above.

[0044] In certain embodiments, the artificially engineered influenza viruses are temperature sensitive influenza viruses, cold adapted influenza viruses and/or attenuated influenza viruses. For example, a temperature sensitive influenza virus according to the invention typically exhibits between about 2.0 and 5.0 logio reduction in growth at 39 °C as compared to a wild type influenza virus. For example, a temperature sensitive virus favorably exhibits at least about 2.0 logio, at least about 3.0 logκ), at least about 4.0 logϊo, or at least about 4.5 logκ) reduction in growth at 39 °C relative to that of a wild type influenza virus. Typically, but not necessarily, a temperature sensitive influenza virus retains robust growth characteristics at 33 °C. An attenuated influenza virus of the invention typically exhibits between about a 2.0 and a 5.0 loglO reduction in growth in a ferret attenuation assay as compared to a wild type influenza virus. For example, an attenuated influenza virus of the invention exhibits at least about a 2.0 logio, frequently about a 3.0 logio, and favorably at least about a 4.0 logio reduction in growth in a ferret attenuation assay relative to wild type influenza virus.

BRIEF DESCRIPTION OF THE DRAWINGS

[0045] Figure 1 : Illustration of pAD3000 plasmid

[0046] Figure 2: Micrographs of infected cells

[0047] Figure 3: Genotyping analysis of rMDV-A and 6:2 H1N1 reassortant virus from plasmid transfection. [0048] Figure 4: Illustration of eight plasmid system for the production of influenza B virus.

[0049] Figure 5: A and B. Characterization of recombinant MDV-B virus by RT-

PCR; C and D. Characterization of recombinant B/Yamanashi/ 166/98 by RT PCR.

[0050] Figure 6: Sequence of pAD3000 in GeneBank format. [0051] Figure 7: Sequence alignment with MDV-B and eight plasmids.

[0052] Figure 8: RT-PCR products derived from simultaneous amplification of HA and NA segments of influenza B strains.

[0053] Figure 9: Bar graph illustrating relative titers of recombinant and reassortant virus. [0054] Figure 10: Bar graph illustrating relative titers of reassortant virus under permissive and restrictive temperatures (temperature sensitivity).

[0055] Figure 11: Graphic representation of reassortant viruses incorporating specific mutations (knock-in) correlating with temperature sensitivity (left panel) and relative titers at permissive and restrictive temperatures (temperature sensitivity) (right panel).

[0056] Figure 12: Determination of ts mutations in a minigenome assay. A. HEp-2 cells were transfected with PBl, PB2, PA, NP and pFlu-CAT, incubated at 33 or 39 °C for 18 hr and cell extracts were analyzed for CAT reporter gene expression. B. CAT mRNA expression by primer extension assay.

[0057] Figure 13: Schematic illustration of triple-gene recombinants with wild type residues in PA, NP, and Ml proteins. [0058] Figure 14: Tabulation of growth of single-gene and double-gene recombinant viruses.

[0059] Figure 15: Tabulation of amino acid residue of the nucleoprotein corresponding to non-ts phenotype.

[0060] Figure 16: Schematic diagram of recombinant PR8 mutants. The mutations introduced in PBl and/or PB2 genes are indicated by the filled dots.

[0061] Figure 17: Bar graph illustrating relative titers at 33 °C and 39 °C.

[0062] Figure 18: Photomicrographs illustrating plaque morphology of PR8 mutants at various temperatures. MDCK cells were infected with virus as indicated and incubated at 33, 37 and39 °C for three days. Virus plaques were visualized by immunostaining and photographed.

[0063] Figure 19: Protein synthesis at permissive and nonpermissive temperatures.

MDCK cells were infected with viruses as indicated and incubated at 33 or 39 °C overnight. Radiolabeled labeled polypeptides were electrophoresed on an SDS-PAGE and autoradiographed. Viral proteins, HA, NP, Ml and NS are indicated. [0064] Figure 20: A. Line graphs illustrating differential replication of MDV-A and MDV-B in Per.C6 cells relative to replication in MDCK cells; B. Line graph illustrating differential replication of MDV-A single gene reassortants in Per.C6 cells.

DETAILED DESCRIPTION

[0065] Many pathogenic influenza virus strains grow only poorly in tissue culture, and strains suitable for production of live attenuated virus vaccines (e.g., temperature sensitive, cold adapted and/or attenuated influenza viruses) have not been successfully grown in cultured cells for commercial production. The present invention provides a multi-plasmid transfection system which permits the growth and recovery of influenza virus strains which are not adapted for growth under standard cell culture conditions. [0066] In a first aspect, the methods of the invention provide vectors and methods for producing recombinant influenza B virus in cell culture entirely from cloned viral DNA. In another aspect, the methods of the present invention are based in part on the development of tissue culture conditions which support the growth of virus strains (both A strain and B strain influenza viruses) with desirable properties relative to vaccine production (e.g., attenuated pathogenicity or phenotype, cold adaptation, temperature sensitivity, etc.) in vitro in cultured cells. Influenza viruses are produced by introducing a plurality of vectors incorporating cloned viral genome segments into host cells, and culturing the cells at a temperature not exceeding 35 °C. When vectors including an influenza virus genome are transfected, recombinant viruses suitable as vaccines can be recovered by standard purification procedures. Using the vector system and methods of the invention, reassortant viruses incorporating the six internal gene segments of a strain selected for its desirable properties with respect to vaccine production, and the immunogenic HA and NA segments from a selected, e.g., pathogenic strain, can be rapidly and efficiently produced in tissue culture. Thus, the system and methods described herein are useful for the rapid production in cell culture of recombinant and reassortant influenza A and B viruses, including viruses suitable for use as vaccines, including live attenuated vaccines, such as vaccines suitable for intranasal administration.

[0067] Typically, a single Master Donor Virus (MDV) strain is selected for each of the A and B subtypes. In the case of a live attenuated vaccine, the Master Donor Virus strain is typically chosen for its favorable properties, e.g., temperature sensitivity, cold adaptation and/or attenuation, relative to vaccine production. For example, exemplary Master Donor Strains include such temperature sensitive, attenuated and cold adapted strains of A Ann Arbor/6/60 and B/Ann Arbor/1/66, respectively. The present invention elucidates the underlying mutations resulting in the ca, ts and att phenotypes of these virus strains, and provides methods for producing novel strains of influenza suitable for use as donor strains in the context of recombinant and reassortant vaccine production.

[0068] For example, a selected master donor type A virus (MDV-A), or master donor type B virus (MDV-B), is produced from a plurality of cloned viral cDNAs constituting the viral genome. In an exemplary embodiment, recombinant viruses are produced from eight cloned viral cDNAs. Eight viral cDNAs representing either the selected MDV-A or MDV-B sequences of PB2, PBl, PA, NP, HA, NA, M and NS are cloned into a bi-directional expression vector, such as a plasmid (e.g., pAD3000), such that the viral genomic RNA can be transcribed from an RNA polymerase I (pol I) promoter from one strand and the viral mRNAs can be synthesized from an RNA polymerase II (pol II) promoter from the other strand. Optionally, any gene segment can be modified, including the HA segment (e.g., to remove the multi-basic cleavage site).

[0069] Infectious recombinant MDV-A or MDV-B virus is then recovered following transfection of plasmids bearing the eight viral cDNAs into appropriate host cells, e.g., Vero cells, co-cultured MDCK/293T or MDCK/COS7 cells. Using the plasmids and methods described herein, the invention is useful, e.g., for generating 6:2 reassortant influenza vaccines by co-transfection of the 6 internal genes (PBl, PB2, PA, NP, M and NS) of the selected virus (e.g., MDV-A, MDV-B) together with the HA and NA derived from different corresponding type (A or B) influenza viruses. For example, the HA segment is favorably selected from a pathogenically relevant HI, H3 or B strain, as is routinely performed for vaccine production. Similarly, the HA segment can be selected from a strain with emerging relevance as a pathogenic strain such as an H2 strain (e.g., H2N2), an H5 strain (e.g., H5N1) or an H7 strain (e.g., H7N7). Reassortants incorporating seven genome segments of the MDV and either the HA or NA gene of a selected strain (7:1 reassortants) can also be produced. In addition, this system is useful for determining the molecular basis of phenotypic characteristics, e.g., the attenuated (att), cold adapted (ca), and temperature sensitive (ts) phenotypes, relevant to vaccine production.

DEFINITIONS

[0070] Unless defined otherwise, all scientific and technical terms are understood to have the same meaning as commonly used in the art to which they pertain. For the purpose of the present invention the following terms are defined below.

[0071] The terms "nucleic acid," "polynucleotide," "polynucleotide sequence" and

"nucleic acid sequence" refer to single-stranded or double-stranded deoxyribonucleotide or ribonucleotide polymers, or chimeras or analogues thereof. As used herein, the term optionally includes polymers of analogs of naturally occurring nucleotides having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids). Unless otherwise indicated, a particular nucleic acid sequence of this invention encompasses complementary sequences, in addition to the sequence explicitly indicated.

[0072] The term "gene" is used broadly to refer to any nucleic acid associated with a biological function. Thus, genes include coding sequences and/or the regulatory sequences required for their expression. The term "gene" applies to a specific genomic sequence, as well as to a cDNA or an mRNA encoded by that genomic sequence.

[0073] Genes also include non-expressed nucleic acid segments that, for example, form recognition sequences for other proteins. Non-expressed regulatory sequences include "promoters" and "enhancers," to which regulatory proteins such as transcription factors bind, resulting in transcription of adjacent or nearby sequences. A "Tissue specific" promoter or enhancer is one which regulates transcription in a specific tissue type or cell type, or types.

[0074] The term "vector" refers to the means by which a nucleic can be propagated and/or transferred between organisms, cells, or cellular components. Vectors include plasmids, viruses, bacteriophage, pro-viruses, phagemids, transposons, and artificial chromosomes, and the like, that replicate autonomously or can integrate into a chromosome of a host cell. A vector can also be a naked RNA polynucleotide, a naked DNA polynucleotide, a polynucleotide composed of both DNA and RNA within the same strand, a poly-lysine-conjugated DNA or RNA, a peptide-conjugated DNA or RNA, a liposome-conjugated DNA, or the like, that are not autonomously replicating. Most commonly, the vectors of the present invention are plasmids.

[0075] An "expression vector" is a vector, such as a plasmid, which is capable of promoting expression, as well as replication of a nucleic acid incorporated therein. Typically, the nucleic acid to be expressed is "operably linked" to a promoter and/or enhancer, and is subject to transcription regulatory control by the promoter and/or enhancer.

[0076] A "bi-directional expression vector" is typically characterized by two alternative promoters oriented in the opposite direction relative to a nucleic acid situated between the two promoters, such that expression can be initiated in both orientations resulting in, e.g., transcription of both plus (+) or sense strand, and negative (-) or antisense strand RNAs. Alternatively, the bi-directional expression vector can be an ambisense vector, in which the viral mRNA and viral genomic RNA (as a cRNA) are expressed from the same strand.

[0077] In the context of the invention, the term "isolated" refers to a biological material, such as a nucleic acid or a protein, which is substantially free from components that normally accompany or interact with it in its naturally occurring environment. The isolated material optionally comprises material not found with the material in its natural environment, e.g., a cell. For example, if the material is in its natural environment, such as a cell, the material has been placed at a location in the cell (e.g., genome or genetic element) not native to a material found in that environment. For example, a naturally occurring nucleic acid (e.g., a coding sequence, a promoter, an enhancer, etc.) becomes isolated if it is introduced by non-naturally occurring means to a locus of the genome (e.g., a vector, such as a plasmid or virus vector, or amplicon) not native to that nucleic acid. Such nucleic acids are also referred to as "heterologous" nucleic acids.

[0078] The term "recombinant" indicates that the material (e.g., a nucleic acid or protein) has been artificially or synthetically (non-naturally) altered by human intervention. The alteration can be performed on the material within, or removed from, its natural environment or state. Specifically, when referring to a virus, e.g., an influenza virus, the virus is recombinant when it is produced by the expression of a recombinant nucleic acid. [0079] The term "reassortant," when referring to a virus, indicates that the virus includes genetic and/or polypeptide components derived from more than one parental viral strain or source. For example, a 7:1 reassortant includes 7 viral genomic segments (or gene segments) derived from a first parental virus, and a single complementary viral genomic segment, e.g., encoding hemagglutinin or neuraminidase, from a second parental virus. A 6:2 reassortant includes 6 genomic segments, most commonly the 6 internal genes from a first parental virus, and two complementary segments, e.g., hemagglutinin and neuraminidase, from a different parental virus.

[0080] The term "introduced" when referring to a heterologous or isolated nucleic acid refers to the incoφoration of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid can be incoφorated into the genome of the cell (e.g., chromosome, plasmid, plastid or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA). The term includes such methods as "infection," "transfection," "transformation" and "transduction." In the context of the invention a variety of methods can be employed to introduce nucleic acids into prokaryotic cells, including electroporation, Calcium phosphate precipitation, lipid mediated transfection (lipofection), etc.

[0081] The term "host cell" means a cell which contains a heterologous nucleic acid, such as a vector, and supports the replication and/or expression of the nucleic acid, and optionally production of one or more encoded products including a polypeptide and/or a virus. Host cells can be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, insect, amphibian, avian or mammalian cells, including human cells. Exemplary host cells in the context of the invention include Vero (African green monkey kidney) cells, Per.C6 cells (human embryonic retinal cells), BHK (baby hamster kidney) cells, primary chick kidney (PCK) cells, Madin-Darby Canine Kidney (MDCK) cells, Madin- Darby Bovine Kidney (MDBK) cells, 293 cells (e.g., 293T cells), and COS cells (e.g., COS1, COS7 cells). The term host cell encompasses combinations or mixtures of cells including, e.g., mixed cultures of different cell types or cell lines.

[0082] The terms "temperature sensitive," "cold adapted" and "attenuated" are well known in the art. For example, the term "temperature sensitive" ("ts") indicates that the virus exhibits a 100 fold or greater reduction in titer at 39 °C relative to 33 °C for influenza A strains, and that the virus exhibits a 100 fold or greater reduction in titer at 37 °C relative to 33 °C for influenza B strains. For example, the term "cold adapted" ("ca") indicates that the virus exhibits growth at 25 °C within 100 fold of its growth at 33 °C. For example, the term "attenuated" ("att") indicates that the virus replicates in the upper airways of ferrets but is not detectable in lung tissues, and does not cause influenza-like illness in the animal. It will be understood that viruses with intermediate phenotypes, i.e., viruses exhibiting titer reductions less than 100 fold at 39 °C (for A strain viruses) or 37 °C (for B strain viruses), exhibiting growth at 25 °C that is more than 100 fold than its growth at 33 °C (e.g., within 200 fold, 500 fold, 1000 fold, 10,000 fold less), and/or exhibit reduced growth in the lungs relative to growth in the upper airways of ferrets (i.e., partially attenuated) and/or reduced influenza like illness in the animal, which possess one or more of the amino acid substitutions described herein are also useful viruses encompassed by the invention. Growth indicates viral quantity as indicated by titer, plaque size or moφhology, particle density or other measures known to those of skill in the art.

[0083] The expression "artificially engineered" is used herein to indicate that the virus, viral nucleic acid or virally encoded product, e.g., a polypeptide, a vaccine, comprises at least one mutation introduced by recombinant methods, e.g., site directed mutagenesis, PCR mutagenesis, etc. The expression "artificially engineered" when referring to a virus (or viral component or product) comprising one or more nucleotide mutations and/or amino acid substitutions indicates that the viral genome or genome segment encoding the virus (or viral component or product) is not derived from naturally occurring sources, such as a naturally occurring or previously existing laboratory strain of virus produced by non-recombinant methods (such as progressive passage at 25 °C), e.g., a wild type or cold adapted A/ Ann Arbor/6/60 or B/Ann Arbor/l/66strain.

I

Influenza Virus [0084] The genome of Influenza viruses is composed of eight segments of linear

(-) strand ribonucleic acid (RNA), encoding the immunogenic hemagglutinin (HA) and neuraminidase (NA) proteins, and six internal core polypeptides: the nucleocapsid nucleoprotein (NP); matrix proteins (M); non-structural proteins (NS); and 3 RNA polymerase (PA, PBl, PB2) proteins. During replication, the genomic viral RNA is transcribed into (+) strand messenger RNA and (-) strand genomic cRNA in the nucleus of the host cell. Each of the eight genomic segments is packaged into ribonucleoprotein complexes that contain, in addition to the RNA, NP and a polymerase complex (PBl, PB2, and PA).

[0085] In the present invention, viral genomic RNA corresponding to each of the eight segments is inserted into a recombinant vector for manipulation and production of influenza viruses. A variety of vectors, including viral vectors, plasmids, cosmids, phage, and artificial chromosomes, can be employed in the context of the invention. Typically, for ease of manipulation, the viral genomic segments are inserted into a plasmid vector, providing one or more origins of replication functional in bacterial and eukaryotic cells, and, optionally, a marker convenient for screening or selecting cells incoφorating the plasmid sequence. An exemplary vector, plasmid pAD3000 is illustrated in Figure 1. [0086] Most commonly, the plasmid vectors of the invention are bi-directional expression vectors capable of initiating transcription of the inserted viral genomic segment in either direction, that is, giving rise to both (+) strand and (-) strand viral RNA molecules. To effect bi-directional transcription, each of the viral genomic segments is inserted into a vector having at least two independent promoters, such that copies of viral genomic RNA are transcribed by a first RNA polymerase promoter (e.g., Pol I), from one strand, and viral mRNAs are synthesized from a second RNA polymerase promoter (e.g., Pol π). Accordingly, the two promoters are arranged in opposite orientations flanking at least one cloning site (i.e., a restriction enzyme recognition sequence) preferably a unique cloning site, suitable for insertion of viral genomic RNA segments. Alternatively, an "ambisense" vector can be employed in which the (+) strand mRNA and the (-) strand viral RNA (as a cRNA) are transcribed from the same strand of the vector.

Expression vectors [0087] The influenza virus genome segment to be expressed is operably linked to an appropriate transcription control sequence (promoter) to direct mRNA synthesis. A variety of promoters are suitable for use in expression vectors for regulating transcription of influenza virus genome segments. In certain embodiments, e.g., wherein the vector is the plasmid pAD3000, the cytomegalovirus (CMV) DNA dependent RNA Polymerase II (Pol JJ) promoter is utilized. If desired, e.g., for regulating conditional expression, other promoters can be substituted which induce RNA transcription under the specified conditions, or in the specified tissues or cells. Numerous viral and mammalian, e.g., human promoters are available, or can be isolated according to the specific application contemplated. For example, alternative promoters obtained from the genomes of animal and human viruses include such promoters as the adenovirus (such as Adenovirus 2), papilloma virus, hepatitis-B virus, polyoma virus, and Simian Virus 40 (SV40), and various retroviral promoters. Mammalian promoters include, among many others, the actin promoter, immunoglobulin promoters, heat-shock promoters, and the like. In addition, bacteriophage promoters can be employed in conjunction with the cognate RNA polymerase, e.g., the T7 promoter. [0088] Transcription is optionally increased by including an enhancer sequence.

