Compositions and methods involving respiratory syncytial virus subgroup B strain 9320

FIELD OF THE INVENTION

[0002] The present invention is in the field of virology. More specifically, the invention relates to human respiratory syncytial virus, including the diagnosis, treatment, and prevention of human RSV infections.

BACKGROUND OF THE INVENTION

[0003] Human Respiratory Syncytial Virus (RSV) is the leading cause of hospitalization for viral respiratory tract disease (e.g., bronchiolitis and pneumonia) in infants and young children worldwide, as well as a significant source of morbidity and mortality in immunocompromised adults and in the elderly (see, e.g., Shay et al. (1999) “Bronchiolitis-associated hospitalizations among U.S. children, 1980-1996” JAMA 282:1440-1446, Falsey et al. (1995) “Respiratory syncytial virus and influenza A infections in the hospitalized elderly” J Infect Dis 172:389-394, Falsey et al. (1992) “Viral respiratory infections in the institutionalized elderly: clinical and epidemiologic findings” J Am Geriatr Soc 40:115-119, Falsey and Walsh (1998) “Relationship of serum antibody to risk of respiratory syncytial virus infection in elderly adults” J Infect Dis 177:463-466, Hall et al. (1986) “Respiratory syncytial viral infection in children with compromised immune function” N Engl J Med 315:77-81, and Harrington et al. (1992) “An outbreak of respiratory syncytial virus in a bone marrow transplant center” J Infect Dis 165:987-993). To date, no vaccines have been approved which are able to prevent the diseases associated with RSV infection. RSV is an enveloped virus that has a single-stranded negative sense non-segmented RNA genome, and it is classified in the Pneumovirus genus of the Paramyxoviridae family (Collins et al. (2001) Respiratory syncytial virus. pp. 1443-1485. In; Knipe and Howley (eds.) Fields Virology vol. 1. Lippincott, Williams and Wilkins, Philadelphia; Lamb and Kolakofsky (2001) Paramyxoviridae: the viruses and their replication pp. 1305-1340. In; Knipe and Howley (eds.) Fields Virology vol. 1. Lippincott, Williams and Wilkins, Philadelphia). Human RSV is classified into two subgroups, subgroups A and B, based on antigenic diversity and nucleotide sequence divergence. For example, the attachment protein G is most divergent and the fusion protein F is relatively conserved between the two subgroups.

[0004] Considerable progress has been made towards understanding the molecular biology of subgroup A RSV; however, much less information is available for subgroup B RSV. Most work to date has focused on subgroup A strains. For example, RSV strain A2 has been sequenced. The genome of the A2 strain RSV is 15,222 nt in length and contains 10 transcriptional units that encode 11 proteins (NS1, NS2, N, P, M, SH, G, F, M2-1, M2-2, and L). The genome is tightly bound by the N protein to form the nucleocapsid, which is the template for the viral RNA polymerase comprising the N, P and L proteins (Grosfeld et al. (1995) J. Virol. 69:5677-5686; Yu et al. (1995) J. Virol. 69:2412-2419). Each transcription unit is flanked by a highly conserved 10-nt gene-start (GS) signal, at which mRNA synthesis begins, and ends with a semiconserved 12- to 13-nt gene-end (GE) signal that directs polyadenylation and release of mRNAs (Harmon et al. (2001) J. Virol. 75:36-44; Kuo et al. (1996) J. Virol. 70:6892-6901). Transcription of RSV genes is sequential, and there is a gradient of decreasing mRNA synthesis due to transcription attenuation (Barik (1992) J. Virol. 66:6813-6818; Dickens et al. (1984) J. Virol. 52:364-369). The viral RNA polymerase must first terminate synthesis of the upstream message in order to initiate synthesis of the downstream mRNA.

[0005] The nucleocapsid protein (N), phosphoprotein (P), and large polymerase protein (L) constitute the minimal components for viral RNA replication and transcription in vitro (Grosfield et al. (1995) J. Virol. 69:5677-5686; Yu et al. (1995) J. Virol. 69:2412-2419). The N protein associates with the genomic RNA to form the nucleocapsid, which serves as the template for RNA synthesis. The L protein is a multifunctional protein that contains RNA-dependent RNA polymerase catalytic motifs and is also probably responsible for capping and polyadenylation of viral mRNAs. However, the L protein alone is not sufficient for the polymerase function; the P protein is also required. Transcription and replication of RSV RNA are also modulated by the M2-1, M2-2, NS1, and NS2 proteins that are unique to the pneumoviruses. M2-1 is a transcription antitermination (or elongation) factor required for processive RNA synthesis and transcription read-through at gene junctions, essential for RNA transcription and virus replication (Collins et al. (1996) “Transcription elongation factor of respiratory syncytial virus, a nonsegmented negative-strand RNA virus” Proc Natl Acad Sci USA 93:81-85; Hardy and Wertz (2000) “The Cys3-His1 motif of the respiratory syncytial virus M2-1 protein is essential for protein function” J Virol 74:5880-5885; Tang et al. (2001) “Requirement of cysteines and length of the human respiratory syncytial virus M2-1 protein for protein function and virus viability” J Virol 75:11328-11335; Collins et al. (2001) in D. M. Knipe et al. (eds.), Fields Virology, 4th ed. Lippincott, Philadelphia; Hardy et al. (1999) J. Virol. 73:170-176; and Hardy andWertz (1998) J. Virol. 72:520-526). M2-2, though not essential for virus replication in tissue culture, is involved in the switch between viral RNA transcription and replication (Bermingham and Collins (1999) Proc. Natl. Acad. Sci. USA 96:11259-11264; Jin et al. (2000) J. Virol. 74:74-82). NS1 and NS2 have been shown to inhibit minigenome synthesis in vitro (Atreya et al. (1998) J. Virol. 72:1452-1461).

[0006] NS1, NS2, SH, M2-2 and G are accessory proteins that can be deleted from the RSV A2 strain without affecting virus viability (Bermingham and Collins (1999) Proc. Natl. Acad. Sci. USA 96:11259-11264; Jin et al. (2000) J. Virol. 74:74-82; Jin et al. (2000) “Recombinant respiratory syncytial viruses with deletions in the NS1, NS2, SH, and M2-2 genes are attenuated in vitro and in vivo” Virology 273:210-218; Bukreyev et al. (1997) “Recombinant respiratory syncytial virus from which the entire SH gene has been deleted grows efficiently in cell culture and exhibits site- specific attenuation in the respiratory tract of the mouse” J Virol 71:8973-8982; Teng and Collins (1999) “Altered growth characteristics of recombinant respiratory syncytial viruses which do not produce NS2 protein” J Virol 73:466-473; Teng et al. (2000) “Recombinant respiratory syncytial virus that does not express the NS1 or M2-2 protein is highly attenuated and immunogenic in chimpanzees” J Virol 74:9317-9321; Karron et al. (1997) “Respiratory syncytial virus (RSV) SH and G proteins are not essential for viral replication in vitro: clinical evaluation and molecular characterization of a cold-passaged, attenuated RSV subgroup B mutant” Proc Natl Acad Sci USA 94:13961-13966). However, except for the SH deletion mutant, most of the gene deletion mutants do not replicate as well as the wild type RSV either in tissue culture or in animal hosts.

[0007] The G and F proteins are the two major surface antigens that elicit anti-RSV neutralizing antibodies to provide protective immunity against RSV infection and reinfection. High levels of circulating antibodies correlate with protection against RSV infections or reduction of disease severity (Crowe (1999) Microbiol. Immunol. 236:191-214). As noted, two antigenic RSV subgroups (A and B) have been recognized based on virus antigenic and sequence divergence (Anderson et al. (1985) J. Infect. Dis. 151:626-633; Mufson et al. (1985) J. Gen. Virol. 66:2111-2124). By using a reciprocal cross-neutralization assay, it has been determined that the F proteins between the two subgroups are 50% related and the G proteins are only 1-7% related (reviewed by Collins et al. (2001) “Respiratory syncytial virus” In: D. M. Knipe et al. (Ed) Fields Virology, pp. 1443-1485, Vol. 1, Lippincott Williams & Wilkins, Philadelphia). This antigenic diversity may be partly responsible for repeated RSV infection. The antigenic diversity of these two RSV subgroups enables viruses from both subgroups to circulate concurrently in a community, and the prevalence of each subgroup can alternate during successive years. Epidemic studies of RSV infection in children have suggested that naturally acquired infection elicits a relatively higher protection against disease caused by the homologous subgroup virus (McIntosh and Chanock (1990) “Respiratory syncytial virus” In: D. M. Knipe et al. (Ed) Second Edition Virology, pp.1045-1072, Raven Press, Ltd., New York). The immunity induced by RSV infection is transient and subsequent reinfection can occur. However, RSV reinfection usually does not cause severe disease. An RSV vaccine is therefore typically targeted to provide protection against severe lower respiratory disease caused by RSV subgroup A and B viruses.

[0008] Efforts to produce a safe and effective RSV vaccine have focused on the administration of purified viral antigen or the development of live attenuated RSV for intranasal administration. For example, a formalin-inactivated virus vaccine not only failed to provide protection against RSV infection, but was shown to exacerbate symptoms during subsequent infection by the wild-type virus in infants (Kapikian et al. (1969) Am. J. Epidemiol. 89:405-421; Chin et al. (1969) Am. J. Epidemiol. 89:449-63). More recently, efforts have been aimed towards developing live attenuated temperature-sensitive mutants by chemical mutagenesis or cold passage of the wild-type RSV (Crowe et al. (1994) Vaccine 12:691-9). Typically, the virus candidates have been either underattenuated or overattenuated (Kim et al. (1973) Pediatrics 52:56-63; Wright et al. (1976) J. Pediatrics 88:931-6), and some of the candidates were genetically unstable, resulting in the loss of the attenuated phenotype (Hodges et al. (1974) Proc Soc. Exp. Bio. Med. 145:1158-64). To date, no live attenuated vaccine has been brought to market.

[0009] Characterization of additional strains of RSV, particularly from subgroup B, will assist in production of effective vaccines (e.g., regions of homology or identity between strains can indicate functionally conserved regions that can be targeted by mutagenesis). Although short regions of various subgroup B strains have been sequenced (e.g., B9320 protein G, SEQ ID NO: 14, from GenBank accession number M73544; a B9320 intergenic region, SEQ ID NO: 15, from GenBank accession number S75820; B9320 G and F gene start and end sequences, SEQ ID NOs:16-19, from Jin et al. (1998) Virology 251:206-214 and Cheng et al. (2001) Virology 283:59-68; and various B18537 coding and intergenic regions, GenBank accession numbers D00334, D00392-D00397, D00736, D01042, and M17213), only one subgroup B strain, strain B1, has been sequenced in its entirety (SEQ ID NO: 13, from GenBank accession number AF013254).

[0010] Accordingly, this invention presents the complete polynucleotide sequence of human RSV subgroup B strain 9320. Polypeptides encoded by the B9320 genome are also provided, as are other benefits which will become apparent upon review of the disclosure.

SUMMARY OF THE INVENTION

[0011] The present invention provides the complete polynucleotide sequence of human respiratory syncytial virus subgroup B strain 9320. Amino acid sequences of proteins encoded by the B9320 genome are also provided. The invention provides isolated or recombinant nucleic acids and polypeptides comprising the novel B9320 sequences. Isolated or recombinant RSV comprising the nucleic acids and polypeptides of the invention (e.g., attenuated recombinant RSV) are also provided, as are immunogenic compositions including such nucleic acids, polypeptides, and RSV that are suitable for use as vaccines. Recovery of infectious recombinant 9320 viruses from cDNAs is described.

[0012] In a first aspect, the present invention provides isolated or recombinant nucleic acids comprising a polynucleotide sequence of the invention. Thus, for example, an isolated or recombinant nucleic acid comprising the polynucleotide sequence of SEQ ID NO:1 or a complementary polynucleotide sequence thereof is a favored embodiment of the invention. An isolated or recombinant nucleic acid comprising at least one unique polynucleotide subsequence of SEQ ID NO:1 or a complementary polynucleotide sequence thereof, with the proviso that the unique polynucleotide subsequence includes at least one subsequence not included in SEQ ID NOs:14-19 or a complementary polynucleotide sequence thereof, is another favored embodiment. The unique polynucleotide subsequence can, for example, comprise at least 10 contiguous nucleotides of SEQ ID NO:1 or a complementary polynucleotide sequence thereof (e.g., at least 20 contiguous nucleotides, at least 50 contiguous nucleotides, at least 100 contiguous nucleotides, at least 500 contiguous nucleotides, or even at least 1000 contiguous nucleotides). In some embodiments, the polynucleotide subsequence includes at least one compete open reading frame (ORF) of SEQ ID NO:1.

[0013] In addition to the sequences explicitly provided in the accompanying sequence listing, polynucleotide sequences that are highly related structurally and/or functionally (e.g., as defined by hybridization and/or sequence identity) are polynucleotides of the invention. For example, a polynucleotide sequence that is greater than 97.8% identical to SEQ ID NO:1 or a complementary polynucleotide sequence thereof, as determined by BLASTN using default parameters, is a polynucleotide of the invention. As another example, a polynucleotide sequence that hybridizes under stringent conditions over substantially the entire length of a polynucleotide subsequence comprising at least 100 contiguous nucleotides of SEQ ID NO:1 or a complementary polynucleotide sequence thereof, wherein the polynucleotide sequence hybridizes to the polynucleotide subsequence of SEQ ID NO:1 or the complementary polynucleotide sequence thereof under said stringent conditions with at least 2× a signal to noise ratio that the polynucleotide sequence hybridizes to a corresponding polynucleotide subsequence of SEQ ID NO:13 or a complementary polynucleotide sequence thereof, is a polynucleotide sequence of the invention. Similarly, polynucleotide sequences of the invention include a polynucleotide sequence encoding a polypeptide of the invention, e.g., encoding an amino acid sequence or unique subsequence selected from the group consisting of SEQ ID NOs:2-11 or an artificial conservative variation thereof.

[0014] A nucleic acid of the invention optionally comprises at least one artificially mutated nucleotide, e.g., at least one artificially deleted, inserted, and/or substituted nucleotide. In certain embodiments, mutation of the polynucleotide sequence results in alteration of an encoded amino acid sequence. Thus, in one class of embodiments, at least one polypeptide encoded by the nucleic acid comprises at least one deleted, inserted, and/or substituted amino acid residue (e.g., at least one conservatively or non-conservatively substituted amino acid residue). For example, the mutated nucleotide can be located in an ORF encoding a polypeptide selected from SEQ ID NOs:2-12.

[0015] Another class of embodiments provides vectors comprising the nucleic acids of the invention. Yet another class of embodiments provides a host cell into which such a vector has been introduced. Another class of embodiments provides methods of producing a recombinant respiratory syncytial virus. In the methods, such a host cell is cultured in a suitable culture medium under conditions permitting expression of the nucleic acid, and the recombinant respiratory syncytial virus is isolated from the host cell and/or the medium. Recombinant RSV produced according to these methods form another feature of the invention, as do recombinant RSV comprising a nucleic acid of the invention. A related class of embodiments provides methods of producing an isolated or recombinant polypeptide. In the methods, a host cell comprising a vector that includes a nucleic acid of the invention is cultured in a suitable culture medium under conditions permitting expression of the nucleic acid, and the polypeptide is isolated from the host cell and/or the medium. Polypeptides produced according to these methods form another feature of the invention, as do polypeptides comprising an amino acid sequence or subsequence that is encoded by a nucleic acid of the invention.

[0016] One aspect of the invention provides isolated or recombinant polypeptides comprising an amino acid sequence of the invention. Thus, for example, an isolated or recombinant polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:2-11 is a favored embodiment of the invention. An isolated or recombinant polypeptide comprising a unique amino acid subsequence comprising at least 7 (e.g., at least 8, at least 10, at least 20, at least 50, or more) contiguous amino acid residues of any one of SEQ ID NOs:2-11 is another favored embodiment. Artificial conservative variations of amino acid sequences or subsequences of the invention are also amino acid sequences of the invention, as are amino acid sequences that are substantially identical to an amino acid sequence of the invention. For example, an amino acid sequence that is greater than 99.3% identical to SEQ ID NO:2, greater than 98.4% identical to SEQ ID NO:3, greater than 99.7% identical to SEQ ID NO:4, greater than 98.3% identical to SEQ ID NO:5, greater than 99.6% identical to SEQ ID NO:6, greater than 97.0% identical to SEQ ID NO:7, greater than 99.3% identical to SEQ ID NO:8, greater than 99.5% identical to SEQ ID NO:9, greater than 96.4% identical to SEQ ID NO:10, or greater than 99.2% identical to SEQ ID NO:11, as determined by BLASTP using default parameters, is an amino acid sequence of the invention. Similarly, an amino acid sequence or subsequence that is specifically bound by an antibody that specifically binds to an amino acid sequence or subsequence encoded by SEQ ID NO:1, wherein said antibody does not specifically bind to an amino acid sequence or subsequence encoded by SEQ ID NO:13 or SEQ ID NO:14, is an amino acid sequence of the invention.

[0017] A polypeptide of the invention optionally comprises at least one artificially altered amino acid, e.g., at least one deleted, inserted, and/or substituted amino acid. For example, one class of embodiments provides an isolated or recombinant polypeptide comprising the amino acid sequence of SEQ ID NO:12 with a deletion of residues 164-197, or an artificial conservative variation thereof.

[0018] Immunogenic compositions comprising an immunologically effective amount of a recombinant respiratory syncytial virus, polypeptide, and/or nucleic acid of the invention form another aspect of the invention. Similarly, another feature of the invention provides methods for stimulating the immune system of an individual to produce a protective immune response against respiratory syncytial virus. In the methods, an immunologically effective amount of a respiratory syncytial virus, polypeptide, and/or nucleic acid of the invention is administered to the individual in a physiologically acceptable carrier.

BRIEF DESCRIPTION OF THE DRAWINGS

[0019]
FIG. 1 schematically illustrates assembly of the full-length antigenomic RSV 9320 cDNA. Positions of various subclones used to assemble the full length antigenomic cDNA are indicated. The cDNA fragments obtained by RT/PCR were ligated through the indicated restriction enzyme sites. The fourth residue of the leader sequence at the antigenomic sense was either C or G as indicated.

[0020]
FIG. 2 schematically illustrates the cloning of pB-L, the assembly of the L coding region from three subclones. Positions of various subclones and primers used to assemble pB-L are indicated.

[0021]
FIG. 3 schematically illustrates cloning of the 5′ portion of the RSV 9320 antigenome. Positions of various subclones and primers are indicated.

[0022]
FIG. 4 presents line graphs illustrating the growth of wild type 9320 (diamonds), rg9320C4 (squares), rg9320G4(triangles), and rg9320ΔG (circles) in Vero cells (Panel A) and HEp-2 cells (Panel B). Vero or BEp-2 cells were infected with each virus at an m.o.i of 0.1 and incubated at 35° C. for 5 days. The viruses released into the culture supernatants at each day were titrated in Vero cells by plaque assay.

DEFINITIONS

[0023] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. The following definitions supplement those in the art and are directed to the current application and are not to be imputed to any related or unrelated case, e.g., to any commonly owned patent or application. Although any methods and materials similar or equivalent to those described herein can be used in the practice for testing of the present invention, the preferred materials and methods are described herein. Accordingly, the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.

