# Patent

## Title
Avian pneumovirus genes, recombinant avian pneumoviruses and methods of making

## Abstract

The present invention is directed to novel avian pneumovirus strain Colorado (APV/CO) genes and intergenic sequences. Also disclosed are methods of making recombinant avian pneumovirus and live-attenuated APV/CO. Further disclosed are methods of diagnosing avian pneumovirus.

## Background
This application is a continuation-in-part of international application number PCT/US03/38123 filed Dec. 2, 2003 and claims the benefit of U.S. provisional application No. 60/430,301 filed Dec. 2, 2002, the contents of which are fully incorporated by reference herein.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The invention relates to the fields of immunology and molecular biology.
2. Related Art
Avian pneumovirus (APV), also known as turkey rhinotracheitis virus, was first reported in South Africa in 1978 (Buys & Du Preez, Turkeys 28:36 (1980)) and, subsequently, was isolated in Europe, Israel and Asia (Alexander, in Barnes et al., eds., Diseases of Poultry, Iowa State University Press, Ames, Iowa (1997), pp. 541-569; Cavanagh and Barett, Virus Res. 11:241-256 (1988); Jones et al., Vet. Rec. 119:599-600 (1986); McDougall and Cook, Vet. Rec. 118:206-207 (1986); Wilding et al., Vet. Rec. 118:735 (1986)). The United States was considered free of APV until 1996, when it was isolated for the first time in Colorado from an outbreak of upper respiratory tract disease in turkeys (Cook et al., Avian Pathol. 28:607-617 (1999); Kleven, in Proceedings of the U.S. Animal Health Association 101st Annual Meeting, U.S. Animal Health Association, Washington, D.C. Report of the Committee: transmissible diseases of poultry and other avian species (1997), pp. 486-491). This first isolate was called APV/Colorado (APV/CO). Subsequently, APV infection was reported in turkeys in Minnesota, from which the virus has spread to the neighboring states of North and South Dakota (Goyal et al., North Central Avian Disease Conference, Minneapolis, Minn. (October, 1999); Panigrahy et al., Avian Dis. 44:17-22 (2000)). APV has emerged as a major problem for turkey industries in Minnesota. In 1999, 37% of the turkey flocks in Minnesota were positive for APV antibodies, causing economic losses of approximately $15 million per year (Gulati et al., J. Clin. Microbiol. 38:4010-4014 (2000)).
APV belongs to the genus Metapneumovirus within the subfamily Pneumovirinae of the family Paramyxoviridae (Pringle, Arch. Virol. 143:1449-1459 (1998)). The genome of Metapneumovirus is a non-segmented, single-stranded, negative-sense RNA with a gene order of 3′-Leader-N-P-M-F-M2-SH-G-L-Trailer-5′. APV was assigned to a new genus because its genome contains eight genes arranged in a different order from the ten genes of members of genus Pneumovirus, such as respiratory syncytial virus (RSV) (Collins et al., “Parainfluenza viruses,” in Fields Virology, Fields et al., eds., Lippincott-Raven, Philadelphia, Pa. (1996), pp. 1205-1241; Ling et al., J. Gen. Virol. 73:1709-1715 (1992); Randhawa et al., J. Virol. 71:9849-9854 (1997)). The newly discovered human metapneumovirus (hMPV) is the only mammalian virus that has been included tentatively in the genus Metapneumovirus (Van den Hoogen et al., Nat. Med. 7:719-724 (2001); Van den Hoogen, et al., Virology 295:119-132 (2002); Njenga et al., Virus Res. 91:163-169 (2003)).
On the basis of level of genetic variation in the attachment (G) protein, European APV isolates have been divided into two subgroups, designated A and B (Juhasz and Easton, J. Gen Virol. 75:2873-2880 (1994)). These two subgroups were also shown to be antigenically distinct (Bayon-Auboyer et al., Arch. Virol. 144:1091-1109 (1999)). Until late 1996, all known APV isolates belonged to either the A or the B subgroup. Surprisingly, the APV isolates from the U.S. were shown to cross-neutralize poorly with European subgroup A and B viruses, suggesting that they belong to a different subgroup. A new subgroup, C, has been proposed for the U.S. isolates of APV (Cook et al., Avian Pathol. 28:607-617 (1998); Kleven, in Proceedings of the U.S. Animal Health Association 101st Annual Meeting, U.S. Animal Health Association, Washington, D.C. Report of the Committee: transmissible diseases of poultry and other avian species (1997), pp. 486-491; Seal, Virus Res. 58:45-52 (1998); Seal, Health Res. Rev. 1:67-72 (2000); Shin et al., J. Clin. Microbiol. 40:1687-1693 (2002)). Recently, a subgroup D strain of APV has been reported (Bayon-Auboyer et al., J. Gen. Virol. 81:2723-2733 (2000)). The U.S. isolates have been shown to be different from Subgroup D strains (Toquin et al., Avian Dis. 44:977-982 (2000)).
The nucleotide sequences of all the eight mRNAs of APV subgroup A have been reported (Randhawa et al., J. Virol. 71:9849-9854 (1997) and references therein). However, the nucleotide and deduced amino acid sequences of only N, P, M, F and M2 genes of APV/CO have been reported (Dar et al., Virus Res. 79 (1-2):15-25 (2001); Seal, Virus Res. 58:45-52 (1998); Seal et al., Virus Res. 66:139-147 (2000); Genbank accession—AF176592).
At present, there is no satisfactory vaccine available for APV and also no method available to genetically manipulate the genome of APV.
BRIEF SUMMARY OF THE INVENTION
In accordance with the invention, there are provided isolated nucleic acid molecules which are at least 95% identical to the coding region of the SH gene (SEQ ID NO:87) of APV/CO. Further provided are isolated nucleic acid molecules encoding the SH protein (SEQ ID NO:88) of APV/CO. The nucleic acid molecules and polypeptides of the present invention are useful for making immunological formulations against, and in the detection of, APV/CO.
In accordance with another aspect of the invention, there are provided methods of making recombinant APV comprising constructing a cDNA encoding the antigenome of APV, transfecting the cDNA into cells, and culturing the cells under conditions suitable to produce the recombinant APV. Also provided are recombinant APV produced by this method.
In accordance with another aspect, there are provided methods of making a live-attenuated APV and APV produced by this method, comprising: constructing a cDNA encoding the antigenome of APV with one or more attenuating mutations, transfecting the cDNA into cells, and culturing the sells under conditions suitable to produce the recombinant APV. The live-attenuated APVs of the present invention are useful as an immunological formulation.
In accordance with yet another aspect of the invention, there are provided methods of diagnosing APV, comprising detecting APV RNA or protein expression in a biological sample.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a schematic genetic map of APV subgroup A. The gene order, gene start, and gene end sequences are shown.
FIG. 2 shows comparative alignments of genomic termini of APV sequences. Comparative alignment of the nucleotide sequences (genomic-sense) of the 3′ leader region is shown in (A) and the 5′ trailer region in (B) of APV/CO (SEQ ID NO:1), APV-A (SEQ ID NO:2), and HMPV isolates 00-1 (SEQ ID NO:3), CAN97-83 (SEQ ID NO:47) and CAN98-75 (SEQ ID NO:48). Perfectly conserved nucleotides relative to APV/CO are indicated by dots. Dashes were included in the HMPV 00-1 sequences since they were primer-based. Complementarity between the 3′ and 5′ ends of APV/CO genomic RNA is shown in (C). The complementary nucleotides are marked by vertical lines.
FIG. 3 shows the confirmation of the gene-order through genome-walk by sequential RT-PCR along APV-genomic RNA: The 3′ to 5′ order of the genes in the genomic RNA of APV/CO is shown. The transcription-signals gene-start (GS) and semi-conserved gene-end (GE) signals of each gene are indicated. Sequence of intergenic region: M-F (SEQ ID NO:4), F-M2 (SEQ ID NO:5), M2-SH (SEQ ID NO:6) and SH-G (SEQ ID NO:7) are shown in bold italics.
FIG. 4 shows an initial sequence of the SH gene (SEQ ID NO:8) and putative SH protein (SEQ ID NO:9) of APV/CO. FIG. 4a shows the results of a subsequent sequencing of the APV/CO SH gene (SEQ ID NO: 87) and the putative SH protein (SEQ ID NO: 88) based on this sequence. The nucleic acid sequences of FIGS. 4 and 4a are greater than 95% identical, with the initial sequence found to possess a six nucleotide insertion. In FIG. 4a: The gene-start (GS) and the gene-end (GE) transcription signals of the SH gene are indicated in italics. In the SH protein: the potential N-linked glycosylation sites are underlined; the most hydrophobic region that corresponds to the probable transmembrane domain is shown in bold italics.
FIG. 5 and 5a show the hydrophilicity profile of APV/CO SH protein from FIG. 4a. The distribution of the hydrophobic and hydrophilic domains along the amino acid sequence was determined using the algorithm of Kyte and Doolittle (1982) with a window size of 7 residues. The Y axis denotes hydrophilicity (hydrophobicity is indicated by negative values) and X axis indicates amino acid position.
FIG. 6 shows the comparative alignment of the predicted amino acid sequence of putative SH protein of APV/CO (SEQ ID NO:9) with Human metapneumovirus (HMPV) (SEQ ID NO:10), APV subgroups A (APV/A) (SEQ ID NO:11). APV subgroups B (APV/B) (SEQ ID NO:12), human respiratory syncytial virus (HRSV) (SEQ ID NO:13), bovine respiratory syncytial virus (BRSV) (SEQ ID NO:14), and Pneumonia virus of mice (PVM) (SEQ ID NO: 15). FIG. 6a shows the comparative alignment of the predicted amino acid sequence of SH protein of APV/CO (SEQ ID NO:88) with APV subgroups A (APV/A) (SEQ ID NO:97) and B (APV/B) (SEQ ID NO:98), Human metapneumovirus (HMPV) (SEQ ID NO:96), bovine (BRSV) (SEQ ID NO:100) and human respiratory syncytial virus (HRSV) (SEQ ID NO:99) and Pneumonia virus of mice (PVM) (SEQ ID NO:101) generated using Clustal W sequence alignment. Gaps are represented by dashes and periods indicate the positions of identical aa residues compared to APV/CO.
FIG. 7 shows the general scheme for the assembly of cDNA fragments of APV/CO genes in pBR 322.
FIG. 8 shows the transfection procedure for the recovery of infectious APV entirely from cloned cDNA. The full length APV cDNA along with support plasmids is transfected into Vero cells infected with a vaccinia virus (MVA-t7) to obtain infectious APV.
FIG. 9 shows the construction of F cleavage site mutant of recombinant APV/CO.
FIG. 10 shows the orientation of APV overlapping nucleic acid material of ATCC Deposit Numbers PTA-5668, PTA-5669, PTA-5670, PTA-5671, PTA-5672, PTA-5673, which are labeled as Clones 1-4, DNA 1 and DNA 2, respectively.
FIG. 11 shows a comparative alignment of the predicted amino acid sequences of three different strains of APV-C, APV/CO, Mn-1a and Mn-2a. Proposed intra-cellular, transmembrane, and extra-cellular domains of the G proteins are indicated above the sequences. Perfectly conserved amino acids relative to APV/CO are indicated by dots, and potential N-linked glycosylation sites are underlined. The amino acid residues forming the highly divergent domain have been highlighted in bold (amino acids 300-450).
FIG. 12 show the structure of the APV/CO genome. Individual genes are indicated by boxes. The gene length and protein length are indicated above and below each gene, respectively. The nucleotide lengths of the 3′ leader, 5′ trailer, and intergenic regions are underlined.
FIG. 13 shows a complete gene map of APV/CO genome (in antigenome-sense). The last nucleotide of the gene-end, the first nucleotide of the gene-start, and the first and last nucleotides of the leader and trailer are numbered. Conserved sequence motifs at the gene-end and the gene-start of each gene are indicated in bold upper case, and a consensus is given below. Translational stop and start codons are underlined. Intergenic sequences are shown between the gene-end and gene-start sequences. In the case of the SH-G intergenic region (91 nucleotides), only the first and last five nucleotides are shown, and the number of the remaining nucleotides is indicated.
FIG. 14 shows a secondary structure prediction of the G gene (cDNA sense) of APV-C. The MFOLD software program was used to predict the secondary structure and a representative model with its stability (kcal/mol) is shown.