Enhancers are typically short, e.g., 10-500 bp, cis-acting DNA elements that act in concert with a promoter to increase transcription. Many enhancer sequences have been isolated from mammalian genes (hemoglobin, elastase, albumin, alpha. -fetoprotein, and insulin), and eukaryotic cell viruses. The enhancer can be spliced into the vector at a position 5' or 3' to the heterologous coding sequence, but is typically inserted at a site 5' to the promoter. Typically, the promoter, and if desired, additional transcription enhancing sequences are chosen to optimize expression in the host cell type into which the heterologous DNA is to be introduced (Scharf et al. (1994) Heat stress promoters and transcription factors Results Probl Cell Differ 20:125-62; Kriegler et al. (1990) Assembly of enhancers, promoters, and splice signals to control expression of transferred genes Methods in Enzymol 185: 512- 27). Optionally, the amplicon can also contain a ribosome binding site or an internal ribosome entry site (IRES) for translation initiation.

[0089] The vectors of the invention also favorably include sequences necessary for the termination of transcription and for stabilizing the mRNA, such as a polyadenylation site or a terminator sequence. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. In one embodiment, e.g., involving the plasmid pAD3000, the SV40 polyadenylation sequences provide a polyadenylation signal.

[0090] In addition, as described above, the expression vectors optionally include one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells, in addition to genes previously listed, markers such as dihydrofolate reductase or neomycin resistance are suitable for selection in eukaryotic cell culture.

[0091] The vector containing the appropriate DNA sequence as described above, as well as an appropriate promoter or control sequence, can be employed to transform a host cell permitting expression of the protein. While the vectors of the invention can be replicated in bacterial cells, most frequently it will be desirable to introduce them into mammalian cells, e.g., Vero cells, BHK cells, MDCK cell, 293 cells, COS cells, for the puφose of expression.

Additional Expression Elements [0092] Most commonly, the genome segment encoding the influenza virus protein includes any additional sequences necessary for its expression, including translation into a functional viral protein. In other situations, a minigene, or other artificial construct encoding the viral proteins, e.g., an HA or NA protein, can be employed. In this case, it is often desirable to include specific initiation signals which aid in the efficient translation of the heterologous coding sequence. These signals can include, e.g., the ATG initiation codon and adjacent sequences. To insure translation of the entire insert, the initiation codon is inserted in the correct reading frame relative to the viral protein. Exogenous transcriptional elements and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of enhancers appropriate to the cell system in use.

[0093] If desired, polynucleotide sequences encoding additional expressed elements, such as signal sequences, secretion or localization sequences, and the like can be incoφorated into the vector, usually, in-frame with the polynucleotide sequence of interest, e.g., to target polypeptide expression to a desired cellular compartment, membrane, or organelle, or into the cell culture media. Such sequences are known to those of skill, and include secretion leader peptides, organelle targeting sequences (e.g., nuclear localization sequences, ER retention signals, mitochondrial transit sequences), membrane localization/anchor sequences (e.g., stop transfer sequences, GPI anchor sequences), and the like.

Influenza virus vaccine [0094] Historically, influenza virus vaccines have been produced in embryonated hens' eggs using strains of virus selected based on empirical predictions of relevant strains. More recently, reassortant viruses have been produced that incoφorate selected hemagglutinin and neuraminidase antigens in the context of an approved attenuated, temperature sensitive master strain. Following culture of the virus through multiple passages in hens' eggs, influenza viruses are recovered and, optionally, inactivated, e.g., using formaldehyde and/or β-propiolactone. However, production of influenza vaccine in this manner has several significant drawbacks. Contaminants remaining from the hens' eggs are highly antigenic, pyrogenic, and frequently result in significant side effects upon administration. More importantly, strains designated for production must be selected and distributed, typically months in advance of the next flu season to allow time for production and inactivation of influenza vaccine. Attempts at producing recombinant and reassortant vaccines in cell culture have been hampered by the inability of any of the strains approved for vaccine production to grow efficiently under standard cell culture conditions. [0095] The present invention provides a vector system, and methods for producing recombinant and reassortant viruses in culture which make it possible to rapidly produce vaccines corresponding to one or many selected antigenic strains of virus. In particular, conditions and strains are provided that result in efficient production of viruses from a multi plasmid system in cell culture. Optionally, if desired, the viruses can be further amplified in Hens' eggs.

[0096] For example, it has not been possible to grow the influenza B master strain

B/Ann Arbor/1/66 under standard cell culture conditions, e.g., at 37 °C. In the methods of the present invention, multiple plasmids, each incoφorating a segment of an influenza virus genome are introduced into suitable cells, and maintained in culture at a temperature less than or equal to 35 °C. Typically, the cultures are maintained at between about 32 °C and 35°C, preferably between about 32 °C and about 34 °C, e.g., at about 33 °C.

[0097] Typically, the cultures are maintained in a system, such as a cell culture incubator, under controlled humidity and CO₂, at constant temperature using a temperature regulator, such as a thermostat to insure that the temperature does not exceed 35 °C.

[0098] Reassortant influenza viruses can be readily obtained by introducing a subset of vectors corresponding to genomic segments of a master influenza virus, in combination with complementary segments derived from strains of interest (e.g., antigenic variants of interest). Typically, the master strains are selected on the basis of desirable properties relevant to vaccine administration. For example, for vaccine production, e.g., for production of a live attenuated vaccine, the master donor virus strain may be selected for an attenuated phenotype, cold adaptation and/or temperature sensitivity. In this context, Influenza A strain ca A/ Ann Arbor/6/60; Influenza B strain ca B/Ann Arbor/1/66; or another strain selected for its desirable phenotypic properties, e.g., an attenuated, cold adapted, and or temperature sensitive strain, such as an artificially engineered influenza A strain as described in Example 4; or an artificially engineered influenza B strain incoφorating one or more of the amino acid substitutions specified in Table 17 are favorably selected as master donor strains.

[0099] In one embodiment, plasmids incoφorating the six internal genes of the influenza master virus strain, (i.e., PBl, PB2, PA, NP, NB, Ml, BM2, NSl and NS2) are transfected into suitable host cells in combination with hemagglutinin and neuraminidase segments from an antigenically desirable strain, e.g., a strain predicted to cause significant local or global influenza infection. Following replication of the reassortant virus in cell culture at appropriate temperatures for efficient recovery, e.g., equal to or less than 35 °C, such as between about 32 °C and 35 °C, for example between about 32 °C and about 34 °C, or at about 33 °C, reassortant viruses is recovered. Optionally, the recovered virus can be inactivated using a denaturing agent such as formaldehyde or β-propiolactone.

Attenuated, temperature sensitive and cold adapted influenza virus vaccines [0100] In one aspect, the present invention is based on the determination of the mutations underlying the ts phenotype in preferred Master Donor Strains of virus. To determine the functional importance of single nucleotide changes in the MDV strain genome, reassortant viruses derived from highly related strains within the A/AA/6/60 lineage were evaluated for temperature sensitivity. The isogenic nature of the two parental strains enables the evaluation of single nucleotide changes on the ts phenotype. Accordingly, the genetic basis for the ts phenotype of MDV-A is mapped at the nucleotide level to specific amino acid residues within PBl, PB2, and NP.

[0101] Previous attempts to map the genetic basis of the ts phenotype of ca

A AA/6/60 utilized classical coinfection/reassortant techniques to create single and multiple gene reassortants between A/AA/6/60 and an unrelated wt strain. These studies suggested that both PB2, and PBl contributed to the ts phenotype (Kendal et al. (1978) Biochemical characteristics of recombinant viruses derived at sub-optimal temperatures: evidence that ts lesions are present in RNA segments 1 and 3, and that RNA 1 codes for the virion transcriptase enzyme, p. 734-743. In B. W. J. Mahy, and R.D. Barry (ed.) Negative Strand Viruses. Academic Press; Kendal et al. (1977) Comparative studies of wild-type and cold mutant (temperature sensitive) influenza viruses: genealogy of the matrix (M) and the non- structural (NS) proteins in recombinant cold-adapted H3N2 viruses J Gen Virol 37:145-159; Kendal et al. (1979) Comparative studies of wild-type and cold-mutant (temperature sensitive) influenza viruses: independent segregation of temperature-sensitivity of virus replication from temperature-sensitivity of virion transcriptase activity during recombination of mutant A/ Ann Arbor/6/60 with wild-type H3N2 strains J Gen Virol 44:443-4560; Snyder et al. (1988) Four viral genes independently contribute to attenuation of live influenza A/ nn Arbor/6/60 (H2N2) cold- adapted reassortant virus vaccines J Virol 62:488-95). Inteφretation of these studies, however, was confounded by constellation effects, which were caused by mixing gene segments from two divergent influenza A strains. Weakened interactions could have occurred through changes between the A/AA/6/60 and wt gene segments other than those specifically involved in expression of the ts phenotype from the A/AA/6/60 background. Constellation effects were also shown to confound the inteφretation of association of the M gene segment with the att phenotype (Subbarao et al. (1992) The attenuation phenotype conferred by the M gene of the influenza A/ nn Arbor/6/60 cold-adapted virus (H2N2) on the A/Korea/82 (H3N2) reassortant virus results from a gene constellation effect Virus Res 25:37-50).

[0102] In the present invention, mutations resulting in amino acid substitutions at positions PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ are identified as functionally important in conferring the temperature sensitive phenotype on the MDV-A strain virus. As will be understood by those of skill in the art, mutations in nucleotides at positions PBl¹¹⁹⁵, PBl¹⁷⁶⁶, PBl²⁰⁰⁵, PB2⁸²¹ and NP¹⁴⁶ designate amino acid substitutions at PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴, respectively. Thus, any nucleotide substitutions resulting in substituted amino acids at these positions are a feature of the invention. Exemplary mutations PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G), singly, and more preferably in combination, result in a temperature sensitive phenotype. Simultaneous reversion of these mutations to wild type abolishes the ts phenotype, while introduction of these mutations onto a wild-type background results in virus with a ts phenotype. Consistent with the stability of these phenotypes during passage of the virus, no single change can individually revert the temperature sensitivity profile of the resulting virus to that of wild-type. Rather, these changes appear to act in concert with one another to fully express the ts phenotype. This discovery permits the engineering of additional strains of temperature sensitive influenza A virus suitable for master donor viruses for the production of live attenuated influenza vaccines.

[0103] Similarly, substitutions of individual amino acids in a Master Donor Virus-

B strain are correlated with the ts phenotype as illustrated in Table 17. Thus, the methods presented herein are adapted to producing novel influenza B strains with temperature sensitive, and optionally attenuated and/or cold adapted phenotypes by introducing one or more specified mutations into an influenza B genome. For example, one or more mutations resulting in an amino acid substitution at a position selected from among PB2⁶³⁰; PA⁴³¹; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³ are introduced into an influenza B strain genome to produce a temperature sensitive influenza B virus. Exemplary amino acid substitutions include the following: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (VI 14A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V).

[0104] Influenza viruses incoφorating the mutations of the invention are a feature of the invention regardless of the method in which they are produced. That is, the invention encompasses influenza strains including the mutations of the invention, e.g., any influenza A virus with an amino acid substitution relative to wild type at one or more positions selected from among: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ or any influenza B virus with an amino acid substitution relative to wild type at one or more positions selected from among: PB2⁶³⁰; PA⁴³¹; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³, with the proviso that the strains ca A/ Ann Arbor/6/60 and B/Ann Arbor/1/66 are not considered a feature of the present invention. In certain preferred embodiments, the influenza A viruses include a plurality of mutations (e.g., two, or three, or four, or five, or more mutations) selected from among PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G); and the influenza B viruses include a plurality of mutations selected from among PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (Ml 83V), respectively. For example, in addition to providing viruses with desired phenotypes relevant for vaccine production, viruses with a subset of mutations, e.g., 1, or 2, or 3, or 4, or 5 selected mutations, are useful in elucidating the contribution of additional mutations to the phenotype of the virus. In certain embodiments, the influenza viruses include at least one additional non-wild type nucleotide (e.g., possibly resulting in an additional amino acid substitution), which optionally refines the desired phenotype or confers a further desirable phenotypic attribute.

Cell Culture [0105] Typically, propagation of the virus is accomplished in the media compositions in which the host cell is commonly cultured. Suitable host cells for the replication of influenza virus include, e.g., Vero cells, Per.C6 cells, BHK cells, MDCK cells, 293 cells and COS cells, including 293T cells, COS7 cells. Commonly, co-cultures including two of the above cell lines, e.g., MDCK cells and either 293T or COS cells are employed at a ratio, e.g., of 1:1, to improve replication efficiency. Typically, cells are cultured in a standard commercial culture medium, such as Dulbecco's modified Eagle's medium supplemented with serum (e.g., 10% fetal bovine serum), or in serum free medium, under controlled humidity and CO₂ concentration suitable for maintaining neutral buffered pH (e.g., at pH between 7.0 and 7.2). Optionally, the medium contains antibiotics to prevent bacterial growth, e.g., penicillin, streptomycin, etc., and/or additional nutrients, such as L-glutamine, sodium pyruvate, non-essential amino acids, additional supplements to promote favorable growth characteristics, e.g., trypsin, β-mercaptoethanol, and the like.

[0106] Procedures for maintaining mammalian cells in culture have been extensively reported, and are known to those of skill in the art. General protocols are provided, e.g., in Freshney (1983) Culture of Animal Cells: Manual of Basic Technique, Alan R. Liss, New York; Paul (1975) Cell and Tissue Culture. 5^th ed., Livingston, Edinburgh; Adams (1980) Laboratory Techniques in Biochemistry and Molecular

Biology-Cell Culture for Biochemists. Work and Burdon (eds.) Elsevier, Amsterdam. Additional details regarding tissue culture procedures of particular interest in the production of influenza virus in vitro include, e.g., Merten et al. (1996) Production of influenza virus in cell cultures for vaccine preparation. In Cohen and Shafferman (eds) Novel Strategies in Design and Production of Vaccines, which is incoφorated herein in its entirety. Additionally, variations in such procedures adapted to the present invention are readily determined through routine experimentation.

[0107] Cells for production of influenza virus can be cultured in serum-containing or serum free medium. In some case, e.g., for the preparation of purified viruses, it is desirable to grow the host cells in serum free conditions. Cells can be cultured in small scale, e.g., less than 25 ml medium, culture tubes or flasks or in large flasks with agitation, in rotator bottles, or on microcarrier beads (e.g., DEAE-Dextran microcarrier beads, such as Dormacell, Pfeifer & Langen; Superbead, Flow Laboratories; styrene copolymer-tri- methylamine beads, such as Hillex, SoloHill, Ann Arbor) in flasks, bottles or reactor cultures. Microcarrier beads are small spheres (in the range of 100-200 microns in diameter) that provide a large surface area for adherent cell growth per volume of cell culture. For example a single liter of medium can include more than 20 million microcarrier beads providing greater than 8000 square centimeters of growth surface. For commercial production of viruses, e.g., for vaccine production, it is often desirable to culture the cells in a bioreactor or fermenter. Bioreactors are available in volumes from under 1 liter to in excess of 100 liters, e.g., Cyto3 Bioreactor (Osmonics, Minnetonka, MN); NBS bioreactors (New Brunswick Scientific, Edison, N.J.); laboratory and commercial scale bioreactors from B. Braun Biotech International (B. Braun Biotech, Melsungen, Germany).

[0108] Regardless of the culture volume, in the context of the present invention, it is important that the cultures be maintained at a temperature less than or equal to 35 °C, to insure efficient recovery of recombinant and/or reassortant influenza virus using the multi plasmid system described herein. For example, the cells are cultured at a temperature between about 32 °C and 35 °C, typically at a temperature between about 32 °C and about 34 °C, usually at about 33 °C.

[0109] Typically, a regulator, e.g., a thermostat, or other device for sensing and maintaining the temperature of the cell culture system is employed to insure that the temperature does not exceed 35 °C during the period of virus replication.

Introduction of vectors into host cells [0110] Vectors comprising influenza genome segments are introduced (e.g., transfected) into host cells according to methods well known in the art for introducing heterologous nucleic acids into eukaryotic cells, including, e.g., calcium phosphate co- precipitation, electroporation, microinjection, lipofection, and transfection employing polyamine transfection reagents. For example, vectors, e.g., plasmids, can be transfected into host cells, such as COS cells, 293T cells or combinations of COS or 293T cells and MDCK cells, using the polyamine transfection reagent TransIT-LTl (Minis) according to the manufacturer's instructions. Approximately 1 μg of each vector to be introduced into the population of host cells with approximately 2 μl of TransIT-LTl diluted in 160 μl medium, preferably serum-free medium, in a total vol. of 200 μl. The DNA:transfection reagent mixtures are incubated at room temperature for 45 min followed by addition of 800 μl of medium. The transfection mixture is added to the host cells, and the cells are cultured as described above. Accordingly, for the production of recombinant or reassortant viruses in cell culture, vectors incoφorating each of the 8 genome segments, (PB2, PBl, PA, NP, M, NS, HA and NA) are mixed with approximately 20 μl TransIT-LTl and transfected into host cells. Optionally, serum-containing medium is replaced prior to transfection with serum-free medium, e.g., Opti-MEM I, and incubated for 4-6 hours.

[0111] Alternatively, electroporation can be employed to introduce vectors incoφorating influenza genome segments into host cells. For example, plasmid vectors incoφorating an influenza A or influenza B virus are favorably introduced into Vero cells using electroporation according to the following procedure. In brief, 5 x 10⁶ Vero cells, e.g., grown in Modified Eagle's Medium (MEM) supplemented with 10% Fetal Bovine Serum (FBS) are resuspended in 0.4 ml OptiMEM and placed in an electroporation cuvette. Twenty micrograms of DNA in a volume of up to 25 μl is added to the cells in the cuvette, which is then mixed gently by tapping. Electroporation is performed according to the manufacturer's instructions (e.g., BioRad Gene Pulser II with Capacitance Extender Plus connected) at 300 volts, 950 microFarads with a time constant of between 28-33 msec. The cells are remixed by gently tapping and approximately 1-2 minutes following electroporation 0.7 ml MEM with 10% FBS is added directly to the cuvette. The cells are then transferred to two wells of a standard 6 well tissue culture dish containing 2 ml MEM, 10% FBS or OPTI-MEM without serum. The cuvette is washed to recover any remaining cells and the wash suspension is divided between the two wells. Final volume is approximately 3.5 mis. The cells are then incubated under conditions permissive for viral growth, e.g., at approximately 33 °C for cold adapted strains.