[0024] As used in this specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a virus” includes a plurality of viruses; reference to “a host cell” includes mixtures of host cells, and the like.

[0025] An “amino acid sequence” is a polymer of amino acid residues (a protein, polypeptide, etc.) or a character string representing an amino acid polymer, depending on context.

[0026] A “polynucleotide sequence” or “nucleotide sequence” is a polymer of nucleotides (an oligonucleotide, a DNA, a nucleic acid, etc.) or a character string representing a nucleotide polymer, depending on context. From any specified polynucleotide sequence, either the given nucleic acid or the complementary polynucleotide sequence (e.g., the complementary nucleic acid) can be determined.

[0027] A “subsequence” is any portion of an entire sequence, up to and including the complete sequence. Typically, a subsequence comprises less than the full-length sequence. A “unique subsequence” is a subsequence that is not found in any previously determined RSV polynucleotide or polypeptide sequence (e.g., the A2, B1, and B18537 sequences listed and/or referenced herein).

[0028] An “artificial mutation” is a mutation introduced by human intervention, e.g., under laboratory conditions. Thus, an “artificially mutated” nucleotide is a nucleotide that has been mutated as a result of human intervention, an “artificially altered” amino acid residue is a residue that has been altered as a result of human intervention, and an “artificial conservative variation” is a conservative variation that has been produced by human intervention. For example, a wild type virus (e.g., one circulating naturally among human hosts) or other parental strain of virus can be “artificially mutated” using recombinant DNA techniques to alter the viral genome (e.g., the viral genome can be altered by in vitro mutagenesis, or by exposing it to a chemical, ionizing radiation, or the like and then performing in vitro or in vivo selection for a temperature sensitive, cold sensitive, or otherwise attenuated strain of virus). As another example, a wild type protein can be “artificially altered” by artificially mutating the gene encoding that protein.

[0029] The term “variant” with respect to a polypeptide refers to an amino acid sequence that is altered by one or more amino acids with respect to a reference sequence. The variant can have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties, e.g., replacement of leucine with isoleucine. Alternatively, a variant can have “nonconservative” changes, e.g., replacement of a glycine with a tryptophan. Analogous minor variation can also include amino acid deletion or insertion, or both. Guidance in determining which amino acid residues can be substituted, inserted, or deleted without eliminating biological or immunological activity can be found using computer programs well known in the art, for example, DNASTAR software. Examples of conservative substitutions are also described below.

[0030] The term “nucleic acid” or “polynucleotide” encompasses any physical string of monomer units that can be corresponded to a string of nucleotides, including a polymer of nucleotides (e.g., a typical DNA or RNA polymer), PNAs, modified oligonucleotides (e.g., oligonucleotides comprising bases that are not typical to biological RNA or DNA in solution, such as 2′-O-methylated oligonucleotides), and the like. A nucleic acid can be e.g., single-stranded or double-stranded. Unless otherwise indicated, a particular nucleic acid sequence of this invention encompasses complementary sequences, in addition to the sequence explicitly indicated.

[0031] 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. 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.

[0032] “Expression of a gene” or “expression of a nucleic acid” means transcription of DNA into RNA (optionally including modification of the RNA, e.g., splicing), translation of RNA into a polypeptide (possibly including subsequent modification of the polypeptide, e.g., posttranslational modification), or both transcription and translation, as indicated by the context.

[0033] The term “vector” refers to the means by which a nucleic acid 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.

[0034] 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.

[0035] 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. 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 HEp-2 cells and Vero cells.

[0036] The term “introduced” when referring to a heterologous or isolated nucleic acid refers to the transfer of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid can be incorporated 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 host cells, including electroporation, calcium phosphate precipitation, lipid mediated transfection (lipofection), etc.

[0037] An “open reading frame” or “ORF” is a possible translational reading frame of DNA or RNA (e.g., of a gene), which is capable of being translated into a polypeptide. That is, the reading frame is not interrupted by stop codons. However, it should be noted that the term ORF does not necessarily indicate that the polynucleotide is, in fact, translated into a polypeptide.

[0038] A “polypeptide” is a polymer comprising two or more amino acid residues (e.g., a peptide or a protein). The polymer can optionally comprise modifications such as glycosylation or the like. The amino acid residues of the polypeptide can be natural or non-natural and can be unsubstituted, unmodified, substituted or modified.

[0039] The term “recombinant” indicates that the material (e.g., a virus, a nucleic acid, or a 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. For example, a “recombinant nucleic acid” is one that is made by recombining nucleic acids, e.g., during cloning, DNA shuffling or other procedures, or by chemical or other mutagenesis; a “recombinant polypeptide” or “recombinant protein” is a polypeptide or protein which is produced by expression of a recombinant nucleic acid; and a “recombinant virus”, e.g., a recombinant respiratory syncytial virus, is produced by the expression of a recombinant nucleic acid.

[0040] The term “isolated” refers to a biological material, such as a virus, 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. An isolated virus, for example, is in an environment (e.g., a cell culture system, or purified from cell culture) other than the native environment of wild-type virus (e.g., the nasopharynx of an infected individual).

[0041] The term “chimeric” or “chimera,” 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. Similarly, the term “chimeric” or “chimera,” when referring to a viral protein, indicates that the protein includes polypeptide components (i.e., amino acid subsequences) derived from more than one parental viral strain or source.

[0042] An RSV “having an attenuated phenotype” or an “attenuated” RSV exhibits a substantially lower degree of virulence as compared to a wild-type virus (e.g., one circulating naturally among human hosts). An attenuated RSV typically exhibits a slower growth rate and/or a reduced level of replication (e.g., a peak titer, e.g., in cell culture, in an animal model of infection, or in a human vacinee's nasopharynx, that is at least about ten fold, preferably at least about one hundred fold, less than that of a wild-type RSV).

[0043] An “immunologically effective amount” of RSV is an amount sufficient to enhance an individual's (e.g., a human's) own immune response against a subsequent exposure to RSV. Levels of induced immunity can be monitored, e.g., by measuring amounts of neutralizing secretory and/or serum antibodies, e.g., by plaque neutralization, complement fixation, enzyme-linked immunosorbent, or microneutralization assay.

[0044] A “protective immune response” against RSV refers to an immune response exhibited by an individual (e.g., a human) that is protective against serious lower respiratory tract disease (e.g., pneumonia and/or bronchiolitis) when the individual is subsequently exposed to and/or infected with wild-type RSV. In some instances, the wild-type (e.g., naturally circulating) RSV can still cause infection, particularly in the upper respiratory tract (e.g., rhinitis), but it can not cause a serious infection. Typically, the protective immune response results in detectable levels of host engendered serum and secretory antibodies that are capable of neutralizing virus of the same strain and/or subgroup (and possibly also of a different, non-vaccine strain and/or subgroup) in vitro and in vivo.

[0045] As used herein, an “antibody” is a protein comprising one or more polypeptides substantially or partially encoded by immunoglobulin genes or fragments of immunoglobulin genes. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. A typical immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kD) and one “heavy” chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (VH) refer to these light and heavy chains respectively. Antibodies exist as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′2, a dimer of Fab which itself is a light chain joined to VH-CH1 by a disulfide bond. The F(ab)′2 may be reduced under mild conditions to break the disulfide linkage in the hinge region thereby converting the (Fab′)2 dimer into a Fab′ monomer. The Fab′ monomer is essentially a Fab with part of the hinge region (see, Fundamental Immunology, W. E. Paul, ed., Raven Press, N.Y. (1999), for a more detailed description of other antibody fragments). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such Fab′ fragments may be synthesized de novo either chemically or by utilizing recombinant DNA methodology. Thus, the term antibody, as used herein, includes antibodies or fragments either produced by the modification of whole antibodies or synthesized de novo using recombinant DNA methodologies. Antibodies include, e.g., polyclonal antibodies, monoclonal antibodies, multiple or single chain antibodies, including single chain Fv (sFv or scFv) antibodies in which a variable heavy and a variable light chain are joined together (directly or through a peptide linker) to form a continuous polypeptide, and humanized or chimeric antibodies.

[0046] An “antigenome” is a polynucleotide that is complementary (typically, perfectly complementary) to a single-stranded viral (e.g., RSV) genome. Since RSV is a negative-sense RNA virus, the genome is the “antisense” strand, and the antigenome is the “sense” strand that corresponds to mRNA.

[0047] A variety of additional terms are defined or otherwise characterized herein.

DETAILED DESCRIPTION

[0048] The present invention provides the complete polynucleotide sequence of human RSV subgroup B strain 9320. The sequence of a B9320 antigenomic cDNA is listed as SEQ ID NO:1. As will be evident, the RSV genome is an RNA with a polynucleotide sequence complementary to that of SEQ ID NO:1.

[0049] The B9320 genome comprises 10 transcriptional units encoding 11 proteins. Amino acid sequences of the proteins are also provided: NS1 is listed as SEQ ID NO:2, NS2 as SEQ ID NO:3, N as SEQ ID NO:4, P as SEQ ID NO:5, M as SEQ ID NO:6, SH as SEQ ID NO:7, G as SEQ ID NO:12, F as SEQ ID NO:8, M2-1 as SEQ ID NO:9, M2-2 as SEQ ID NO:10, and L as SEQ ID NO:11.

[0050] The invention provides isolated or recombinant polynucleotides and polypeptides comprising the novel B9320 sequences. Recombinant RSV comprising the nucleic acids and/or polypeptides (e.g., attenuated recombinant RSV suitable for use in attenuated live viral vaccines) are also provided.

[0051] Polynucleotides of the Invention

[0052] One aspect of the present invention provides isolated or recombinant nucleic acids comprising a polynucleotide sequence of the invention. Polynucleotide sequences of the invention include the polynucleotide sequence represented by SEQ ID NO:1, with the caveat that SEQ ID NOs:14-19, representing limited subsequences of RSV B9320, have been previously described (e.g., in GenBank accession numbers M73544 and S75820; Jin et al. (1998) Virology 251:206-214; and Cheng et al. (2001) Virology 283:59-68). Thus, for example, an isolated or recombinant nucleic acid comprising the polynucleotide sequence of SEQ ID NO:1 or a complementary polynucleotide sequence thereof is a favored embodiment of the invention. An isolated or recombinant nucleic acid comprising at least one unique polynucleotide subsequence of SEQ ID NO:1 (e.g., a unique coding subsequence) or a complementary polynucleotide sequence thereof, with the proviso that the unique polynucleotide subsequence includes at least one subsequence not included in SEQ ID NOs:14-19 or a complementary polynucleotide sequence thereof, is another favored embodiment. The unique polynucleotide subsequence can, for example, comprise at least 10 contiguous nucleotides of SEQ ID NO:1 or a complementary polynucleotide sequence thereof (e.g., at least 20 contiguous nucleotides, at least 50 contiguous nucleotides, at least 100 contiguous nucleotides, at least 500 contiguous nucleotides, or even at least 1000 contiguous nucleotides).

[0053] In addition to the sequences explicitly provided in the accompanying sequence listing, polynucleotide sequences that are highly related structurally and/or functionally are polynucleotides of the invention. Thus, polynucleotide sequences of the invention include a polynucleotide sequence that hybridizes under stringent conditions over substantially the entire length of the polynucleotide sequence of SEQ ID NO:1 (or a complementary sequence thereof) with at least 2× a signal to noise ratio (e.g., at least 5× or at least 10× the signal to noise ratio) that the polynucleotide sequence hybridizes to the polynucleotide sequence of SEQ ID NO:13 or a complementary polynucleotide sequence thereof. Polynucleotide sequences of the invention also include a polynucleotide sequence that hybridizes under stringent conditions over substantially the entire length of a polynucleotide subsequence comprising at least 100 contiguous nucleotides of SEQ ID NO:1 or its complementary sequence (e.g., a unique subsequence) with at least 2× a signal to noise ratio (e.g., at least 5× or at least 10× the signal to noise ratio) that the polynucleotide sequence hybridizes to the corresponding subsequence of SEQ ID NO:13 or a complementary polynucleotide sequence thereof (or, optionally, the corresponding subsequence of a genome of another naturally occurring respiratory syncytial virus or a complementary polynucleotide sequence thereof).

[0054] Similarly, polynucleotide sequences of the invention include a polynucleotide sequence encoding an amino acid sequence or unique subsequence selected from the group consisting of SEQ ID NOs:2-11 or an artificial conservative variation thereof.

[0055] In addition to the polynucleotide sequences of the invention, e.g., listed in SEQ ID NO:1, polynucleotide sequences that are substantially identical to a polynucleotide of the invention can be used in the compositions and methods of the invention. Substantially identical or substantially similar polynucleotide sequences are defined as polynucleotide sequences that are identical, on a nucleotide by nucleotide basis, with at least a subsequence of a reference polynucleotide, e.g., selected from SEQ ID NO:1. Such polynucleotides can include, e.g., insertions, deletions, and substitutions relative to SEQ ID NO:1. For example, isolated or recombinant nucleic acids comprising polynucleotide sequences (or subsequences) having greater than 97.8% sequence identity to SEQ ID NO:1 or a complementary polynucleotide sequence thereof, as determined by BLASTN using default parameters, with the proviso that the polynucleotide sequence includes at least one subsequence not selected from SEQ ID NOs:14-19, are favored embodiments of the invention. For example, the polynucleotide sequences (or subsequences) can be at least 98.5% (e.g., at least 99.0%, at least 99.5%, or more) identical to SEQ ID NO:1 or a complementary polynucleotide sequence thereof.

[0056] The nucleic acids of the invention can be, e.g., single-stranded or double-stranded, and can be, e.g., a DNA (e.g., a cDNA), an RNA, or an artificial nucleic acid (e.g., a peptide nucleic acid). SEQ ID NO:1 presents the DNA sequence of the antigenomic B9320 cDNA; however, it will be understood that the complementary genomic polynucleotide sequence can readily be determined from SEQ ID NO:1 and that U in an RNA sequence corresponds to T in a DNA sequence.

[0057] Nucleic acids of the invention include nucleic acids encoding polypeptides of the invention. In one general class of embodiments, the nucleic acid comprises at least one unique polynucleotide subsequence of SEQ ID NO:1 (or a complementary polynucleotide sequence thereof) encoding at least 20 contiguous amino acid residues of any one of SEQ ID NOs:2-12 (e.g., at least 50, at least 100, at least 200, or more contiguous amino acid residues). In one class of embodiments, the unique polynucleotide subsequence comprises at least one complete ORF, preferably at least one complete ORF encoding a polypeptide selected from among SEQ ID NOs: 2-12. In some embodiments, the nucleic acid comprises a plurality of complete open reading frames.

[0058] A nucleic acid of the invention optionally comprises at least one artificially mutated nucleotide, e.g., at least one artificially deleted, inserted, and/or substituted nucleotide (e.g., in a noncoding region, e.g., a C to G change at the fourth position of the antigenomic sequence, and/or in a coding region). For example, the nucleic acid can comprise a plurality of artificially mutated nucleotides. The artificially mutated nucleotide(s) can be introduced.by site-directed mutagenesis, chemical mutagenesis, or the like.

[0059] In certain embodiments, mutation of the polynucleotide sequence results in alteration of an encoded amino acid sequence. Thus, in one class of embodiments, at least one polypeptide encoded by the nucleic acid comprises at least one deleted, inserted, and/or substituted amino acid residue (e.g., at least one conservatively or non-conservatively substituted amino acid residue). For example, the mutated nucleotide can be located in an ORF encoding a polypeptide selected from SEQ ID NOs:2-12. Thus, in one class of example embodiments, the at least one artificially mutated nucleotide is located in the open reading frame encoding the polypeptide of SEQ ID NO:12. The artificially mutated nucleotide(s) can comprise, e.g., a deletion, e.g., a deletion resulting in a deletion of one or more amino acid residues from the G protein encoded by SEQ ID NO:12 (e.g., a deletion of residues 164-197), or a deletion resulting in a deletion of the open reading frame encoding G. In another class of example embodiments, the at least one artificially mutated nucleotide is located in the open reading frame encoding the polypeptide of SEQ ID NO:10. The artificially mutated nucleotide(s) can comprise, e.g., a deletion, e.g., a deletion resulting in a deletion of one or more amino acid residues from the M2-2 protein encoded by SEQ ID NO:10, or a deletion resulting in a deletion of the open reading frame encoding M2-2. As another example, at least one of the nucleotides encoding amino acid residue 1, amino acid residue 4 and/or amino acid residue 10 of M2-2 can be mutated (e.g., substituted or deleted, e.g., forcing use of the second and/or third start codon and resulting in a deletion of amino acid residues 1-3 or 1-9 of M2-2).

[0060] The nucleic acids of the invention include chimeric nucleic acids, for example, a nucleic acid comprising at least one subsequence of SEQ ID NO:1 or a complementary polynucleotide sequence thereof and at least one polynucleotide subsequence from a different strain of virus. The subsequence of SEQ ID NO:1 is preferably a unique polynucleotide subsequence that comprises at least 10 contiguous nucleotides of SEQ ID NO:1 or its complement and that includes at least one subsequence not included in SEQ ID NOs:14-19 or a complementary polynucleotide sequence thereof. The different strain of virus can be, e.g., a different strain of human RSV (e.g., A2, B1, or the like) or a different species of virus (e.g., another paramyxovirus, e.g., pneumonia virus of mice, bovine RSV, or metapneumovirus). Such chimeric nucleic acids can, for example, encode chimeric proteins and/or chimeric viruses (e.g., for use in vaccines to induce a protective immune response against one or more strains of RSV and/or another virus). For example, in certain embodiments, the nucleic acid comprises at least one complete open reading frame of SEQ ID NO:1 and at least one complete open reading frame of the different strain of virus.

[0061] Another class of embodiments provides vectors comprising the nucleic acids of the invention. Yet another class of embodiments provides a host cell into which such a vector has been introduced.

[0062] Polypeptides of the Invention

[0063] One aspect of the present invention provides RSV B9320 polypeptides and variants thereof, for example, a polypeptide comprising an amino acid sequence or subsequence that is encoded by a nucleic acid of the invention, with the proviso that the amino acid sequence or subsequence is not encoded by SEQ ID NO:14.

[0064] One general class of embodiments provides isolated or recombinant polypeptides comprising an amino acid sequence of the invention. Thus, for example, an isolated or recombinant polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:2-11 is a favored embodiment of the invention. An isolated or recombinant polypeptide comprising a unique amino acid subsequence comprising at least 7 (e.g., at least 8, at least 10, at least 20, at least 50, or more) contiguous amino acid residues of any one of SEQ ID NOs:2-11 is another favored embodiment. Artificial conservative variations of amino acid sequences or subsequences of the invention are also amino acid sequences of the invention. Such polypeptides are optionally immunogenic.