DETAILED DESCRIPTION OF THE INVENTION
The present inventors have identified the coding and amino acid sequence of the small hydrophobic (SH) gene of the avian pneumovirus strain Colorado (APV/CO). The sequences of the SH gene and deduced protein are shown in FIG. 4a (SEQ ID NOs:87 and 88). The SH gene sequence reported in SEQ ID NO:87 is greater than 95% identical to the sequence reported in SEQ ID NO:8; the invention therefore encompasses both sequences and the putative protein sequences based upon them. The SH gene of APV/CO reported in FIG. 4a is 622 nucleotides in length. Comparison of the deduced amino acid sequence of the SH protein of APV/CO with the corresponding published sequences of other members of genera metapneumovirus showed 24% identity with the newly discovered human metapneumovirus (hMPV). Additionally, the predicted amino acid sequences for the G glycoprotein genes of APV subgroup C members APV/CO, Mn-1a, and Mn-2a have also been identified and are shown in FIG. 11 (SEQ ID NOs:56, 57, and 58). The complete nucleotide sequence of the APV/CO G gene is 1758 nucleotides in length, encoding a polypeptide of 585 amino acids. Though the G protein of APV-CO showed structural and biochemical features similar to those of the HMPVs, it showed only 21 to 25% amino acid identity with those of the HMPVs and less in comparison with other APVs. Also provided are the nucleotide sequences of transcription-signals and the N-P, P-M, M-F, F-M2, M2-SH, SH-G, and G-L intergenic regions, and the 3′ leader and 5′ trailer regions of APV/CO (FIG. 13).
In accordance with an aspect of the present invention, there is provided an isolated nucleic acid molecule comprising a nucleotide sequence encoding the SH protein (SEQ ID NO: 88) or a nucleotide sequence of the SH gene (SEQ ID NO:87). Isolated nucleic acid molecules of the present invention include polynucleotides comprising the exact sequence shown in SEQ ID NO:87, and polynucleotides which comprise a sequence substantially different from those described above but which, due to the degeneracy of the genetic code, still encode the SH protein. Of course, the genetic code is well known in the art. Thus, it would be routine for one skilled in the art to generate the degenerate variants described herein.
Unless otherwise indicated, each “nucleotide sequence” set forth herein is presented as a sequence of deoxyribonucleotides (abbreviated A, G, C and T) or ribonucleotides (A, G, C and U). However, by “nucleotide sequence” of a nucleic acid molecule or polynucleotide is intended, for a DNA molecule or polynucleotide, a sequence of deoxyribonucleotides, and for an RNA molecule or polynucleotide, the corresponding sequence of ribonucleotides (A, G, C and U), where each thymidine deoxyribonucleotide (T) in the specified deoxyribonucleotide sequence is replaced by the ribonucleotide uridine (U).
Polynucleotides useful in the present invention may be in the form of RNA or in the form of DNA, which DNA includes cDNA, genomic DNA, and synthetic DNA. The DNA may be double stranded or single-stranded, and if single stranded may be the coding strand or non-coding (anti-sense) strand.
The polynucleotide which encodes for the polypeptide of SEQ ID NO:88 may include: only the coding sequence for the polypeptide; the coding sequence for the polypeptide and additional coding sequence such as a leader or secretary sequence or a proprotein sequence; the coding sequence for the polypeptide (and optionally additional coding sequence) and non-coding sequence, such as intron or non-coding sequence 5′ and/or 3′ of the coding sequence for the predicted SH polypeptide.
Thus, the term “polynucleotide encoding a polypeptide” encompasses a polynucleotide which includes only coding sequence for the polypeptide as well as a polynucleotide which includes additional coding and/or non-coding sequence.
The present invention further relates to variants of the hereinabove described polynucleotides which encode for fragments, analogs and derivatives of the polypeptide having the deduced amino acid sequence of SEQ ID NO:88. The variant of the polynucleotide may be a naturally occurring allelic variant of the polynucleotide or a non-naturally occurring variant of the polynucleotide. As known in the art, an allelic variant is an alternate form of a polynucleotide sequence which may have a substitution, deletion or addition of one or more nucleotides, which does not substantially alter the function of the encoded polypeptide.
The present invention also includes polynucleotides, wherein the coding sequence for the polypeptide may be fused in the same reading frame to a polynucleotide sequence which aids in expression and secretion of a polypeptide from a host cell, for example, a leader sequence which functions as a secretory sequence for controlling transport of a polypeptide from the cell. The polypeptide having a leader sequence is a preprotein and may have the leader sequence cleaved by the host cell to form the mature form of the polypeptide. The polynucleotides may also encode for proprotein which is the protein plus additional 5′ amino acid residues. A mature protein having a prosequence is a proprotein and is an inactive form of the protein. Once the prosequence is cleaved an active mature protein remains.
Thus, for example, the polynucleotide may encode for a SH protein alone, or for a protein having a prosequence or for a protein having both prosequence and a presequence (leader sequence).
The polynucleotides useful in the present invention may also have the coding sequence fused in frame to a marker sequence which allows for purification of the polypeptide of the present invention. The marker sequence may be a hexahistidine tag supplied by a pQE-9 vector to provide for purification of the polypeptide fused to the marker in the case of a bacterial host, or, for example, the marker sequence may be a hemagglutinin (HA) tag when a mammalian host, e.g. COS-7 cells, is used. The HA tag corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson, I. et al., Cell 37:767 (1984)).
The term “gene” means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons).
Further embodiments of the invention include isolated nucleic acid molecules comprising a polynucleotide having a nucleotide sequence at least 90% identity, and more preferably at least 95%, 97%, 98% or 99% identity to (a) a nucleotide sequence encoding the SH polypeptide having the complete amino acid sequence in FIG. 4a (SEQ ID NO:88); (b) a nucleotide sequence having the complete coding region of the SH gene in FIG. 4a (SEQ ID NO:87); (c) a nucleotide sequence having the complete sequence of the SH gene in FIG. 4a (SEQ ID NO:87); (d) a nucleotide sequence encoding any of the SH analogs or deletion mutants described below; or (e) a nucleotide sequence which is fully complementary to any of the nucleotide sequences in (a), (b), (c) or (d).
Preferred, are nucleic acid molecules having sequences at least 90%, 95%, 96%, 97%, 98% or 99% identical to the nucleic acid sequence shown in FIG. 4a (SEQ ID NO:87) which encode a polypeptide having SH protein activity. By “a polypeptide having SH activity” is intended polypeptides exhibiting activity similar, but not necessarily identical, to an activity of the wild-type SH protein or an activity that is enhanced over that of the wild-type SH protein, as measured in a particular biological assay. Particular preferred are polypeptides which are specifically antigenic, that is, induce an immune response which is specific for the wild-type SH protein.
Of course, due to the degeneracy of the genetic code, one of ordinary skill in the art will immediately recognize that a large number of the nucleic acid molecules having a sequence at least 90%, 95%, 96%, 97%, 98%, or 99% identical to the reference nucleic acid sequence will encode a polypeptide “having SH protein activity.” In fact, since degenerate variants of these nucleotide sequences all encode the same polypeptide, this will be clear to the skilled artisan even without performing the above described comparison assay. It will be further recognized in the art that, for such nucleic acid molecules that are not degenerate variants, a reasonable number will also encode a polypeptide having SH protein activity. This is because the skilled artisan is fully aware of amino acid substitutions that are either less likely or not likely to significantly effect protein function (e.g., replacing one aliphatic amino acid with a second aliphatic amino acid). Thus, the invention further includes variations of the SH polypeptide which show substantial SH polypeptide activity or which include regions of SH protein which are antigenic. Such mutants include deletions, insertions, inversions, repeats, and type substitutions (for example, substituting one hydrophilic residue for another, but not strongly hydrophilic for strongly hydrophobic as a rule). Small changes or such “neutral” amino acid substitutions will generally have little effect on activity.