Recovery of viruses [0112] Viruses are typically recovered from the culture medium, in which infected

(transfected) cells have been grown. Typically crude medium is clarified prior to concentration of influenza viruses. Common methods include filtration, ultrafiltration, adsoφtion on barium sulfate and elution, and centrifugation. For example, crude medium from infected cultures can first be clarified by centrifugation at, e.g., 1000-2000 x g for a time sufficient to remove cell debris and other large particulate matter, e.g., between 10 and 30 minutes. Alternatively, the medium is filtered through a 0.8 μm cellulose acetate filter to remove intact cells and other large particulate matter. Optionally, the clarified medium supernatant is then centrifuged to pellet the influenza viruses, e.g., at 15,000 x g, for approximately 3-5 hours. Following resuspension of the virus pellet in an appropriate buffer, such as STE (0.01 M Tris-HCl; 0.15 M NaCl; 0.0001 M EDTA) or phosphate buffered saline (PBS) at pH 7.4, the virus is concentrated by density gradient centrifugation on sucrose (60%-12%) or potassium tartrate (50%-10%). Either continuous or step gradients, e.g., a sucrose gradient between 12% and 60% in four 12% steps, are suitable. The gradients are centrifuged at a speed, and for a time, sufficient for the viruses to concentrate into a visible band for recovery. Alternatively, and for most large scale commercial applications, virus is elutriated from density gradients using a zonal-centrifuge rotor operating in continuous mode. Additional details sufficient to guide one of skill through the preparation of influenza viruses from tissue culture are provided, e.g., in Furminger. Vaccine Production, in Nicholson et al. (eds) Textbook of Influenza pp. 324- 332; Merten et al. (1996) Production of influenza virus in cell cultures for vaccine preparation, in Cohen & Shafferman (eds) Novel Strategies in Design and Production of Vaccines pp. 141-151, and United States patents no. 5,690,937. If desired, the recovered viruses can be stored at -80°C in the presence of sucrose-phosphate-glutamate (SPG) as a stabilizer Methods and Compositions for prophylactic administration of vaccines

[0113] Recombinant and reassortant viruses of the invention can be administered prophylactically in an appropriate carrier or excipient to stimulate an immune response specific for one or more strains of influenza virus. Typically, the carrier or excipient is a pharmaceutically acceptable carrier or excipient, such as sterile water, aqueous saline solution, aqueous buffered saline solutions, aqueous dextrose solutions, aqueous glycerol solutions, ethanol, allantoic fluid from uninfected Hens' eggs (i.e., normal allantoic fluid "NAF") or combinations thereof. The preparation of such solutions insuring sterility, pH, isotonicity, and stability is effected according to protocols established in the art. Generally, a carrier or excipient is selected to minimize allergic and other undesirable effects, and to suit the particular route of administration, e.g., subcutaneous, intramuscular, intranasal, etc.

[0114] Generally, the influenza viruses of the invention are administered in a quantity sufficient to stimulate an immune response specific for one or more strains of influenza virus. Preferably, administration of the influenza viruses elicits a protective immune response. Dosages and methods for eliciting a protective immune response against one or more influenza strains are known to those of skill in the art. For example, inactivated influenza viruses are provided in the range of about 1-1000 HID₅₀ (human c o infectious dose), i.e., about 10 -10 pfu (plaque forming units) per dose administered. Alternatively, about 10-50 μg, e.g., about 15 μg HA is administered without an adjuvant, with smaller doses being administered with an adjuvant. Typically, the dose will be adjusted within this range based on, e.g., age, physical condition, body weight, sex, diet, time of administration, and other clinical factors. The prophylactic vaccine formulation is systemically administered, e.g., by subcutaneous or intramuscular injection using a needle and syringe, or a needleless injection device. Alternatively, the vaccine formulation is administered intranasally, either by drops, large particle aerosol (greater than about 10 microns), or spray into the upper respiratory tract. While any of the above routes of delivery results in a protective systemic immune response, intranasal administration confers the added benefit of eliciting mucosal immunity at the site of entry of the influenza virus. For intranasal administration, attenuated live virus vaccines are often preferred, e.g., an attenuated, cold adapted and/or temperature sensitive recombinant or reassortant influenza virus. While stimulation of a protective immune response with a single dose is preferred, additional dosages can be administered, by the same or different route, to achieve the desired prophylactic effect.

[0115] Alternatively, an immune response can be stimulated by ex vivo or in vivo targeting of dendritic cells with influenza viruses. For example, proliferating dendritic cells are exposed to viruses in a sufficient amount and for a sufficient period of time to permit capture of the influenza antigens by the dendritic cells. The cells are then transferred into a subject to be vaccinated by standard intravenous transplantation methods.

[0116] Optionally, the formulation for prophylactic administration of the influenza viruses, or subunits thereof, also contains one or more adjuvants for enhancing the immune response to the influenza antigens. Suitable adjuvants include: saponin, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil or hydrocarbon emulsions, bacille Calmette-Guerin (BCG), Corynebacterium parvum, and the synthetic adjuvants QS-21 and MF59.

[0117] If desired, prophylactic vaccine administration of influenza viruses can be performed in conjunction with administration of one or more immunostimulatory molecules. Immunostimulatory molecules include various cytokines, lymphokines and chemokines with immunostimulatory, immunopotentiating, and pro-inflammatory activities, such as interleukins (e.g., IL-1, IL-2, IL-3, IL-4, IL-12, IL-13); growth factors (e.g., granulocyte-macrophage (GM)-colony stimulating factor (CSF)); and other immunostimulatory molecules, such as macrophage inflammatory factor, Flt3 ligand, B7.1; B7.2, etc. The immunostimulatory molecules can be administered in the same formulation as the influenza viruses, or can be administered separately. Either the protein or an expression vector encoding the protein can be administered to produce an immunostimulatory effect.

[0118] In another embodiment, the vectors of the invention including influenza genome segments can be employed to introduce heterologous nucleic acids into a host organism or host cell, such as a mammalian cell, e.g., cells derived from a human subject, in combination with a suitable pharmaceutical carrier or excipient as described above. Typically, the heterologous nucleic acid is inserted into a non-essential region of a gene or gene segment, e.g., the M gene of segment 7. The heterologous polynucleotide sequence can encode a polypeptide or peptide, or an RNA such as an antisense RNA or ribozyme. The heterologous nucleic acid is then introduced into a host or host cells by producing recombinant viruses incoφorating the heterologous nucleic, and the viruses are administered as described above.

[0119] Alternatively, a vector of the invention including a heterologous nucleic acid can be introduced and expressed in a host cells by co-transfecting the vector into a cell infected with an influenza virus. Optionally, the cells are then returned or delivered to the subject, typically to the site from which they were obtained. In some applications, the cells are grafted onto a tissue, organ, or system site (as described above) of interest, using established cell transfer or grafting procedures. For example, stem cells of the hematopoietic lineage, such as bone marrow, cord blood, or peripheral blood derived hematopoietic stem cells can be delivered to a subject using standard delivery or transfusion techniques.

[0120] Alternatively, the viruses comprising a heterologous nucleic acid can be delivered to the cells of a subject in vivo. Typically, such methods involve the administration of vector particles to a target cell population (e.g., blood cells, skin cells, liver cells, neural (including brain) cells, kidney cells, uterine cells, muscle cells, intestinal cells, cervical cells, vaginal cells, prostate cells, etc., as well as tumor cells derived from a variety of cells, tissues and or organs. Administration can be either systemic, e.g., by intravenous administration of viral particles, or by delivering the viral particles directly to a site or sites of interest by a variety of methods, including injection (e.g., using a needle or syringe), needleless vaccine delivery, topical administration, or pushing into a tissue, organ or skin site. For example, the viral vector particles can be delivered by inhalation, orally, intravenously, subcutaneously, subdermally, intradermally, intramuscularly, intraperitoneally, intrathecally, by vaginal or rectal administration, or by placing the viral particles within a cavity or other site of the body, e.g., during surgery. [0121] The above described methods are useful for therapeutically and/or prophylactically treating a disease or disorder by introducing a vector of the invention comprising a heterologous polynucleotide encoding a therapeutically or prophylactically effective polypeptide (or peptide) or RNA (e.g., an antisense RNA or ribozyme) into a population of target cells in vitro, ex vivo or in vivo. Typically, the polynucleotide encoding the polypeptide (or peptide), or RNA, of interest is operably linked to appropriate regulatory sequences as described above in the sections entitled "Expression Vectors" and "Additional Expression Elements." Optionally, more than one heterologous coding sequence is incoφorated into a single vector or virus. For example, in addition to a polynucleotide encoding a therapeutically or prophylactically active polypeptide or RNA, the vector can also include additional therapeutic or prophylactic polypeptides, e.g., antigens, co-stimulatory molecules, cytokines, antibodies, etc., and/or markers, and the like.

[0122] The methods and vectors of the present invention can be used to therapeutically or prophylactically treat a wide variety of disorders, including genetic and acquired disorders, e.g., as vaccines for infectious diseases, due to viruses, bacteria, and the like.

Kits [0123] To facilitate use of the vectors and vector systems of the invention, any of the vectors, e.g., consensus influenza virus plasmids, variant influenza polypeptide plasmids, influenza polypeptide library plasmids, etc., and additional components, such as, buffer, cells, culture medium, useful for packaging and infection of influenza viruses for experimental or therapeutic puφoses, can be packaged in the form of a kit. Typically, the kit contains, in addition to the above components, additional materials which can include, e.g., instructions for performing the methods of the invention, packaging material, and a container.

Manipulation of viral nucleic acids and Proteins [0124] In the context of the invention, influenza virus nucleic acids and/or proteins are manipulated according to well known molecular biology techniques. Detailed protocols for numerous such procedures, including amplification, cloning, mutagenesis, transformation, and the like, are described in, e.g., in Ausubel et al. Current Protocols in

Molecular Biology (supplemented through 2000) John Wiley & Sons, New York ("Ausubel"); Sambrook et al. Molecular Cloning - A Laboratory Manual (2nd Ed.), Vol.

1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1989 ("Sambrook"), and Berger and Kimmel Guide to Molecular Cloning Techniques. Methods in

Enzymology volume 152 Academic Press, Inc., San Diego, CA ("Berger").

[0125] In addition to the above references, protocols for in vitro amplification techniques, such as the polymerase chain reaction (PCR), the ligase chain reaction (LCR), Qβ-replicase amplification, and other RNA polymerase mediated techniques (e.g., NASBA), useful e.g., for amplifying cDNA probes of the invention, are found in Mullis et al. (1987) U.S. Patent No. 4,683,202; PCR Protocols A Guide to Methods and Applications (Innis et al. eds) Academic Press Inc. San Diego, CA (1990) ("Innis"); Arnheim and Levinson (1990) C&EN 36; The Journal Of NM Research (1991) 3:81; Kwoh et al. (1989) Proc Natl Acad Sci USA 86. 1173; Guatelli et al. (1990) Proc Natl Acad Sci USA 87:1874: Lomell et al. (1989) J Clin Chem 35:1826; Landegren et al.

(1988) Science 241: 1077; Van Brunt (1990) Biotechnology 8:291; Wu and Wallace

(1989) Gene 4: 560; Barringer et al. (1990) Gene 89:117, and Sooknanan and Malek (1995) Biotechnology 13:563. Additional methods, useful for cloning nucleic acids in the context of the present invention, include Wallace et al. U.S. Pat. No. 5,426,039. Improved methods of amplifying large nucleic acids by PCR are summarized in Cheng et al. (1994) Nature 369:684 and the references therein.

[0126] Certain polynucleotides of the invention, e.g., oligonucleotides can be synthesized utilizing various solid-phase strategies including mononucleotide- and/or trinucleotide-based phosphoramidite coupling chemistry. For example, nucleic acid sequences can be synthesized by the sequential addition of activated monomers and/or trimers to an elongating polynucleotide chain. See e.g., Caruthers, M.H. et al. (1992) Meth Enzvmol 211:3.

[0127] In lieu of synthesizing the desired sequences, essentially any nucleic acid can be custom ordered from any of a variety of commercial sources, such as The Midland Certified Reagent Company (mcrc@oligos.com), The Great American Gene Company (www.genco.com), ExpressGen, Inc. (www.expressgen.com), Operon Technologies, Inc. (www.operon.com), and many others.

[0128] In addition, substitutions of selected amino acid residues in viral polypeptides can be accomplished by, e.g., site directed mutagenesis. For example, viral polypeptides with amino acid substitutions functionally correlated with desirable phenotypic characteristic, e.g., an attenuated phenotype, cold adaptation, temperature sensitivity, can be produced by introducing specific mutations into a viral nucleic acid segment encoding the polypeptide. Methods for site directed mutagenesis are well known in the art, and described, e.g., in Ausubel, Sambrook, and Berger, supra. Numerous kits for performing site directed mutagenesis are commercially available, e.g., the Chameleon Site Directed Mutagenesis Kit (Stratagene, La Jolla), and can be used according to the manufacturers instructions to introduce, e.g., one or more amino acid substitutions described in Table 6 or Table 17, into a genome segment encoding a influenza A or B polypeptide, respectively.

EXAMPLES

EXAMPLE 1: CONSTRUCTION OF pAD3000

[0129] The plasmid pHW2000 (Hoffmann et al. (2000) A DNA transfection system or generation of influenza A virus from eight plasmids Proc Natl Acad Sci USA 97:6108- 6113) was modified to replace the bovine growth hormone (BGH) polyadenylation signals with a polyadenylation signal sequences derived from Simian virus 40 (SV40).

[0130] Sequences derived from SV40 were amplified with Taq MasterMix

(Qiagen) using the following oligonucleotides, designated in the 5' to 3' direction: polyA.l: AACAATTGAGATCTCGGTCACCTCAGACATGATAAGATACATTGATGAGT (SEQ ID NO:l) ρolyA.2: TATAACTGCAGACTAGTGATATCCTTGTTTATTGCAGCTTATAATGGTTA (SEQ ID NO:2) [0131] The plasmid pSV2His was used as a template. A fragment consistent with the predicted 175 bp product was obtained and cloned into pcDNA3.1, using a Topo TA cloning vector (Invitrogen) according to the manufacturer's directions. The desired 138 bp fragment containing the SV40 polyadenylation signals was excised from the resulting plasmid with EcoRV and BstEII, isolated from an agarose gel, and ligated between the unique PvuU and BstEII sites in pHW2000 using conventional techniques (see, e.g., Ausubel, Berger, Sambrook). The resulting plasmid, pAD3000 (Figure 1), was sequenced and found to contain the SV40 polyadenylation site in the correct orientation. Nucleotides 295-423 in pAD3000 correspond to nucleotides 2466-2594, respectively, in SV40 strain 777 (AF332562).

EXAMPLE 2: EIGHT PLASMID SYSTEM FOR PRODUCTION OF MDV-A [0132] A cold-adapted influenza virus type A strain A/AA/6/60 variant has commonly been used as a master donor virus for the production of nasally administered Influenza A vaccines. This strain is an exemplary Master Donor Virus (MDV) in the context of the present invention. For simplicity, this strain A/AA/6/60 variant is designated herein MDV-A. MDV-A viral RNA was extracted using the RNeasy mini kit (Qiagen) and the eight corresponding cDNA fragments were amplified by RT-PCR using the primers listed in Table 1.

Table 1. Sequence of the primers used for cloning MDV-A eight segments

MDV-A REVERSE PRIMERS

SEQ ID Aarl PB2-long CCT AAC ATA TCA CCT GCC TCG TAT TAG TAG AAA CAA GGT CGT TT

NO: 11

SEQ ID BsmBI-PBl ATA TCG TCT CGT ATT AGT AGA AAC AAG GCA TTT

NO: 12

SEQ ID BsmBI-PA ATA TCG TCT CGT ATT AGT AGA AAC AAG GTA CTT

NO: 13

SEQ ID BsmBI-NP ATA TCG TCT CGT ATT AGT AGA AAC AAG GGT ATT

NO: 14

SEQ ID Aarl HA-long CCT AAC ATA TCA CCT GCC TCG TAT TAG TAG AAA CAA GGG TGT T

NO: 15

SEQ ID BsmBI-NA ATA TCG TCT CGT ATT AGT AGA AAC AAG GAG TTT

NO: 16

SEQ ID BsmBI-M ATA TCG TCT CGT ATT AGT AGA AAC AAG GTA GTT

NO: 17

SEQ ID BsmBI-NS ATA TCG TCT CGT ATT AGT AGA AAC AAG GGT GTT

NO: 18

[0133] With the exception of the influenza genome segments encoding HA and

PB2, which were amplified using the primers containing Aar I restriction enzyme recognition site, the remaining 6 genes were amplified with primers containing the BsmB I restriction enzyme recognition site. Both Aarl and BsmB I cDNA fragments were cloned between the two BsmB I sites of the pAD3000 vector.

[0134] Sequencing analysis revealed that all of the cloned cDNA fragments contained mutations with respect to the consensus MDV-A sequence, which were likely introduced during the cloning steps. The mutations found in each gene segment are summarized in Table 2.

Table 2. Mutations introduced into the MDV-A clones in pAD3000

[0135] All the mutations were corrected back to the consensus MDV-A sequence using a QuikChange Site-directed Mutagenesis Kit (Stratagene) and synthetic oligonucleotide primers as shown in Table 3. Table 3. Primers used for correcting the mutations in the MDV-A clones

REASSORTED INFLUENZA VIRUS

[0136] Madin-Darby canine kidney (MDCK) cells and human COS7 cells were maintained in modified Eagle Medium (MEM) containing 10% fetal bovine serum (FBS). Human embryonic kidney cells (293T) were maintained in Opti-MEM I (Life Technologies) containing 5% FBS. MDCK and either COS7 or 293T cells were co- cultured in 6-well plates at a ratio of 1:1 and the cells were used for transfection at a confluency of approximately 80%. 293T and COS7 cells have a high transfection efficiency, but are not permissive for influenza virus replication. Co-culture with MDCK cells ensures efficient replication of the recombinant viruses. Prior to transfection, serum- containing media were replaced with serum free medium (Opti-MEM I) and incubated for 4-6 hours. Plasmid DNA transfection was performed using TransIT-LTl (Mirus) by mixing 1 μg of each of the 8 plasmid DNAs (PB2, PBl, PA, NP, M, NS, HA and NA) with 20 μl of TransIT-LTl diluted in 160 μl Opti-MEM I in a total volume of 200 μl. The DNA:transfection reagent mixtures were incubated at room temperature for 45 min followed by addition of 800 μl of Opti-MEM I. The transfection mixture was then added to the co-cultured MDCK 293T or MDCK/COS7 cells. The transfected cells were incubated at 35 °C or 33 °C for between 6 hours and 24 hours, e.g., overnight, and the transfection mixture was replaced with 1 ml of Opti-MEM I in each well. After incubation at 35 °C or 33 °C for 24 hours, 1ml of Opti-MEM I containing lμg/ml TPCK-trypsin was added to each well and incubated for an additional 12 hours. The recovered virus was then amplified in confluent MDCK cells or directly amplified in embryonated chick eggs. MDCK cells in 12-well plate were infected with 0.2 ml of the transfection mixture for 1 hour at room temperature, the mixture was then removed and replaced with 2ml of Opti- MEM I containing lμg/ml TPCK-trypsin. The cells were incubated at 35 °C or 33 °C for 3-4 days. The amplified viruses were stored at -80°C in the presence of SPG stabilizer or plaque-purified and amplified in MDCK cells or chicken embryonic eggs.