[0065] In addition to the amino acid sequences of the invention, e.g., listed in SEQ ID NOs:2-11, amino acid sequences that are substantially identical to an amino acid sequence of the invention can be used in the compositions and methods of the invention. Substantially identical or substantially similar polypeptide sequences are defined as amino acid sequences that are identical, on an amino acid by amino acid basis, with at least a subsequence of a reference polypeptide, e.g., selected from among SEQ ID NOs:2-11. Such amino acid sequences can include, e.g., insertions, deletions, and substitutions relative to SEQ ID NOs:2-11. For example, an isolated or recombinant polypeptide comprising an amino acid sequence that is greater than 99.3% identical to SEQ ID NO:2, an amino acid sequence that is greater than 98.4% identical to SEQ ID NO:3, an amino acid sequence that is greater than 99.7% identical to SEQ ID NO:4, an amino acid sequence that is greater than 98.3% identical to SEQ ID NO:5, an amino acid sequence that is greater than 99.6% identical to SEQ ID NO:6, an amino acid sequence that is greater than 97.0% identical to SEQ ID NO:7, an amino acid sequence that is greater than 99.3% identical to SEQ ID NO:8, an amino acid sequence that is greater than 99.5% identical to SEQ ID NO:9, an amino acid sequence that is greater than 96.4% identical to SEQ ID NO:10, or an amino acid sequence that is greater than 99.2% identical to SEQ ID NO:11, as determined by BLASTP using default parameters, is a favored embodiment of the invention. For example, the isolated or recombinant polypeptide can comprise an amino acid sequence (or subsequence) that is at least 99.5% identical to SEQ ID NO:2, at least 98.6% identical to SEQ ID NO:3, at least 99.9% identical to SEQ ID NO:4, at least 98.5% identical to SEQ ID NO:5, at least 99.8% identical to SEQ ID NO:6, at least 97.2% identical to SEQ ID NO:7, at least 99.5% identical to SEQ ID NO:8, at least 99.7% identical to SEQ ID NO:9, at least 96.6% identical to SEQ ID NO:10, or at least 99.4% identical to SEQ ID NO:11, as determined by BLASTP using default parameters.

[0066] A polypeptide of the invention optionally comprises at least one artificially altered amino acid, e.g., at least one deleted, inserted, and/or substituted amino acid. For example, the polypeptide can comprise a plurality of artificially altered amino acids.

[0067] One class of embodiments provides an isolated or recombinant polypeptide comprising the amino acid sequence of SEQ ID NO:12 with a deletion of residues 164-197, or an artificial conservative variation thereof.

[0068] Methods of producing isolated or recombinant polypeptides form another aspect of the invention. In the methods, a host cell into which a vector (e.g., an expression vector, e.g., an expression vector comprising one or more ORFs, or a vector comprising an entire viral genome or antigenome) comprising a nucleic acid of the invention has been introduced is cultured in a suitable culture medium under conditions permitting expression of the nucleic acid. The polypeptide is then isolated from the host cell and/or the medium. For example, the polypeptide can be purified from the host cell and/or the medium such that the resulting purified polypeptide is enriched at least 5× as compared to its initial state. Polypeptides produced according to the methods described herein are also features of the invention. Such polypeptides can comprise, e.g., subsequences (e.g., unique subsequences, immunogenic subsequences, etc.) of SEQ ID NOs:2-11 from a few amino acids (e.g., 7 or more, 10 or more, or 20 or more) up to the full length proteins.

[0069] Determining Sequence Relationships

[0070] A variety of methods for determining relationships (e.g., identity, similarity and/or homology) between two or more sequences, such as SEQ ID NO:1 and SEQ ID NO:13, are available and well known in the art. The methods include manual alignment, computer assisted sequence alignment, and combinations thereof. A number of algorithms (which are generally computer implemented) for performing sequence alignment are widely available, or can be produced by one of skill. These methods include, e.g., the local homology algorithm of Smith and Waterman (1981) Adv. Appl. Math. 2:482; the homology alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443; the search for similarity method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. (USA) 85:2444; and/or by computerized implementations of these algorithms (e.g., GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.).

[0071] For example, software for performing sequence identity (and sequence similarity) analysis using the BLAST algorithm is described in Altschul et al. (1990) J. Mol. Biol. 215:403-410. This software is publicly available, e.g., through the National Center for Biotechnology Information on the world wide web at ncbi.nlm.nih.gov. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold. These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP (BLAST Protein) program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see, Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).

[0072] Additionally, the BLAST algorithm performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul (1993) Proc. Nat'l. Acad. Sci. USA 90:5873-5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence (and, therefore, in this context, homologous) if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, or less than about 0.01, and or even less than about 0.001.

[0073] Another example of a useful sequence alignment algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng and Doolittle (1987) J. Mol. Evol. 35:351-360. The method used is similar to the method described by Higgins and Sharp (1989) CABIOS 5:151-153. The program can align, e.g., up to 300 sequences of a maximum length of 5,000 letters. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster can then be aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences can be aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program can also be used to plot a dendogram or tree representation of clustering relationships. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison.

[0074] An additional example of an algorithm that is suitable for multiple DNA, or amino acid, sequence alignments is the CLUSTALW program (Thompson, J. D. et al. (1994) Nucl. Acids. Res. 22: 4673-4680). CLUSTALW performs multiple pairwise comparisons between groups of sequences and assembles them into a multiple alignment based on homology. Gap open and Gap extension penalties can be, e.g., 10 and 0.05 respectively. For amino acid alignments, the BLOSUM algorithm can be used as a protein weight matrix. See, e.g., Henikoff and Henikoff (1992) Proc. Natl. Acad. Sci. USA 89: 10915-10919.

[0075] Nucleic Acid Hybridization

[0076] Similarity between nucleic acids can also be evaluated by “hybridization” between single stranded (or single stranded regions of) nucleic acids with complementary or partially complementary polynucleotide sequences. Hybridization is a measure of the physical association between nucleic acids, typically, in solution, or with one of the nucleic acid strands immobilized on a solid support, e.g., a membrane, a bead, a chip, a filter, etc. Nucleic acid hybridization occurs based on a variety of well characterized physico-chemical forces, such as hydrogen bonding, solvent exclusion, base stacking and the like. Numerous protocols for nucleic acid hybridization are well known in the art. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biologv—Hvbridization with Nucleic Acid Probes, part I, chapter 2, “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” (Elsevier, N.Y.), as well as in Ausubel et al. Current Protocols in Molecular Biology (supplemented through 2003) John Wiley & Sons, New York (“Ausubel”); Sambrook et al. Molecular Cloning—A Laboratory Manual (3rd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2001 (“Sambrook”), and Berger and Kimmel Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif. (“Berger”). Hames and Higgins (1995) Gene Probes 1, IRL Press at Oxford University Press, Oxford, England (Hames and Higgins 1) and Hames and Higgins (1995) Gene Probes 2, IRL Press at Oxford University Press, Oxford, England (Hames and Higgins 2) provide details on the synthesis, labeling, detection and quantification of DNA and RNA, including oligonucleotides.

[0077] Conditions suitable for obtaining hybridization, including differential hybridization, are selected according to the theoretical melting temperature (Tm) between complementary and partially complementary nucleic acids. Under a given set of conditions, e.g., solvent composition, ionic strength, etc., the Tm is the temperature at which the duplex between the hybridizing nucleic acid strands is 50% denatured. That is, the Tm corresponds to the temperature corresponding to the midpoint in transition from helix to random coil; it depends on length, nucleotide composition, and ionic strength for long,stretches of nucleotides.

[0078] After hybridization, unhybridized nucleic acids can be removed by a series of washes, the stringency of which can be adjusted depending upon the desired results. Low stringency washing conditions (e.g., using higher salt and lower temperature) increase sensitivity, but can produce nonspecific hybridization signals and high background signals. Higher stringency conditions (e.g., using lower salt and higher temperature that is closer to the Tm) lower the background signal, typically with primarily the specific signal remaining. See, also, Rapley, R. and Walker, J. M. eds., Molecular Biomethods Handbook (Humana Press, Inc. 1998).

[0079] “Stringent hybridization wash conditions” or “stringent conditions” in the context of nucleic acid hybridization experiments, such as Southern and northern hybridizations, are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993), supra, and in Hames and Higgins 1 and Hames and Higgins 2, supra.

[0080] An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 2×SSC, 50% formamide at 42° C., with the hybridization being carried out overnight (e.g., for approximately 20 hours). An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see Sambrook, supra for a description of SSC buffer). Often, the wash determining the stringency is preceded by a low stringency wash to remove signal due to residual unhybridized probe. An example low stringency wash is 2×SSC at room temperature (e.g., 20° C. for 15 minutes).

[0081] In general, a signal to noise ratio of at least 2× (or higher, e.g., at least 5×, 10×, 20×, 50×, 100×, or more) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Detection of at least stringent hybridization between two sequences in the context of the present invention indicates relatively strong structural similarity to, e.g., the nucleic acids of the present invention provided in the sequence listings herein.

[0082] For purposes of the present invention, generally, “highly stringent” hybridization and wash conditions are selected to be about 5° C. or less lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH (as noted below, highly stringent conditions can also be referred to in comparative terms). Target sequences that are closely related or identical to the nucleotide sequence of interest (e.g., “probe”) can be identified under stringent or highly stringent conditions. Lower stringency conditions are appropriate for sequences that are less complementary.

[0083] For example, in determining stringent or highly stringent hybridization (or even more stringent hybridization) and wash conditions, the hybridization and wash conditions are gradually increased (e.g., by increasing temperature, decreasing salt concentration, increasing detergent concentration and/or increasing the concentration of organic solvents, such as formamide, in the hybridization or wash), until a selected set of criteria are met. For example, the hybridization and wash conditions are gradually increased until a probe comprising one or more polynucleotide sequences of the invention, e.g., sequences or unique subsequences selected from SEQ ID NO:1 and/or complementary polynucleotide sequences, binds to a perfectly matched complementary target (again, a nucleic acid comprising one or more nucleic acid sequences or subsequences selected from SEQ ID NO:1 and/or complementary polynucleotide sequences thereof), with a signal to noise ratio that is at least 2× (and optionally 5×, 10×, or 100× or more) as high as that observed for hybridization of the probe to an unmatched target (e.g., a polynucleotide sequence comprising the corresponding one or more sequences or subsequences selected from SEQ ID NO:13 and/or complementary polynucleotide sequences thereof), as desired. Preferably, the sequences or subsequences are selected from a portion of SEQ ID NO:1 that includes at least a subsequence that is not included in SEQ ID NOs:14-19

[0084] Using the polynucleotides of the invention, or subsequences thereof, novel target nucleic acids can be obtained; such target nucleic acids are also a feature of the invention. For example, such target nucleic acids include sequences that hybridize under stringent conditions to a unique oligonucleotide probe corresponding to any of the polynucleotides of the invention, e.g., SEQ ID NO:1.

[0085] Higher ratios of signal to noise can be achieved by increasing the stringency of the hybridization conditions such that ratios of about 15×, 20×, 30×, 50× or more are obtained. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a colorimetric label, a radioactive label, or the like.

[0086] Nucleic acids which do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.

[0087] Defining Proteins by Immunoreactivity

[0088] Because the polypeptides of the invention provide a variety of new polypeptide sequences, the polypeptides also provide new structural features which can be recognized, e.g., in immunological assays. The generation of antibodies or antisera which specifically bind the polypeptides of the invention, as well as the polypeptides which are bound by such antibodies or antisera, and the antibodies or antisera themselves, are a feature of the invention.

[0089] Thus, the proteins of the invention can also be identified by immunoreactivity; e.g., a polypeptide of the invention can include an amino acid sequence or subsequence that is specifically bound by an antibody that specifically binds to an amino acid sequence or subsequence encoded by SEQ ID NO:1, wherein the antibody does not specifically bind to an amino acid sequence or subsequence encoded by SEQ ID NO:13 or SEQ ID NO:14 (or, optionally, to an amino acid sequence or subsequence encoded by the genome of another naturally occurring respiratory syncytial virus).

[0090] Methods of producing antibodies, performing immunoassays, and the like are well known in the art. See e.g., the section entitled “Antibodies” below and references therein.

[0091] In one typical format, an immunoassay to identify a polypeptide of the invention uses a polyclonal antiserum which was raised against one or more of the RSV 9320 polypeptides of the invention (e.g., a polypeptide comprising SEQ ID NOs:2-11 or SEQ ID NO:12 with a deletion of residues 164-197), or a substantial subsequence thereof (i.e., at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or 98% or more of the full length sequence provided). The full set of potential polypeptide immunogens derived from one or more of the RSV 9320 polypeptides of the invention are collectively referred to below as “the immunogenic polypeptides.” The resulting antisera is optionally selected to have low cross-reactivity against the control RSV B1 polypeptides and/or other known, e.g., naturally occurring, RSV polypeptides, and any such cross-reactivity is removed by immunoabsorption with one or more of the control RSV polypeptides, prior to use of the polyclonal antiserum in the immunoassay.

[0092] In order to produce antisera for use in an immunoassay, one or more of the immunogenic polypeptides is produced and purified as described herein. For example, recombinant protein can be produced in a mammalian cell line. An inbred strain of mice (used in this assay because results are more reproducible due to the virtual genetic identity of the mice) is immunized with the immunogenic polypeptide(s) in combination with a standard adjuvant, such as Freund's adjuvant, and a standard mouse immunization protocol (see Harlow and Lane (1988) Antibodies, A Laboratory Manual Cold Spring Harbor Press, New York, for a standard description of antibody generation, immunoassay formats and conditions that can be used to determine specific immunoreactivity). Alternatively, one or more synthetic or recombinant polypeptides derived from the sequences disclosed herein is conjugated to a carrier protein and used as an immunogen.

[0093] Polyclonal sera are collected and titered against the immunogenic polypeptide(s) in an immunoassay, for example, a solid phase immunoassay with one or more of the immunogenic polypeptides immobilized on a solid support. Polyclonal antisera with a titer of 106 or greater are selected, pooled and subtracted with the control RSV polypeptides to produce subtracted pooled titered polyclonal antisera.

[0094] The subtracted pooled titered polyclonal antisera are tested for cross reactivity against the control RSV polypeptides. Preferably at least two of the immunogenic RSV 9320 polypeptides are used in this determination, preferably in conjunction with at least two of the control RSV polypeptides, to identify antibodies which are specifically bound by the immunogenic polypeptides(s).

[0095] In this comparative assay, discriminatory binding conditions are determined for the subtracted titered polyclonal antisera which result in at least about a 5-10 fold higher signal to noise ratio for binding of the titered polyclonal antisera to the immunogenic RSV 9320 polypeptides as compared to binding to the control RSV polypeptides. That is, the stringency of the binding reaction is adjusted by the addition of non-specific competitors, such as albumin or non-fat dry milk, or by adjusting salt conditions, temperature, or the like. These binding conditions are used in subsequent assays for determining whether a test polypeptide is specifically bound by the pooled subtracted polyclonal antisera. In particular, a test polypeptide which shows at least a 2-5× higher signal to noise ratio than the control polypeptides under discriminatory binding conditions, and at least about a ½ signal to noise ratio as compared to the immunogenic polypeptide(s), shares substantial structural similarity or homology with the immunogenic polypeptide(s) as compared to the control RSV polypeptides, and is, therefore, a polypeptide of the invention.

[0096] In another example, immunoassays in the competitive binding format are used for detection of a test polypeptide. For example, as noted, cross-reacting antibodies are removed from the pooled antisera mixture by immunoabsorption with the control RSV polypeptides. The immunogenic polypeptide(s) are then immobilized to a solid support which is exposed to the subtracted pooled antisera. Test proteins are added to the assay to compete for binding to the pooled subtracted antisera. The ability of the test protein(s) to compete for binding to the pooled subtracted antisera as compared to the immobilized protein(s) is compared to the ability of the immunogenic polypeptide(s) added to the assay to compete for binding (the immunogenic polypeptides compete effectively with the immobilized immunogenic polypeptides for binding to the pooled antisera). The percent cross-reactivity for the test proteins is calculated, using standard calculations.

[0097] In a parallel assay, the ability of the control proteins to compete for binding to the pooled subtracted antisera is determined as compared to the ability of the immunogenic polypeptide(s) to compete for binding to the antisera. Again, the percent cross-reactivity for the control polypeptides is calculated, using standard calculations. Where the percent cross-reactivity is at least 5-10× as high for the test polypeptides, the test polypeptides are said to specifically bind the pooled subtracted antisera, and are, therefore, polypeptides of the invention.

[0098] In general, the immunoabsorbed and pooled antisera can be used in a competitive binding immunoassay as described herein to compare any test polypeptide to the immunogenic polypeptide(s). In order to make this comparison, the two polypeptides are each assayed at a wide range of concentrations and the amount of each polypeptide required to inhibit 50% of the binding of the subtracted antisera to the immobilized protein is determined using standard techniques. If the amount of the test polypeptide required is less than twice the amount of the immunogenic polypeptide that is required, then the test polypeptide is said to specifically bind to an antibody generated to the immunogenic polypeptide, provided the amount is at least about 5-10× as high as for a control polypeptide.

[0099] As a final determination of specificity, the pooled antisera is optionally fully immunosorbed with the immunogenic polypeptide(s) (rather than the control polypeptides) until little or no binding of the resulting immunogenic polypeptide subtracted pooled antisera to the immunogenic polypeptide(s) used in the immunoabsorption is detectable. This fully immunosorbed antisera is then tested for reactivity with the test polypeptide. If little or no reactivity is observed (i.e., no more than 2× the signal to noise ratio observed for binding of the fully immunosorbed antisera to the immunogenic polypeptide), then the test polypeptide is specifically bound by the antisera elicited by the immunogenic protein.

[0100] Sequence Variations

[0101] Silent Variations

[0102] Due to the degeneracy of the genetic code, any of a variety of nucleic acid sequences encoding polypeptides and/or viruses of the invention are optionally produced, some which can bear lower levels of sequence identity to the RSV nucleic acid and polypeptide sequences in the figures. The following provides a typical codon table specifying the genetic code, found in many biology and biochemistry texts.

1TABLE 1Codon TableAmino acidsCodonAlanineAlaAGCAGCCGCGGCUCysteineCysCUGCUGUAspartic acidAspDGACGAUGlutamic acidGluEGAAGAGPhenylalaninePheFUUCUUUGlycineGlyGGGAGGCGGGGGUHistidineHisHCACCAUIsoleucineIleIAUAAUCAUULysineLysKAAAAAGLeucineLeuLUUAUUGCUACUCCUGCUUMethionineMetMAUGAsparagineAsnNAACAAUProlineProPCCACCCCCGCCUGlutamineGlnQCAACAGArginineArgRAGAAGGCGACGCCGGCGUSerineSerSAGCAGUUCAUCCUCGUCUThreonineThrTACAACCACGACUValineValVGUAGUCGUGGUUTryptophanTrpWUGGTyrosineTyrYUACUAU

[0103] The codon table shows that many amino acids are encoded by more than one codon. For example, the codons AGA, AGG, CGA, CGC, CGG, and CGU all encode the amino acid arginine. Thus, at every position in the nucleic acids of the invention where an arginine is specified by a codon, the codon can be altered to any of the corresponding codons described above without altering the encoded polypeptide. It is understood that U in an RNA sequence corresponds to T in a DNA sequence.

[0104] As an example, a nucleic acid sequence corresponding to the amino acid sequence FEV (residues 164-166 of SEQ ID NO:12) is TTTGAAGTG. A silent variation of this sequence includes TTCGAGGTA (also encoding FEV).