Typically seen as conservative substitutions are the replacements, one for another, among the aliphatic amino acids Ala, Val, Leu and Ile; interchange of the hydroxyl residues Ser and Thr, exchange of the acidic residues Asp and Glu, substitution between the amide residues Asn and Gln, exchange of the basic residues Lys and Arg and replacements among the aromatic residues Phe, Tyr.
For example, guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie, J. U. et al., “Deciphering the Message in Protein Sequences: Tolerance to Amino Acid Substitutions,” Science 247:1306-1310 (1990), wherein the authors indicate that there are two main approaches for studying the tolerance of an amino acid sequence to change. The first method relies on the process of evolution, in which mutations are either accepted or rejected by natural selection. The second approach uses genetic engineering to introduce amino acid changes at specific positions of a cloned gene and selections or screens to identify sequences that maintain functionality. As the authors state, these studies have revealed that proteins are surprisingly tolerant of amino acid substitutions. The authors further indicate which amino acid changes are likely to be permissive at a certain position of the protein. For example, most buried amino acid residues require nonpolar side chains, whereas few features of surface side chains are generally conserved. Other such phenotypically silent substitutions are described in Bowie, J. U. et al., Science 247:1306-1310 (1990) and the references cited therein.
The present invention further relates to an SH polypeptide which has the deduced amino acid sequence of FIG. 4a (SEQ ID NO:88), as well as fragments, analogs and derivatives of such polypeptide. The terms “fragment,” “derivative” and “analog” when referring to a polypeptide of the invention, means a polypeptide which retains essentially the same biological function or activity as such polypeptide, preferably antigenicity. Thus, an analog includes a protein which can be activated by cleavage of the protein portion to produce an active polypeptide.
The fragment, derivative or analog of the polypeptide of FIG. 4a (SEQ ID NO:88) may be (i) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code, or (ii) one in which one or more of the amino acid residues includes a substituent group, or (iii) one in which the polypeptide is fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol), or (iv) one in which the additional amino acids are fused to the polypeptide, such as a leader or secretary sequence or a sequence which is employed for purification of the polypeptide or a protein sequence. Such fragments, derivatives and analogs are deemed to be within the scope of those skilled in the art from the teachings herein.
By a fragment of an isolated the SH polypeptide, for example, is intended to encompass polypeptide fragments contained in SEQ ID NO:88 or encoded by SEQ ID NO:87. Protein fragments may be “free-standing,” or comprised within a larger polypeptide of which the fragment forms a part or region, most preferably as a single continuous region. Polypeptide fragments can be at least 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, or 150 amino acids in length. In this context “about” includes the particularly recited ranges, larger or smaller by several (5, 4, 3, 2, or 1) amino acids, at either extreme or at both extremes.
Even if deletion of one or more amino acids from the N- or C-terminus of a protein results in modification of loss of one or more biological functions of the protein, other functional activities (e.g., biological activities, ability to multimerize, ability to raise antibodies) may still be retained. For example, the ability of shortened SH mutants to induce and/or bind to antibodies which recognize the complete form of the polypeptides generally will be retained when less than the majority of the residues of the complete polypeptide are removed from the N- or C-terminus. Whether a particular polypeptide lacking N-terminal residues of a complete polypeptide retains such immunologic activities can readily be determined by routine methods described herein and otherwise known in the art. It is not unlikely that an SH mutant with a large number of deleted terminal amino acid residues may retain some biological or immunogenic activities. In fact, peptides composed of as few as six amino acid residues may often evoke an immune response.
A further embodiment of the invention relates to a polypeptide which comprises the amino acid sequence of a SH polypeptide having an amino acid sequence which contains at least one amino acid substitution, but not more than 50 amino acid substitutions, even more preferably, not more than 40 amino acid substitutions, still more preferably, not more than 30 amino acid substitutions, and still even more preferably, not more than 20 amino acid substitutions. Of course, it is highly preferable for a peptide or polypeptide to have an amino acid sequence which comprises the amino acid sequence of a SH polypeptide, which contains at least one, but not more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 amino acid substitutions. Also provided are polynucleotides encoding such polypeptides.
The polypeptides and polynucleotides of the present invention are preferably provided in an isolated form, and preferably are purified to homogeneity. By “isolated” is intended a polynucleotide or polypeptide removed from its native environment. Thus, a polynucleotide or polypeptide produced and/or contained within a recombinant host cell is considered isolated for purposes of the present invention. Also intended are polypeptides that have been purified, partially or substantially, from a recombinant host cell or a native source. Recombinant DNA molecules contained in a vector are considered isolated for the purposes of the present invention. Further examples of isolated DNA molecules include recombinant DNA molecules maintained in heterologous host cells or purified (partially or substantially) DNA molecules in solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the DNA molecules of the present invention. Isolated nucleic acid molecules according to the present invention further include such molecules produced synthetically.
The polypeptides of the present invention include the polypeptide of SEQ ID NO:88 as well as polypeptides which have at least 90%, 95%, 96%, 97%, 98%, 99% identity to the polypeptide of SEQ ID NO:88 and also include portions of such polypeptides with such portion of the polypeptide generally containing at least 30 amino acids and more preferably at least 40, 50, 60, 70, 80 or 100 amino acids.
By a polypeptide having an amino acid sequence at least, for example, 95% “identical” to a reference amino acid sequence polypeptide is intended that the amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
By a polypeptide having an amino acid sequence at least, for example, 95% “identical” to a query amino acid sequence of the present invention, it is intended that the amino acid sequence of the subject polypeptide is identical to the query sequence except that the subject polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the query amino acid sequence. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a query amino acid sequence, up to 5% of the amino acid residues in the subject sequence may be inserted, deleted, or substituted with another amino acid. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
As a practical matter, whether any particular polypeptide or polynucleotide is at least 90%, 95%, 96%, 97%, 98% or 99% identical to another polypeptide or polynucleotide can be determined conventionally using known computer programs. A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci. 6:237-245 (1990)). In a sequence alignment the query and subject sequences are either both nucleotide sequences or both amino acid sequences. The result of said global sequence alignment is in percent identity. Another known computer programs for determining percent identity is the Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, 575 Science Drive, Madison, Wis. 53711). When using Bestfit or any other sequence alignment program to determine whether a particular sequence is, for instance, 95% identical to a reference sequence according to the present invention, the parameters are set, of course, such that the percentage of identity is calculated over the full length of the reference amino acid or nucleotide sequence and that gaps in homology of up to 5% of the total number of amino acid or nucleotide residues in the reference sequence are allowed.
The present invention is also directed to recombinant nucleic acid molecules comprising APV/CO genes and/or intergenetic sequences. Since the sequence of the intergenic sequences of APV/CO and the sequence of the SH gene are provided here, and the sequences of the N, P, M, F and M2 genes are known, one of ordinary skill can construct a recombinant nucleic acid molecule comprising one or more of these genes or intergenetic sequences. Especially preferred are isolated nucleic acid molecules comprising the SH gene in combination with one or more of the following sequences: the 5′ trailer sequence; the N gene; the P gene; the M gene; the F gene; the M2 gene; the M-F intergenetic sequence; the F-M2 intergenetic sequence; the M2-SH intergenic sequence; and the SH-G intergenic sequence.