Functional expression of MDV-A polymerase proteins [0137] Functional activity of the four MDV-A polymerase proteins, PB2, PBl, PA and NP, were analyzed by their ability to replicate an influenza virus minigenome encoding an EGFP reporter gene. A set of 8 expression plasmids (see, e.g., Table 4)

(Hoffmann et al. (2001) Eight plasmid rescue system for influenza A virus; Options for the control of influenza International Congress Series 1219:1007-1013) that contained the cDNAs of A/PR/8/34 strain (H1N1) and an influenza virus minigenome containing a reporter gene encoding the enhanced green fluorescent protein (EGFP, pHW72-EGFP). [0138] The MDV-A PB 1 , PB2, PA and NP or PB 1 , PA, NP (-PB2 as a negative control) were transfected into the co-cultured MDCK/293T cells together with a plasmid representing an influenza A virus EGFP minigenome (pHW72-EGFP)(Hoffmann et al. (2000) "Ambisense" approach for the generation of influenza A virus: vRNA and mRNA synthesis from one template Virology 15:267(2):310-7). The transfected cells were observed under phase contrast microscope or fluorescence microscope at 48 hours post- transfection. Alternatively, flow cytometry can be employed to detect EGFP expression. [0139] As shown in Figure 2, green fluorescence, indicating expression of the

EGFP minigenome was observed in the cells transfected with PB2, PBl, PA and NP of MDV-A, but not in the cells transfected with only three polymerase proteins. This indicated that the MDV-A polymerase proteins in pAD3000 were functional.

[0140] In other assays a minigenome including the chloramphenicol acetyl transferase (CAT) gene, designated pFlu-CAT is utilized to measure polymerase activity. In such an assay, CAT expression is measured at the protein (e.g., by ELISA) or RNA level, as an indicator of minigenome replication.

Analysis of the MDV-A plasmids by single gene reassortant experiment [0141] Each of the 8 MDV-A genome segments cloned in pAD3000 was shown to be functionally expressed in a reassortant experiment by co-transfecting a single gene segment from MDA-A together with the complementary seven segments from control

A PR/8/34 strain. All eight single genome segment plasmids in combination with complementary control segments generated infectious reassortant virus, which caused cytopathic effects in infected MDCK cells, indicating that all eight plasmids encode functional MDV-A proteins. Table 4.

Table 4. Recovery of 7+1 reassortants by plasmids

[0142] To further determine the packaging constraints of influenza A virus, the NS segment was separated into two separate gene segments: one encoding the NSl genomic segment and the other encoding the NS2 genomic segment. The nine plasmids incoφorating the genomic segments of influenza A were transfected into MDCK/COS cells as described above, and the recovered viruses were amplified in embryonated chicken eggs prior to titration on MDCK cells. Reduced plaque size was observed for the nine-plasmid system as compared to the eight-plasmid system described above. RT-PCR analysis demonstrated that only the NS2 segment was present in the virions, and that the NS 1 gene segment was not packaged.

Recovery of MDV-A and 6:2 reassortant viruses [0143] Following the procedures described above, three days post transfection with either the 8 MDV-A plasmids (recombinant), or with plasmids incoφorating the 6

MDV-A internal genes, and HA and NA derived from A PR/8/34 (6:2 reassortant), transfected culture supematants were used to infect fresh MDCK cells, and the infected cells were incubated at 33°C for three days in the presence of lμg/ml TPCK-trypsin. The cytoplasmic effect of the recombinant virus on infected MDCK cells was observed using a microscope. Expression of viral hemagglutinin was monitored using a standard hemagglutination assay (HA). HA assays were performed by mixing 50μl of serially 2- fold diluted culture supematants with 50μl of 1% chick red blood cells in 96-well plates. A HA titer of approximately 1:254-1:1024 was detected for the amplified viruses derived from either the transfected 8 MDV-A plasmids, or the 6:2 reassortant virus. The transfection reaction using the 8 A/PR/8/34 plasmid obtained from Dr. E. Hoffman was used as a positive control. Infectious influenza viruses were produced from these three transfection reactions as indicated in Table 5.

Table 5. Plasmids used for recovery of A/PR/8/34. MDV-A and 6:2 reassortant

[0144] RT-PCR was performed to map the genotypes of the recovered viruses.

Viral RNA was isolated from the infected cell culture supernatant using the RNeasy mini Kit (Qiagen) and the eight influenza vims segments were amplified by RT-PCR using primers specific to each MDV-A gene segment and HI- and Nl-specific primers. As shown in Figure 3, rMDV-A contained PB2, PBl, NP, PA, M and NS that were specific to MDV-A and HA and NA specific to the H2 and N2 subtype. The 6:2 reassortant contained the 6 internal genes derived from MDV-A, and the HA and NA derived from A/PR/8/34 (HlNl). This confirmed that viruses generated from the transfected plasmids had the correct genotypes.

[0145] The rescued viruses were titrated by plaque assay on MDCK cells and the plaques were confirmed to be influenza vims by immunostaining using chicken serum raised against MDV-A. MDCK cells at 100% confluency on 12-well plates were infected with 100 μl of 10-fold serially diluted vims at RT for 1 hour with gentle rocking. The inoculum was removed and the cells were overlaid with IX L15 containing 0.8 % agarose and lμg/ml TPCK-trypsin. The plates were incubate at 35°C or 33°C for three days, fixed with 100% methanol, blocked by 5% milk in PBS, and incubated with 1:2000 diluted chicken anti-MDV-A antisemm for 1 hour followed by incubation with HRP-conjugated rabbit anti-chicken IgG for 1 hr. The plaques were visualized by addition of the HRP substrate solution (DAKO). All the recovered vimses exhibited positive immunostaining.

EXAMPLE 4: MAPPING THE GENETIC BASIS OF CA. TS. ATT PHENOTYPES OF MDV-A

[0146] The MDV-A influenza vims vaccine strain has several phenotypes relevant to the production of vaccines, e.g., live attenuated vaccines: cold adaptation (ca), temperature sensitivity (ts) and attenuation (att). Sequence comparison of the MDV-A strain with the non-ts vimlent wt A/AA/6/60 strain revealed that a minimal of 17nt differences between these two strains (Table 6). Several of the changes in the MDV-A sequence are unique to this strain as compared to all the available influenza type A vimses in the GeneBank database, suggesting that one or more of these amino acid substitutions is functionally related to the att, ca and ts phenotype(s). The single amino acid change at PB2⁸²¹ was the only nucleotide position that had been previously reported as a determinant in the ts phenotype of MDV-A (Subbarao et al. (1995) Addition of Temperature-Sensitive Missense Mutations into the PB2 Gene of Influenza A Transfectant Viruses Can Effect an Increase in Temperature Sensitivity and Attenuation and Permits the Rational Design of a Genetically Engineered Live Influenza A Virus Vaccine J. Virol. 69:5969-5977). [0147] In order to pinpoint the minimal substitutions involved in the MDV-A phenotypes, the nucleotides in the MDV-A clone that differ from wt A/AA/6/60 were individually changed to those of wt A/AA/6/60 (i.e., "reverted"). Each reverted gene segment was then introduced into host cells in combination with complementary segments of MDV-A to recover the single gene reassortants. In addition, the reverted gene segment and the corresponding MDV-A segment can also be transfected in combination with segments derived from other wild type strains, e.g., strain A/PR/8/34, to assess the contribution of each gene segment to the vims phenotypes. Using the recombinant MDV- A plasmid system described above, site-directed mutagenesis was performed to further modify the six internal genes to produce a non-ts reassortant. A total of 15 nucleotides substitution mutations were introduced into the six MDV-A plasmids to represent the recombinant wild type A/AA/6/60 genome (rWt, Flu064) as listed in Table 6. Madin- Darby canine kidney (MDCK) cells and COS-7 cells were maintained and transfected as described above. The recovered vims was then passaged in MDCK cells once, followed by amplification in the allantoic cavities of embryonic chicken eggs. Transfection and vims growth in MDCK and eggs were performed at 33 °C, a temperature permissive for both ca and wt vimses to minimize any temperature selection pressures. Vims genotype was confirmed by sequence analysis of cDNA fragments amplified from viral RNA.

Numbers in bo d represent the differences between rMDV-A and rWt. Words in bold (15) are the changes between rmdv-a and rwt.

[0148] Phenotypic characteristics were determined by procedures known in the art, e.g., as previously described in United States Patent 6,322,967 to Parkin entitled "Recombinant tryptophan mutants of influenza," which is incoφorated herein in its entirety. Briefly, temperature sensitivity of the recombinant vimses was determined by plaque assay on MDCK cells at 33, 38 and 39 °C. MDCK cells in 6-well plates were infected with 400 μl of 10-fold serially diluted virus and adsorbed at room temperature for 60 min. The innoculants were removed and replaced with lx L15/MEM containing 1% agarose and 1 μg/ml TPCK-trypsin. The infected cells were incubated at 33 °C in a CO₂ incubator or in water-tight containers containing 5% CO₂ submerged in circulating water baths maintained at 38 ±0.1 °C or 39 ±0.1 °C (Parkin et al. (1996) Temperature sensitive mutants of influenza A virus generated by reverse genetics and clustered charged to alanine mutagenesis. Vir. Res. 46:31-44). After three days' incubation, the monolayers were immunostained using chicken anti-MDV polyclonal antibodies and the plaques were enumerated. Plaque counts obtained at each of the temperatures were compared to assess the ts phenotype of each vims and each assay was performed a minimum of three times. The shut-off temperature was defined as the lowest temperature that had a titer reduction of 100-fold or greater compared to 33 °C.

[0149] Infectious vims obtained from the cocultured COS-7/MDCK cells transfected with the eight plasmids (pMDV-PB2, pMDV-PBl, pMDV-PA, pMDV-NP, pMDV-HA, pMDV-NA, pMDV-M, and pMDV-NS) was amplified in chicken embryonated eggs, and was shown to exhibit the characteristic ts phenotype of nonrecombinant, biological derived MDV-A (Table 7). Neither MDV-A nor rMDV-A formed distinct plaques at 39 °C, although both formed easily visualized plaques at 33 °C.

Table 7. Replication of MDV/Wt reassortants at various temperatures

* Indicates reduction in plaque size compared to rWt. The underlined indicates that no plaques were detected at 10^"4-fold dilution [0150] In order to perform a systematic, detailed analysis of the genetic basis of the ts phenotype of MDV-A, the sequences of several closely related non-ts, non-att wt A/AA/6/60 strains with 17-48 nt differences from the ca A/AA/6/60, including the highly related isolate, wt A/AA/6/60 E10SE2, were utilized for comparison. A total of 19 nt differences exist between E10SE2 and MDV-A (Table 6). E10SE2 was shown to be non-ts (Table 7) and non-att in ferrets. In order to generate a recombinant non-ts vims, the MDV-A plasmids were altered by site directed mutagenesis to incoφorate 15 of the 19 differences representing 10 amino acids changes. Four of the nucleotide positions, PB2- 1182, 1212, PB1-123, and NP-1550, that differed between MDV-A and E10SE2 were not altered from the MDV-A sequence, since these nucleotides were observed in other non-ts isolates of A/AA/6/60 and, therefore, not expected to have a role in expression of the ts phenotype (Herlocher et al. (1996) Sequence comparisons of A/AA/6/60 influenza viruses: mutations which may contribute to attenuation. Virus Research 42: 11-25). Recombinant virus (rWt, Flu064), encoding the 15 nucleotide changes, was obtained from the cocultured COS-7/MDCK cells transfected with a set of 8 plasmids, ρWt-PB2, pWt-PBl, pWt-PA, pWt-NP, pWt-M, pWt-NS, pMDV-HA, and pMDV-NA. Sequencing analysis indicated that rWt contained the designed genetic changes and was non-ts at 39 °C, identical to the biologically derived wt A/AA/6/60. These observations demonstrated that the ts phenotype mapped to a subset of these 15 nt changes.

Contribution of the six internal gene segments to vims ts phenotype [0151] The effect of each wt gene segment on the MDV-A ts phenotype was assessed by creating recombinant, single-gene reassortants (Table 7). Introduction of wt PB2 into rMDV-A resulted in a vims that was only non-ts at 38 °C; however, it remained ts at 39 °C. The reduction in virus titer at 38 °C and 39°C (relative to 33 °C) was 0.6 log₁₀ and 2.7 logio , respectively, as measured by plaque assay in MDCK cells. The reassortant containing the wt PBl gene segment was non- ts, with respect to its ability to form plaques at both 38 and 39 °C. The plaque size of this recombinant, however, was influenced by increased temperature and was significantly reduced at 39 °C as compared to rWt.

Introduction of the wt NP gene segment into rMDV-A resulted in a vims that was also non-ts at 38 °C, but in contrast to the wt PB2 recombinant, the vims containing the wt NP gene segment did not form plaques at 39 °C. Introduction of wt PA, M or NS gene segments independently into rMDV-A did not alter the ts phenotype, indicating that these three gene segments had minimal role in maintenance of this phenotype.

[0152] Because neither wt PBl, wt PB2 or wt NP expressed individually on the

MDV-A background could create a plaque efficiency and plaques size profile identical to non-ts rWT, these gene segments were introduced into MDV-A in various combinations. The combination of wt PBl and wt PB2 resulted in a vims that was non-ts at both 38 and 39 °C (Table 7). Although the plaque size was larger than that of either single gene reassortant, it was significantly smaller than rWt. The triple combination of wt PB 1/PB2/NP in rMDV-A resulted in a vims that was similar or identical to rWt in its plaquing efficiency and plaque size at 39 °C. Therefore, whereas the wt PB2, PBl and NP gene segments only partially reverted the ts phenotype when introduced individually, the combination of all three wt gene segments was able to fully revert the ts phenotype to a non-ts behavior identical to rWt. [0153] In order to determine whether these 3 gene segments were capable of imparting the characteristic MDV-A ts phenotype to rWt, the six internal gene segments derived from MDV-A were introduced into rWt individually or in combination. Introduction of single PBl, PB2, or NP gene segment into rWt resulted in a reduction of vims titer at 38 °C and a greater reduction at 39 °C, however, none of these single gene reassortants was as restricted at high temperature as rMDV-A (Figure 10). The PA, M and NS gene segments derived from MDV-A did not influence the non-ts phenotype of rWt. Consistent with the previous reasortments, it was demonstrated that introduction of both MDV-A PBl and PB2 genes into rWt backbone greatly increased vims ts phenotype at 38 °C; however, complete reversion of vims ts phenotype required addition of the NP gene. Thus, the PBl, PB2 and NP gene segments derived from MDV-A were important in conferring the complete ts phenotype.

Mapping the genetic loci that determined MDV-A ts phenotype. [0154] The specific differences between the PBl, PB2 and NP gene segments of rWt and rMDV-A were addressed systematically to identify those changes that played a significant role in the ts phenotype. The NP gene of rMDV-A differed from rWt NP only at nt 146 (G34D, Table 6). The PB2 gene of rMDV-A differed from rWt at three sites, but only nt 821 resulted in an amino acid change (N265S, Table 6) and presumably represented the ts locus located in the PB2 gene segment. The PBl gene of MDV-A differed from wt PBl at 6 nt positions, of which 4 were coding changes (Table 6). Each of the wt amino acid residue substitutions was substituted individually into the PB 1 gene segment of rMDV-A to assess their role in the ts phenotype. 1395G (Glu-457) and 2005G

(Ala) did not affect the MDV-A ts phenotype. 1195A (Lys-391) and 1766A (Glu-581) each resulted in a slight reduction in the ts phenotype at 38 °C, but had no effect at 39 °C (Table 8). These data indicated that 1195A and 1766A were the likely ts loci in the PBl gene segment. However, combination of both 1195 A and 1766 A did not produce a ts phenotype similar to wt PBl (Table 6). Addition of 2005G but not 1395 A to PBl - 1195A/1766A further decreased the vims ts phenotype at 39 °C, demonstrating that 2005A also had a role in the expression of the ts phenotype specified by the PBl segment of MDV-A.

Table 8: Mapping the residues in PBl that determine ts phenotype V Viirruuss 3 333 ° °CC 38 °C 33 °C/ 38 °C 39 °C 33 °C/ 39 °C with Wt sequence logio PFU/mL rMDV-A 8.67 6.00 2.67 <4O^t >4.67 rWt 9.04 9.01 0.03 9.03 0.01

PB1-1195A 8.06 6.68 1.38 <4O >4.06 P PBB11--11339955GG 8 8..7722 5.88 2.85 <4O >4.72

PB1-1766A 8.07 6.70 1.37 <4O >4.07

PB1-2005G 8.76 6.31 2.45 <4O >4.76

PB1-1195A1766A 8.65 7.60 1.05 5.98* 2.68

PB1-1195A1395G1766A 8.84 8.13 0.71 6.38* 2.46 P PBB11--11119955AA11776666AA22000055GG 8 8..7799 8.12 0.66 7.14* 1.64

PB1 PB2/NP 8.26 8.63 0.12 8.59 0.16

PB2/NP 8.81 8.21 0.59 7.56* 1.25

PB1-1195A/PB2/NP 8.86 8.81 0.05 7.60* 1.26

PB1-1766A/PB2/NP 9.33 8.84 0.50 8.71* 0.62 P PBB11--11776666AA22000055GG//PPBB22//NNPP 8 8..3300 8.22 0.08 8.11* 0.18

PB 1 - 1766A 1395G/PB2/NP 8.88 8.85 0.03 8.39* 0.49

PB1-1195A1766A/PB2/NP 8.45 8.48 0.06 8.10 0.35

* Indicates reduction in plaque size compared to rWt. The underlined indicates that no plaques were detected at 10^"4-fold dilution.