[0105] Such “silent variations” are one species of “conservatively modified variations”, discussed below. One of skill will recognize that each codon in a nucleic acid (except ATG, which is ordinarily the only codon for methionine, and TTG, which is ordinarily the only codon for tryptophan) can be modified by standard techniques to encode a functionally identical polypeptide. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in any described sequence. The invention, therefore, explicitly provides each and every possible variation of a nucleic acid sequence encoding a polypeptide of the invention that could be made by selecting combinations based on possible codon choices. These combinations are made in accordance with the standard triplet genetic code (e.g., as set forth in Table 1, or as is commonly available in the art) as applied to the nucleic acid sequence encoding an RSV polypeptide of the invention. All such variattions of every nucleic acid herein are specifically provided and described by consideration of the sequence in combination with the genetic code. One of skill is fully able to make these silent substitutions using the methods herein.

[0106] Conservative Variations

[0107] “Conservatively modified variations” or, simply, “conservative variations” of a particular nucleic acid sequence or polypeptide are those which encode identical or essntially indentical amino acid sequences. One of skill will recognize that individual substitutions, deletions or additions which alter, add or delete a single amino acid or a small percentage of amino acids (typically less than 5%, more typically less than 4%, 2% or 1%) in an encoded sequence are “conservatively modified variations” where the alterations result in the deletion of an amino acid, addition of an amino acid, or substitution of an amino acid with a chemically similar amino acid.

[0108] Conservative substitution tables providing functionally similar amino acids are well known in the art. Table 2 sets forth six groups which contain amino acids that are “conservative substitutions” for one another. Alternative conservative substitution charts are available in the art and can be used in a similar manner.

2TABLE 2Conservative Substitution Groups1Alanine (A)Serine (S)Threonine (T)2Aspartic acid (D)Glutamic acid (E)3Asparagine (N)Glutamine (Q)4Arginine (R)Lysine (K)5Isoleucine (I)Leucine (L)Methionine (M)Valine (V)6Phenylalanine (F)Tyrosine (Y)Tryptophan (W)

[0109] Thus, “conservatively substituted variations” of a polypeptide sequence of the present invention include substitutions of a small percentage, typically less than 5%, more typically less than 2% or 1%, of the amino acids of the polypeptide sequence, with a conservatively selected amino acid of the same conservative substitution group.

[0110] For example, a conservatively substituted variation of the RSV strain B9320 M2-1 polypeptide in SEQ ID NO:9 will contain “conservative substitutions”, e.g., according to the six groups defined above, in up to about 10 residues (i.e., about 5% of the amino acids) in the full-length polypeptide.

[0111] In a further example, if conservative substitutions were localized in the region corresponding to amino acids 10-12 of RSV 9320 M2-1 (EIR), examples of conservatively substituted variations of this region include conservative substitutions of DLK or DMR (or any others that can be made according to Table 2) for EIR.

[0112] Listing of a protein sequence herein, in conjunction with the above substitution table, provides an express listing of all conservatively substituted proteins.

[0113] Finally, the addition or deletion of sequences which do not alter the encoded activity of a nucleic acid molecule, such as the addition or deletion of a non-functional sequence, an epitope tag, a polyhistidine tag, GFP, or the like, is a conservative variation of the basic nucleic acid or polypeptide.

[0114] One of skill will appreciate that many conservative variations of the nucleic acid constructs which are disclosed yield a functionally identical construct. For example, as discussed above, owing to the degeneracy of the genetic code, “silent substitutions” (i.e., substitutions in a nucleic acid sequence which do not result in an alteration in an encoded polypeptide) are an implied feature of every nucleic acid sequence which encodes an amino acid. Similarly, “conservative amino acid substitutions,” in which one or a few amino acids in an amino acid sequence are substituted with different amino acids with highly similar properties, are also readily identified as being highly similar to a disclosed construct. Such conservative variations of each disclosed or claimed virus, nucleic acid or protein are a feature of the present invention. Such conservative (e.g., silent) variations can be used, e.g., to produce antibodies for detection of or immunoprotection against RSV.

[0115] Production of Viral Nucleic Acids

[0116] In the context of the invention, viral (e.g., RSV) 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 2003) John Wiley & Sons, New York (“Ausubel”); Sambrook et al. Molecular Cloning—A Laboratory Manual (3rd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2001 (“Sambrook”), and Berger and Kimmel Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif. (“Berger”).

[0117] 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 polynucleotides of the invention, are found in Mullis et al. (1987) U.S. Pat. No. 4,683,202; PCR Protocols A Guide to Methods and Applications (Innis et al. eds) Academic Press Inc. San Diego, Calif. (1990) (“Innis”); Arnheim and Levinson (1990) C&EN 36; The Journal Of NIH 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.

[0118] 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 Enzymol 211:3.

[0119] 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 (www.mcrc.com), The Great American Gene Company (www.genco.com), ExpressGen, Inc. (www.expressgen.com), QIAGEN (http://oligos.qiagen.com), and many others.

[0120] 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 and/or temperature sensitivity, can be produced by introducing specific mutations into a viral nucleic acid segment (e.g., a cDNA) encoding the polypeptide. Methods for site directed mutagenesis are well known in the art, and are described, e.g., in Ausubel, Sambrook, and Berger, supra. Numerous kits for performing site directed mutagenesis are commercially available, e.g., the ExSite™ and Chameleon™ site directed mutagenesis kits (Stratagene, La Jolla), and can be used according to the manufacturer's instructions to introduce, e.g., one or more nucleotide substitutions specifying one or more amino acid substitutions into an RSV polynucleotide.

[0121] Various types of mutagenesis are optionally used in the present invention, e.g., to modify nucleic acids and encoded polypeptides and/or viruses to produce conservative or non-conservative variants. Any available mutagenesis procedure can be used. Such mutagenesis procedures optionally include selection of mutant nucleic acids and polypeptides for one or more activity of interest. Procedures that can be used include, but are not limited to: site-directed point mutagenesis, random point mutagenesis, in vitro or in vivo homologous recombination (DNA shuffling), mutagenesis using uracil containing templates, oligonucleotide-directed mutagenesis, phosphorothioate-modified DNA mutagenesis, mutagenesis using gapped duplex DNA, point mismatch repair, mutagenesis using repair-deficient host strains, restriction-selection and restriction-purification, deletion mutagenesis, mutagenesis by total gene synthesis, double-strand break repair, and many others known to persons of skill. In one embodiment, mutagenesis can be guided by information known about the naturally occurring molecule or altered or mutated naturally occurring molecules, e.g., sequence, sequence comparisons, physical properties, crystal structure or the like. In another class of embodiments, modification is essentially random (e.g., as in classical DNA shuffling).

[0122] Several of these procedures are set forth in Sambrook and Ausubel, herein. Additional information on these procedures is found in the following publications and the references cited therein: Arnold (1993) “Protein engineering for unusual environments” Current Opinion in Biotechnology 4:450-455; Bass et al. (1988) “Mutant Trp repressors with new DNA-binding specificities” Science 242:240-245; Botstein and Shortle (1985) “Strategies and applications of in vitro mutagenesis” Science 229:1193-1201; Carter et al. (1985) “Improved oligonucleotide site-directed mutagenesis using M13 vectors” Nucl. Acids Res. 13: 4431-4443; Carter (1986) “Site-directed mutagenesis” Biochem. J. 237:1-7; Carter (1987) “Improved oligonucleotide-directed mutagenesis using M13 vectors” Methods in Enzymol. 154: 382-403; Dale et al. (1996) “Oligonucleotide-directed random mutagenesis using the phosphorothioate method” Methods Mol. Biol. 57:369-374; Eghtedarzadeh and Henikoff (1986) “Use of oligonucleotides to generate large deletions” Nucl. Acids Res. 14: 5115; Fritz et al. (1988) “Oligonucleotide-directed construction of mutations: a gapped duplex DNA procedure without enzymatic reactions in vitro” Nucl. Acids Res. 16: 6987-6999; Grundstrom et al. (1985) “Oligonucleotide-directed mutagenesis by microscale ‘shot-gun’ gene synthesis” Nucl. Acids Res. 13: 3305-3316; Kunkel (1987) “The efficiency of oligonucleotide directed mutagenesis” in Nucleic Acids and Molecular Biology (Eckstein, F. and Lilley, D. M. J. eds., Springer Verlag, Berlin)); Kunkel (1985) “Rapid and efficient site-specific mutagenesis without phenotypic selection” Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) “Rapid and efficient site-specific mutagenesis without phenotypic selection” Methods in Enzymol. 154, 367-382; Kramer et al. (1984) “The gapped duplex DNA approach to oligonucleotide-directed mutation construction” Nucl. Acids Res. 12: 9441-9456; Kramer and Fritz (1987) “Oligonucleotide-directed construction of mutations via gapped duplex DNA” Methods in Enzymol. 154:350-367; Kramer et al. (1984) “Point Mismatch Repair” Cell 38:879-887; Kramer et al. (1988) “Improved enzymatic in vitro reactions in the gapped duplex DNA approach to oligonucleotide-directed construction of mutations” Nucl. Acids Res. 16: 7207; Ling et al. (1997) “Approaches to DNA mutagenesis: an overview” Anal Biochem. 254(2): 157-178; Lorimer and Pastan (1995) Nucleic Acids Res. 23, 3067-8; Mandecki (1986) “Oligonucleotide-directed double-strand break repair in plasmids of Escherichia coli: a method for site-specific mutagenesis” Proc. Natl. Acad. Sci. USA 83:7177-7181; Nakamaye and Eckstein (1986) “Inhibition of restriction endonuclease Nci I cleavage by phosphorothioate groups and its application to oligonucleotide-directed mutagenesis” Nucl. Acids Res. 14: 9679-9698; Nambiar et al. (1984) “Total synthesis and cloning of a gene coding for the ribonuclease S protein” Science 223: 1299-1301; Sakamar and Khorana (1988) “Total synthesis and expression of a gene for the a-subunit of bovine rod outer segment guanine nucleotide-binding protein (transducin)” Nucl. Acids Res. 14: 6361-6372; Sayers et al. (1988) “Y-T Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis” Nucl. Acids Res. 16:791-802; Sayers et al. (1988) “Strand specific cleavage of phosphorothioate-containing DNA by reaction with restriction endonucleases in the presence of ethidium bromide” Nucl. Acids Res. 16: 803-814; Sieber et al.(2001) Nature Biotechnology 19:456-460; Smith (1985) “In vitro mutagenesis” Ann. Rev. Genet. 19:423-462; Methods in Enzymol. 100: 468-500 (1983); Methods in Enzymol. 154: 329-350 (1987); Stemmer (1994) Nature 370, 389-91; Taylor et al. (1985) “The use of phosphorothioate-modified DNA in restriction enzyme reactions to prepare nicked DNA” Nucl. Acids Res. 13: 8749-8764; Taylor et al. (1985) “The rapid generation of oligonucleotide-directed mutations at high frequency using phosphorothioate-modified DNA” Nucl. Acids Res. 13: 8765-8787; Wells et al. (1986) “Importance of hydrogen-bond formation in stabilizing the transition state of subtilisin” Phil. Trans. R. Soc. Lond. A 317: 415-423; Wells et al. (1985) “Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites” Gene 34:315-323; Zoller and Smith (1982) “Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any DNA fragment” Nucleic Acids Res. 10:6487-6500; Zoller and Smith (1983) “Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors” Methods in Enzymol. 100:468-500; and Zoller and Smith (1987) “Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template” Methods in Enzymol. 154:329-350. Additional details on many of the above methods can be found in Methods in Enzymology Volume 154, which also describes useful controls for trouble-shooting problems with various mutagenesis methods.

[0123] Vectors, Promoters and Expression Systems

[0124] The present invention includes recombinant constructs incorporating one or more of the nucleic acid sequences described above. Such constructs include a vector, for example, a plasmid, a cosmid, a phage, a virus, a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC), etc., into which one or more of the polynucleotide sequences of the invention, for example, SEQ ID NO:1 or subsequences thereof, e.g., including at least one ORF selected from SEQ ID NO:1, has been inserted, in a forward or reverse orientation. For example, the inserted nucleic acid can include all or part of at least one of the polynucleotide sequences of the invention. Typically the vector is selected based on the characteristics, e.g., size of the selected polynucleotide sequence, and on the intended use, e.g., expression, amplification, etc. In a preferred embodiment, the construct further comprises regulatory sequences, including, for example, a promoter, operably linked to the sequence. Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available.

[0125] The polynucleotides of the present invention can be included in any one of a variety of vectors suitable for generating sense or antisense RNA, and optionally, polypeptide (or peptide) expression products, e.g., selected from SEQ ID NOs:2-11. Such vectors include chromosomal, nonchromosomal and synthetic DNA sequences, e.g., derivatives of SV40; bacterial plasmids; phage DNA; baculovirus; yeast plasmids; vectors derived from combinations of plasmids and phage DNA, viral DNA such as vaccinia, adenovirus, fowl pox virus, pseudorabies, adenovirus, adeno-associated virus, retroviruses, and many others, as well as viral amplicon vectors. Any vector that is capable of introducing genetic material into a cell, and, if replication is desired, which is replicable in the relevant host, can be used.

[0126] In an expression vector, the polynucleotide sequence, commonly a subsequence of SEQ ID NO:1, e.g., comprising an ORF, such as an ORF encoding a polypeptide (or peptide) selected from among SEQ ID NOs: 2-11 (or variants thereof, e.g., conservative variations thereof), is physically arranged in proximity and orientation to an appropriate transcription control sequence (promoter, and optionally, one or more enhancers) to direct mRNA synthesis. For example, a subsequence of SEQ ID NO:1, e.g., encoding a polypeptide selected from a subsequence of one of SEQ ID NOs:2-11, can be inserted into an expression vector to produce antigenic peptide for the production of antibodies, e.g., for diagnostic or therapeutic purposes. That is, the polynucleotide sequence of interest is operably linked to an appropriate transcription control sequence. Examples of such promoters include: LTR or SV40 promoter, E. coli lac or trp promoter, phage lambda PL promoter, and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. The expression vector typically also contains a ribosome binding site for translation initiation, and a transcription terminator. The vector optionally includes appropriate sequences for amplifying expression. In addition, the expression vectors optionally comprise one or more selectable marker genes to provide a phenotypic trait for selection of transformed host cells, such as dihydrofolate reductase or neomycin resistance for eukaryotic cell culture, or such as tetracycline or ampicillin resistance in E. coli.

[0127] Where translation of polypeptide encoded by a nucleic acid comprising a polynucleotide sequence of the invention is desired, additional translation specific initiation signals can improve the efficiency of translation. These signals can include, e.g., an ATG initiation codon and adjacent sequences. In some cases, for example, full-length cDNA molecules or chromosomal segments including a coding sequence incorporating, e.g., a polynucleotide sequence of the invention, a translation initiation codon and associated sequence elements are inserted into the appropriate expression vector simultaneously with the polynucleotide sequence of interest. In such cases, additional translational control signals are not required. However, in cases where only a polypeptide coding sequence, e.g., encoding an amino acid sequence selected from among SEQ ID NOs:2-11 or a portion thereof, is inserted, exogenous translational control signals, including an ATG initiation codon is provided for expression of the relevant sequence. The initiation codon is put in the correct reading frame to ensure transcription of the polynucleotide sequence of interest. 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 (Scharf D et al. (1994) Results Probl Cell Differ 20:125-62; Bittner et al. (1987) Methods in Enzymol 153:516-544).

[0128] Polypeptide Production and Recovery

[0129] The present invention also relates to the introduction of vectors incorporating the polynucleotides of the invention (e.g., polynucleotides including all or part of one or more ORFs selected from SEQ ID NO:1) into host cells and the production of polypeptides of the invention, e.g., one or more polypeptide selected from SEQ ID NOs:2-11 or subsequences thereof (e.g., unique subsequences thereof) by recombinant techniques. Recombinant and/or isolated polypeptides encoded by the polynucleotides of the invention, e.g., SEQ ID NOs:2-11, or subsequences (e.g., unique subsequences) thereof are used, for example, as antigens to produce antibodies in animal or human subjects. For example, antigenic polypeptides (or peptides) corresponding to all or part of a polypeptide represented by SEQ ID NOs:2-11 can be injected into an experimental animal to produce antibodies specific for one or more strains of RSV, as further described in the section entitled “Antibodies” below. Additionally, the antigenic polypeptides can be administered, e.g., as a vaccine, to human subjects to elicit an immune response specific for one or more strains of RSV. For example, such an elicited immune response can be a protective immune response.

[0130] To produce the polypeptides of the invention, host cells are genetically engineered (e.g., transduced, transformed or transfected) with a vector, such as an expression vector, of this invention. As described above, the vector can be in the form of a plasmid, a viral particle, a phage, etc. Examples of appropriate expression hosts include: bacterial cells, such as E. coli, Streptomyces, and Salmonella typhimurium; fungal cells, such as Saccharomyces cerevisiae, Pichia pastoris, and Neurospora crassa; insect cells such as Drosophila and Spodoptera frugiperda; mammalian cells such as 3T3, COS, CHO, BHK, HEK 293 or Bowes melanoma; plant cells, etc.

[0131] The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the inserted polynucleotide sequences. The culture conditions, such as temperature, pH and the like, are typically those previously used with the host cell selected for expression, and will be apparent to those skilled in the art and in the references cited herein, including, e.g., Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique, third edition, Wiley-Liss, New York and the references cited therein. In addition to Sambrook, Berger and Ausubel, details regarding cell culture can be found in Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips (eds) (1995) Plant Cell, Tissue and Organ Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg N.Y.) and Atlas and Parks (eds) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, Fla.

[0132] In bacterial systems, a number of expression vectors can be selected depending upon the use intended for the expressed product. For example, when large quantities of a polypeptide or fragments thereof are needed for the production of antibodies, vectors which direct high level expression of fusion proteins that are readily purified are favorably employed. Such vectors include, but are not limited to, multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene), in which the coding sequence of interest, e.g., a polynucleotide of the invention as described above, can be ligated into the vector in-frame with sequences for the amino-terminal translation initiating Methionine and the subsequent 7 residues of beta-galactosidase producing a catalytically active beta galactosidase fusion protein; pIN vectors (Van Heeke and Schuster (1989) J Biol Chem 264:5503-5509); pET vectors (Novagen, Madison Wis.); and the like.

[0133] Similarly, in the yeast Saccharomyces cerevisiae a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase and PGH can be used for production of the desired expression products. For reviews, see Berger, Ausubel, and, e.g., Grant et al. (1987) Methods in Enzymology 153:516-544.

[0134] Vectors suitable for replication in mammalian cells are also known in the art. Exemplary vectors include those derived from SV40, retroviruses, bovine papilloma virus, vaccinia virus, other herpesviruses and adenovirus. Such suitable mammalian expression vectors optionally contain a promoter to mediate transcription of foreign DNA sequences and, optionally, an enhancer. Suitable promoters are known in the art and include viral promoters such as those from SV40, cytomegalovirus (CMV), Rous sarcoma virus (RSV), adenovirus (ADV), and bovine papilloma virus (BPV).