The present invention also relates to vectors which include the isolated nucleic molecules of the present invention, host cells which are genetically engineered with the recombinant vectors, and the production of APV polypeptides or fragments thereof by recombinant techniques.
Host cells are genetically engineered (transduced or transformed or transfected) with the vectors of this invention which may be, for example, a cloning vector or an expression vector. The vector may be, for example, in the form of a plasmid, a viral particle, a phage, etc. The engineered host cells can be cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants or amplifying the APV genes. The culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
The polynucleotides of the present invention may be employed for producing polypeptides by recombinant techniques. Thus, for example, the polynucleotide may be included in any one of a variety of expression vectors for expressing a polypeptide. 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, and pseudorabies. However, any other vector may be used as long as it is replicable and viable in the host.
The appropriate DNA sequence may be inserted into the vector by a variety of procedures. In general, the DNA sequence is inserted into an appropriate restriction endonuclease site(s) by procedures known in the art. Such procedures and others are deemed to be within the scope of those skilled in the art.
The DNA sequence in the expression vector is operatively linked to an appropriate expression control sequence (promoter) to direct cDNA synthesis. As representative examples of such promoters, there may be mentioned: LTR or SV40 promoter, the E. coli. lac or trp, the phage lambda PL promoter and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. The expression vector also contains a ribosome binding site for translation initiation and a transcription terminator. The vector may also include appropriate sequences for amplifying expression.
In addition, the expression vectors preferably contain 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, kanamycin or ampicillin resistance in E. coli. 
The vector containing the appropriate DNA sequence as hereinabove described, as well as an appropriate promoter or control sequence, may be employed to transform an appropriate host to permit the host to express the protein.
As representative examples of appropriate hosts, there may be mentioned: bacterial cells, such as E. coli, Streptomyces, Salmonella typhimurium; fungal cells, such as yeast; insect cells such as Drosophila S2 and Spodoptera Sf9; animal cells such as CHO, COS or Bowes melanoma; adenoviruses; plant cells, etc. The selection of an appropriate host is deemed to be within the scope of those skilled in the art from the teachings herein.
More particularly, the present invention also includes recombinant constructs comprising one or more of the sequences as broadly described above. The constructs comprise a vector, such as a plasmid or viral vector, into which a sequence of the invention has been inserted, in a forward or reverse orientation. In a preferred aspect of this 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. The following vectors are provided by way of example; Bacterial: pQE70, pQE60, pQE-9 (Qiagen), pBS, pDlO, phagescript, psiX174, pbluescript SK, pbsks, pNH8A, pNH16a, pNH18A, pNH46A (Stratagene); ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 (Pharmacia); Eukaryotic: pWLNEO, pSV2CAT, pOG44, pXT1, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL (Pharmacia). However, any other plasmid or vector may be used as long as they are replicable and viable in the host.
Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, PL and trp. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art.
In a further embodiment, the present invention relates to host cells containing the above-described constructs. The host cell can be a higher eukaryotic cell, such as a mammalian cell, or a lower eukaryotic cell, such as a yeast 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, or electroporation (Davis, L. et al., Basic Methods in Molecular Biology (1986)). Preferably, the host cell is an ompT-deficient prokaryotic cell. Particularly preferred ompT-deficient prokaryotic cells are gram-negative bacteria, Psudomonas, Klebsiella, E. coli and Salmonella. 
The constructs in host cells can be used in a conventional manner to produce the gene product encoded by the recombinant sequence. Alternatively, the polypeptides of the invention can be synthetically produced by conventional peptide synthesizers.
APV proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described by Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y. (1989), the disclosure of which is hereby incorporated by reference.
Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter is induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period.
Cells are typically harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification.
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, such methods are well known to those skilled in the art.
The polypeptide can be recovered and purified from recombinant cell cultures by methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Protein refolding steps can be used, as necessary, in completing configuration of the APV protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps.
Reverse genetics systems for bovine RSV (Yunus et al., Virus Genes 23:157-164 (2001)) and NDV strains Badette C and LaSota (Huan et al., J. Gen. Virol. 82:1729-1736 (2001)) are known. APV is closely related to bovine RSV and DNV in genome organization; therefore, the reagents and techniques used for the development of reverse genetics systems for bovine RSV and NDV should be directly applicable for the development of a similar system for APV.
The ability to recover infectious APV from cDNA greatly facilitates vaccine development and molecular biologic studies, which can provide fundamental information on APV. With regard to vaccine development, this makes it possible to (i) identify attenuating mutations, (ii) create new types of attenuating mutations, including deletion of the viral genome, (iii) combine attenuating mutations to create a stable vaccine virus, and (iv) modify vaccine virus to accommodate antigenic drift in circulating virus. In addition, it becomes possible to insert foreign sequences into the APV genome for coexpression. For example, the G genes of APV subgroups A and B viruses, the gene for protective antigen of another avian pathogen or the genes for cytokines can be inserted into the APV genome for coexpression. Also, direct engineering of infectious APV will lead the way for basic studies of APV molecular biology and pathogenesis. For the first time, it will be possible to study the function of each APV gene in an authentic virus system. Lastly, these studies may provide information useful for studies involving non-U.S. APV isolates and human metapneumovirus.
APV causes a severe respiratory tract disease in turkeys. It is considered to be one of the most important emerging viral diseases in the United States and is of great economic threat to the U.S. poultry industry. APV has become a major problem for the turkey industry in Minnesota. Economic losses due to APV infection in the Minnesota turkey industry alone have been estimated at $15 million annually. Recent studies have shown that APV has already spread to several neighboring states, suggesting that the virus will probably spread to other states across the nation. Since U.S. APV isolates are antigenically and genetically different from those from other parts of the world, it is necessary to understand the molecular biology and pathogenesis of the U.S. isolates and develop effective vaccines for control of the virus.
At present there are no satisfactory live-attenuated or inactivated vaccines available for the prevention of APV infection in the United States (Goyal et al., North Central Avian Disease Conference, Minneapolis, Minn., October 1999)). Therefore, an alternative safe and efficacious vaccine would be beneficial to the U.S. turkey industry. Live attenuated vaccines are inexpensive and have been proven effective against many viral infections; but, live-attenuated vaccines are made empirically, and the molecular basis of attenuation is in most cases, not understood. Since the genomes typically contain many changes, the ability to directly engineer mutations into cDNA makes it possible to generate defined attenuated strains where cDNA serves as a stable vaccine “seed.” Another limitation of currently used, live-attenuated vaccines is their reversion to virulence. This limitation can be overcome by designing attenuating mutations in the genome that are less likely to revert to virulence. Due to recent technological advances, it is now possible to design attenuated vaccine strains of nonsegmented negative-stranded RNA viruses by direct genetic manipulation at the cDNA level. To date, complete infectious recombinant virus has been recovered from full-length cDNA for several nonsegmented negative-strand viruses (Baron and Barrett; J. Virol. 71:1265-1271 (1997); Clarke et al., J. Virol. 74:4831-4838 (2000); Collins et al., PNAS (USA) 92:11563-11567 (1995); Garcin et al., EMBO J. 14:6087-6094 (1995); Gassen et al., J. Virol. 74:10737-44 (2000); Hoffman and Banerjee, J. Virol 71:4272-4277 (1997); Peeters et al., J. Virol 73:5001-5009 (1999); and Radecke et al., EMBO J. 14:5773-5784 (1995)).