[0155] PBl single site mutations were then introduced together with wt PB2 and wt NP into rMDV-A. Wt PB2/NP and rMDV-A reassortant was non-ts at 38 °C and had a titer reduction of 1.25 logio at 39 °C but its plaque size was much reduced compared to rWt. Addition of either PB 1-1195A or 1766A did not significantly change the phenotype of wt PB2/NP reassortant. Only the combination of PB1-1195A and 1766A, together with a wt PB2 and wt NP, resulted in a vims that had the same non-ts phenotype as wt PB1/PB2/NP and rMDV-A reassortant (Table 8). Addition of PB1-1395G or 2005G to wt PB1-1766/PB2/NP did not convert the vims to a characteristic rWt non-ts phenotype. These data, therefore, demonstrated that the four amino acids distributed in the three PBl, PB2 and NP genes could completely revert the MDV-A ts phenotype.

Host cell restriction of MDV-A and reassortant viruses

[0156] In addition to the temperature sensitivity and attenuation phenotypes exhibited by the MDV-A vims and reassortant vimses with one or more MDV-A derived segment as described above, the MDV-A vims exhibited host cell restriction as indicated by reduced growth in Per.C6 cells relative to growth in MDCK cells. MDV-A and reassortant viruses with MDV-A derived PBl and PB2 segments exhibited significantly reduced growth in Per.C6 cells relative to their growth in MDCK cells, as shown in Figure

20 A and B.

Engineering of a temperature sensitive, attenuated vims strain [0157] To determine whether the five amino acids identified in the PBl, PB2 and NP gene segments of MDV-A would reproduce the ts and att phenotypes of MDV-A,

PB1-391E, 581G, 661T, PB2-265S, NP-34G were introduced into a divergent wild type vims strain (A/PR/8/34; "PR8"), and the resulting vims exhibited 1.9 logio reduction in vims titer at 38 °C and 4.6 logio reduction at 39 °C, which was very similar to that of rMDV-A (Figure 11). [0158] Sequence comparison between the PBl, PB2 and NP genes of ca

A/AA/6/60 (MDV-A) and A/PR/8/34 revealed that the four substituted amino acids identified in the PBl and PB2 genes of MDV-A are unique. NP³⁴ is conserved between MDV-A and PR8, Therefore, the three ts sites, PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G) and PBl⁶⁶¹ (A661T), identified in the PBl gene of MDV-A were introduced into PBl of A/PR/8/34 and the PB2²⁶⁵ (N265S) was introduced into PB2 of A/PR/8/34 by site-directed mutagenesis. The mutations introduced into the PBl and PB2 genes were verified by sequencing analysis. The primer pairs used for mutagenesis reaction are listed as in Table 9. These vimses are shown schematically in Figure 16. Table 9. Primers used for introducing ts mutations into PR8 PBl and PB2 genes

HJ240 PR8-PB 1 Al 195G 5 ' GAAAGAAGATTGAAGAAATCCGACCGCTC (SEQ ID NO:79)

HJ241 PR8-PB 1 Al 195G.as 5' GAGCGGTCGGATTTCTTCAATCTTCTTTC (SEQ ID NO:80)

HJ242 PR8-PB1A1766G 5' GAAATAAAGAAACTGTGGGGGCAAACCCGTTCC (SEQ ID NO:81)

HJ243 PR8-PBlA1766G.as 5' GGAACGGGTTTGCCCCCACAGTTTCTTTATTTC (SEQ ID NO:82)

HJ244 PR8-PB 1G2005A 5' GTATGATGCTGTTACAACAACACACTC C (SEQ ID NO:83)

HJ245 PR8-PB lG2005A.as 5' GGAGTGTGTTGTTGTAACAGCATCATAC (SEQ ID NO:84)

HJ246 PR8-PB2A821G 5' ATTGCTGCTAGGAGCATAGTGAGAAGAGC (SEQ ID NO:85)

HJ247 PR8-PB2A821G.as 5' GCTCTTCTCACTATGCTCCTAGCAGCAAT (SEQ ID NO:86)

[0159] To examine if the ts mutations introduced into PB 1 and PB2 genes of PR8 confer the ts phenotype in vitro, a minigenome assay was performed. The influenza minigenome reporter, designated pFlu-CAT, contained the negative sense CAT gene cloned under the control of the pol I promoter. Expression of the CAT protein depended on the expression of influenza PBl, PB2, PA, and NP proteins.

[0160] Briefly, HEp-2 cells were transfected with 1 μg of each of PB 1 , PB2, PA,

NP and pFlu-CAT minigenome by lipofectamine 2000 (Invitrogen). After overnight (approximately 18 hour) incubation at 33 °C or 39 °C, the cell extracts were analyzed for CAT protein expression by CAT ELISA kit (Roche Bioscience). The level of CAT mRNA was measured by primer extension assay. At 48 hr post-transfection, total cellular RNA was extracted by TRIzol reagent (Invitrogen) and 1/3 of RNA was mixed with an excess of DNA primer (5'-ATGTTCTTTACGATGCGATTGGG) labeled at its 5' end with [r-³²P]-ATP and T4 polynucleotide kinase in 6ul of water. Following denaturing at 95 °C for 3 min, primer extension was performed after addition of 50 U of superscript reverse transcriptase (Invitrogen) in the reaction buffer provided with the enzyme containing 0.5mM dNTP for 1 hr at 42 °C. Transcription products were analyzed on 6% polyacrylamide gels containing 8M urea in TBE buffer and were detected by autoradiograph.

[0161] As shown in Fig. 12A and B, the PBl gene carrying three amino acid substitutions (PR8-3s), PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G) and PBl⁶⁶¹ (A661T), had reduced activity at 33°C compared to PR8 control. A greater reduction in CAT protein expression (Fig. 12A) was observed for this mutant at 39 °C, indicating PBl gene with the three introduced MDV-A ts sites exhibited temperature sensitive replication in this in vitro assay. Introduction of PB2²⁶⁵ (N265S) into PR8 had very little effect on its activity at both permissive (33 °C) and nonpermissive temperatures (39 °C). Combination of both PBl-3s and PB2-ls resulted in greater reduction in protein activity (PR8-4s), which appeared to be even more ts than MDV-A. As expected, a low level activity (15%) was detected in cells transfected with PBl, PB2, PA, NP genes derived from MDV-A at 39 °C compared to wt A/AA/6/60 (wt A/AA). [0162] PR8 mutant vimses were generated and recovered as described above. In brief, co-cultured cos7 and MDCK cells were transfected with eight plasmids encoding PR8 HA, NA, PBl, PB2, PA, NP, M and NS genes derived from PR8. To make a vims carrying four ts loci (PR8-4s), PBl-3s containing three changes in PBl at positions nt 1195 (K391E), nt 1766 (E581G) and nt 2005 (A661T) and PBl-ls containing one change in PB2 at position 821 (N265S) were used. In addition, PR8 vims carrying either three mutations in PBl (PR8-3s) or one mutation in PB2 (PR8-ls) was also recovered separately. These vimses are shown schematically in Figure 16. All four of the recombinant mutant PR8 vimses grew to very high titer in embryonic eggs, reaching a titer of 9.0 loglOpfu/ml or greater as shown in Table 10. [0163] To examine viral protein synthesis in infected cells, MDCK cells were infected with vims at an m.o.i of 5 and cells were labeled with ³⁵S-Trans at 7 hr post- infection for lhr. The labeled cell lysate was electrophoresed on 1.5% polyacrylamide gel containing SDS and autoradiographed. Protein synthesis was also studied by Western blotting. Vims infected cells were harvested at 8 hr postinfection and electrophoresed on 4-15% gradient gel. The blot was probed with anti-Ml antibody or chicken anti-MDV-A polyclonal antibody, followed by incubation with HRP-conjugated secondary antibody. The antibody-conjugated protein bands were detected by the Chemiluminescent Detection System (Invitrogen) followed by exposure to X-ray film.

[0164] As shown in Fig. 19, all had a similar level of protein synthesis at 33 °C, however, at 39 °C the level of protein synthesis was reduced slightly for PR8-ls but greatly reduced in PR8-3s and PR8-4s infected cells. Western blotting analysis also showed that reduced protein synthesis in the order of PR8-4s>PR8-3s>PR8-ls. Thus, the reduced replication of the ts mutants was likely the result of their reduced replication at the nonpermissive temperatures. [0165] Temperature sensitivity of the PR8 mutant vimses was determined by plaque assay on MDCK cells at 33 °C, 37 °C, 38 °C and 39 °C. The recovered vimses were amplified in embryonic eggs and introduced into cells as described above. After incubation of vims-infected cells for three days at the designated temperatures, cell monolayers were immunostained using chicken anti-MDV polyclonal antibodies and the plaques were enumerated. Plaque counts obtained at each of the temperatures were compared to assess the ts phenotype of each vims. The shut-off temperature was defined as the lowest temperature that had a titer reduction of 100-fold or greater compared to 33 °C.

[0166] As shown in Table 10 and Fig. 17, all mutants replicated well at 33 °C although a slight reduction in vims titer was observed. At 38 °C, a significant reduction in vims titer was observed for all the mutants. At 39 °C, a reduction in vims titer greater than 4.0 logio was observed for vimses carrying the three ts loci in the PBl gene (PR8-3s and PR8-4s). PR8-ls was also ts at 39 °C. The ts phenotype of PR8-4s was very similar to that of MDV-A that had a reduction of 4.6 logio at 39 °C compared to 33 °C. Although all the three PR8 mutants did not have greater than 2.0 logio reduction in vims titer at 37 °C, their plaque moφhology was different from those at 33 °C. As shown in Fig. 18, the plaque size for each mutant was only slightly reduced at 33 °C compared to PR8. A significant reduction in plaque size at 37 °C was observed for PR8-3s and greater for PR8-4s. PR8-ls did not have significant reduction in plaque size at 37 °C. At 39 °C, only a few pin-point sized plaques were observed for both PR8-3s and PR8-4s. The plaque size of approximately 30% of that wt PR8 was observed for PR8-ls.

Table 10. Temperature sensitivity of PR8 with the introduced ts loci

Vims titer (logiopfu/ml)

Vims 33 °C 37 °C 38 °C 39 °C

MDV-A 8.6 7.0 6.4 4*

Wt A/AA 8.7 8.7 8.9 8.3

PR8 9.6 9.5 9.5 9

PB8-ls 9.4 8.9 7.7 7.4

PB8-3s 9.2 8.8 7.8 5.2

PB8-4s 9.5 7.8 7.1 4.4

A titer of 4.0 was assigned when no virus was detected at 10,000 dilutions.

[0167] Attenuation of the mutant PR8 viruses was examined in ferrets. In brief, male ferrets 9-10 weeks old were used to assess vims replication in the respiratory tracts of an animal host. Ferrets were housed individually and inoculated intranasally with 8.5 logiopfu of vims. Three days after infection, ferrets were sedated with ketamine-HCL, lungs and nasal turbinates (NT) were harvested. The lung tissue homogenates were serially diluted and titrated in 10-day-old embryonated chicken eggs. Vims titer (logioEIDso/ml) in lungs was calculated by the Karber methods. Vims replication in NT was determined by plaque assay and expressed as logiopfu/ml. [0168] The levels of vims replication in lungs and nasal turbinates were measured by EID50 or plaque assays (Table 11). Three days after infection, PR8 replicated to a level of 5.9 logιoEID50/gram lung tissues. However, PR8-ls exhibited a 3.0 logio reduction in replication of ferret lungs and very little replication was detected for PR8-3s. No replication was detected for PR8-4s that was studied in two vims groups infected with vims obtained independently. Vims detection limit in ferret lungs by EJD50 assay is 1.5 loglO and thus a titer of 1.5 logιoEID50 was assigned for PR8-4s. As a control, MDV-A did not replicate in ferret lungs and wt A/AA/6/60 replicated to a titer of 4.4 logι₀. Vims replication in nasal turbinates (NT) was examined by plaque assay on MDCK cells. PR8 replicated to a titer of 6.6 logiopfu/g in the nose. Only slight reductions in vims titer were observed for PR8-ls and PR8-3s. A reduction of 2.2 logio was observed for PR8-4s (A), whereas a 4.3 logio reduction was observed for PR8-4s (B), which carried a change in the PBl gene (E390G). The greatly reduced replication of PR8-4s (B) correlates well with its ts phenotype at 37 °C. An infectious dose of 8.5 loglOpfu was used here instead of 7.0 loglOpfu that was usually used for evaluating the attenuation phenotype of MDV-A derived influenza vaccines. This result indicated that PR8 carrying the four ts loci derived from MDV-A was attenuated in replication in the lower respiratory tracts of ferrets.

Table 11. Replication of PR 8 mutants in ferrets

a) no vims was detected and a titer of 1.5 logιoEID50/g was assigned b) The vims contains an additional change in PB1-1193 (E390G)

[0169] In both the ts and att assays, the PR8 mutant vims exhibited both ts and att phenotypes that were very similar to that of MDV-A. These data indicate that introduction of the unique amino acid substitutions of the MDV-A into a divergent influenza vims strain results in a virus exhibiting the temperature sensitive and attenuated phenotypes desirable for producing, e.g., live attenuated, vaccines. Additionally, the ts, att, PR-8 vims grew to a high titer that suitable for use as a master donor vims for the production of live attenuated or inactivated influenza vaccines. These results indicate that the five MDV-A mutations: PB1-391E, PB1-581G, PB1-661T, PB2-265S, and NP-34G can impart the ts and att phenotypes to any influenza A strains. Similarly, novel ts, att B strains suitable for vaccine production can be produced by introducing the mutations of the MDV-B strain into influenza B strain viruses. In addition to producing live attenuated virus vaccines, introduction of these mutations into donor strains will lead to the production of safer inactivated vaccines.

EXAMPLE 5: EIGHT PLASMID SYSTEM FOR PRODUCTION OF MDV-B [0170] Viral RNA from a cold adapted variant of influenza B/Ann Arbor/1/66

(ca/Master Ann Arbor/1/66 PI Aviron 10/2/97), an exemplary influenza B master donor strain (MDV-B) was extracted from 100 μl of allantoic fluid from infected embryonated eggs using the RNeasy Kit (Qiagen, Valencia, CA), and the RNA was eluted into 40 μl H₂0. RT-PCR of genomic segments was performed using the One Step RT-PCR kit (Qiagen, Valencia, CA) according to the protocol provided, using 1 μl of extracted RNA for each reaction. The RT-reaction was performed 50 min at 50 °C, followed by 15 min at 94 °C. The PCR was performed for 25 cycles at 94 °C for 1 min, 54 °C for 1 min, and 72 °C for 3 min. The P-genes were amplified using segment specific primers with RsmBI - sites that resulted in the generation of two fragments (Table 12). Table 12. RT-PCR primers for amplification of the eight vRNAs of influenza ca B/Ann Arbor/1/66.

Forward primer Reverse primer

PBl Bm-PBlb-1 : ( SEQ ID NO : 53 ) Bm-PBlb-1200R: (SEQ ID NO: 54)

[1A] TATTCGTCTCAGGGAGCAGAAGCGGAGCCTTTAAGATG TATTCGTCTCGATGCCGTTCCTTCT CA GAAGAATGG

PBl Bm-PBlb-1220: (SEQ ID NO: 55) Bm-PBlb-2369R: (SEQ ID NO: 56)

[IB] TATTCGTCTCGGCATCTTTGTCGCCTGGGATGATGATG ATATCGTCTCGTATTAGTAGAAACACGAGCCTT

PB2 Bm-PB2b-l: (SEQ ID NO: 57) Bm-PB2b-1145R: (SEQ ID NO:58)

[2A] TATTCGTCTCAGGGAGCAGAAGCGGAGCGTTTTCAAGATG TATTCGTCTCTCTCATTTTGCTCTTTTTTAATATTCCCC

PB2 Bm-PB2b-1142: (SEQ ID NO: 59) Bm-PB2b-2396R: (SEQ ID NO: 60)

[2B] TATTCGTCTCATGAGAATGGAAAAACTACTAATAAATTCAGC ATATCGTCTCGTATTAGTAGAAACACGAGCATT

PA Bm-Pab-1: (SEQ ID NO: 61) Bm-PAb-126lR: (SEQ ID NO: 62)

[3A] TATTCGTCTCAGGGAGCAGAAGCGGTGCGTTTGA TATTCGTCTCCCAGGGCCCTTTTACTTGTCAGAGTGC

PA Bm-Pab-1283: (SEQ ID NO: 63) Bm-PAb-2308R: (SEQ ID NO: 64)

[3B] TATTCGTCTCTCCTGGATCTACCAGAAATAGGGCCAGAC ATATCGTCTCGTATTAGTAGAAACACGTGCATT

HA MDV-B S'BsmBI-HA: (SEQ ID NO: 65) MDV-B S'BsmBI-HA: (SEQ ID NO: 66)

TATTCGTCTCAGGGAGCAGAAGCAGAGCATTTTCTAATATC ATATCGTCTCGTATTAGTAGTAACAAGAGCATTTTTC

NP Ba-NPb-1: (SEQ ID NO: 67) Ba-NPb-1842R: (SEQ ID NO: 68)

TATTGGTCTCAGGGAGCAGAAGCACAGCA TTTCTTGT ATATGGTCTCGTATTAGTAGAAACAACAGCATTT

NA MDV-B 5'BsmBI-NA: (SEQ ID NO: 69) MDV-B 3'BsmBI-NA: (SEQ ID NO:70)

TATTCGTCTCAGGGAGCAGAAGCAGAGCATCTTCTCAAAAC ATATCGTCTCGTATTAGTAGTAACAAGAGCATTTTTCAG

M MDV-B 5'BsmBI-M: (SEQ ID NO: 71) MDV-B 3'BsmBI-M: (SEQ ID NO: 72)

TATTCGTCTCAGGGAGCAGAAGCACGCACTTTCTTAAAATG ATATCGTCTCGTATTAGTAGAAACAACGCACTTTTTCCAG

NS MDV-B 5'BsmBI-NS: (SEQ ID NO: 73) MDV-B 3'BsmBI-NS: (SEQ ID NO: 74)

TATTCGTCTCAGGGAGCAGAAGCAGAGGATTTGTTTAGTC ATATCGTCTCGTATTAGTAGTAACAAGAGGATTTTTAT

[0171] The sequences complementary to the influenza sequences are shown in bold. The 5 '-ends have recognition sequences for the restriction endonucleases RsmBI (Bin) or Bsal (Ba).

Cloning of plasmids [0172] PCR fragments were isolated, digested with RsmBI (or Bsal for NP) and inserted into pAD3000 (a derivative of pHW2000 which allows the transcription of negative sense vRNA and positive mRNA) at the RsmBI site as described above. Two to four each of the resultant plasmids were sequenced and compared to the consensus sequence of MDV-B based on sequencing the RT-PCR fragments directly. Plasmids which had nucleotide substitutions resulting in amino acid changes different from the consensus sequence were "repaired" either by cloning of plasmids or by utilizing the Quikchange kit (Stratagene, La Jolla, CA). The resultant B/Ann Arbor/1/66 plasmids were designated pAB121-PBl, pAB122-PB2, pAB123-PA, pAB124-HA, pAB125-NP, pAB126-NA, pAB127-M, and pAB128-NS. Using this bi-directional transcription system all viral RNAs and proteins are produced intracellularly, resulting in the generation of infectious influenza B vimses (Figure 4).