[0135] The optional presence of an enhancer, combined with the promoter described above, will typically increase expression levels. An enhancer is any regulatory DNA sequence that can stimulate transcription up to 1000-fold when linked to endogenous or heterologous promoters, with synthesis beginning at the normal mRNA start site. Enhancers are also active when placed upstream or downstream from the transcription initiation site, in either normal or flipped orientation, or at a distance of more than 1000 nucleotides from the promoter. See, e.g., Maniatis (1987) Science 236:1237 and Alberts (1989) Molecular Biology of the Cell, 2nd Ed. (or later). Enhancers derived from viruses may be particularly useful, because they typically have a broader host range. Examples include the SV40 early gene enhancer (see Dijkema (1985) EMBO J. 4:761) and the enhancer/promoters derived from the long terminal repeat (LTR) of the RSV (see Gorman (1982) Proc. Natl. Acad. Sci. 79:6777) and from human cytomegalovirus (see Boshart (1985) Cell 41:521). Additionally, some enhancers are regulatable and become active only in the presence of an inducer, such as a hormone or metal ion (see Sassone-Corsi and Borelli (1986) Trends Genet. 2:215); Maniatis (1987) Science 236:1237), In addition, the expression vector can and will typically also include a termination sequence and poly(A) addition sequences which are operably linked to the heterologous coding sequence.

[0136] Sequences that cause amplification of the gene may also be desirably included in the expression vector or in another vector that is co-translated with the expression vector, as are sequences which encode selectable markers. Selectable markers for mammalian cells are known in the art, and include, for example, thymidine kinase, dihydrofolate reductase (together with methotrexate as a DHFR amplifier), aminoglycoside phosphotransferase, hygromycin B phosphotransferase, asparagine synthetase, adenosine deaminase, metallothionien, and antibiotic resistant genes such as neomycin.

[0137] Mammalian cell lines available as hosts for expression are known in the art and include many immortalized cell lines available from the American Type Culture Collection (ATCC) as well as primary cultured cells and established cell lines, including but not limited to Vero, HEp-2, 3T3, COS, CHO, HeLa, BHK, MDCK, 293, WI38, Hep G2, MRC-5, and many others.

[0138] Host cells containing the vectors (e.g., expression vectors) described above are also a feature of the invention. The host cell can be a eukaryotic cell, such as a mammalian cell, a yeast cell, or a plant cell, or the host cell can be a prokaryotic cell, such as a bacterial cell. Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-Dextran mediated transfection, electroporation, encapsulation of the polynucleotide(s) in liposomes, direct microinjection of the DNA into nuclei, or other common techniques (see, e.g., Davis, L., Dibner, M., and Battey, I. (1986) Basic Methods in Molecular Biology).

[0139] A host cell strain is optionally chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the protein include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation. Post-translational processing which cleaves a precursor form into a mature form of the protein is sometimes important for correct insertion, folding and/or function. Different host cells have specific cellular machinery and characteristic mechanisms for such post-translational activities and can be chosen to ensure the correct modification and processing of the introduced, foreign protein.

[0140] Host cells transformed with a nucleotide sequence encoding a polypeptide of the invention are optionally cultured under conditions suitable for the expression and recovery of the encoded protein from cell culture. The protein or fragment thereof produced by a recombinant cell can be secreted, membrane-bound, or contained intracellularly, depending on the sequence -and/or the vector used.

[0141] Following transduction of a suitable host cell line or strain and growth of the host cells to an appropriate cell density, the selected promoter is induced if necessary by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period. The secreted polypeptide product is then recovered from the culture medium. Alternatively, cells can be harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification. Eukaryotic or microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents, or other methods, which are well know to those skilled in the art.

[0142] Expressed polypeptides can be recovered and purified from recombinant cell cultures by any of a number of methods well known in the art, including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography (e.g., using any of the tagging systems noted herein), hydroxylapatite chromatography, and lectin chromatography. Protein refolding steps can be used, as desired, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed in the final purification steps. In addition to the references noted above, a variety of purification methods are well known in the art, including, e.g., those set forth in Deutscher, Methods in Enzymology Vol. 182: Guide to Protein Purification, Academic Press, Inc. N.Y. (1990); Sandana (1997) Bioseparation of Proteins, Academic Press, Inc.; Bollag et al. (1996) Protein Methods, 2nd Edition Wiley-Liss, NY; Walker (1996) The Protein Protocols Handbook Humana Press, NJ; Harris and Angal (1990) Protein Purification Applications: A Practical Approach IRL Press at Oxford, Oxford, U.K.; Scopes (1993) Protein Purification: Principles and Practice 3rd Edition Springer Verlag, NY; Janson and Ryden (1998) Protein Purification: Principles, High Resolution Methods and Applications, Second Edition Wiley-VCH, NY; and Walker (1998) Protein Protocols on CD-ROM Humana Press, NJ.

[0143] Alternatively, cell-free transcription/translation systems can be employed to produce polypeptides comprising an amino acid sequence or subsequence encoded by the polynucleotides of the invention. A number of suitable in vitro transcription and translation systems are commercially available. A general guide to in vitro transcription and translation protocols is found in Tymms (1995) In vitro Transcription and Translation Protocols: Methods in Molecular Biology Volume 37, Garland Publishing, NY. Cell free transcription/translation systems can be particularly useful for the production of polypeptides, including proteins for administration to human subjects.

[0144] In addition, the polypeptides, or subsequences thereof, e.g., subsequences comprising antigenic peptides, can be produced manually or by using an automated system, by direct peptide synthesis using solid-phase techniques (see, e.g., Stewart et al. (1969) Solid-Phase Peptide Synthesis, W H Freeman Co, San Francisco; Merrifield J (1963) J. Am. Chem. Soc. 85:2149-2154). Exemplary automated systems include the Applied Biosystems 431A Peptide Synthesizer (Perkin Elmer, Foster City, Calif.). If desired, subsequences can be chemically synthesized separately, and combined using chemical methods to provide full-length polypeptides.

[0145] Modified Amino Acids

[0146] Expressed polypeptides of the invention can contain one or more modified amino acid. The presence of modified amino acids can be advantageous in, for example, (a) increasing polypeptide serum half-life, (b) reducing polypeptide antigenicity or (c) increasing polypeptide storage stability. Amino acid(s) are modified, for example, co-translationally or post-translationally during recombinant production (e.g., N-linked glycosylation at N-X-S/T motifs during expression in mammalian cells) or are modified by synthetic means (e.g., via PEGylation).

[0147] Non-limiting examples of a modified amino acid include a glycosylated amino acid, a sulfated amino acid, a prenlyated (e.g., famesylated, geranylgeranylated) amino acid, an acetylated amino acid, an acylated amino acid, a PEG-ylated amino acid, a biotinylated amino acid, a carboxylated amino acid, a phosphorylated amino acid, and the like, as well as amino acids modified by conjugation to, e.g., lipid moieties or other organic derivatizing agents. References adequate to guide one of skill in the modification of amino acids are replete throughout the literature. Example protocols are found in Walker (1998) Protein Protocols on CD-ROM Human Press, Towata, N.J.

[0148] Antibodies

[0149] The polypeptides of the invention can be used to produce antibodies specific for the polypeptides comprising amino acid sequences or subsequences encoded by the polynucleotides of the invention. Antibodies specific for antigenic peptides encoded by, e.g., SEQ ID NO:1 (e.g., SEQ ID NOs:2-11), and related variant polypeptides are useful, e.g., for diagnostic and therapeutic purposes, e.g., related to the activity, distribution, and expression of target polypeptides.

[0150] Antibodies specific for the polypeptides of the invention can be generated by methods well known in the art. Such antibodies can include, but are not limited to, polyclonal, monoclonal, chimeric, humanized, single chain, Fab fragments and fragments produced by an Fab expression library.

[0151] Polypeptides do not require biological activity for antibody production. However, the polypeptide or oligopeptide is antigenic. Peptides used to induce specific antibodies typically have an amino acid sequence of at least about 5 amino acids, and often at least 10 or 20 amino acids. Short stretches of a polypeptide, e.g., encoded by a polynucleotide of the invention such a sequence selected from SEQ ID NO:1 (such as a polypeptide selected from among SEQ ID NOs:2-11) can optionally be fused with another protein, such as keyhole limpet hemocyanin (KLH), and antibodies produced against the fusion protein or polypeptide.

[0152] Numerous methods for producing polyclonal and monoclonal antibodies are known to those of skill in the art, and can be adapted to produce antibodies specific for the polypeptides or peptides of the invention. See, e.g., Coligan (1991) Current Protocols in Immunology Wiley/Greene, NY; and Harlow and Lane (1989) Antibodies: A Laboratory Manual Cold Spring Harbor Press, NY; Stites et al. (eds.) Basic and Clinical Immunology (4th ed.) Lange Medical Publications, Los Altos, Calif., and references cited therein; Goding (1986) Monoclonal Antibodies: Principles and Practice (2d ed.) Academic Press, New York, N.Y.; Fundamental Immunology, e.g., 4th Edition (or later),W. E. Paul (ed.), Raven Press, N.Y. (1998); and Kohler and Milstein (1975) Nature 256: 495-497. Other suitable techniques for antibody preparation include selection of libraries of recombinant antibodies in phage or similar vectors. See, Huse et al. (1989) Science 246: 1275-1281; and Ward, et al. (1989) Nature 341: 544-546. Specific monoclonal and polyclonal antibodies and antisera will usually bind with a KD of at least about 0.1 μM, preferably at least about 0.01 μM or better, and most typically and preferably, 0.001 μM or better.

[0153] For certain therapeutic applications (e.g., administration of an antibody or anitserum specific for one or more strains of RSV to provide passive immunity to a subject, e.g., a human, to prevent or decrease the severity of RSV disease), humanized antibodies are desirable. Detailed methods for preparation of humanized antibodies can be found in U.S. Pat. No. 5,482,856. Additional details on humanization and other antibody production and engineering techniques can be found in Borrebaeck (ed) (1995) Antibody Engineering. 2nd Edition Freeman and Company, NY (Borrebaeck); McCafferty et al. (1996) Antibody Engineering, A Practical Approach IRL at Oxford Press, Oxford, England (McCafferty), and Paul (1995) Antibody Engineering Protocols Humana Press, Towata, N.J. (Paul). Additional details regarding specific procedures can be found, e.g., in Ostberg et al. (1983) Hybridoma 2: 361-367, Ostberg, U.S. Pat. No. 4,634,664, and Engelman et al. U.S. Pat. No. 4,634,666.

[0154] Diagnostic Assays

[0155] The novel nucleic acid sequences of the present invention can be used in diagnostic assays to detect RSV in a sample, to detect RSV B9320-like sequences, and to detect strain differences in clinical isolates of RSV using either chemically synthesized or recombinant RSV B9320 polynucleotide fragments, e.g., selected from SEQ ID NO:1. For example, fragments of the novel B9320 sequences (SEQ ID NO:1) comprising at least between 10 and 20 nucleotides can be used as primers to amplify nucleic acids using polymerase chain reaction (PCR) methods well known in the art (e.g., reverse transcription-PCR) and as probes in nucleic acid hybridization assays to detect target genetic material such as RSV RNA in clinical specimens.

[0156] The novel RSV B9320 polynucleotide sequences can be used in their entirety or as fragments to detect the presence of RNA sequences or transcription products in cells, tissues, samples and the like using hybridization techniques known in the art or in conjunction with one of the methods discussed herein. The probes can be either DNA or RNA molecules, such as fragments of viral RNA, isolated restriction fragments of cloned DNA, cDNAs, amplification products, transcripts, and oligonucleotides, and can vary in length from oligonucleotides as short as about 10 nucleotides in length to viral RNA fragments or cDNAs in excess of one or more kilobases. For example, in some embodiments, a probe of the invention includes a polynucleotide sequence or subsequence (e.g., a unique subsequence) selected from SEQ ID NO:1 or sequences complementary thereto. Preferably the polynucleotide sequence (or subsequence) is selected from a portion of SEQ ID NO:1 that includes at least a subsequence that is not included in SEQ ID NOs:14-19. Alternatively, polynucleotide sequences that are variants of one of the above designated sequences are used as probes. Most typically, such variants include one or a few nucleotide variations. For example, pairs (or sets) of oligonucleotides can be selected, in which the two (or more) polynucleotide sequences are substantially identical variants of each other, wherein one polynucleotide sequence or set corresponds identically to a first viral strain (e.g., B9320) and the other sequence(s) or set(s) correspond identically to additional viral strains (e.g., B1, A2, etc.). Such pairs of oligonucleotide probes are particularly useful, for example, in the context of an allele specific hybridization experiment to determine the identity of an RSV virus or viral nucleic acid, e.g., for diagnostic or monitoring purposes. In other applications, probes are selected that are more or less divergent, that is probes that are at least about 70% (or 80%, 90%, 95%, 98%, or 99%) identical are selected.

[0157] The probes of the invention, e.g., as exemplified by unique subsequences selected from SEQ ID NO:1, can also be used to identify additional useful polynucleotide sequences (such as to characterize additional strains of RSV) according to procedures routine in the art. In one set of preferred embodiments, one or more probes, as described above, are utilized to screen libraries of expression products or cloned viral nucleic acids (i.e., expression libraries or genomic libraries) to identify clones that include sequences identical to, or with significant sequence identity to SEQ ID NO:1. In turn, each of these identified sequences can be used to make probes, including pairs or sets of variant probes as described above. It will be understood that in addition to such physical methods as library screening, computer assisted bioinformatic approaches, e.g., BLAST and other sequence homology search algorithms, and the like, can also be used for identifying related polynucleotide sequences.

[0158] The probes of the invention are particularly useful for detecting the presence and for determining the identity of RSV nucleic acids in cells, tissues or other biological samples (e.g., a nasal wash or bronchial lavage). For example, the probes of the invention are favorably utilized to determine whether a biological sample, such as a subject (e.g., a human subject) or model system (such as a cultured cell sample) has been exposed to, or become infected with, RSV. Detection of hybridization of the selected probe to nucleic acids originating in (e.g., isolated from) the biological sample or model system is indicative of exposure to or infection with the virus (or a related virus) from which the probe polynucleotide is selected. For example, a polynucleotide sequence that hybridizes preferentially to a subsequence of SEQ ID NO:1 as compared to the corresponding subsequence of SEQ ID NO:13 (or the genome of another naturally occurring RSV strain) can be used to distinguish RSV B 9320 from RSV B1 (or another RSV strain).

[0159] It will be appreciated that probe design is influenced by the intended application. For example, where several allele-specific probe-target interactions are to be detected in a single assay, e.g., on a single DNA chip, it is desirable to have similar melting temperatures for all of the probes. Accordingly, the length of the probes are adjusted so that the melting temperatures for all of the probes on the array are closely similar (it will be appreciated that different lengths for different probes may be needed to achieve a particular Tm where different probes have different GC contents). Although melting temperature is a primary consideration in probe design, other factors are optionally used to further adjust probe construction, such as selecting against primer self-complementarity and the like.

[0160] In other circumstances, e.g., relating to functional attributes of cells or organisms expressing the polynucleotides and polypeptides of the invention, probes that are polypeptides, peptides or antibodies are favorably utilized. For example, polypeptides, polypeptide fragments and peptides encoded by or having subsequences encoded by the polynucleotides of the invention, e.g., SEQ ID NO:1, are favorably used to identify and isolate antibodies or other binding proteins, e.g., from phage display libraries, combinatorial libraries, polyclonal sera, and the like.

[0161] Antibodies specific for a polypeptide subsequence encoded by any subsequence (e.g., unique subsequence) or ORF of SEQ ID NO:1 are likewise valuable as probes for evaluating expression products, e.g., from cells or tissues. For example, suitable polypeptide sequences are selected from among the amino acid sequences represented by SEQ ID NOs:2-11. In addition, antibodies are particularly suitable for evaluating expression of proteins comprising amino acid subsequences encoded by SEQ ID NO:1 (e.g., SEQ ID NOs:2-11), e.g., in a sample from a subject infected with or exposed to RSV. Antibodies can be directly labeled with a detectable reagent as described below, or detected indirectly by labeling of a secondary antibody specific for the heavy chain constant region (i.e., isotype) of the specific antibody. Additional details regarding production of specific antibodies are provided above in the section entitled “Antibodies.”

[0162] Labeling and Detecting Probes

[0163] Numerous methods are available for labeling and detection of the nucleic acid and polypeptide (or peptide or antibody) probes of the invention. These include: 1) fluorescence (using, e.g., fluorescein, Cy-5, rhodamine or other fluorescent tags); 2) isotopic methods, e.g., using end-labeling, nick translation, random priming, or PCR to incorporate radioactive isotopes into the probe polynucleotide/oligonucleotide; 3) chemifluorescence, e.g., using alkaline phosphatase and the substrate AttoPhos (Amersham) or other substrates that produce fluorescent products; 4) chemiluminescence (e.g., using either horseradish peroxidase and/or alkaline phosphatase with substrates that produce photons as breakdown products; kits providing reagents and protocols are available from such commercial sources as Amersham, Boehringer-Mannheim, and Life TechnologieslGibco BRL); and, 5) colorimetric methods (again using, e.g., horseradish peroxidase and/or alkaline phosphatase with substrates that produce a colored precipitate; kits are available from Life Technologies/Gibco BRL, and Boehringer-Mannheim). Other methods for labeling and detection will be readily apparent to one skilled in the art.

[0164] More generally, a probe can be labeled with any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical, chemical or other available means. Useful labels in the present invention include spectral labels such as fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red, rhodamine, and the like), radiolabels (e.g., 3H, 125I, 35S, 14C, 32P, 33P, etc.), enzymes (e.g., horse-radish peroxidase, alkaline phosphatase, etc.), spectral calorimetric labels such as colloidal gold or colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads. The label may be coupled directly or indirectly to a component of the detection assay (e.g., a probe, such as an oligonucleotide, isolated DNA, amplicon, restriction fragment, or the like) according to methods well known in the art. As indicated above, a wide variety of labels may be used, with the choice of label depending on sensitivity required, ease of conjugation with the compound, stability requirements, available instrumentation, and disposal provisions. In general, a detector which monitors a probe-target nucleic acid hybridization is adapted to the particular label which is used. Typical detectors include spectrophotometers, phototubes and photodiodes, microscopes, scintillation counters, cameras, film and the like, as well as combinations thereof. Examples of suitable detectors are widely available from a variety of commercial sources known to persons of skill. Commonly, an optical image of a substrate comprising a nucleic acid array with particular set of probes bound to the array is digitized for subsequent computer analysis.

[0165] Because incorporation of radiolabeled nucleotides into nucleic acids is straightforward, this detection represents one favorable labeling strategy. Exemplary technologies for incorporating radiolabels include end-labeling with a kinase or phosphatase enzyme, nick translation, incorporation of radio-active nucleotides with a polymerase and many other well known strategies.