A recent breakthrough in the field of nonsegmented negative-strand RNA viruses is the establishment of a system to recover infectious virus entirely from cloned DNA. This new technology has made it possible to introduce mutations into viral genomes and hence, allow reverse genetics. This has significant implications for our understanding of fundamental aspects of the replication of these viruses and the development of vaccines. To date, several nonsegmented negative-strand RNA viruses have been rescued from cDNA clones. However, a reverse genetics rescue system is not currently available for APV. Therefore, we are proposing to develop a rescue system for APV. Availability of a rescue system for APV will enable us to understand the pathogenesis of this virus and develop immunological formulations.
Thus, in accordance with another aspect of the invention, there are provided cDNA molecules encoding the APV antigenome. These cDNA molecules are useful in constructing recombinant APV, as well as live-attenuated APV for use as immunological formulations.
In accordance with another aspect of the invention, there are also provided method of producing recombinant APV viruses using a cDNA molecule encoding the APV antigenome. Recombinant APV viruses may be produced by constructing a cDNA encoding the APV antigenome, transfecting the cDNA into a host cell, and culturing the host cell under conditions suitable to express the APV cDNA and produce APV.
In accordance with another aspect of the invention, there are provided methods of producing live-attenuated APV. Live-attenuated APV is produced by constructing a cDNA molecule encoding the APV antigenome with one or more attenuating mutations incorporated therein, transfecting the cDNA into a host cell, and culturing the host cell under conditions suitable to express the APV cDNA and produce APV. Also provided are viruses produced by such methods.
An attenuating mutation refers to a nucleotide mutation or amino acid coded for in view of such a mutation which results in a decreased probability of causing disease in its host (i.e., a loss of virulence), in accordance with standard terminology in the art. The attenuating mutation may be a substitution, deletion or insertion.
In an embodiment of the invention, random mutations are made in the cDNA molecule encoding the APV antigenome. Viruses produced by this method are tested for virulence. The sequence of the RNA genome isolated from the attenuated virus is determined and compared to a control sequence of either the prototype strain or parent strain. Nucleotide sequence variations between the virulent strain and the attenuated strain can be identified.
The ability to generate viral progeny through plasmid-mediated introduction of a viral genome can also be used to produce viruses with defined molecular changes. In this embodiment of the invention, stable virus stocks can be produced that contain altered sequences that confer desired properties on the virus, for example, reduced virulence. This approach can also be used to assess the effect of molecular changes on various properties of the virus, i.e. antigenic type, virulence, or attenuation by introducing desired sequence changes into the viral genome, producing virus progeny from the genome, and recovering the virus progeny for characterization. In addition, this approach can be used to construct a virus with heterologous sequences inserted into the viral genome that are concurrently delivered by the virus to generate an immune response against other diseases.
Construction of viral genomes with defined molecular changes can be accomplished using standard techniques such as oligonucleotide-directed, linker-scanning or polymerase chain reaction-based mutagenesis techniques known to those skilled in the art (Zoller and Smith, DNA 3:479-488; (1984); Botstein and Shortle, Science 229:1193 (1985)). Ligation of the genome into a suitable vector for transfer may be accomplished through standard techniques known to those skilled in the art.
Transfection of cells with the RNA transcript coded by the full length genomic cDNA can be achieved by any suitable means, such as, for example, by treating the cells with DEAE dextran, treating the cells with Lipofectin, treating cells with calcium-phosphate and by electroporation. APV-permissive cells are cells which, upon transfection with the viral cDNA antigenome, are capable of producing viral particles. Examples of such cells include, but are not limited to, Vero cells, QT23, chicken embryo fibroblast and tracheal organ culture.
Another aspect of the invention relates to a method for inducing an immunological response in a bird which comprises inoculating the bird with a live-attenuated APV adequate to produce antibody and/or T cell immune response to protect said bird from APV infection. Yet another aspect of the invention relates to a method of inducing immunological response in a bird which comprises delivering one or more APV proteins via a vector directing expression of the APV polynucleotide encoding such proteins in vivo in order to induce such an immunological response to produce antibody to protect such bird from APV infection.
Further aspects of the invention relates to an immunological formulation (composition) which, when introduced into a bird, induces an immunological response in that mammal to APV wherein the composition comprises a live-attenuated APV, an APV polypeptide or an APV polynucleotide construct. The immunological formulation may further comprise a suitable carrier. The immunological formulation can be administered intraperitoneally, parenterally, intranasally, epidurally or orally. The immunological formulation may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, oculonasal, rectal and intestinal mucosa, etc.). It is preferable that the immunological formulation be administered parenterally (including subcutaneous, intramuscular, intravenous, intradermal etc. injection). Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use. The immunological formulation may also include adjuvant systems for enhancing the immunogenicity of the formulation, such as oil-in water systems and other systems known in the art. The dosage will depend on the specific activity of the immunological formulation and can be readily determined by routine experimentation.
In another aspect of the invention, there are provided methods of diagnosis of APV infection in birds. Preferred birds include chickens and turkeys. Particularly preferred are turkeys. It is believed that APV genes and levels of APV protein can be detected in certain body fluids (e.g., sera, plasma, urine, and spinal fluid) and body tissues (especially tissues derived from the lung) from birds (especially chickens and turkeys).
Thus, the present invention provides a method for diagnosis of APV infection in birds, comprising assaying the presence of one or more APV RNA sequences or the expression of one or more APV proteins in a biological sample derived from a putatively infected bird. Higher levels of APV RNA or protein compared to a negative control is indicative of APV infection. The diagnostic method can be used to detect one or more APV RNA sequences and/or proteins.
Any APV gene or protein sequence can be detected using these techniques, including: the 3′ leader sequence, N, P, M, F, M2, SH, G, L, and the 5′ trailer sequence. Particularly preferred are SH and G. In addition, intergenic RNA sequences of APV can be detected, including the N-P, P-M, M-F, F-M2, M2-SH, SH-G, and G-L sequence.
By “assaying the presence of APV RNA or the expression level of APV proteins” is intended qualitatively or quantitatively measuring or estimating the level of the APV RNA or protein in a biological sample either directly (e.g., by determining or estimating absolute RNA or protein) or relatively (e.g., by comparing to the APV RNA or protein level in a second biological sample).
By “biological sample” is intended any biological sample obtained from an individual, cell line, tissue culture, or other source which contains APV RNA or protein. Biological samples include mammalian body fluids (such as sera, plasma, urine, synovial fluid and spinal fluid) which contain APV protein, and tissues or cells which become infected with APV, such as lung tissue, pneumocytes, sinus, harderian glands, or trachea.