[0173] It is noteworthy that pAB121-PBl and pAB124-HA had 2 and pAB128-

NS had 1 silent nucleotide substitution compared to the consensus sequence (Table 13). These nucleotide changes do not result in amino acid alterations, and are not anticipated to affect viral growth and rescue. These silent substitutions have been retained to facilitate genotyping of the recombinant vimses.

Table 13. Plasmid set representing the eight segments of B/Ann Arbor/1/66 (MDV-B)

Seg. plasmids nucleotides protein

PBl PAB121-PB1 A924>G924; C1701>T1701 silent

PB2 PAB122-PB2 consensus —

PA PAB123-PA consensus —

HA PAB124-HA T150>C150; T153>C153 silent

NP PAB125-NP consensus —

NA PAB126-NA consensus —

M PAB127-M consensus —

NS PAB128-NS A416>G416 NSl: silent

[0174] For constmction of the plasmids with nucleotide substitution in PA, NP, and Ml genes the plasmids pAB123-PA, pAB125-NP, pAB127-M were used as templates. Nucleotides were changed by Quikchange kit (Stratagene, La Jolla, CA). Alternatively, two fragments were amplified by PCR using primers which contained the desired mutations, digested with RsmBI and inserted into pAD3000-RsmBI in a three fragment ligation reaction. The generated plasmids were sequenced to ensure that the cDNA did not contain unwanted mutations.

[0175] The sequence of template DNA was determined by using Rhodamine or dRhodamine dye-terminator cycle sequencing ready reaction kits with AmpliTaq® DNA polymerase FS (Perkin-Elmer Applied Biosystems, Inc,Foster City, CA). Samples were separated by electrophoresis and analyzed on PE/ABI model 373, model 373 Stretch, or model 377 DNA sequencers. [0176] In a separate experiment, viral RNA from influenza B/Yamanshi/166/98 was amplified and cloned into pAD3000 as described above with respect to the MDV-B strain, with the exception that amplification was performed for 25 cycles at 94 °C for 30 seconds, 54 °C for 30 seconds and 72 °C for 3 minutes. Identical primers were used for amplification of the B/Yamanashi/166/98 strain segments, with the substitution of the following primers for amplification of the NP and NA segments: MDV-B 5'BsmBI-NP: TATTCGTCTCAGGGAGCAGAAGCACAGCATTTTCTTGTG (SEQ ID NO:75) and MDV-B 3'BsmBI-NP:ATATCGTCTCGTATTAGTAGAAACAACAGCATTTTTTAC (SEQ ID NO:76) and Bm-NAb-1: TATTCGTCTCAGGGAGCAGAAGCAGAGCA (SEQ ID NO:77) and Bm- NAb-1557R:ATATCGTCTCGTATTAGTAGTAACAAGAGCATTTT (SEQ ID NO:78), respectively. The B/Yamanashi/ 166/98 plasmids were designated pAB251-PBl, pAB252- PB2, pAB253-PA, pAB254-HA, pAB255-NP, pAB256-NA, pAB257-M, and pAB258- NS. Three silent nucleotide differences were identified in PA facilitating genotyping of recombinant and reassortant B/Yamanashi/166/98 vims.

EXAMPLE 6: GENERATION OF INFECTIOUS RECOMBINANT INFLUENZA B AND REASSORTED INFLUENZA VIRUS

[0177] To overcome the obstacles encountered in attempting to grow influenza B in a helper vims free cell culture system, the present invention provides novel vectors and protocols for the production of recombinant and reassortant B strain influenza vimses. The vector system used for the rescue of influenza B vims is based on that developed for the generation of influenza A vims (Hoffmann et al. (2000) A DNA transfection system for generation of influenza A virus from eight plasmids Proc Natl Acad Sci USA 97:6108- 6113; Hoffmann & Webster (2000) Unidirectional RNA polymerase I-polymerase II transcription system for the generation of influenza A virus from eight plasmids J Gen Virol 81:2843-7). 293T or COS-7 cells (primate cells with high transfection efficiency and poll activity) were co-cultured with MDCK cells (permissive for influenza vims), 293T cells were maintained in OptiMEM I-AB medium containing 5% FBS cells, COS-7 cells were maintained in DMEM I-AB medium containing 10% FBS. MDCK cells were maintained in lx MEM, 10 % FBS with the addition of antibiotic and antimycotic agents. Prior to transfection with the viral genome vectors, the cells were washed once with 5 ml PBS or medium without FBS. Ten ml trypsin-EDTA was added to confluent cells in a 75 cm² flask (MDCK cells were incubated for 20-45 min, 293T cells were incubated for 1 min). The cells were centrifuged, and resuspended in 10 ml OptiMEM I-AB. One ml of each suspended cell line was then diluted into 18 ml OptiMEM I-AB, and mixed. The cells were then aliquoted into a 6 well plate at 3 ml/well. After 6-24 hours, 1 μg of each plasmid was mixed in an 1.5 ml Eppendorf tube with OptiMEM I-AB to the plasmids ( x μl plasmids + x μl OptiMEM I-AB + x μl TransIT-LTl = 200 μl); 2 μl TransIT-LTl per μg of plasmid DNA. The mixture was incubated at room temperature for 45 min. Then 800 μl of OptiMEM I-AB was added. The medium was removed from the cells, and the transfection mixture was added to the cells (t = 0) at 33 °C for 6-15 hours. The transfection mixture was slowly removed from the cells, and 1 ml of OptiMEM I-AB was added, and the cells were incubated at 33 °C for 24 hours. Forty-eight hours following transfection, 1 ml of OptiMEM I-AB containing 1 μg/ml TPCK-trypsin was added to the cells. At 96 hours post-transfection, 1 ml of OptiMEM I-AB containing 1 μg/ml TPCK- trypsin was added to the cells.

[0178] Between 4 days and 7 days following transfection 1 ml of the cell culture supernatant was withdrawn and monitored by HA or plaque assay. Briefly, 1 ml of supernatant was aliquoted into an Eppendorf tube and centrifuge at 5000 rpm for 5 min. Nine hundred μl of supernatant was transferred to a new tube, and serial dilutions were performed at 500 μl/well to MDCK cells (e.g., in 12 well plates). The supernatant was incubated with the cells for 1 hour then removed, and replaced with infection medium (lxMEM) containing lμg/ml of TPCK-trypsin. HA assay or plaque assays were then performed. For example, for the plaque assays supematants were titrated on MDCK cells which were incubated with an 0.8% agarose overlay for three days at 33 °C. For infection of eggs the supernatant of transfected cells were harvested six or seven days after transfection, 100 μl of the vims dilutions in Opti-MEM I were injected into 11 days old embryonated chicken eggs at 33 °C. The titer was determined three days after inoculation by TCID₅₀ assay in MDCK cells.

[0179] To generate MDV-B, either co-cultured 293T-MDCK or COS-7-MDCK cells were transfected with 1 μg of each plasmid. When examined at 5 to 7 days post- transfection the co-cultured MDCK cells showed cytopathic effects (CPE), indicating the generation of infectious MDV-B vims from cloned cDNA. No CPE was observed in cells transfected with seven plasmids (Table 14). To determine the efficiency of the DNA transfection system for virus generation, supematants of cells were titrated seven days after transfection on MDCK cells and the vims titer was determined by plaque assay. The vims titer of the supernatant of co-cultured 293T-MDCK was 5.0 x 10⁶ pfu/ml and 7.6 x 10⁶ pfu/ml in COS7-MDCK cells.

Table 14. Generation of infectious Influenza-B vims from eight plasmids segment 1 2 3 4

PBl pAB121-PBl PAB121-PB1 —

PB2 pAB122-PB2 pAB122-PB2 PAB122-PB2 pAB122-PB2

PA pAB123-PA pAB123-PA pAB123-PA pAB123-PA

HA pAB124-HA pAB124-HA pAB124-HA pAB124-HA

NP pAB125-NP pAB125-NP pAB125-NP pAB125-NP

NA pAB126-NA pAB126-NA pAB126-NA pAB126-NA

M pAB127-M pAB127-M pAB127-M pAB127-M

NS pAB128-NS pAB128-NS pAB128-NS pAB128-NS co-cultured 293T-MDCK cells co-cultured COS-7 -MDCK cells

CPE + - + pfu/ml 5.0 x 10° 0 7.6 x 10⁶ 0

[0180] Transiently co-cultured 293T-MDCK (1 , 2) or co-cultured COS7-MDCK cells (3, 4) were transfected with seven or eight plasmids. Cytopathic effect (CPE) was monitored seven days after transfection in the co-cultured MDCK cells. Seven days after transfection the supematants of transfected cells were titrated on MDCK cells. The data of pfu/ml represent the average of multiple, (e.g., three or four) transfection experiments.

[0181] Comparable results were obtained in transfection experiments utilizing the

B/Yamanashi/166/98 plasmid vectors. These results show that the transfection system allows the reproducible de novo generation of influenza B vims from eight plasmids.

Genotypin of recombinant Influenza B [0182] After a subsequent passage on MDCK cells, RT-PCR of the supernatant of infected cells was used to confirm the authenticity of the generated vims. RT-PCR was performed with segment specific primers for all eight segments (Table 12). As shown in

Figure 5A, PCR products were generated for all segments. Direct sequencing of the PCR products of the PBl, HA, and NS segments revealed that the four nucleotides analyzed were the same as found in the plasmid pAB121-PBl, pAB124-HA, and pAB128-NS.

These results confirmed that the generated vims was generated from the designed plasmids and exclude (in addition to the negative controls) any possible laboratory contamination with the parent vims (Figure 5B).

[0183] Similarly, following transfection with the B/Yamanashi/166/98 plasmid vectors, vims was recovered and the region encompassing nucleotides 1280-1290 of the PA segment were amplified. Sequencing confirmed that the recovered vims corresponded to the plasmid-derived recombinant B/Yamanashi/166/98 (Figures 5C and D).

Phenotvpin of rMDV-B [0184] The MDV-B vims shows two characteristic phenotypes: temperature sensitivity (ts) and cold adaptation (ca). By definition a 2 log (or higher) difference in vims titer at 37 °C compared to 33 °C defines ts, ca is defined by less than 2 log difference in vims growth at 25 °C compared to 33 °C. Primary chicken kidney (PCK) cells were infected with the parent vims MDV-B and with the transfected vims derived from plasmids to determine the viral growth at three temperatures.

[0185] For plaque assay confluent MDCK cells (ECACC) in six well plates were used. Vims dilutions were incubated for 30-60 min. at 33 °C. The cells were overlayed with an 0.8 % agarose overlay. Infected cells were incubated at 33 °C or 37 °C. Three days after infection the cells were stained with 0.1% crystal violet solution and the number of plaques determined.

[0186] The ca-ts phenotype assay was performed by TCID₅₀ titration of the vims samples at 25, 33, and 37 °C. This assay format measures the TCID₅o titer by examining the cytopathic effect (CPE) of influenza virus on primary chick kidney cell monolayers in 96-well cell culture plates at different temperatures (25 °C, 33 °C, 37 °C). This assay is not dependent on the plaque morphology, which varies with temperature and virus strains; instead it is dependent solely on the ability of influenza vims to replicate and cause CPE. Primary chicken kidney (PCK) cell suspension, prepared by trypsinization of the primary tissue, were suspended in MEM (Earl's) medium containing 5% FCS. PCK cells were seeded in 96 well cell culture plates for 48 hours in order to prepare monolayer with >90% confluency. After 48hrs, the PCK cell monolayer were washed for one hour with semm free MEM medium containing 5mM L-Glutamine, antibiotics, non-essential amino acid, referred as Phenotype Assay Medium (PAM). Serial ten-fold dilution of the vims samples were prepared in 96 well blocks containing PAM. The diluted vims samples were then plated onto the washed PCK monolayer in the 96 well plates. At each dilution of the vims sample, replicates of six wells were used for infection with the diluted vims. Un-infected cells as cell control were included as replicate of 6 wells for each sample. Each vims sample was titered in 2-4 replicates. Phenotype control virus with pre-determined titers at 25 °C, 33 °C, and 37 °C is included in each assay. In order to determine the ts phenotype of the vims samples, the plates were incubated for 6 days at 33 °C and 37 °C in 5% CO₂ cell culture incubators. For ca-phenotype characterization the plates were incubated at 25 °C for 10 days. The vims titer was calculated by the Karber Method and reported as Logio Mean (n=4) TCID₅₀ Titer/ml + Standard Deviation. The standard deviations of the vims titers presented in Fig.1-3 ranged from 0.1 to 0.3. The difference in vims titer at 33 °C and 37 °C were used to determine the ts phenotype and difference in titer at 25 °C and 33 °C of the vims were used to determine the ca phenotype.

[0187] The plasmid derived recombinant MDV-B (recMDV-B) vims expressed the two characteristic phenotypes in cell culture, ca and ts, as expected. The ca phenotype, efficient replication at 25 °C, is functionally measured as a differential in titer between 25 °C and 33 °C of less than or equal to 2 loglO when assayed on PCK cells. Both the parental MDV-B and recMDV-B expressed ca; the difference between 25 °C and 33 °C was 0.3 and 0.4 loglO, respectively (Table 15). The ts phenotype is also measured by observing the titers at two different temperatures on PCK cells; for this phenotype, however, the titer at 37 °C should be less than the titer at 33 °C by 2 loglO or more. The difference between 33 °C and 37 °C for the parental MDV-B and recMDV-B was 3.4 and 3.7 loglO, respectively (Table 15). Thus, the recombinant plasmid-derived MDV-B vims expressed both the ca and ts phenotypes.

[0188] The recombinant vims had a titer of 7.0 logio TCID₅o/ml at 33 °C and 3.3 TCIDso/ml at 37 °C and 8.8 logio TdD₅o/ml at 25 °C (Table 15). Thus, the recombinant vims derived from transfection with the eight influenza MDV-B genome segment plasmids has both the ca and ts phenotype. Table 15. Phenotype assay for MDV-B and rMDV-B generated from plasmids

Temperature ( 0C) Phenotype

25 33 37

Virus

LoglO TCID50/ml (Mean + SD) ca B/Ann Arbor/01/66 (MDV-B) 8.8 + 0.3 8.5 + 0.05 5.1 + 0.1 ca, ts RecMDV-B 7.4 + 0.3 7.0 + 0.13 3.3 + 0.12 ca, ts

Rec53-MDV-B 5.9 + 0.1 5.7 + 0.0 5.3 + 0.1 ca, non-ts

Primary chicken kidney cells were infected with the parent vims MDV-B and the plasmid- derived recombinant vims (recMDV-B). The vims titer was determined at three different temperatures. EXAMPLE 7: PRODUCTION OF REASSORTANT B/YAMANASHI/166/98 VIRUS [0189] The HA and NA segments of several different strains representing the major lineages of influenza B were amplified and cloned into pAD3000, essentially as described above. The primers were optimized for simultaneous RT-PCR amplification of the HA and NA segments. Comparison of the terminal regions of the vRNA representing the non coding region of segment 4 (HA) and segment 6 (NB/NA) revealed that the 20 terminal nucleotides at the 5' end and 15 nucleotides at the 3 'end were identical between the HA and NA genes of influenza B vimses. A primer pair for RT-PCR (underlined sequences are influenza B vims specific) Bm-NAb-1: TAT TCG TCT CAG GGA GCA GAA GCA GAG CA (SEQ ID NO:79); Bm-NAb-1557R: ATA TCG TCT CGT ATT AGT AGT AAC AAG AGC ATT TT (SEQ ID NO: 80) was synthesized and used to simultaneously amplify the HA and NA genes from various influenza B strains (Fig. 8). The HA and NA PCR-fragments of B/Victoria/504/2000, B/Hawaii/ 10/2001, and B/Hong Kong/330/2001 were isolated, digested with RsmBI and inserted into pAD3000. These results demonstrated the applicability of these primers for the efficient generation of plasmids containing the influenza B HA and NA genes from several different wild type vimses representing the major lineages of influenza B. The RT-PCR products can be used for sequencing and/or cloning into the expression plasmids.

[0190] In order to demonstrate the utility of B/Yamanashi/166/98 (a

B/Yamagata/16/88-like vims) to efficiently express antigens from various influenza B lineages, reassortants containing PBl, PB2, PA, NP, M, NS from B/Yamanashi/166/98 and the HA and NA from strains representing both the Victoria and Yamagata lineages (6 +2 reassortants) were generated. Transiently cocultured COS7-MDCK cells were cotransfected with six plasmids representing B/Yamanashi/166/98 and two plasmids containing the cDNA of the HA and NA segments of two strains from the B/Victori a/2/87 lineage, B/Hong Kong/330/2001 and B/Hawaii/10/2001, and one strain from the B/Yamagata/16/88 lineage, B/Victoria/504/2000, according to the methods described above. Six to seven days after transfection the supematants were titrated on fresh MDCK cells. All three 6+2 reassortant vimses had titers between 4 - 9 x 10⁶ pfu/ml (Table 16). These data demonstrated that the six internal genes of B/Yamanashi/166/98 could efficiently form infectious vims with HA and NA gene segments from both influenza B lineages.

[0191] Supematants of cocultured COS7-MDCK cells were titrated six or seven days after transfection and the viral titer determined by plaque assays on MDCK cells.

Table 16:Plasmid set used for the generation of B/Yamanashi/166/98 and 6 + 2 reassortants. segment

1 — pAB251-PBl pAB251-PBl pAB251-PBl pAB251-PBl

2 pAB252-PB2 pAB252-PB2 pAB252-PB2 pAB252-PB2 pAB252-PB2

3 pAB253-PA pAB253-PA pAB253-PA pAB253-PA pAB253-PA

4 pAB254-HA pAB254-HA pAB281-HA pAB285-HA pAB287-HA

5 pAB255-NP pAB255-NP pAB255-NP pAB255-NP pAB255-NP

6 pAB256-NA pAB256-NA pAB291-NA pAB295-NA pAB297-NA

7 pAB257-M pAB257-M pAB257-M pAB257-M pAB257-M

8 pAB258-NA pAB258-NA pAB258-NA pAB258-NA PAB258-NA

Recombinant virus 8 6 + 2 6 + 2 6 + 2

B/Υamanashi/ B/Victoria/504/ B/Hawaii/10/2001 B/Hong

166/98 2000 Kong/330/2001 pfu/ml^a 0 4 x l0⁶ 9 x 10" 6 x 10" 7 x l0⁶

[0192] Relatively high titers are obtained by replication of wild type

B/Yamanashi/166/98 in eggs. Experiments were performed to determine whether this property was an inherent phenotype of the six "internal" genes of this vims. To evaluate this property, the yield of wild type B/Victoria/504/2000, which replicated only moderately in eggs, was compared to the yield of the 6+2 reassortant expressing the B/Victoria/504/2000 HA and NA. These vimses in addition to wild type and recombinant B/Yamanashi/166/98 were each inoculated into 3 or 4 embryonated chicken eggs, at either 100 or 1000 pfu. Three days following infection, the allantoic fluids were harvested from the eggs and the TCID₅₀ titers determined on MDCK cells. The 6+2 reassortants produced similar quantities of vims in the allantoic fluid to the wt and recombinant B/Yamanashi/166/98 strain (Fig. 9). The difference in titer between B/Victoria/504/2000 and the 6+2 recombinant was approximately 1.6 logio TCID50 (0.7-2.5 logio TCIDso mL, 95% CI). The difference between B/Nictoria/504/2000 and the 6+2 recombinant were confirmed on three separate experiments (P <0.001). These results demonstrated that the egg growth properties of B/Yamanashi/166/98 could be conferred to HA and ΝA antigens that are normally expressed from strains that replicated poorly in eggs.