[0166] Fluorescent labels are desirable, having the advantage of requiring fewer precautions in handling, and being amenable to high-throughput visualization techniques. Preferred labels are typically characterized by one or more of the following: high sensitivity, high stability, low background, low environmental sensitivity and high specificity in labeling. Fluorescent moieties, which are incorporated into the labels of the invention, are generally are known, including Texas red, fluorescein isothiocyanate, rhodamine, etc. Many fluorescent tags are commercially available from SIGMA chemical company (Saint Louis, Mo.), Molecular Probes (Eugene, Oreg.), R&D systems (Minneapolis, Minn.), Pharmacia LKB Biotechnology (Piscataway, N.J.), CLONTECH Laboratories, Inc. (Palo Alto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee, Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc. (Gaithersberg, Md.), Fluka Chemica-Biochemika Analytika (Fluka Chemie AG, Buchs, Switzerland), and Applied Biosystems (Foster City, Calif.) as well as other commercial sources known to one of skill. Similarly, moieties such as digoxygenin and biotin, which are not themselves fluorescent but are readily used in conjunction with secondary reagents, i.e., anti-digoxygenin antibodies, avidin (or streptavidin), that can be labeled, are suitable as labeling reagents in the context of the probes of the invention.

[0167] The label is coupled directly or indirectly to a molecule to be detected (a product, substrate, enzyme, or the like) according to methods well known in the art. As indicated above, a wide variety of labels are used, with the choice of label depending on the sensitivity required, ease of conjugation of the compound, stability requirements, available instrumentation, and disposal provisions. Non radioactive labels are often attached by indirect means. Generally, a ligand molecule (e.g., biotin) is covalently bound to a nucleic acid such as a probe, primer, amplicon, or the like. The ligand then binds to an anti-ligand (e.g., streptavidin) molecule which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound. A number of ligands and anti-ligands can be used. Where a ligand has a natural anti-ligand, for example, biotin, thyroxine, and cortisol, it can be used in conjunction with labeled anti-ligands. Alternatively, any haptenic or antigenic compound can be used in combination with an antibody. Labels can also be conjugated directly to signal generating compounds, e.g., by conjugation with an enzyme or fluorophore or chromophore. Enzymes of interest as labels will primarily be hydrolases, particularly phosphatases, esterases and glycosidases, or oxidoreductases, particularly peroxidases. Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc. Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol. Means of detecting labels are well known to those of skill in the art. Thus, for example, where the label is a radioactive label, means for detection include a scintillation counter or photographic film as in autoradiography. Where the label is optically detectable, typical detectors include microscopes, cameras, phototubes and photodiodes and many other detection systems which are widely available.

[0168] Production of Recombinant Virus

[0169] Negative strand RNA viruses can be genetically engineered and recovered using a recombinant reverse genetics approach (U.S. Pat. No. 5,166,057 to Palese et al.). Although this method was originally applied to engineer influenza viral genomes (Luytjes et al. (1989) Cell 59:1107-1113; Enami et al. (1990) Proc. Natl. Acad. Sci. USA 92:11563-11567), it has been successfully applied to a wide variety of segmented and nonsegmented negative strand RNA viruses, e.g., rabies (Schnell et al. (1994) EMBO J. 13: 4195-4203); VSV (Lawson et al. (1995) Proc. Natl. Acad. Sci. USA 92: 4477-4481); measles virus (Radecke et al.(1995) EMBO J. 14:5773-5784); rinderpest virus (Baron and Barrett (1997) J.Virol. 71: 1265-1271); human parainfluenza virus (Hoffman and Banerjee (1997) J. Virol. 71: 3272-3277; Dubin et al. (1997) Virology 235:323-332); SV5 (He et al. (1997) Virology 237:249-260); canine distemper virus (Gassen et al. (2000) J. Virol. 74:10737-44); and Sendai virus (Park et al. (1991) Proc. Natl. Acad. Sci. USA 88: 5537-5541; Kato et al. (1996) Genes to Cells 1:569-579).

[0170] Recently, a system for producing recombinant subgroup A RSV (e.g., attenuated recombinant RSV suitable for vaccine production) has been described by the inventors and coworkers in WO 02/44334 by Jin et al. entitled “Recombinant RSV virus expression systems and vaccines,” the disclosure of which is incorporated herein in its entirety. Rescue of subgroup A RSV has also been described, e.g., in Jin et al. (1998) Virology 251:206-214 and Collins et al. (1995) Proc. Natl. Acad. Sci. USA 92:11563-11567. (See also e.g., Jin et al. (2000) J. Virol. 74:74-82; Jin et al. (2000) Virology 273:210-218; Cheng et al. (2001) Virology 283:59-68; Tang et al. (2001) J. Virol. 75:11328-11335; U.S. patent application Ser. No. 60/444,287 (filed on Jan. 31, 2003) by Jin et al. entitled “Functional mutations in respiratory syncytial virus”; and U.S. patent application Ser. No. 10/672,302 (filed on Sep. 26, 2003) by Jin et al. entitled “Functional mutations in respiratory syncytial virus.”) Rescue of subgroup B RSV is briefly described below and in the examples herein.

[0171] In brief, recombinant RSV incorporating the nucleic acids of this invention are generated, for example, in a suitable cell line (e.g., Vero or Hep-2 cells) by transfection of the cells with an antigenomic cDNA. Typically, the antigenomic cDNA is flanked by a T7 RNA polymerase promoter and a hepatitis delta virus ribozyme plus the T7 transcriptional terminator. Plasmids expressing the viral N, P, and L proteins (and optionally also the M2-1 protein) are also introduced into the cells, and a T7 RNA polymerase is typically expressed in the transfected cells (e.g., by infection of the cells with a modified vaccinia virus Ankara expressing T7 RNA polymerase). Recombinant RSV can also be produced by infection of suitable cells with previously isolated recombinant virus. Techniques for propagation, separation from host cell cellular components, and/or further purification of RSV are well known to those skilled in the art.

[0172] Methods of producing recombinant RSV are a feature of the invention. In the methods, a host cell into which a vector comprising a nucleic acid of the invention has been introduced is cultured in a suitable culture medium under conditions permitting expression of the nucleic acid (e.g., coexpression of RSV N, P, and L and optionally M2-1 and/or T7 RNA polymerase). The recombinant respiratory syncytial virus is then isolated from the host cell and/or the medium. Typically, the nucleic acid comprises an entire RSV genome or antigenome. Alternatively, the nucleic acid can comprise a portion of an RSV genome or antigenome (e.g., one or more open reading frames encoding proteins to be assembled with an RSV genome from another source to form the recombinant virus).

[0173] Recombinant RSV (e.g., attenuated recombinant RSV) produced according to the methods described herein are also a feature of the invention, as are recombinant RSV (e.g., attenuated recombinant RSV) comprising one or more nucleic acids and/or polypeptides of the invention.

[0174] Cell Culture

[0175] Typically, propagation of a recombinant virus (e.g., recombinant RSV) is accomplished in the media compositions in which the host cell is commonly cultured. Suitable host cells for the replication of RSV include, e.g., Vero cells and HEp-2 cells. 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.

[0176] 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, 5th ed., Livingston, Edinburgh; Adams (1980) Laboratory Techniques in Biochemistry and Molecular Biology-Cell Culture for Biochemists, Work and Burdon (eds.) Elsevier, Amsterdam. Additionally, variations in such procedures adapted to the present invention are readily determined through routine experimentation.

[0177] Cells for production of RSV can be cultured in serum-containing or serum free medium. In some cases, e.g., for the preparation of purified viruses, it is desirable to grow the host cells in serum free conditions. For example, cells can be grown to the desired density in serum-containing medium, infected, and then maintained in serum-free medium. 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, Minn.); NBS bioreactors (New Brunswick Scientific, Edison, N.J.); and laboratory and commercial scale bioreactors from B. Braun Biotech International (B. Braun Biotech, Melsungen, Germany).

[0178] Other useful references, e.g. for cell isolation and culture (e.g., of bacterial cells containing recombinant nucleic acids, e.g., for subsequent nucleic acid isolation) include Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique, third edition, Wiley-Liss, New York and the references cited therein; Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips (eds) (1995) Plant Cell, Tissue and Organ Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg N.Y.) and Atlas and Parks (eds) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, Fla.

[0179] Introduction of Vectors Into Host Cells

[0180] Vectors, e.g., vectors incorporating RSV polynucleotides, 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, e.g., Vero cells or Hep-2 cells, using the transfection reagent LipofectACE or Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. Alternatively, electroporation can be employed to introduce vectors incorporating RSV genome segments into host cells.

[0181] Model Systems

[0182] Attenuated RSV, e.g. those described herein comprising all or part of SEQ ID NO:1 or variations thereof, can be tested in in vitro and in vivo models to confirm adequate attenuation, genetic stability, and/or immunogenicity for vaccine use. In in vitro assays, e.g., replication in cultured cells, the virus can be tested, e.g., for genetic stability, temperature sensitivity of virus replication and/or a small plaque phenotype. RSV can be further tested in animal models of infection. A variety of animal models, e.g., primate (e.g., chimpanzee, African green monkey) and rodent (e.g., cotton rat), are known in the art, as described briefly herein and in U.S. Pat. No. 5,922,326 to Murphy et al. (Jul. 13, 1999) entitled “Attenuated respiratory syncytial virus compositions”; U.S. Pat. No. 4,800,078; Meignier et al. eds. (1991) Animal Models of Respiratory Syncvtial Virus Infection, Merieux Foundation Publication; Prince et al. (1985) Virus Res. 3:193-206; Richardson et al. (1978) J. Med. Virol. 3:91-100; Wright et al. Infect. Immun. (1982) 37:397-400; and Crowe et al. (1993) Vaccine 11:1395-1404.

[0183] Methods and Compositions for Prophylactic Administration of Vaccines

[0184] One aspect of the invention provides immunogenic compositions (e.g., vaccines) comprising an immunologically effective amount of a recombinant RSV of the invention (e.g., an attenuated live recombinant RSV), an immunologically effective amount of a polypeptide of the invention, and/or an immunologically effective amount of a nucleic acid of the invention.

[0185] A related aspect of the invention provides methods for stimulating the immune system of an individual to produce a protective immune response against respiratory syncytial virus. In the methods, an immunologically effective amount of a recombinant RSV of the invention, an immunologically effective amount of a polypeptide of the invention, and/or an immunologically effective amount of a nucleic acid of the invention is administered to the individual in a physiologically acceptable carrier.

[0186] The RSV, polypeptides, and nucleic acids 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 RSV. 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, 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, oral, topical, etc. The resulting aqueous solutions can e.g., be packaged for use as is or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration

[0187] Generally, the RSV (or RSV components) of the invention are administered in a quantity sufficient to stimulate an immune response specific for one or more strains of RSV (e.g., an immunologically effective amount of RSV or an RSV component is administered). Preferably, administration of RSV elicits a protective immune response. Dosages and methods for eliciting a protective anti-viral immune response, adaptable to producing a protective immune response against RSV, are known to those of skill in the art. See, e.g., U.S. Pat. No. 5,922,326; Wright et al. (1982) Infect. Immun. 37:397-400; Kim et al. (1973) Pediatrics 52:56-63; and Wright et al. (1976) J. Pediatr. 88:931-936. For example, virus can be provided in the range of about 103-106 pfu (plaque forming units) per dose administered (e.g., 104-105 pfu per dose administered). Typically, the dose will be adjusted based on, e.g., age, physical condition, body weight, sex, diet, mode and time of administration, and other clinical factors. The prophylactic vaccine formulation can be systemically administered, e.g., by subcutaneous or intramuscular injection using a needle and syringe or a needleless injection device. Preferably, the vaccine formulation is administered intranasally, e.g., by drops, aerosol (e.g., 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 virus. For intranasal administration, attenuated live virus vaccines are often preferred, e.g., an attenuated, cold adapted and/or temperature sensitive recombinant RSV, e.g., a chimeric recombinant RSV. As an alternative or in addition to attenuated live virus vaccines, killed virus vaccines, nucleic acid vaccines, and/or polypeptide subunit vaccines, for example, can be used, as suggested by Walsh et al. (1987) J. Infect. Dis. 155:1198-1204 and Murphy et al. (1990) Vaccine 8:497-502.

[0188] Typically, the attenuated recombinant RSV of this invention as used in a vaccine is sufficiently attenuated such that symptoms of infection, or at least symptoms of serious infection, will not occur in most individuals immunized (or otherwise infected) with the attenuated RSV. In embodiments in which viral components (e.g., the nucleic acids or polypeptides herein) are used as vaccine or immunogenic components, serious infection is not typically an issue. In some instances, the attenuated RSV (or RSV components of the invention) can still be capable of producing symptoms of mild illness (e.g., mild upper respiratory illness) and/or of dissemination to unvaccinated individuals. However, virulence is sufficiently abrogated such that severe lower respiratory tract infections do not typically occur in the vaccinated or incidental host.

[0189] 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. In neonates and infants, for example, multiple administrations may be required to elicit sufficient levels of immunity. Administration can continue at intervals throughout childhood, as necessary to maintain sufficient levels of protection against wild-type RSV infection. Similarly, adults who are particularly susceptible to repeated or serious RSV infection, such as, for example, health care workers, day care workers, family members of young children, the elderly, and individuals with compromised cardiopulmonary function may require multiple immunizations to establish and/or maintain protective immune responses. Levels of induced immunity can be monitored, for example, by measuring amounts of neutralizing secretory and serum antibodies, and dosages adjusted or vaccinations repeated as necessary to elicit and maintain desired levels of protection.

[0190] Alternatively, an immune response can be stimulated by ex vivo or in vivo targeting of dendritic cells with virus. 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 RSV antigens by the dendritic cells. The cells are then transferred into a subject to be vaccinated by standard intravenous transplantation methods.

[0191] Optionally, the formulation for prophylactic administration of the RSV also contains one or more adjuvants for enhancing the immune response to the RSV antigens. Suitable adjuvants include, for example: complete Freund's adjuvant, incomplete Freund's adjuvant, 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 adjuvant QS-21.

[0192] If desired, prophylactic vaccine administration of RSV 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 RSV, or can be administered separately. Either the protein or an expression vector encoding the protein can be administered to produce an immunostimulatory effect.

[0193] Although vaccination of an individual with an attenuated RSV of a particular strain of a particular subgroup can induce cross-protection against RSV of different strains and/or subgroups, cross-protection can be enhanced, if desired, by vaccinating the individual with attenuated RSV from at least two strains, e.g., each of which represents a different subgroup. Similarly, the attenuated RSV vaccines of this invention can optionally be combined with vaccines that induce protective immune responses against other infectious agents.

[0194] Kits and Reagents

[0195] The present invention is optionally provided to a user as a kit. For example, a kit of the invention contains one or more nucleic acid, polypeptide, antibody, or cell line described herein. Most often, the kit contains a diagnostic nucleic acid or polypeptide (e.g., an antibody or a probe, e.g., as a cDNA microarray packaged in a suitable container) or other nucleic acid such as one or more expression vector. The kit typically further comprises one or more additional reagents, e.g., substrates, labels, primers, tubes and/or other accessories, reagents for collecting samples, buffers, hybridization chambers, cover slips, etc. The kit optionally further comprises an instruction set or user manual detailing preferred methods of using the kit components.

[0196] Digital Systems

[0197] The present invention provides digital systems, e.g., computers, computer readable media and integrated systems comprising character strings corresponding to the sequence information herein for the polypeptides and nucleic acids herein, including, e.g., those sequences listed herein and the various silent substitutions and conservative substitutions thereof. Integrated systems can further include, e.g., gene synthesis equipment for making genes and/or peptide synthesis equipment for making polypeptides corresponding to the character strings.

[0198] Various methods known in the art can be used to detect homology or similarity between different character strings, or can be used to perform other desirable functions such as to control output files, provide the basis for making presentations of information including the sequences and the like. Examples include BLAST, discussed supra. Computer systems of the invention can include such programs, e.g., in conjunction with one or more data file or data base comprising a sequence as noted herein.

[0199] Thus, different types of homology and similarity of various stringency and length can be detected and recognized in the integrated systems herein. For example, many homology determination methods have been designed for comparative analysis of sequences of biopolymers, for spell-checking in word processing, and for data retrieval from various databases. With an understanding of double-helix pair-wise complement interactions among 4 principal nucleobases in natural polynucleotides, models that simulate annealing of complementary homologous polynucleotide strings can also be used as a foundation of sequence alignment or other operations typically performed on the character strings corresponding to the sequences herein (e.g., word-processing manipulations, construction of figures comprising sequence or subsequence character strings, output tables, etc.).

[0200] Thus, standard desktop applications such as word processing software (e.g., Microsoft Word™ or Corel WordPerfec™) and database software (e.g., spreadsheet software such as Microsoft Excel™, Corel Quattro Pro™, or database programs such as Microsoft Access™or Paradox™) can be adapted to the present invention by inputting a character string corresponding to one or more polynucleotides and polypeptides of the invention (either nucleic acids or proteins, or both). For example, a system of the invention can include the foregoing software having the appropriate character string information, e.g., used in conjunction with a user interface (e.g., a GUI in a standard operating system such as a Windows, Macintosh or LINJX system) to manipulate strings of characters corresponding to the sequences herein. As noted, specialized alignment programs such as BLAST can also be incorporated into the systems of the invention for alignment of nucleic acids or proteins (or corresponding character strings).

[0201] Systems in the present invention typically include a digital computer with data sets entered into the software system comprising any of the sequences herein. The computer can be, e.g., a PC (Intel x86 or Pentium chip- compatible DOS™, OS2™ WIDOWS™ WINDOWS NT™, WINDOWS95™, WINDOWS98™ LINUX based machine, a MACINTOSH™, Power PC, or a UNIX based (e.g., SUN™ work station) machine) or other commercially common computer which is known to one of skill. Software for aligning or otherwise manipulating sequences is available, or can easily be constructed by one of skill using a standard programming language such as Visualbasic, Fortran, Basic, Java, or the like.

[0202] Any controller or computer optionally includes a monitor which is often a cathode ray tube (“CRT”) display, a flat panel display (e.g., active matrix liquid crystal display, liquid crystal display), or others. Computer circuitry is often placed in a box which includes numerous integrated circuit chips, such as a microprocessor, memory, interface circuits, and others. The box also optionally includes a hard disk drive, a floppy disk drive, a high capacity removable drive such as a writeable CD-ROM, and other common peripheral elements. Inputting devices such as a keyboard or mouse optionally provide for input from a user and for user selection of sequences to be compared or otherwise manipulated in the relevant computer system.

[0203] The computer typically includes appropriate software for receiving user instructions, either in the form of user input into a set parameter fields, e.g., in a GUI, or in the form of preprogrammed instructions, e.g., preprogrammed for a variety of different specific operations. The software then converts these instructions to appropriate language, e.g., for instructing the operation of equipment, e.g., gene and/or peptide synthesis equipment, to carry out the desired operation.

[0204] The software can also include output elements for controlling nucleic acid synthesis (e.g., based upon a sequence or an alignment of a sequences herein) or other operations.

[0205] In an additional aspect, the present invention provides system kits embodying the methods, composition, systems and apparatus herein. System kits of the invention optionally comprise one or more of the following: (1) an apparatus, system, system component or apparatus component as described herein; (2) instructions for practicing the methods described herein, and/or for operating the apparatus or apparatus components herein and/or for using the compositions herein. In a further aspect, the present invention provides for the use of any apparatus, apparatus component, composition or kit herein, for the practice of any method or assay herein, and/or for the use of any apparatus or kit to practice any assay or method herein.