Total cellular RNA can be isolated from a biological sample using the single-step guanidinium-thiocyanate-phenol-chloroform method described in Chomczynski and Sacchi, Anal. Biochem. 162:156-159 (1987). Levels of APV RNA are then assayed using any appropriate method. These include Northern blot analysis (Harada et al., Cell 63:303-312 (1990)), S1 nuclease mapping (Fujita et al., Cell 49:357-367 (1987)), the polymerase chain reaction (PCR), reverse transcription in combination with the polymerase chain reaction (RT-PCR) (Makino et al., Technique 2:295-301 (1990)), and reverse transcription in combination with the ligase chain reaction (RT-LCR).
Assaying APV protein levels in a biological sample can occur using antibody-based techniques. For example, APV protein expression in tissues can be studied with classical immunohistological methods (Jalkanen, M., et al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, M., et al., J. Cell. Biol. 105:3087-3096 (1987)). Other antibody-based methods useful for detecting APV protein gene expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA).
Suitable labels are known in the art and include enzyme labels, such as, glucose oxidase, and radioisotopes, such as iodine (125I, 121I), carbon (14C), sulfur (35S), tritium (3H), indium (112In), and technetium (99mTc); luminescent labels, such as luminol; and fluorescent labels, such as fluorescein and rhodamine, and biotin.
Having generally described the invention, the same will be more readily understood by reference to the following examples, which are provided by way of illustration and are not intended as limiting.
EXAMPLES
Example 1
Cloning of the 3′ Leader and 5′ Trailer Sequences of APV/CO
The nucleotide sequence of the 3′ and 5′ extragenic leader and trailer regions was determined for the genomic viral RNA (vRNA) of APV/CO (SEQ ID NO:1). To obtain the sequence of the 3′ leader and 5′ trailer regions, vRNA was extracted from purified virions and amplified with consensus primers based upon HMPV isolate 00-1 leader and trailer regions. Briefly, to obtain the 3′ leader sequence, the APV/CO genomic RNA was reverse-transcribed with a positive-sense consensus 3′ end leader primer, le-For (5′ GGAGGACGAGAAAAAAAC-GC 3′) (SEQ ID NO: 79). The resulting cDNA was subjected to PCR with le-For primer and a N gene-specific negative-sense primer, N-540 (5′ GATTGTTGATGCCAGCTTCGTGAA 3′) (SEQ ID NO: 80). The PCR product was cloned, and the clones were hybridized with a N gene-specific radio-labeled probe, spanning regions 55-540 nucleotides. The 3′ leader sequence was obtained from nucleotide sequencing of numerous hybridization-positive clones. However, to confirm the leader sequence and to determine the presence of primer sequence at the 3′ end of the genome, the GeneRacer kit (Invitrogen) was utilized. Briefly, viral RNA was polyadenylated at its 3′ end using poly (A) polymerase (Invitrogen) and reverse-transcribed with an oligo dT primer. PCR was performed using a GeneRacer 3′ forward primer (supplied with the kit) and the above-described N-540 primer. The amplified cDNA was either directly sequenced or cloned, and several clones were sequenced to obtain the nucleotide sequence of the 3′ leader region of the APV-C genome. The sequence of the 5′ trailer region was obtained in a similar manner. The APV/CO genomic RNA was reverse-transcribed with an L gene-specific positive-sense primer, L-5787 (5′ GTTGGAGGCAGCAGGGTCATAGAATC 3′) (SEQ ID NO: 81), and PCR was performed with L-5787 and a negative-sense consensus 5′ end trailer primer, tr-Rev (5′ GGAGGACGAGAAAAAAACCGTAT 3′) (SEQ ID NO: 82). The resulting RT-PCR product was either directly sequenced, or cloned and then sequenced, thus giving the nucleotide sequence of the 5′ trailer region of APV-CO. The sequence of the 5′ trailer region was further confirmed, using the 5′ RACE method described by Krishnamurthy & Samal (J. Gen. Virol. 79: 2419-2424 (1998)). The cDNA from the above RT reaction was tailed with dCTP using terminal deoxynucleotidyl transferase (Invitrogen), and PCR-amplified with L-5787 and an oligo dG anchor primer (Invitrogen). The PCR product was then cloned, and several clones from independent 5′ RACE reactions were sequenced to obtain the nucleotide sequence of the 5′ trailer region of the APV-C genome.
The 3′ leader of APV/CO is 40 nucleotides in length, which is one nucleotide shorter than those of APV subgroup A (Randhawa et al., J. Virol. 71:9849-9854 (1997)) and human metapneumovirus (van den Hoogen et al., Virology 295:119-132 (2002)). Twenty-nine of the 40 nucleotides are identical between APV/CO and the human metapneumovirus. The results show that the leader region of APV/CO is more closely related to the human metapneumovirus than to the leader region of APV subgroup A.
The 5′ trailer region of APV-CO was 39 nucleotides in length. Both the Canadian isolates of HMPV showed greater sequence similarity to the trailer region of APV/CO than did that of APV-A.
It was observed that both the leader and trailer regions of APV-CO showed higher degrees of resemblance to those of HMPV than to those of APV-A. The leader and trailer regions of APV/CO were also highly complementary to each other; 11 of the first 13 nt and 18 of the terminal 30 nt were exact complements.
Example 2
Cloning of the SH Gene and M-F, F-M2, M2-SH, SH-G Intergenic Regions of APV/CO
The APV/CO isolate was obtained from National Veterinary Services Laboratories (Ames, Iowa) and propagated in Vero cells. The cells were harvested 4-5 days post-infection when maximum cytopathic effect in the form of extensive syncytia was observed. The infected cells were scraped into the medium and lysed by three cycles of freezing and thawing to release the intracellular virus. The cell-lysate was clarified by centrifugation at 3000×g for 15 minutes. The supernatants from infected cells were made 10% with respect to PEG 8000 and incubated for 3 h at 4° C. The virus was pelleted by centrifugation at 3000×g for 30 min at 4° C. The virus pellet was resuspended in PBS and stored at 4° C. APV genomic RNA was extracted from purified APV by TRIzol reagent (Invitrogen Corporation) according to the supplier's protocol except that one additional extraction with phenol plus chloroform was added to the procedure.
The “genome-walking” strategy was employed for obtaining the sequences of the SH gene and M-F, F-M2, M2-SH & SH-G intergenic regions of APV/CO. The genome-walking technique was based on sequential cDNA synthesis from the known genes at the 3′ end of the negative-sense genomic RNA traversing into the regions of the genome located at the 5′ end. Briefly, we used APV genomic RNA and gene specific positive sense primers within M, F or M2 genes in Reverse Transcription-PCR (RT-PCR) reactions. The first RT-PCR reaction with the M gene primer (5′-GGTGCAGGAGTTCAGGTAATAGTGGAG-3′; (SEQ ID NO:16) Genbank accession: AF262571) yielded M-F intergenic sequence and the second RT-PCR with an F gene primer (5′-GCATGGTGGCCTTATCACCACTGGGTGCT-3′ (SEQ ID NO:17); Genbank accession: AF187152) yielded the F-M2 intergenic sequence. In order to obtain the SH gene sequence, a third reverse transcription reaction was initiated within the M2 gene with the positive sense primer (5′-GCGGAGAACATGGCCTGATCTTCCTGA-3′ (SEQ ID NO:18); Genbank accession: AF176592). The first strand cDNA was purified using a nucleotide removal kit (Qiagen). The purified cDNA was tailed with C nucleotides in a tailing reaction catalyzed by terminal deoxynucleotidyl transferase enzyme (Invitrogen Corporation). A PCR was set up with dC-tailed cDNA template and the positive sense M2 forward primer and a poly dG-anchor reverse primer (Invitrogen Corporation). The amplified PCR product was cloned into a TA cloning vector (Invitrogen Corporation) and transformed using DH10B cells (Invitrogen Corporation). The resulting colonies were hybridized with a radiolabelled M2 cDNA probe. Several hybridization-positive clones, each containing a long insert, were selected and sequenced. Several of the positive clones yielded the entire SH gene, including the M2-SH and SH-G intergenic regions.
The cDNA synthesis initiated at the M gene yielded lead to the sequence for M-F intergenic region. Similarly, cDNA synthesis initiated within the F gene yielded the sequence for F-M2 intergenic region. Subsequently, cDNA initiated within the M2 gene traversed the M2-SH intergenic region into the SH gene, followed by the SH-G intergenic region and entered the G gene. The M-F, F-M2, M2-SH intergenic regions of APV/CO are each two nucleotides in length and identical in sequence, 3′-UU-5′ (FIG. 3). However, the SH-G intergenic region was considerably longer consisting of 91 nucleotides (FIG. 3). Thus, during the cloning of the SH gene we traversed the APV genome in the order 3′-M-F-M2-SH-G-5′ (FIG. 3). These data confirmed the presence and the location of the SH gene and showed that the gene order of the APV/CO isolate indeed conforms to the genus Metapneumovirus (Pringle, Arch. Virol. 143:1449-1459 (1998)).