EXAMPLE 8: MOLECULAR BASIS FOR ATTENUATION OF CA B/ANN ARBOR/1/66

[0193] The MDV-B vims (ca B/Ann Arbor/1/66) is attenuated in humans, shows an attenuated phenotype in ferrets and shows a cold adapted and temperature sensitive phenotype in cell culture. The deduced amino acid sequences of the internal genes of

MDV-B were compared with sequences in the Los Alamos influenza database (on the world wide web at: flu.lanl.gov) using the BLAST search algorithm. Eight amino acids unique to MDV-B, and not present in any other strain were identified (Table 17). Genome segments encoding PBl, BM2, NSl, and NS2 show no unique substituted residues. The PA and Ml proteins each have two, and the NP protein has four unique substituted amino acids (Table 17). One substituted amino acid is found in PB2 at position 630 (an additional strain B/Harbin/7/94 (AF170572) also has an arginine residue at position 630).

[0194] These results suggested that the gene segments PB2, PA, NP and Ml may be involved in the attenuated phenotype of MDV-B. In a manner analogous to that described above for MDV-A, the eight plasmid system can be utilized to generate recombinant and reassortant (single and/or double, i.e., 7:1; 6:2 reassortants) in a helper independent manner simply by co-transfection of the relevant plasmids into cultured cells as described above with respect to MDV-A. For example, the 6 internal genes from B/Lee/40 can be used in conjunction with HA and NA segments derived from MDV-B to generate 6 + 2 reassortants. Table 17. Unique substituted amino acids of B/Ann Arbor/1/66

Nr. ca B/Ann Aligned sequences Number of Arbor/1/66 (wild type vimses) aligned sequences pos. amino codon amino codon acid acid

PBl 0 - - 23

PB2 1 630 Arg630 AGA Ser630 AGC 23

PA 2 431 Met431 ATG Val431 GTG 23

497 His497 CAT Tyr497 TAT

NP 4 55 Ala55 GCC Thr55 ACC 26

114 A 14 GCG Vail 14 GTG

410 His410 CAT Pro410 CCT, CCC

509 Thr509 GAC Ala509 GGC

Ml 2 159 Gin 159 CAA Hisl59 CAT 24

183 Vail 83 GTG M183 ATG

BM2 0 - - 24

NSl 0 - - 80

NS2 0 - - 80

The deduced amino acid sequence of eight proteins of ca B/Ann Arbor was used in a BLAST search. Amino acid position which were different between MDV-B and the aligned sequences are shown. The nucleotides in the codons that are underlined represent the substituted positions.

[0195] In order to determine whether the 8 unique amino acid differences had any impact on the characteristic MDV-B phenotypes, a recombinant vims was constructed in which all eight nucleotide positions encoded the amino acid reflecting the wt influenza genetic complement. A set of plasmids was constmcted in which the eight residues of the PA, NP, and Ml genes were changed by site directed mutagenesis to reflect the wild type amino acids (as indicated in Table 17). A recombinant with all eight changes, designated rec53-MDV-B, was generated by cotransfection of the constmcted plasmids onto cocultured COS7-MDCK cells. The coculturing of MDCK cells and growth at 33 °C ensured that the supernatant contained high vims titers six to seven days after transfection. The supematants of the transfected cells were titrated and the titer determined on MDCK cells by plaque assay and PCK cells at 33 °C and 37 °C.

[0196] As shown in Fig. 13, in two different independent experiments, recMDV-B expressed the ts-phenotype in both MDCK cells and PCK cells. The triple reassortant vims rec53-MDV-B designed harboring all eight amino acid changes expressed the non- ts-phenotype, the difference in titer between 33 °C and 37 °C was only 0.7 logio in PCK cells. This titer was less than the required 2 logio difference characteristic of the ts definition and significantly lower than the ~3 logio difference observed with recMDV-B. These results show that the alteration of the eight amino acids within PA, NP, and Ml proteins was sufficient to generate a non-ts, wild type-like virus with both homologous and heterologous glycoprotein s.

[0197] The contribution of each gene segment to the ts phenotype was then determined. Plasmid derived recombinants harboring either the PA, NP, or M gene segment with the wild-type amino acid complement were generated by the DNA cotransfection technique. All single gene recombinants exhibited growth restriction at 37 °C in MDCK cells and in PCK cells (Fig. 14), indicating that changes in no one gene segment were capable of reverting the ts phenotype. In addition, recombinant viruses that carried both the NP and M or PA and M gene segments together also retained the ts- phenotype. In contrast, recombinant vimses that harbored both the PA and NP gene segments had a difference in titer between 37 °C and 33 °C of 2.0 logio or less, similar to the rec53-MDV-B. These results show that the NP and PA genes have a major contribution to the ts-phenotype.

[0198] To determine whether all of the four amino acids in the NP protein and two in the PA protein contribute to non-ts, triple gene and double-gene recombinants with altered NP and PA genes were generated (Fig. 15). The substitution of two amino acids Al 14 → VI 14 and H410 — > P410 resulted in non-ts phenotype. Vimses with single substitution H410 — > P410 in the nucleoprotein showed non-ts phenotype in MDCK and PCK. On the other hand, the single substitution A55 — ^■» T55 showed a ts-phenotype. These results indicate that the P410 in NP is involved in efficient growth at 37 °C. These results show that from the six amino acids of PA and NP four residues contribute to the non-ts phenotype.

[0199] Based on prior evidence, a ts-phenotype and an attenuated phenotype are highly correlated. It is well established that ca B/Ann Arbor/1/66 vims is not detectable in lung tissue of infected ferrets, whereas non attenuated influenza B vimses vimses are detectable in lungs after intranasal infection. To determine whether identical mutation underlie the ts and att phenotypes, the following studies were performed. [0200] Recombinant vimses obtained after transfection were passaged in embryonated chicken eggs to produce a vims stock. Nine week old ferrets were inoculated intranasaly with 0.5 ml per nostril of vimses with titers of 5.5, 6.0 or 7.0 logio pfu/ml. Three days after infection ferrets were sacrificed and their lungs and turbinates were examined as described previously.

[0201] Ferrets (four animals in each group) were infected intranasaly with recMDV-B or rec53-MDV-B. Three days after infection vims nasal turbinates and lung tissue were harvested and the existence of virus was tested. No vims was detected in lung tissues of ferrets infected with 7.0 logio p u recMDV-B. From the four animals infected with rec53-MDV-B vims with 7.0 logio pfu in three animals vims was detected in lung tissue (one animal in this group for unknown reasons). In two out of four lung tissues of ferrets infected with rec53-MDV-B at a lower dose (5.5 log pfu/ml) virus could be isolated from lung tissue. Thus, the change of the eight unique amino acids in PA, NP, and Ml protein into wild type residues were sufficient to convert a att phenotype into a non-att phenotype.

[0202] Since the data in cell culture showed that PA and NP are main contributors to the ts-phenotype, in a second experiment, ferrets were infected with rec53-MDV-B (PA,NP,M), rec62-MDV-B (PA), NP rec71 -MDV-B (NP) with 6 log pfu. Two out of four animals infected with rec53-MDV-B had vims in the lung. None of the lung tissues of ferrets infected with single and double reassortant vimses had detectable levels of vims. Thus, in addition to the amino acids in the PA and NP proteins, the Ml protein is important for the att phenotype. Vims with wt PA and NP did not replicate in ferret lung, indicating that a subset of the mutations involved in attenuation are involved in the ts phenotype. [0203] Thus, the ts-phenotype of B/Ann Arbor/1/66 is determined by at most three genes. The conversion of eight amino acids in the PA, NP, and Ml protein into wild type residues resulted in a recombinant vims that replicated efficiently at 37 °C. Similarly, a 6+2 recombinant vims representing the six internal genes of MDV-B with the HA and NA segments from B/HongKong/330/01 showed a ts-phenotype and the triple recombinant was non-ts. [0204] As described above with respect to influenza A strains, substitution of the residues indicated above, e.g., PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (Ml 83 V), confers the ts and att phenotypes. Accordingly, artificially engineered variants of influenza B strain vims having one or more of these amino acid substitutions exhibit the ts and att phenotypes and are suitable for use, e.g., as master donor strain vimses, in the production of attenuated live influenza vims vaccines.

EXAMPLE 9: RESCUE OF INFLUENZA FROM EIGHT PLASMIDS BY ELECTROPORATION OF VERO CELLS [0205] Previously it has been suggested that recombinant influenza A can be rescued from Vero cells (Fodor et al. (1999) Rescue of influenza A virus from recombinant DNA J. Virol. 73:9679-82; Hoffmann et al. (2002) Eight-plasmid system for rapid generation of influenza virus vaccine Vaccine 20:3165-3170). The reported method requires the use of lipid reagents and has only been documented for a single strain of a highly replication competent laboratory strains of influenza A (A/WSN/33 and

A/PR/8/34), making it of limited application in the production of live attenuated virus suitable for vaccine production. The present invention provides a novel method for recovering recombinant influenza virus from Vero cells using electroporation. These methods are suitable for the production of both influenza A and influenza B strain vimses, and permit the recovery of, e.g., cold adapted, temperature sensitive, attenuated vims from Vero cells grown under semm free conditions facilitating the preparation of live attenuated vaccine suitable for administration in, e.g., intranasal vaccine formulations. In addition to its broad applicability across virus strains, electroporation requires no additional reagents other than growth medium for the cell substrate and thus has less potential for undesired contaminants. In particular, this method is effective for generating recombinant and reassortant vims using Vero cells adapted to growth under serum free condition, such as Vero cell isolates qualified as pathogen free and suitable for vaccine production. This characteristic supports the choice of electroporation as an appropriate method for commercial introduction of DNA into cell substrates. [0206] Electroporation was compared to a variety of methods for introduction of

DNA into Vero cells, including transfection using numerous lipid based reagents, calcium phosphate precipitation and cell microinjection. Although some success was obtained using lipid based reagents for the rescue of influenza A, only electroporation was demonstrated to rescue influenza B as well as influenza A from Vero cells.

[0207] One day prior to electroporation, 90 - 100% confluent Vero cells were split, and seeded at a density of 9 x 10⁶ cells per T225 flask in MEM supplemented with pen/strep, L-glutamine, nonessential amino acids and 10% FBS (MEM, 10% FBS). The following day, the cells were trypsinized and resuspend in 50 ml phosphate buffered saline (PBS) per T225 flask. The cells are then pelleted and resuspend in 0.5 ml OptiMEM I per T225 flask. Optionally, customized OptiMEM medium containing no human or animal- derived components can be employed. Following determination of cell density, e.g., by counting a 1:40 dilution in a hemocytometer, 5 x 10⁶ cells were added to a 0.4 cm electroporation cuvette in a final volume of 400 μl OptiMEM I. Twenty μg DNA consisting of an equimolar mixture of eight plasmids incorporating either the MDV-A or MDV-B genome in a volume of no more than 25 μl was then added to the cells in the cuvette. The cells were mixed gently by tapping and electroporated at 300 volts, 950 microFarads in a BioRad Gene Pulser II with Capacitance Extender Plus connected (BioRad, Hercules, CA). The time constant should be in the range of 28 - 33 msec.

[0208] The contents of the cuvette were mixed gently by tapping and 1-2 min after electroporation, 0.7ml MEM, 10% FBS was added with a 1 ml pipet. The cells were again mixed gently by pipetting up and down a few times and then split between two wells of a 6 well dish containing 2 ml per well MEM, 10% FBS. The cuvette was then washed with 1 ml MEM, 10% FBS and split between the two wells for a final volume of approximately 3.5 ml per well.

[0209] In alternative experiments, Vero cells adapted to semm free growth conditions, e.g., in OptiPro (SFM) (Invitrogen, Carlsbad, CA) were electroporated as described above except that following electroporation in OptiMEM I, the cells were diluted in OptiPro (SFM) in which they were subsequently cultured for rescue of vims.

[0210] The electroporated cells were then grown under conditions appropriate for replication and recovery of the introduced vims, i.e., at 33 °C for the cold adapted Master Donor Strains. The following day (e.g., approximately 19 hours after electroporation), the medium was removed, and the cells were washed with 3 ml per well OptiMEM I or OptiPro (SFM). One ml per well OptiMEM I or OptiPro (SFM) containing pen/strep was added to each well, and the supematants were collected daily by replacing the media. Supematants were stored at - 80 °C in SPG. Peak vims production was typically observed between 2 and 3 days following electroporation.

Table 18: Results of 8 Plasmid Rescue of MDV strains on Different Cell Types and by Different Transfection Methods

Substrate Method No of Test Result (Infectious Virus Recovered)

MDV-B

COS-7/MDCK Lipo 3 positive

COS-7/MDCK CaP04 2 positive

MRC-5 Lipo 5 negative

MRC-5 CaP04 3 negative

MRC-5 Electroporation 2 negative

WI-38 Lipo 2 negative

WI-38 Electroporation 4 negative

WI-38 Microinjection 1 negative

LF1043 Lipo 1 negative

LF1043 CaP04 2 negative

Vero Lipo 7 negative

Vero CaP04 2 negative

Vero/MDCK Lipo 1 negative

Vero (serum) Electroporation 5 positive (5/5)

Vero (serum free) Electroporation 4 positive (4/4)

MDV-A

Vero (serum) Electroporation 3 positive (3/3)

Vero (serum Free) Electroporation 3 positive (3/3)

EXAMPLE 10: INFLUENZA VIRUS VECTOR SYSTEM FOR GENE DELIVERY [0211] The vectors of the present invention can also be used as gene delivery systems and for gene therapy. For such applications, it is desirable to generate recombinant influenza vims, e.g., recombinant influenza A or B vims expressing a foreign protein. For example, because segment 7 of the influenza B vims is not spliced, it provides a convenient genetic element for the insertion of heterologous nucleic acid sequences. The mRNA contains two cistrons with two open reading frames encoding the Ml and BM2 proteins. The open reading frame of BM2 or Ml is substituted by the heterologous sequence of interest, e.g., a gene encoding the enhanced green fluorescent protein (EGFP). Using the plasmid based vector system of the present invention, the cDNA encoding the open reading frame of Ml-EGFP and BM2 are cloned on two different plasmids. The open reading frame is flanked by the non coding region of segment 7, which contains the signals required for replication and transcription. Alternatively, two plasmids are constmcted: one containing Ml ORF and the other containing EGFP-BM2. Co-transfection of the resultant nine plasmids results in the generation of a recombinant influenza B vims containing the heterologous gene sequence. Similarly, EGFP can be expressed from the NSl segment of influenza A. [0212] The exemplary "green" influenza B vims can be used for standardization in virus assays, such as micro neutralization assays. The combination of the plasmid based technology and the simple detection of protein expression (fluorescence derived from EGFP can be monitored by microscopy, as illustrated in Figure 2), permits the optimization of protein expression. [0213] While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be clear to one skilled in the art from a reading of this disclosure that various changes in form and detail can be made without departing from the tme scope of the invention. For example, all the techniques and apparatus described above may be used in various combinations. All publications, patents, patent applications, or other documents cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent, patent application, or other document were individually indicated to be incorporated by reference for all purposes.

Claims

CLAIMSWHAT IS CLAIMED IS:

1. A method for producing influenza vimses in cell culture, the method comprising: i) introducing a plurality of vectors comprising an influenza vims genome into a population of host cells, which population of host cells is capable of supporting replication of influenza vims; ii) culturing the population of host cells at a temperature less than or equal to 35 °C; and, iii) recovering a plurality of influenza viruses.

2. The method of claim 1, wherein the influenza vimses comprise at least one of: an attenuated influenza vims, a cold adapted influenza vims and a temperature sensitive influenza vims.

3. The method of claim 1, wherein the influenza vimses possess one or more phenotypic attributes selected from the group consisting of: attenuation, temperature sensitivity and cold adaptation.

4. The method of claim 1, wherein the influenza vimses are suitable for administration in an intranasal vaccine formulation.

5. The method of claim 1, comprising introducing a plurality of vectors comprising at least one of a) an influenza A/ Ann Arbor/6/60 vims or an artificially engineered influenza A vims comprising at least one substituted amino acid, which substituted amino acid influences the characteristic biological properties of A/ Ann Arbor/6/60; and, b) an influenza B/Ann Arbor/1/66 vims or an artificially engineered influenza B vims comprising at least one substituted amino acid, which substituted amino acid influences the characteristic biological properties of B/Ann Arbor/1/66.

6. The method of claim 5, comprising introducing a plurality of vectors comprising at least one of: a) an artificially engineered influenza A vims comprising at least one substituted amino acid, which substituted amino acid corresponds to a unique amino acid of influenza A/ Ann Arbor/6/60; and, b) an artificially engineered influenza B virus comprising at least one substituted amino acid, which substituted amino acid corresponds to a unique amino acid of influenza B/Ann Arbor/1/66.

7. The method of claim 5, wherein the influenza viruses comprise at least one of: a) an influenza A strain vims comprising at least one substituted amino acid selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴; and, b) an influenza B strain vims comprising at least one substituted amino acid selected from the group consisting of: PB2⁶³⁰; PA⁴³¹; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³.

8. The method of claim 7, wherein the influenza vimses comprise at least one of: a) an influenza A strain vims comprising at least one substituted amino acid selected from the group consisting of: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G); and, b) influenza B strain viruses comprising at least one substituted amino acid selected from the group consisting of: PB2⁶³⁰ (S630R); PA⁴³¹

(V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V).

9. The method of claim 7, wherein the influenza vimses comprise a plurality of substituted amino acids.

10. The method of claim 8, wherein the plurality comprises two, three, four, five, six, seven, eight or nine substituted amino acids.