EXAMPLES

[0206] The following sets forth a series of experiments that demonstrate construction of RSV B9320 cDNAs and recovery of recombinant RSV from the cDNAs. It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. Accordingly, the following examples are offered to illustrate, but not to limit, the claimed invention.

Materials and Methods

[0207] Cells and Viruses

[0208] Monolayer cultures of HEp-2 and Vero cells (obtained from the American Type Culture Collection, ATCC) were maintained in minimal essential medium (MEM) containing 5% fetal bovine serum. RSV A2 was obtained from the ATCC and grown in Vero cells in Opti-MEM. RSV subgroup B strain 9320, originally isolated in Massachusetts in 1977 (Hierholzer and Hirsch (1979) J. Infect. Dis. 140:826-828), was obtained from the ATCC and grown in Vero cells in Opti-MEM. Infected cells were maintained in serum-free Opti-MEM medium. Modified vaccinia virus Ankara expressing bacteriophage T7 RNA polymerase (MVA-T7; Sutter et al. (1995) FEBS Lett. 371:9-12 and Wyatt et al. (1995) Virology 210:202-205) was provided by Dr. Bernard Moss and amplified in CEK cells. Recombinant fowlpox virus expressing the T7 RNA polymerase (FPV-T7; Britton et al. (1996) “Expression of bacteriophage T7 RNA polymerase in avian and mammalian cells by a recombinant fowlpox virus” J Gen Virol 77:963-7) was obtained from Dr. Michael Skinner and grown in CEK cells.

[0209] Sequencing

[0210] RSV B9320 was grown in Vero cells and viral RNA was extracted from virus purified by ultracentrifugation from infected cell culture supernatant. 9320 genome sequences were obtained by sequencing DNA fragments generated by RT-PCR; the cDNA full length clone was also sequenced for comparison. All sequencing was done by Sequetech, Mountain View Calif. (www.sequetech.com).

[0211] Sequence Analysis

[0212] Sequence analysis was performed with Vector NTI version 6.0 and 8.0 ContigExpress and AlignX (Informax, Inc., www.informaxinc.com). Pairwise nucleic acid or polypeptide sequence alignments were performed with Vector NTI AlignX using default parameters set by the provider.

[0213] Construction of Full-length cDNA of RSV Subgroup B9320 Strain and Recovery of Infectious Respiratory Syncytial Virus from cDNA

[0214] Construction of RSV 9320 Protein Expression Plasmids

[0215] The 9320 N, P, and L protein coding regions were each cloned into a pCITE vector (Novagen, Madison, Wis.) under control of a T7 RNA polymerase promoter, to produce expression plasmids pB-N, pB-P, and pB-L.

[0216] pB-N: The N gene was amplified by RT-PCR from 9320 RNA extracted from virus particles purified by ultracentrifugation, using primers XC19 (5′-GATCCCATGGCTCTTAGCAAAGTCAAG-3′ containing Nco I site, SEQ ID NO:20) and XC020 (5′-GTACGGATCCGTTGACTTATTTGCCCCGTAT-3′ containing BamHI site, SEQ ID NO:21), and cloned between the NcoI and BamHI sites of pCITE2a/3a (Novagen) under the control of T7 promoter. This N protein expression plasmid was designated as AD740.

[0217] pB-P: The P gene was amplified by RT-PCR using primers XC17 (5′-GATCCCATGGAGAAGTTTTGCACCTG-3′ with Nco I site, SEQ ID NO:22) and XC018 (5′-GTACGGATCCTGAGTGAGTTGATCACTG-3′ with BamH I site, SEQ ID NO:23) and cloned between the NcoI and BamHI sites of pCITE2a/3a. This clone was designated as AD741.

[0218] pB-L: The L gene was cloned from three cDNA subclones obtained by RT-PCR and the clone was assigned as AD778.

[0219] To obtain one subclone, primers XC0O3 (5′ GCTTGGCCATAACGATTCTATATCATCC-3′, SEQ ID NO:24) and XC014 (5′-GGTAGTATAATGTTGTGCACTTTAG-3′, SEQ ID NO:25) were used to amplify 9320 L from nt8511 to nt11685 and the cDNA was cloned into T/A vector (Invitrogen, pCR 2.1) to generate subclone AD762.

[0220] To obtain the second subclone, primers XC011 (5′-GGTCACGATTTACAAGATAAGCTCC-3′, SEQ ID NO:26) and XC007 (5′-CAGATCCTTTTAACTTGCTACCTAGGCACA-3′ SEQ ID NO:27) were used to amplify nt 11686 to nt14495 and the BamH I to Avr II fragment was cloned into the T/A vector as AD763.

[0221] To obtain the third subclone, primers XC009 (5′-CTTACGTGTGCCTAGGTAGCAAG-3′, SEQ ID NO:28) and XC010 (5′-ACGAGAAAAAAAGTGTCAAAAACTAATGTCTCG, SEQ ID NO:29) were used to amplify 9320 nt 14495 to 15225, producing a first PCR product. To add the ribozyme cleavage sequence (RBZ) and T7 terminator sequence (T7ø), a second PCR product was obtained using XC015 (5′-GTTTTTGACACTTTTTTTCTCGTGGCCGGCATGGTCCCAGCC-3′, SEQ ID NO:30) and XC016 (5′-GATCTAGAGCTCCAAGCTTGCGGCCGCGTCGAC-3′ containing the Kpn I site, SEQ ID NO:31) as primers and pRSV-A2 full-length antigenomic cDNA (Jin et al. (1998) Virology 251:206-214) as template. Since primers XC010 and XC015 contained overlapping sequences, these two PCR products were annealed, extended and amplified by PCR using XC009 and XC016 as primers. The cDNA was cloned into the T/A vector and designated as AD764.

[0222] The three subclones were verified by sequence analysis. To join the three L subclones together, the Avrll and Kpn I fragment was removed from AD764 and cloned into AD763 and the larger clone was designated as AD767. The BamHI to NotI restriction fragment from nt11685 to the sequence downstream of the T7 terminator was removed from AD767 and cloned into pCITE2a/3a vector under the control of the T7 promoter and the plasmid was designated as AD766. The BamHI fragment from nt 8511 to nt 11685 was removed from clone AD762 and inserted into the BamH I site of AD766. The second BamHI site at position of nt 11685 was then knocked out by site-directed mutagenesis and the clone is designated as pB-L (AD778).

[0223] The functions of the pB-N, pB-P, and pB-L expression plasmids were examined by the RSV minigenome assay (as described in, e.g., Tang et al. (2002) Virology 302:207-216). A level of the CAT reporter gene similar to those of A2 expression plasmids was detected in cells transfected with pB-N, pB-P, pB-L and pRSVCAT minigenome, indicating all three of these plasmids are functional.

[0224] Assembly of Full-length Antigenomic cDNA of RSV 9320 Strain

[0225] An antigenomic cDNA spanning the entire RSV 9320 genome was assembled by sequential ligation of RSV cDNA fragments with the indicated unique restriction sites (FIG. 1). In brief, six cDNA fragments (B1-B6) were generated from 9320 viral RNA by RT-PCR using the pfu polymerase (Stratagene, La Jolla, Calif.) and cloned into a modified pET vector containing the RSV 9320 unique restriction enzyme sites (Xma I, Avr II, Sac I, BamH I, and BssHII). The Xma I-Avr II cDNA fragment (B1) containing the T7 RNA polymerase promoter proximal to the 5′ antigenomic sense DNA was joined with the Avr II-Sac I cDNA fragment (B2) to form the B7 fragment (through a SacI site, as described below). The B7 fragment was used to replace the corresponding region in a full-length RSV A2-B9320 chimera containing the G, F and M2 sequence (B3). The Sac I restriction site at nt 2310 in the resulting pUC-B8 was mutated without affecting the coding sequence of the SH gene. The L gene fragment (B10) was assembled from B4 and B9 fragments. The hepatitis delta virus ribozyme (RBZ) and the T7 RNA polymerase terminator sequence was amplified from RSV A2 antigenomic cDNA (Jin et al. (1998) “Recombinant human respiratory syncytial virus (RSV) from cDNA and construction of subgroup A and B chimeric RSV” Virology 251:206-214) and ligated to the trailer sequence through PCR (B6). Ligation of B5 and B6 fragments were mediated through the Avr II and Not I restriction sites. The BamH I site at nt position 11685 was deleted from B10 cDNA by mutagenesis without affecting the protein coding sequence. The L gene (B10) was cloned into the chimeric clone that contained the 9320 B8 fragment and A2 L to replace the A2-L sequence through the BamH I and Not I restriction sites. The antigenomic cDNA clone (B11) encoding the complete RSV 9320 genome was designated pB9320C4. In addition, an antigenomic cDNA clone containing a single C to G change at the fourth position of the leader sequence was also obtained by mutagenesis and designated pB9320G4. A more detailed description of the cDNA construction follows.

[0226] Positions of various primers and subclones used in cloning the full length cDNA are illustrated in FIGS. 1-3. The 3′ genome was amplified by RT-PCR using PFU polymerase with primer V1964 (5′-GGGTACCCCCGGGTAATACGACTCACTATAGGGACGGGAAAAAATG-3′ containing Xma I restriction enzyme, the T7 promoter and the leader sequences, SEQ ID NO:32) and XC051 (5′-GTTAACTTAGAGCTCTACATCATC-3′ containing the Sac I restriction site present in 9320 genome at position of nt 2310, SEQ ID NO:33). The PCR fragment was cloned between the Xma I and SacI sites of the modified pET vector (pET21b was cut with BspEI, and the pET21b was ligated with a polylinker with XmaI, SmaI, SacI, MscI, BamHI, SpeI, PmII, and BssHII restriction sites to produce the modified pET-21b vector) and designated as AD803. A second PCR DNA that contained nt 2106 to 4494 was obtained by RT/PCR using XC034 (5′-GTGTGGTCCTAGGCAATGCAGCAG-3′, SEQ ID NO:34) and XC032 (5′-GACACAGCATGATGGTAGAGCTCTATGTG-3′, SEQ ID NO:35) as primers and was cloned into the Sac I site of the pET vector for sequence analysis. This SacI fragment was then moved to AD803 through the Sac I site in AD803 (producing B7). In order to ligate the cDNA encoding NS1, NS2, N, P, M and SH genes with the rest of the 9320 cDNA, the Sac I site at position nt 2310 was removed by mutagenesis and the resulting clone was designated as AD816. The Xma I to Sac I fragment from AD816 was released to replace the corresponding region of the A2 sequence in the chimeric cDNA AD379 that had the G and F genes of 9320 in place of A2 G and F genes (in a pUC19 backbone, Cheng et al. (2001) Virology 283:59-68). This clone was designated as AD827.

[0227] The cDNA containing the G, F, and M2 genes of 9320 strain was derived by RT-PCR using XC063 (5′-GCTAAGTGAACATAAAACATTCTGTAAC-3′, SEQ ID NO:36) as RT primer and XC006 (5′-CCATTAATAATGGGATCCATTTTGTC-3′ with SacI site, SEQ ID NO:37) and XC062 (5′-CACATAGAGCTCTACCATCATGCTGTGTC-3′ with BamH I site, SEQ ID NO:38) as PCR primers and was initially cloned into pET vector as AD835 for sequence analysis. The SacI to BamH I fragment from AD835 was then moved to AD827 and the clone was designated as AD848.

[0228] The BamHI and NotI fragment from pB-L (AD869 encoding 9320 L with the two Sac I sites at positions of nt 10376 and nt 14951 knocked-out) was swapped into AD848 to complete the assembly of a full length antigenomic cDNA of RSV 9320.

[0229] Three mutations introduced by PCR during the cloning process were corrected by site-directed mutagenesis in their respective subclones, as follows. To reverse a His to Asn change in L at amino acid position 209, site-directed mutagenesis was performed to correct the His with primers XC081 (5′-CATGGTTAATACACTGGTTCAATTTATATACA-3′, SEQ ID NO:41) and XC082 (5′-TGTATATAAATTGAACCAGTGTATTAACCATG-3′, SEQ ID NO:42). To correct an Arg to Lys change in N at amino acid position 194 (nt 1748), site directed mutagenesis was performed with primers XC086 (5′-GTCTTAAAAAACGAAATAAAACGCTACAAGGGCCTCATACC-3′, SEQ ID NO:43) and XC087 (5′GGTATGAGGCCCTTGTAGCGTTTTATTTCGTTTTTTAAGAC-3′, SEQ ID NO:44). A Ser to Asn change in NS1 at amino acid position 108 was not corrected.

[0230] The recombinant 9320 cDNA has the following genetic tags that are different from wild-type 9320 virus. (The enclosed sequence, SEQ ID NO:1, is the wild type RSV 9320 strain and does not reflect the recombinant DNA sequence.) First, Sac I sites at nt 2310, 10376 and 14951 were removed without changing the protein coding sequences, using the following primers: SacI at 2310 nt, XC049 (5′-GATGATGTAGAGCTTTAAGTTAAC-3′, SEQ ID NO:45) and XC050 (5′-GTTAACTTAAAGCTCTACATCATC-3′, SEQ ID NO:46); SacI at 10376 nt, XC088 (5′-CTAACTGGTAAAGAAAGAGAGCTTAGTGTAGGTAGAATGTTTGC-3′, SEQ ID NO: 47) and XC089 (5′-GCAAACATTCTACCTACACTAAGCTCTCTTTCTTTACCAGTTAG-3′, SEQ ID NO: 48); and SacI at 14951 nt, XC090 (5′-GTTTAACAACCAATGAGCTTAAAAAGCTGATTAAAATTAC-3′, SEQ ID NO:49) and XC091 (5′-GTAATTTTAATCAGCTTTTAAGCTCATTGGTTGTTAAAC-3′, SEQ ID NO:50). The removal of the two Sac I sites at positions nt 10376 and 14951 in the L gene from AD864 to generate AD869 did not alter the amino acid sequence of L. Second, a BamH I site at nt 11685 was removed using primers XC067 (5′-CATTAATGAGGGACCCACAGGCTTTAG-3′, SEQ ID NO:39) and XC068 (5′-CTAAAGCCTGTGGGTCCCTCATTAATG-3′, SEQ ID NO:40). Third, a Sac I site at nt 4477 was added using XC032 (5′-GACACAGCATGATGGTAGAGCTCTATGTG, SEQ ID NO:35).

[0231] It was previously reported that changing the C at the fourth nucleotide position of the leader region of RSV A2 to a G increased the promoter strength, resulting in increased transcription/replication of an RSV minigenome (Collins et al. (1993) “Rescue of a 7502-nucleotide (49.3% of full-length) synthetic analog of respiratory syncytial virus genomic RNA” Virology 195:252-256) and higher virus recovery efficiency (Jin et al. (1998) Virology 251:206-214). Thus, as noted, a 9320 cDNA with a C4 to G change in the leader sequence at the antigenomic sense was made to increase the promoter strength, and the resulting clone was designated as AD897 (pB9320G4).

[0232] Construction of G Gene Deletion Mutants

[0233] Two mutants were constructed to determine if the G gene of RSV B9320 strain is dispensable, e.g., for viral replication in tissue culture and/or an animal host. In one mutant, the entire open reading frame of the G gene was removed from the 9320 cDNA. In the other mutant, the region encoding the cysteine noose and heparin binding sites of G was removed from the 9320 cDNA.

[0234] For the RSV A2 strain, the G protein has been shown to be dispensable for virus replication in vitro (Techaarpomkul et al. (2001) “Functional analysis of recombinant respiratory syncytial virus deletion mutants lacking the small hydrophobic and/or attachment glycoprotein gene” J Virol 75:6825-34 and Teng et al. (2001) “Contribution of the respiratory syncytial virus G glycoprotein and its secreted and membrane-bound forms to virus replication in vitro and in vivo” Virology 289:283-96). However, rA2ΔG (RSV A2 lacking G) replicated poorly in HEp-2 cells, and its replication was attenuated in the respiratory tracts of mice. Previously, it was also shown that a cold-adapted RSV B1 strain, cp-52, had both the SH and G genes deleted (Karron et al. (1997) Proc Natl Acad Sci USA 94:13961-13966). However, this deletion mutant replicated poorly and was over-attenuated in animals and in humans. To determine whether the G protein was also dispensable for 9320 replication in vitro, an antigenomic cDNA was constructed in which the entire G gene (957 nt) including the gene start and gene end sequences was deleted from the cDNA and the new SH-F intergenic region contained 75 nt.

[0235] To construct the 9320 antigenomic cDNA that had the G gene deleted, deletion mutagenesis was performed on a pET-S/B cDNA subclone that contained sequences of the 9320 G, F and M2 genes using a pair of PCR primers flanking the G open reading frame in opposite orientations (5′-GATCCCATACTAATAATTCATCATTATG-3′, SEQ ID NO:51, and 5′-AGCAGAGAACCGTGATCTATCAAGCAAG-3′, SEQ ID NO:52) using the ExSite PCR-based Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.). The deletion was confirmed by restriction enzyme digestion and nucleotide sequencing analysis. The Sac I-BamH I fragment containing only the F and M2 genes was introduced into pB9320G4, and the antigenomic cDNA was designated pB9320ΔG.

[0236] To delete only the cysteine noose and heparin binding sites of G (amino acids 164-197), a small cDNA fragment of nt 5179-5280 nt was deleted from the 9320 G gene using primers XC079 (5′-GTAATCATCTTTTGGTTTTTTTGGTGG-3′, SEQ ID NO:53) and XC080 (5′-CCAACCATCAAACCCACAAACAAACCAACCGTC-3′, SEQ ID NO:54). The cDNA containing the desired deletion was then removed from the subclone by digestion with Sac I and BamHI and shuffled into the full-length 9320 antigenomic cDNA. The resulting antigenomic cDNA was designated pB9320ΔHBS.

[0237] Recovery of Recombinant Viruses from cDNAs

[0238] Recovery of 9320 viruses (rg9320C4, rg9320G4, rg9320ΔG and rg9320ΔHBS) by reverse genetics (rg) was performed as described previously (Jin et al. (1998) Virology 251:206-214). Briefly, HEp-2 cells were infected with MVA-T7 at an m.o.i. of 5.0 and transfected with 0.4 μg of pB-N (pN), 0.4 μg of pB-P (pP), 0.2 μg of pB-L (pL), and 0.8 μg of pB9320C4, pB9320G4, pB9320ΔG or pB9320ΔHBS by Lipofectamine™ 2000 (Invitrogen, Carlsbad, Calif.). In some transfection reactions, 0.2 μg pRSV-M2-1 (encoding the RSV A2 M2-1 protein) was also included. Alternatively, Vero cells were infected with FPV-T7 (Britton et al. (1996) J Gen Virol 77:963-7) at an m.o.i. of 1.0 for 1 hr and transfected with the DNAs as above. Transfected cells were incubated at 35° C. Three days after transfection, the culture supernatant was used to infect Vero cells to amplify the recovered viruses. Six days after infection, the culture supernatant was harvested and virus-infected cells were identified by immunostaining using polyclonal anti-RSV A2 serum (Biogenesis, Kingston, N.H.). The recombinant virus from the culture supernatant was plaque purified and amplified in Vero cells.