The nucleotide and deduced amino acid sequence of the SH gene of APV/CO is shown in FIG. 4a. The SH gene, from gene start (GS) to gene end (GE), is 622 nucleotides in length (SEQ ID NO:87). The SH gene starts with a conserved GS sequence, 3′-CCCUGUUCA-5′ (part of SEQ ID NO. 1) and ends in a semi-conserved GE sequence of 3′-UCAAUAAAUUUU-5′ (SEQ ID NO 46) (nucleotides GGGACAAGTCAACATGGAGCCCCTGAAAGTCTCTGGAAGTG GAGGGATACCGATGAAGACAAGGCTTAATATCATACTTGAG AAGTCAATCAATAAAATCTTGATCATTTTAGGATTACTATTA ACTGCCTCAACTGTAATTACAATCACACTCACAGTGGAGTAT ATAAGAGTAGAAAATGAATTGCAACTTTGCAAGATGGAAGC AGAGGTGGCCAAGACAACTCCGGAACCACCAACACAGCCAA CGAAGACAACTCCTACACTAACCAGAACCAGATCAACCACC GCATCCCTCAAAACCAGACCAGTTTCAAGGACCACTCATCCC ACCAATCCCAGCTGCTGGAGAGAGGAGGAAAAGTGCCAGA ATATCACAGCTAAATGGTCCAATTGTTTTGGCACATCTCTAC CTGTGAGGGTGAACTGCACGGTACTAAGAGAATTGTGTGAT GAGCAGCCAGGCAATCACACAACAGTTCAAGTATCAAGGAG GTGTACATGCATATATGCATTAAATTGGGATTGTAGTTATGC TTGAGAGAGAGACTACACTAGCCGACCCTAATGAGGTCCAC AGAAAAAGATTAAAAGCATAAACCAATTTTTTAGTTATTTAA AAA of SEQ ID NO:87). The results showed that the gene-start sequences were perfectly conserved in all the APV/CO genes; whereas, the gene-end sequences were less conserved in all the APV/CO genes.
The longest ORF, which is in the most favorable context, encodes a polyprotein of 175 amino acids (molecular weight=19.54 kilodaltons), is the putative SH protein of APV/CO (SEQ ID NO:88). Two other downstream ORFs encoding smaller proteins of 164 amino acids and 114 amino acids were also identified. The putative ORF of the SH protein APV/CO is the second longest in the genus pneumovirus, after hMPV SH protein, which is 183 amino acids long. The ORF of the SH protein of APV/CO is longer than the ORF of SH protein of APV/A by one amino acid (Ling et al., 1992; Genbank accession: CAD42709). In contrast, the SH protein of PVM, HRSV, and BRSV are comparatively shorter, consisting of 92, 73 and 64 amino acids, respectively (Collins et al., J. Gen. Virol. 71:1571-1576 (1990); Easton and Chambers, Virus Res. 48:27-33 (1997); Samal and Zamora, J. Gen. Virol. 72:1715-1720 (1991)).
The amino acid (aa) composition of the SH protein of APV/CO is relatively similar to that of the hMPV, APV/A, RSV and BRSV with a high percentage (22%) of threonine and serine residues (Collins et al., J. Gen. Virol. 71:1571-1576 (1990); Easton and Chambers, Virus Res. 48:27-33 (1997); Samal and Zamora, J. Gen. Virol. 72:1715-1720 (1991); Van den Hoogen et al., Nat. Med. 7:719-724 (2001)). The putative SH protein of APV/CO contains 9 cysteine residues, whereas the corresponding proteins of hMPV and APV/A contain 10 and 16 cysteine residues, respectively (van den Hoogen et al., Virology 295:119-132 (2002)). The putative SH protein of APV/CO contains 3 potential N-linked glycosylation sites (FIG. 4a).
The hydrophilicity profile for putative SH protein of APV/CO showed a hydrophilic N-terminus followed by a hydrophobic domain, which can serve as a potential membrane-spanning domain (amino acid 28 to 51 for APV/CO), and a predominantly hydrophilic C terminus (FIG. 5a). As with other pneumovirus SH proteins, this result is consistent with the APV/CO SH protein being a type II glycoprotein, having an uncleaved signal-anchor sequence proximal to the N-terminus with the C-terminus being extracellular. Comparison of the hydrophilicity profile for the putative SH protein of APV/CO with the hydrophilicity profiles of SH proteins of hMPV, APV/A, and APV/B revealed similar characteristics (Ling et al., J. Gen. Virol. 73:1709-1715 (1992), Van den Hoogen et al., Virology 295:119-132 (2002)).
Clustal W alignment (FIG. 6a) showed that the SH protein of APV/CO shares a higher amino acid sequence identity with the SH protein of hMPV than with the SH proteins of APV/A, APV/B and BRSV (Collins et al., J. Gen. Virol. 71:1571-1576 (1990); Easton and Chambers, Virus Res. 48:27-33 (1997); Samal and Zamora, J. Gen. Virol. 72:1715-1720 (1991)). It was somewhat surprising to find that the SH protein of APV/CO shares a higher sequence identity with a mammalian Metapneumovirus than with its avian counterparts.
A phylogenetic tree based on SH protein sequences of APV/CO and other members of genus Pneumovirus was constructed. These results agree with the previous finding based on a phylogenetic relationship deduced on the basis of more conserved proteins, M2-1 and L of hMPV, that the mammalian metapneumovirus is closely related to APV/CO among the metapneumoviruses, isolated thus far (Van den Hoogen et al., Nat. Med. 7:719-724 (2001)).
The G protein has been most often used to define the antigenic polymorphisms in Pneumovirus (Collins et al., “Parainfluenza viruses,” in Fields Virology, Fields et al., eds., Lippincott-Raven, Philadelphia, Pa. (1996), pp. 1205-1241). The highest sequence divergence in terms of low amino acid (aa) and nucleotide (nt) sequence identity especially in G-ectodomain among different strains, has been extensively used to draw phylogenetic relationships. Based on G sequence and its reactivity to monoclonal antibodies, two antigenic subgroups A and B have been defined for BRSV and HRSV strains, respectively (Anderson et al., J. Inf. Dis. 151:626-633 (1985); Johnson et al., PNAS (USA) 84:5625-5629 (1987); Mallipeddi and Samal, J. Gen. Virol. 74:2001-2004 (1993)). Similarly, in Avian Metapneumovirus, based on 38% nt identity and 56% predicted aa identity in the G gene of different groups of European isolates, two subgroups A and B of APV have been defined in Europe (Juhasz & Easton, J. Gen Virol. 75:2873-2880 (1994)). Based on polymorphisms observed in the nt and aa sequences of N, P, M, F and M2 genes of 15 U.S. strains, a 89-94% nt sequence identity and 81-95% aa sequence identity (Shin et al., J. Clin. Microbiol. 40:1687-1693 (2002); Njenga et al., Virus Res. 91:163-169 (2003)) was found, indicating that these APV isolates are closely related. The above five genes from the U.S. viruses had 41-77% nt sequence identity and 52-78% aa sequence identity with European subgroups A or B viruses, thus suggesting that the APV-US viruses are genetically distinct from the European subgroups A or B and hence classified as subgroup C or APV/C (Shin et al., J. Clin. Microbiol. 40:1687-1693 (2002); Njenga et al., Virus Res. 91:163-169 (2003)). This study reveals that the sequence of APV/CO SH protein shares a very low aa sequence identity with that of European subgroups A or B, thus supporting the classification of APV/CO into subgroup C. Similarly, comparative sequence similarity analysis of F gene from two APV strains isolated in France in 1985 showed low nt (56.6%) and aa (31.2%) sequence identity with APV/A, APV/B, and APV/C viruses, thus leading to the proposed existence of a forth, subgroup APV/D (Bayon-Auboyer et al., Arch. Virol. 144:1091-1109 (1999); Bayon-Auboyer et al., J. Gen. Virol. 81:2723-2733 (2000)).
Example 3
Sequence Analysis of the G Genes of APV-C Strains APV/CO, Mn-1a, and Mn-2a
The nucleotide and deduced amino acid sequences of the G genes of APV/CO, Mn-1a, and Mn-2a were determined using G mRNA as a template. All RT reactions of mRNAs isolated from virus-infected cells were performed using the ProtoScript first strand cDNA synthesis kit (New England Biolabs, Massachusetts). Three separate RT reactions were performed for each virus using an oligo dT primer (supplied with the kit) and two G gene-specific reverse primers, G-1589 (5′ CAGTGCCGTCCCCAAAACAT 3′) (SEQ ID NO: 83) and G-1640 (5′ CATCATAGCAACCAGC-CGGC 3′) (SEQ ID NO: 84), which were designed based on the sequence obtained from viral genomic RNA. PCR was performed with TaKaRa LA Taq polymerase and GC buffer II (TaKaRa, Japan), and G-513 and G-1589 primers. The following cycle parameters were used in the PCR: initial denaturation at 94° C. for 1 m, 30 cycles of 94° C./30 s, 60° C./30 s and 72° C./2 m, and a final elongation step of 72° C. for 5 m. This yielded a single 1.1 kb PCR product. The entire RT-PCR was performed three times, each time with a new viral mRNA preparation, and each time a single RT-PCR product of 1.1 kb was amplified. The 1.1 kb RT-PCR product was either directly sequenced or was cloned and subsequently sequenced. The nucleotide sequencing procedures utilized BigDye terminator cycle-sequencing kit (Applied Biosystems) in the presence of 5% v/v DMSO or 1M (final concentration) of betaine in the sequencing reaction mixture. This sequence, along with the sequences at the 5′ and 3′ ends obtained from the RT reactions with genomic RNA, yielded the complete nucleotide sequence of the G gene.
The complete nucleotide sequence derived from RT-PCR of the viral genomic and mRNAs revealed that the G gene of APV/CO was 1798 nucleotides in length from gene-start to gene-end, and the major ORF was 1758 nucleotides (nt) long, encoding a polypeptide of 585 amino acids (aa). The gene length and the predicted protein length of G genes of Mn-1a and Mn-2a strains of APV-C were exactly the same as those of the APV/CO (Table 1).