11. The method of claim 1 , comprising introducing a plurality of vectors comprising an influenza B vims.

12. The method of claim 1, comprising introducing a plurality of vectors comprising an influenza A vims.

13. The method of claim 1, comprising introducing a plurality of vectors comprising: (a) at least 6 internal genome segments of a first influenza strain; and, (b) at least one genome segment encoding an immunogenic influenza surface antigen of a second influenza strain.

14. The method of claim 1, comprising introducing a plurality of vectors comprising: (a) at least 6 internal genome segments of a first influenza strain, which influenza strain is attenuated, cold adapted, and/or temperature sensitive; and, (b) at least one genome segment encoding an immunogenic influenza surface antigen of a second influenza strain.

15. The method of claim 1, comprising introducing a plurality of vectors comprising: (a) at least 6 internal genome segments of a first influenza strain, which influenza strain is attenuated, cold adapted, and temperature sensitive; and, (b) at least one genome segment encoding an immunogenic influenza surface antigen of a second influenza strain.

16. The method of claim 1, comprising introducing a plurality of vectors comprising: (a) at least 6 internal genome segments of influenza B/Ann Arbor/1/66 or influenza strain A/ Ann Arbor/6/60 or an artificially engineered influenza vims comprising at least one substituted amino acid, which substituted amino acid corresponds to a unique amino acid of influenza B/Ann Arbor/1/66 or influenza A/ Ann Arbor/6/60; and, (b) at least one genome segment encoding an immunogenic influenza surface antigen of a different influenza strain.

17. The method of claim 16, comprising introducing a plurality of vectors comprising: (a) 6 internal genome segments of influenza B/Ann Arbor/1/66 or influenza strain A/ Ann Arbor/6/60 or an artificially engineered influenza vims comprising at least one substituted amino acid, which substituted amino acid corresponds to a unique amino acid of influenza B/Ann Arbor/1/66 or influenza A/ Ann Arbor/6/60; and, (b) two genome segments encoding the HA and NA antigens of an influenza strain other than B/Ann Arbor/1/66 or A/ Ann Arbor/6/60.

18. The method of claim 16, comprising introducing a plurality of vectors comprising: (a) 7 internal genome segments of influenza B/Ann Arbor/1/66 or influenza strain A/ Ann Arbor/6/60 or an artificially engineered influenza vims comprising at least one substituted amino acid, which substituted amino acid corresponds to a unique amino acid of influenza B/Ann Arbor/1/66 or influenza A/ Ann Arbor/6/60; (b) and either a genome segment encoding the HA antigen or a genome segment encoding the NA antigen of an influenza strain other than B/Ann Arbor/1/66 or A/ Ann Arbor/6/60.

19. The method of claim 1, comprising introducing a plurality of plasmid vectors.

20. The method of claim 1, wherein the population of host cells comprises one or more of: Vero cells, Per.Cό cells, MDCK cells, 293T cells, or COS cells.

21. The method of claim 20, wherein the population of cells comprises a mixture of least two of MDCK cells, 293T cells, and COS cells.

22. The method of claim 1, comprising culturing the population of host cells at a temperature between about 32 °C and 35 °C.

23. The method of claim 1, comprising culturing the population of host cells at a temperature between about 32 °C and about 34 °C.

24. The method of claim 1, comprising culturing the population of host cells at a temperature of about 33 °C.

25. The method of claim 1, comprising recovering recombinant influenza vimses.

26. The method of claim 1, comprising recovering reassortant influenza vimses.

27. The method of claim 1, further comprising inactivating the influenza vimses.

28. An influenza vims produced by the method of claim 1.

29. A method for producing influenza B vimses in cell culture, the method comprising: i) introducing a plurality of vectors comprising an influenza B vims genome into a population of host cells, which population of host cells is capable of supporting replication of influenza vims; ii) culturing the population of host cells under conditions permissive for viral replication; and, iii) recovering a plurality of influenza B viruses.

30. The method of claim 29, comprising a helper free method for producing influenza B vims in cell culture, the method comprising introducing a plurality of vectors comprising an influenza B vims genome into a population of host cells in the absence of a helper vims.

31. The method of claim 29, comprising culturing the population of host cells at a temperature less than or equal to 35 °C.

32. The method of claim 29, comprising culturing the population of host cells at a temperature between about 32 °C and 35 °C.

33. The method of claim 29, comprising culturing the population of host cells at a temperature between about 32 °C and about 34 °C.

34. The method of claim 29, comprising culturing the population of host cells at a temperature of about 33 °C.

35. The method of claim 29, comprising recovering recombinant influenza vimses.

36. The method of claim 29, comprising recovering reassortant influenza vimses.

37. An influenza vims produced by the method of claim 29.

38. A method for producing influenza vimses in cell culture, the method comprising: i) introducing a plurality of vectors comprising an influenza vims genome into a population of Vero cells by electroporation; ii) culturing the population of Vero cells under conditions permissive for viral replication; and, iii) recovering a plurality of influenza vimses.

39. The method of claim 38, wherein the influenza vimses possess one or more phenotypic attributes selected from the group consisting of: attenuation, temperature sensitivity and cold adaptation.

40. The method of claim 38, wherein the influenza vimses comprise an attenuated, cold adapted, temperature sensitive influenza vims.

41. The method of claim 38, wherein the influenza vims is suitable for administration in an intranasal vaccine formulation.

42. The method of claim 38, comprising introducing a plurality of vectors comprising an influenza B vims.

43. The method of claim 38, comprising introducing a plurality of vectors comprising an influenza A vims.

44. The method of claim 38, comprising culturing the population of host cells at a temperature less than or equal to 35 °C.

45. The method of claim 38, comprising culturing the Vero cells in semm free medium.

46. A method for producing a recombinant influenza vims vaccine, the method comprising: i) introducing a plurality of vectors comprising an influenza vims genome into a population of host cells, which population of host cells is capable of supporting replication of influenza vims; ii) culturing the host cell at a temperature less than or equal to 35 °C; and, iii) recovering an influenza vims capable of eliciting an immune response upon administration to a subject.

47. The method of claim 46, wherein the influenza vims possesses at least one phenotypic attribute selected from the group consisting of: temperature sensitivity, cold adaptation and attenuation.

48. The method of claim 46, comprising introducing a plurality of vectors comprising an influenza B vims.

49. The method of claim 46, comprising introducing a plurality of vectors comprising an influenza A vims.

50. The method of claim 46, the recombinant influenza virus vaccine comprising a reassortant influenza vims.

51. The method of claim 46, wherein the influenza vims vaccine comprises a live attenuated influenza virus vaccine.

52. The method of claim 46, further comprising inactivating the influenza vims.

53. An influenza vims vaccine produced by the method of claim 46.

54. A bi-directional expression vector comprising: a plasmid comprising a comprising a first promoter inserted between a second promoter and a bi-directional polyadenylation site.

55. The vector of claim 54, wherein the first promoter and the second promoter are situated in opposite orientations flanking at least one cloning site.

56. The vector of claim 54, wherein the bi-directional polyadenylation site comprises an SV40 polyadenylation site.

57. The vector of claim 54, comprising pAD3000.

58. The vector of claim 54, further comprising a double stranded nucleic acid comprising at least one segment of an influenza vims genome inserted into the cloning site.

59. The vector of claim 1, wherein the first and second promoters are operably linked to alternative strands of the same double stranded viral nucleic acid comprising a segment of the influenza vims genome.

60. The bi-directional expression vector of claim 54, the vector comprising: a plasmid comprising a comprising a first promoter inserted between a second promoter and an SV40 polyadenylation site; wherein the first promoter and the second promoter are situated in opposite orientations flanking at least one segment of an influenza vims.

61. A kit comprising one or more expression vectors of claim 54, and one or more of: a cell, a buffer, a culture medium, an instmction set, a packaging material, and a container.

62. The kit of claim 61, comprising a plurality of expression vectors each comprising at least one segment of an influenza vims genome.

63. The kit of claim 62, comprising a plurality of expression vectors comprising at least 6 internal genome segments of a first influenza strain, which influenza strain possesses at least one phenotypic attribute selected from the group consisting of: temperature sensitivity, cold adaptation and attenuation.

64. The kit of claim 62, wherein the plurality of expression vectors comprises a library of nucleic acids encoding variant HA and/or NA antigens.

65. A composition comprising: a productively growing cell culture comprising at least one cell, which at least one cell comprises a plurality of vectors, which plurality of vectors comprises an influenza vims genome, at a temperature less than or equal to 35 °C.

66. The composition of claim 65, further comprising a cell culture medium.

67. The composition of claim 65, wherein the plurality of vectors comprise bi- directional expression vectors.

68. The composition of claim 67, the bi-directional expression vectors comprising a first promoter inserted between a second promoter and a SV40 polyadenylation site; wherein the first promoter and the second promoter are situated in opposite orientations flanking at least one segment of an influenza vims.

69. A cell culture system comprising: a productively growing cell culture comprising at least one cell, which at least one cell comprises a plurality of vectors, which plurality of vectors comprises an influenza vims genome; and, a regulator for maintaining the culture at a temperature less than or equal to

35 °C.

70. The cell culture system of claim 69, further comprising a cell culture medium.

71. The cell culture system of claim 69, wherein the plurality of vectors comprise bidirectional expression vectors.

72. The cell culture system of claim 69, the bi-directional expression vectors comprising a first promoter inserted between a second promoter and a SV40 polyadenylation site; wherein the first promoter and the second promoter are situated in opposite orientations flanking at least one segment of an influenza vims.

73. An artificially engineered recombinant or reassortant influenza virus comprising an influenza A vims comprising one or more amino acid substitutions at a position selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ or an influenza B vims comprising one or more amino acid substitutions at a position selected from the group consisting of: PB2⁶³⁰; PA⁴³¹; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³.

74. The influenza vims of claim 73, wherein the influenza A vims comprises one or more amino acid substitutions selected from the group consisting of: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G) or wherein the influenza B vims comprises one or more amino acid substitutions selected from the group consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V).

75. The influenza A vims of claim 73, comprising a plurality of amino acid substitutions selected from the group consisting of PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G).

76. The influenza A vims of claim 73, comprising a plurality of amino acid substitutions consisting of PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G).

77. The influenza B vims of claim 73, comprising a plurality of amino acid substitutions selected from the group consisting of PB2⁶³⁰ (S630R); PA⁴³¹ (V43 IM); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V).

78. The influenza B vims of claim 73, comprising a plurality of amino acid substitutions consisting of PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (Ml 83 V).

79. The influenza A vims of claim 73, comprising a PR8 strain influenza A vims.

80. The influenza vims of claim 73, wherein the influenza vims possesses one or more phenotypic attributes selected from the group consisting of: temperature sensitivity, cold adaptation and attenuation.

81. The influenza vims of claim 73, further comprising at least one additional non wild-type amino acid.

82. The influenza vims of claim 73, wherein the influenza vims exhibits at least a 3.0 log₅o reduction in replication in a feπet attenuation assay.

83. The influenza virus of claim 73, wherein the influenza vims exhibits undetectable replication in a feπet attenuation assay.

84. A method of producing a temperature sensitive (ts) influenza vims, the method comprising:

(a) introducing at least one mutation resulting in an amino acid substitution at a position selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and

NP³⁴ into an influenza A vims genome or introducing at least one mutation resulting in an amino acid substitution at a position selected from the group consisting of: PB2⁶³⁰; PA⁴ ; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³ into an influenza B vims genome; and

(b) replicating the mutated influenza vims genome under conditions whereby vims is produced.

85. The method of claim 84, wherein the influenza vims A genome comprises a PR8 genome.

86. The method of claim 84, comprising introducing at least one mutation encoding a substituted amino acid selected from the group consisting of: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G) into an influenza A vims genome or introducing at least one mutation encoding a substituted amino acid selected from the group consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V) into an influenza B vims genome.

87. The method of claim 84, comprising introducing a plurality of mutations encoding a substituted amino acid selected from the group consisting of: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G) into an influenza A vims genome or introducing a plurality of mutations encoding a substituted amino acid selected from the group consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (Ml 83V) into an influenza B virus genome.

88. The method of claim 84, comprising introducing mutations resulting in a plurality of amino acid substitutions consisting of: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G) into an influenza A vims genome or introducing a plurality of amino acid substitutions consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V) into an influenza B vims genome.

89. The method of claim 84, comprising replicating the mutated influenza vims genome in hens'eggs.

90. The method of claim 84, comprising replicating the mutated influenza A vims genome in cell culture.

91. The method of claim 90, further comprising amplifying the virus in hens' eggs.

92. The method of claim 90, comprising culturing the cells at a temperature at less than or equal to 35 °C.

93. The method of claim 90, wherein the cell culture comprises one or more of Vero cells, MDCK cells, 293T cells and COS cells.

94. A method of producing a live attenuated influenza vims vaccine, the method comprising: (a) introducing at least one mutation resulting in an amino acid substitution selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴ into an influenza A vims genome or introducing at least one mutation resulting in an amino acid substitution selected from the group consisting of: PB2⁶³⁰, PA⁴³¹, PA⁴⁹⁷, NP⁵⁵, NP¹¹⁴, NP⁴¹⁰, NP⁵¹⁰, Ml¹⁵⁹ and Ml¹⁸³ into an influenza B vims genome; (b) replicating the mutated influenza virus genome under conditions whereby vimses are produced; and,

(c) recovering the influenza vimses.

95. The method of claim 94, wherein the influenza vims comprises genomic segments encoding the HA and NA antigens derived from at least a second strain of vims.

96. The method of claim 95, wherein the HA and NA antigens are capable of eliciting a protective immune response against at least one strain of influenza vims.

97. An artificially engineered recombinant or reassortant temperature sensitive (ts) influenza A vims comprising at least one introduced amino acid substitution selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴.

98. The ts influenza A vims of claim 97, comprising at least one introduced amino acid substitutions selected from the group consisting of PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G).

99. The ts influenza A vims of claim 97, comprising a plurality of introduced amino acid substitutions selected from the group consisting of PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G).

100. The ts influenza A vims of claim 97, comprising a plurality of introduced amino acid substitutions consisting of: PBl³⁹¹ (K391E), PBl⁵⁸¹ (E581G), PBl⁶⁶¹ (A661T), PB2²⁶⁵ (N265S) and NP³⁴ (D34G).

101. The ts influenza A vims of claim 97, wherein the temperature sensitive influenza A vims exhibits between about 2.0 and about 5.0 logio reduction in growth at 39 °C as compared to a wild type influenza A vims.

102. The ts influenza A virus of claim 101, wherein the temperature sensitive influenza A vims exhibits a logio reduction in growth at 39 °C selected from the group consisting of: at least about 2.0 logio, at least about 3.0 logio, at least about 4.0 logio, and at least about 4.5 logio.

103. The ts influenza A virus of claim 97, wherein the influenza A exhibits between about a 2.0 and a 5.0 logio reduction in growth in a ferret attenuation assay as compared to a wild type influenza A vims.

104. The ts influenza A vims of claim 103, wherein the reduction in growth in a ferret attenuation assay is selected from the group consisting of: at least about 2.0 logio, at least about 3.0 logio, and at least about 4.0 logio-

105. The reassortant ts influenza A vims of claim 97, comprising one or more genomic segments encoding at least one of the HA or NA antigen derived from a second strain of

Influenza A vims.

106. A recombinant or reassortant influenza A vaccine comprising an influenza A vims or an influenza A viral protein comprising a plurality of introduced amino acid substitutions selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴.

107. A recombinant or isolated nucleic acid comprising a polynucleotide sequence encoding an influenza A polypeptide comprising one or more introduced amino acid substitutions at a position selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴.

108. A recombinant or isolated Influenza A polypeptide comprising a one or more introduced amino acid substitutions at a position selected from the group consisting of: PBl³⁹¹, PBl⁵⁸¹, PBl⁶⁶¹, PB2²⁶⁵ and NP³⁴.

109. An artificially engineered recombinant or reassortant temperature sensitive (ts) influenza B virus comprising at least one introduced amino acid substitution selected from the group consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V).

110. The ts influenza B vims of claim 109, comprising at least one introduced amino acid substitution selected from the group consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V).

111. The ts influenza B vims of claim 109, comprising a plurality of introduced amino acid substitutions selected from the group consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (M183V).

112. The ts influenza B virus of claim 109, comprising a plurality of introduced amino acid substitutions consisting of: PB2⁶³⁰ (S630R); PA⁴³¹ (V431M); PA⁴⁹⁷ (Y497H); NP⁵⁵ (T55A); NP¹¹⁴ (V114A); NP⁴¹⁰ (P410H); NP⁵¹⁰ (A510T); Ml¹⁵⁹ (H159Q) and Ml¹⁸³ (Ml 83V).

113. The ts influenza B vims of claim 109, wherein the temperature sensitive influenza A virus exhibits between about 2.0 and about 5.0 logio reduction in growth at 39 °C as compared to a wild type influenza B vims.

114. The ts influenza B vims of claim 113, wherein the temperature sensitive influenza B vims exhibits a logio reduction in growth at 39 °C selected from the group consisting of: at least about 2.0 logio, at least about 3.0 logio, at least about 4.0 logio, and at least about 4.5 logio.

115. The ts influenza B virus of claim 109, wherein the influenza B exhibits between about a 2.0 and a 5.0 logio reduction in growth in a feπet attenuation assay as compared to a wild type influenza B virus.

116. The ts influenza B vims of claim 117, wherein the reduction in growth in a feπet attenuation assay is selected from the group consisting of: at least about 2.0 logio, at least about 3.0 logio, and at least about 4.0 logio.

117. The reassortant ts influenza B vims of claim 109, comprising one or more genomic segments encoding at least one of the HA or NA antigen derived from a second strain of Influenza B vims.

118. A recombinant or reassortant influenza B vaccine comprising an influenza B virus or an influenza B viral protein comprising a plurality of introduced amino acid substitutions selected from the group consisting of: PB2⁶³⁰; PA⁴³¹; PA⁴⁹⁷; NP⁵⁵; NP¹¹⁴; NP ¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³.

119. A recombinant or isolated nucleic acid comprising a polynucleotide sequence encoding an influenza B polypeptide comprising one or more introduced amino acid substitutions at a position selected from the group consisting of: PB2 ³⁰; PA⁴³¹; PA^{4 7}; NP⁵⁵; NP¹¹⁴; NP⁴¹⁰; NP⁵¹⁰; Ml¹⁵⁹ and Ml¹⁸³.

120. A recombinant or isolated Influenza B polypeptide comprising one or more introduced amino acid substitutions selected from the group consisting of: PB2⁶³⁰, PA⁴³¹, NP -,55 NF 11"4 NF -,41^,0^U, NP -,510 Ml¹⁵⁹ and Ml¹⁸³.