[0239] Replication of rg9320C4, rg9320G4, rg9320ΔG in Tissue Culture

[0240] Replication of rg9320C4, rg9320G4 and rg9320ΔG in Vero and HEp-2 cells was compared with replication of wild type 9320. Vero or HEp-2 cell monolayers in 6-well plates were infected with each virus in duplicate at an m.o.i. of 0.1. After 1 hr adsorption at room temperature, the infected cells were washed with PBS three times and incubated with 2 ml of OptiMEM at 35° C. At 24 hr intervals, aliquots of 250 μl of culture supernatant were removed and stored at −80° C. prior to virus titration. Each aliquot taken was replaced with the same amount of fresh media. The virus titer was determined by plaque assay on Vero cells using an overlay consisting of 1% methylcellulose and 1×MEM/L15 (JRH Bioscience, Lenexa, Kans.) containing 2% FBS. After incubation at 35° C. for 6 days, the monolayers were fixed with methanol and plaques enumerated by immunostaining.

[0241] Western Blotting Analysis of Virus Infected Cells

[0242] Vero or HEp-2 cells were infected with virus at an m.o.i of 5.0 and the infected cells were lysed in Laemmli protein sample buffer (Bio-Rad, Hercules, Calif.). The cell lysates were electrophoresed on 12% polyacrylamide gels containing 0.1% SDS, and then transferred to a nylon membrane. The blots were incubated with either polyclonal anti-RSV A2 serum or a mixture of four monoclonal antibodies against the G protein of RSV B strain (2434DB3, 2218BD5, 2218AE7 and 2218DG7) obtained from Dr. Gregory Storch (Storch et al. (1991) “Antigenic and genomic diversity within group A respiratory syncytial virus” J Infect Dis 163:858-861). Viral proteins were visualized by incubation with horseradish peroxidase (HRP)-conjugated secondary antibodies followed by chemiluminescent detection (Amersham Biosciences, Piscataway, N.J.).

Results and Discussion

[0243] We have described the construction of a full-length antigenomic cDNA derived from RSV subgroup B9320 strain and recovery of infectious virus from the cDNA. The antigenomic sequence (complementary to the wild-type RSV 9320 genome and not including the changes introduced into our recombinant RSV) is listed as SEQ ID NO:1. The sequence is being deposited in GenBank (accession number AY353550).

[0244] The RSV 9320 genome contains 15,225 nucleotides and shares 97.8% and 86% identity compared to RSV B1 and A2 strains, respectively. As noted previously, the A2 genome contains 15,222 nucleotides; the B1 genome contains 15,225 nucleotides (Karron et al. (1997) Proc Natl Acad Sci USA 94:13961-13966). Like the RSV A2 strain, 9320 contains 10 transcriptional units encoding 11 proteins in the order of NS1/NS2/N/P/M/SH/G/F/M2-1/M2-2/L. Amino acid sequences of the proteins are also provided: NS1 is listed as SEQ ID NO:2, NS2 as SEQ ID NO:3, N as SEQ ID NO:4, P as SEQ ID NO:5, M as SEQ ID NO:6, SH as SEQ ID NO:7, G as SEQ ID NO:12, F as SEQ ID NO:8, M2-1 as SEQ ID NO:9, M2-2 as SEQ ID NO:10, and L as SEQ ID NO:11.

[0245] Table 3 lists the size of each of the 11 proteins for the 9320, B1, and A2 strains.

3TABLE 3Length of protein (amino acids)B9320B 1A2NS 1139139139NS 2124124124N391391391P241241241M256256256SH656564G292299298F574574574M2-1195195194M2-2939390L216621662165

[0246] Table 4 lists the length of the intergenic regions for the three RSV strains.

4TABLE 4Length of intergenic region (nucleotides)INTERGENICB9320B 1A2NS 1/NS 2161619NS 2/N232326N/P331P/M999M/SH999SH/G444444G/F525252F/M2565646GS L/GE M2464646

[0247] Table 5 lists the percentage amino acid sequence identity between strains B9320 and B1, 9320 and A2, and A2 and B1 for each protein. The SH, G and M2-2 proteins display the greatest differences between A2 and 9320, while the other proteins have an amino acid identity greater than 86%.

5TABLE 5Amino acid identity (%)RSV GeneB9320/B1B9320/A2A2/B1NS 199.386.387NS 298.490.492N99.795.996P98.390.991M99.692.291SH97.071.276G90.352.253F99.389.289M2-199.592.8N/AM2-296.462.492L99.292.493

[0248] Recovery of Infectious 9320 from cDNA

[0249] A reverse genetics system for the A2 strain of subgroup A RSV was established several years ago (Collins et al. (1995) Proc. Natl. Acad. Sci. USA 92:11563-11567 and Jin et al. (1998) Virology 251:206-214). However, a system for recovery of subgroup B RSV has not previously been available. Herein we describe construction of an antigenomic cDNA derived from RSV subgroup B9320 and recovery of infectious RSV from cDNA. Similar to the A2 strain, rescue of 9320 depends on the expression of the viral polymerase proteins N, P and L. The M2-1 expression plasmid is not required for RSV 9320 recovery in either the FPV-T7 infected Vero or the MVA-T7 infected HEp-2 cells. However, M2-1 function was probably supplied by cryptic expression of the M2-1 protein from the transfected full-length antigenomic cDNA (Collins et al. (1999) Virology 259:251-255). The establishment of the reverse genetics system for the 9320 strain should greatly aid studies of viral protein structure and function of this divergent RSV subgroup.

[0250] Recovery of infectious RSV requires co-transfection of a minimum of three plasmids encoding the N, P and L proteins (Jin et al. (1998) Virology 251:206-214). In addition, the elongation function of M2-1 is also required for the virus recovery from cDNA (Collins et al. (1999) “Support plasmids and support proteins required for recovery of recombinant respiratory syncytial virus” Virology 259:251-255 and Collins et al. (1995) “Production of infectious human respiratory syncytial virus from cloned cDNA confirms an essential role for the transcription elongation factor from the 5′ proximal open reading frame of the M2 mRNA in gene expression and provides a capability for vaccine development” Proc. Natl. Acad. Sci. USA 92:11563-11567). The expression plasmids encoding the 9320 N, P, and L proteins were constructed and their functions were examined in the RSV minigenome assay using the pRSV/CAT replicon that contained the negative sense CAT gene flanked by the leader and trailer sequences derived from RSV A2 strain (Tang et al. (2001) J Virol 75:11328-11335). The minigenome assay indicated that the 9320 N, P and L expression plasmids functioned as well as those of RSV A2 strain.

[0251] To recover virus from RSV 9320 cDNA, pB9320C4 or pB9320G4 was transfected into MVA-T7 infected BEp-2 cells or FPV-T7 infected Vero cells together with the 9320 N, P and L expression plasmids with or without the RSV A2 M2-1 plasmid. Several days after inoculation of Vero cells with the transfected culture supernatant, syncytia formation was observed in the infected Vero cells and virus infection was confirmed by immunostaining.

[0252] Table 6 lists the recovery efficiency of recombinant RSV in the presence or absence of the M2-1 expression plasmid. FPV-T7 infected Vero cells or MVA-T7 infected HEp-2 cells were transfected with p9320C4 or p9320G4 in triplicate wells together with N, P, L expression plasmids with or without M2-1. Three days after transfection, the culture supernatants were titrated on Vero cells and the plaque numbers in pfu/ml from each well are shown. The average plaque number is given in parentheses.

6TABLE 6Average plague number (pfu/ml)MVA-T7 infectedFPV-T7 infected Vero cells (pfu/ml)HEp-2 cells (pfu/ml)Virus+M2-1−M2-1+M2-1−M2-1rg93200470, 210, 93 (124)40, 40, 75 (52)55, 5, 3 (21)18, 0, 0 (6)rg9320G41075, 1860, 1280 (1405)1140, 890, 900 (977)285, 3, 0 (96)18, 28, 0 (15)

[0253] As shown in Table 6, rg9320G4 was rescued more efficiently than rg9320 in both the FPV-T7 infected Vero cells and the MVA-T7 infected HEp-2 cells. Inclusion of the M2-1 expression plasmid slightly increased rescue efficiency in both cell types.

[0254] For vaccine production, the vaccine is typically produced from a qualified cell line that is free of any adventitious agents. The BEp-2 cells currently used for recovery of infectious RSV A2 (e.g., Collins et al. (1995) Proc. Natl. Acad. Sci. USA 92:11563-11567 and Jin et al. (1998) Virology 251:206-214) are not suitable for vaccine production. Vero cells were therefore explored as the cell substrate for recovering 9320 virus from its cDNA. It was very difficult to recover virus from MVA-T7-infected Vero cells. FPV-T7 has been shown to have a less cytopathic effect in infected Vero cells and thus result in more efficient virus rescue of other viruses (Britton et al. (1996) J Gen Virol 77:963-7 and Das et al. (2000) “Improved technique for transient expression and negative strand virus rescue using fowlpox T7 recombinant virus in mammalian cells” J Virol Meth 89:119-127). Similarly, the recombinant RSV described here were more efficiently recovered from FPV-T7 infected Vero cells than from MVA-T7 infected cells, which may pave the way for recovering RSV vaccine candidates for clinical studies.

[0255] rg9320C4 and rg9320G4 were plaque purified and amplified in Vero cells, both reaching a titer of 1×107 pfu/ml. A recombinant virus with the G gene deleted from rg9320G4 was also obtained and the virus was designated rg9320ΔG.

[0256] The identity of the recombinant viruses generated from cDNA was analyzed by RT/PCR of each viral RNA using primer pairs spanning the introduced marker sites or the G deletion region. Digestion of the RT/PCR DNA product from nt 2104 to nt 3096 by the Sac I restriction enzyme showed that the Sac I site was present in 9320 virus but not in the recombinant viruses rg9320C4 and rg9320ΔG. Digestion of the RT/PCR product from nt 11593 to nt 11822 by BamH I confirmed that the BamH I site in the recombinant viruses was also abolished. RT/PCR using a pair of primers spanning the G gene confirmed that the G gene was deleted from rg9320ΔG, since its DNA product was approximately 1 kb shorter than that of rg9320. Sequencing of the G deletion junction region confirmed the expected deleted sequence.

[0257] The lack of G protein expression in rg9320ΔG infected cells was also confirmed by Western blotting analysis using monoclonal antibodies against the G protein of subgroup B RSV (Storch et al. (1991) J Infect Dis 163:858-861). The G protein was not expressed in rg9320ΔG-infected cells. Western blotting using a polyclonal antibody against RSV revealed an equivalent level of other viral proteins (F, N and P) synthesized by rg9320ΔG compared with rg9320G4.

[0258] Replication of the G Deletion Mutant in Tissue Culture

[0259] Replication of recombinant 9320 and its G deletion mutant were compared with replication of the biologically derived 9320 strain. Vero or HEp-2 cells were infected with 9320, rg9320C4, rg9320G4 or rg9320ΔG at an m.o.i. of 0.1, and the accumulated level of viruses released into the culture supernatant at each day was titrated in Vero cells. As shown in FIG. 4 Panel A, the growth kinetics of rg9320C4, rg9320G4 and rg9320ΔG were very similar to those of 9320 in Vero cells, reaching peak titers of 6.0 log10 pfu/ml at 96 hours post infection. In HEp-2 cells (FIG. 4 Panel B), rg9320C4 grew similarly to 9320 whereas rg9320G4 grew slightly slower. Replication of rg9320ΔG was reduced by 5-fold compared to rg9320G4.

[0260] The plaque morphology of rg9320ΔG was compared to that of rg9320G4 in Vero and HEp-2 cells. The spread of rg9320ΔG in Vero and HEp-2 cells in liquid medium was similar to that of rg9320G4. rg9320ΔG also formed plaques of similar size in both the Vero and HEp-2 cells. These data indicated that the deletion of G from 9320 did not have significant impact on virus replication in Vero and Hep-2 cells.

[0261] We have demonstrated that the G protein is not essential for RSV 9320 replication in tissue culture cells. However, deletion of G from RSV A2 strain severely affected virus replication in HEp-2 cells; rA2ΔG had a reduction of more than 3.0 log10 and did not form distinct plaques in HEp-2 cells (Teng et al. (2001) Virology 289:283-96). A study by Techaarpornkul et al. (Techaarpornkul et al. (2001) J Virol 75:6825-34) showed that rA2ΔG had 1-2 logs lower titer in HEp-2 cells and formed smaller plaques in HEp-2 cells. The G protein enhances virus binding to target cells, but it has no role in virus penetration once virus has attached the cells (Techaarpornkul et al. (2001) J Virol 75:6825-34). In Vero cells, rA2ΔG replicated as well as wt A2 strain, indicating an alternative pathway might be present in Vero cells for efficient virus entry that is independent of the G protein (Teng et al. (2001) Virology 289:283-96). Like rA2ΔG, rg9320ΔG replicated efficiently in Vero cells; however, in contrast to rA2ΔG, its replication was only slightly reduced in HEp-2 cells. The reduction of rg9320ΔG virus in HEp-2 cells was 5-fold compared to the parental rg9320G4 virus and the plaque size reduction in HEp-2 cells was also less apparent. Therefore, 9320 appears to be less dependent on the G protein for infectivity in HEp-2 cells than RSV A2.

[0262] rg9320ΔHBS, a recombinant 9320 virus with a partial deletion of G (the cysteine noose and heparin binding sites) was also recovered from cDNA as described above. Like rg9320ΔG, replication of rg9320ΔHBS in Vero cells is not significantly impaired.

[0263] Virus Replication in Cotton Rats

[0264] Subgroup B RSV typically replicates better in cotton rats than in mice. Therefore, in vivo replication of recombinant viruses rg9320C4, rg9320G4, rg9320ΔG and rg9320ΔHBS was examined in cotton rats (Sigmodon hispidus). Cotton rats in groups of five were inoculated intranasally with 150 μl of inoculum containing 106 pfu of the specified virus per animal. Animals were sacrificed four days after inoculation. Lung tissues were harvested and homogenized, and virus titer was determined by plaque assay on Vero cells. Table 7 lists the mean viral titer for each recombinant virus. rg9320C4 and rg9320G4 replicated to a titer of 3.1 and 3.0 log10 pfu/g, respectively, in the lungs of cotton rats. Both G deletion mutants (rg9320ΔG and rg9320ΔHBS) replicated poorly, indicating G deletion affected RSV 9320 replication in the animal host. rg9320ΔG and rg9320ΔHBS are thus potential candidates for live attenuated RSV vaccines.

7TABLE 7Virus replication in cotton rat lungviruslog10 mean pfu/g tissue +/− SErg9320C43.1 +/− 0.2rg9320G43.0 +/− 0.1rg9320ΔG0.4 +/− 0.4rg9320ΔHBS1.0 +/− 0.6

[0265] Recombinant 9320 and Vaccines

[0266] An RSV vaccine would preferably provide protection against both subgroup A and subgroup B RSV infection, which tend to circulate concurrently in communities. Most RSV vaccines developed in the past have been based on the RSV A2 strain. However, it remains to be determined whether an RSV vaccine based solely on a subgroup A strain would provide sufficient immunity to both RSV subgroups. Although recombinant technology has been employed to express subgroup B RSV antigens in the A2 strain, including the replacement of the G and F genes by those of BI (Whitehead et al. (1999) “Replacement of the F and G proteins of respiratory syncytial virus (RSV) subgroup A with those of subgroup B generates chimeric live attenuated RSV subgroup B vaccine candidates” J Virol 73:9773-9780) or 9320 (Cheng et al. (2001) “Chimeric subgroup A respiratory syncytial virus with the glycoproteins substituted by those of subgroup B and RSV without the M2-2 gene are attenuated in African green monkeys” Virology 283:59-68) or the insertion of the 9320 G gene in the A2 strain (Jin et al. (1998) Virology 251:206-214), subgroup B RSV vaccine development currently lags significantly behind subgroup A vaccine development. Availability of the subgroup B RSV rescue system described herein permits manipulation of the subgroup B RSV genome, e.g., for vaccine development. For example, RSV B9320 can optionally be attenuated by methods used to attenuate subgroup A strains. The methods that have been used to attenuate RSV subgroup A RSV include, e.g., mutagenesis of the viral internal proteins (Lu et al. (2002) “Identification of temperature-sensitive mutations in the phosphoprotein of respiratory syncytial virus that are likely involved in its interaction with the nucleoprotein” J Virol 76:2871-2880; Lu et al. (2002) “The major phosphorylation sites of the respiratory syncytial virus phosphoprotein are dispensable for virus replication in vitro” J Virol 76:10776-10784; Tang et al. (2002) “Clustered charged-to-alanine mutagenesis of human respiratory syncytial virus L polymerase generated temperature-sensitive viruses” Virology 302(207-216); and Tang et al. (2001) “Requirement of cysteines and length of the human respiratory syncytial virus M2-1 protein for protein function and virus viability” J Virol 75:11328-11335), deletion of the accessory genes (Bermingham and Collins (1999) Proc. Natl. Acad. Sci. USA 96:11259-11264; Jin et al. (2000) J. Virol. 74:74-82; Jin et al. (2000) Virology 273:210-218; Bukreyev et al. (1997) J Virol 71:8973-8982; Teng and Collins (1999) J Virol 73:466-473); and introduction of attenuating mutations from different strains to fine-tune the level of attenuation of a vaccine strain (Firestone et al. (1996) “Nucleotide sequence analysis of the respiratory syncytial virus subgroup A cold-passaged (cp) temperature sensitive (ts) cpts-248/404 live attenuated virus vaccine candidate” Virology 225:419-422 and Whitehead et al. (1999) “Addition of a missense mutation present in the L gene of respiratory syncytial virus (RSV) cpts530/1030 to RSV vaccine candidate cpts248/404 increases its attenuation and temperature sensitivity” J Virol 73:871-877). As one example, from the gene deletion approach, it appears that rA2ΔM2-2 exhibits some desired features for further clinical evaluation (Cheng et al. (2001) Virology 283:59-68; Jin et al. (2003) “Evaluation of recombinant respiratory syncytial virus gene deletion mutants in African green monkeys for their potential as live attenuated vaccine candidates” Vaccine 21:3647-3652; and Teng et al. (2000) J Virol 74:9317-9321); 9320 with a deletion of the M2-2 gene is thus an attenuated 9320 vaccine candidate. Similarly, forcing use of the second or third start codon of the A2 M2-2 mRNA (instead of the first or all three start codons) results in a decrease in M2-2 activity (U.S. patent application Ser. No. 10/672,302 (attorney docket number 26-000320US), filed on Sep. 26, 2003, Jin et al. entitled “Functional mutations in respiratory syncytial virus”). 9320 with a mutation (e.g., substitution or deletion) in the first, second, and/or third start codon of M2-2 is thus an attenuated 9320 vaccine candidate.

[0267] As noted, recombinant 9320 viruses with complete or partial deletions of the G gene, e.g., as described herein, are attenuated 9320 vaccine candidates.

[0268] 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 true scope of the invention. For example, all the compositions and techniques described above can be used in various combinations. All publications, patents, patent applications, and/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, and/or other document were individually indicated to be incorporated by reference for all purposes.

	Number	Date	Country
	60458331	Mar 2003	US
	60508320	Oct 2003	US

Compositions and methods involving respiratory syncytial virus subgroup B strain 9320

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