TABLE 1







Features of G proteins of the metapneumoviruses










Molec-














ular
Percentage
No. of














Length of
Weight
G + C

Serine +
cysteine


Virus
ORF (aa)
(kDa)
content
Proline
Threonine
residues
















APV/CO
585
58.8
61.7
7.2
23.1
18


APV-
585
58.3
62.9
7.2
22.2
18


Mn1a


APV-
585
61.6
54.0
7.7
27.4
18


Mn2a


APV-A
391
43.0
48.5
6.7
23.5
20


APV-B
414
44.6
49.5
8.5
24.6
20


APV-D
389
41.8
49.7
9.5
23.9
20


HMPV-
236
25.8
47.0
8.5
33.9
1


00-1


CAN97-
219
23.7
46.4
7.8
32.0
1


83


CAN98-
236
25.5
46.6
5.5
33.9
2


75









The G gene of APV/CO possesses the gene-start signal 5′ GGGACAAGU 3′ (mRNA sense) (SEQ ID NO: 85). The gene-end signal 5′ UAGUUAAUUAAAAA 3′ (SEQ ID NO: 86) for the G gene of APV/CO was observed 13 nt downstream of the termination codon. Four potential secondary ORFs [ORF2—146-1771 nt (541 aa); ORF3—155-1771 nt (538 aa); ORF4—167-1771 nt (534 aa) and ORF5—1312-1608 nt (99 aa)] were observed in the G gene of APV/CO. ORFs 2, 3 and 4 possessed the exact carboxy-terminal as that of the major ORF. The signal peptide prediction also showed that a eukaryotic cleavage sequence was present between 46-47 aa residues. These observations denote that the polypeptides encoded from these secondary ORFs could probably be secreted forms of APV-C G protein. The G genes of APV-C strains Mn-1a and Mn-2a G also exhibited similar characteristics.
The predicted molecular mass of the G protein of APV/CO was 58,754 daltons, having a net charge of 8.27 at neutral pH and an isoelectric point of 8.28. The G+C residue content of the entire G gene of APV/CO was 61%. However, the G+C residue content of the G gene of Mn-2a was slightly lower (54%) than that of Mn-1a (62%) or APV-CO. Sequence alignment of the G genes of APV/CO and Mn-1a revealed 21 synonymous nucleotide substitutions (20 A→G and 1 C→T) across the length of the gene, resulting in 11 amino acid changes in the G protein of Mn-1a. On the other hand, the G gene of Mn-2a showed extensive sequence divergence from that of APV/CO and contained 195 nucleotide substitutions (190 synonymous and 5 non-synonymous), which ultimately resulted in 110 amino acid changes in the G protein of Mn-2a. The majority (60%) of these changes lay within amino acid 300 to 450 on the predicted protein, thus forming a highly-divergent domain on the G protein (FIG. 11).
The G protein of APV/CO contained 7.2% proline and 23.1% serine and threonine residues. The Mn-2a strain contained higher serine-threonine content (27.4%), while Mn-1a had values similar to APV-CO. The G ORF of APV/CO and Mn-2a contained five potential N-linked glycosylation sites; whereas, Mn1a contained four N-linked glycosylation sites (FIG. 11).
Hydropathy analysis of the G protein of APV/CO showed characteristics of an anchored type II membrane glycoprotein. The predicted hydrophobicity profile of APV/CO G protein included an amino-terminal intra-cellular domain (amino acids 1-31), followed by a hydrophobic TM domain (amino acids 32-54) and the extracellular domain (amino acids 55-585), consisting mainly of hydrophilic residues. Both Mn-1a and Mn-2a exhibited the same hydrophobicity profiles as that of APV/CO.
Though the G protein of APV/CO showed structural and biochemical features similar to those of the HMPVs, it showed only 21 to 25% amino acid identity with those of the HMPVs. However, the levels of amino acid identity with the G protein of other APVs were still lower, ranging only 14-16% (Table 2).







TABLE 2







Percent amino acid identity between the putative ORF's


of APV-C and those of other metapneumoviruses.
















N
P
M
F
M2
SH
G
L





APV-A
70
53
78
72
70
18
14
64


APV-B
70
52
77
71
65
13
14
—


APV-D
—
—
—
—
—
—
16
—


HMPV-
88
66
86
81
85
24
23
80


00-1


CAN97-
88
67
87
81
84
23
25
80


83


CAN98-
88
67
87
80
85
20
21
80


75





—: sequence not available






Among the U.S. strains, the G protein of APV/CO showed 98% and 81% amino acid identities with those of the strains Mn-1a and Mn-2a, respectively. The G proteins of strains Mn-1a and Mn-2a exhibited 79% amino acid identity between themselves. In addition, sequence comparison of the three membrane-associated glycoproteins (F, SH and G) of the three US APV strains revealed that the G protein is the most variable glycoprotein (Table 3).







TABLE 3







Percent amino acid identity between the membrane glycoproteins


of the US isolates of APVs.














APV/CO vs

APV/CO vs

Mn-1a vs




Mn-1a

Mn-2a

Mn-2a
















nt
aa
nt
aa
nt
aa



















F
99.8
99.4
99
98
99
98



SH
100
100
99
98
99
98



G
99
98
87
81
86
79










Example 4
Sequence Analysis of the L Gene of APV/CO
Two different methods are used to determine the sequence of L gene. (a) RT-PCR of genomic RNA isolated from purified APV. APV is purified by the methods used for other paramyxoviruses. Briefly, Vero cells infected with APV/CO are harvested when maximum CPE is observed. The cells are scraped into the medium and lysed by several cycles of freezing and thawing. The cell lysates are centrifuged at 3000×g for 15 min to remove cell debris. Supernatants from infected cells are made 10% with respect to PEG 8000 and incubated for 3 hrs at 4° C. The virus is be pelleted by centrifugation at 4500×g for 30 min at 4° C. and resuspended in 1 mL of TNE buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH 7.5). Genomic RNA is isolated from purified APV by TRIzol reagent (Invitrogen Corporation) according to the manufacturer's protocol, except that one additional extraction with chloroform is included.
The “genome-walking” strategy used for obtaining sequences of SH and G genes is employed to determine the sequence of L gene. Briefly, an mRNA-sense primer specific to the 5′ region of the G gene is used to synthesize cDNA from the genomic RNA with a Thermoscipt RT kit (Invitrogen Corporation). The single-stranded cDNA is then purified using a nucleotide removal kit (Qiagen). A homopolymer (dc) tail is added to the 3′ end of the purified cDNA using terminal deoxynucleotide transferase, and an aliquot is used in PCR-mediated amplification using the G gene-specific primer and Oligo(dG) anchor primer (Invitrogen Corporation). The amplified product is cloned into TA cloning vector (Invitrogen Corporation) and is used to transform DH10B cells. The resultant colonies are hybridized with a radioactively labeled DNA probe derived from the 3′ end region of the G gene. Several positive clones containing large size inserts are sequenced. Sequences from several clones are compared to obtain the correct sequence. This process of genome walking is repeated to obtain the entire sequence of the L gene. In each round of genome walking, approximately 1 kb of new sequence is obtained; therefore, it will take four to five rounds of cDNA cloning to obtain the entire L gene sequence.
Determination of L Gene Sequence from mRNA
It is imperative that the L gene sequence obtained by genome walking be confirmed by sequencing the L mRNA. Vero cells are infected with APV/CO at a multiplicity of 1 PFU/cell. Total cellular is be isolated from cells at 24 h post-infection, using guanidinium thiocyanate and centrifugation through CsCl (Chirgwin et al., Biochem. 18:5294-5299 (1979)). Poly (A)+RNA is isolated using Oligo-dT-cellulose chromatography (Aviv and Leder PNAS (USA) 69:1408-1412 (1972)). A cDNA library is constructed using Oligo-dT primer (Invitrogen Corporation). The library is screened by hybridization with a radioactively-labeled gene specific probe obtained by the RT-PCR of genomic RNA. Both strands of the L gene-specific inserts are sequenced.







TABLE 4







ATCC deposits of the following nucleic acid material were made:










Nucleotides
ATCC Deposit



Contained
Number











Clone Number










1
G > Forward to G < 615
PTA-5668


2
G > 538 to L < 713
PTA-5669


3
L > 703 to L < 2880
PTA-5670


4
L > 5007 to APV trailer
PTA-5671


DNA Number


1
L > 2775 to L < 4000
PTA-5672


2
L > 3740 to L < 5650
PTA-5673









As shown in Table 4 and in FIG. 10, APV clones 1-4 and DNA PCR products DNA 1 and DNA 2 are overlapping. Therefore, one can obtain the complete sequence of the L gene by utilizing the deposited nucleic acid material, ATCC Deposit Numbers PTA-5668, PTA-5669, PTA-5670, PTA-5671, PTA-5672, PTA-5673, the sequence information of which is fully incorporated by reference herein.
With the completion of the entire genomic sequence of APV-CO, the aa identity of each protein of APV/CO was compared with the corresponding proteins of other MPVs (Table 4). All eight proteins of APV/CO invariably showed higher levels of aa identity with the corresponding proteins of HMPVs than to those of the APVs. The N protein was the most identical protein between the HMPVs and APV/CO, while the M protein was the most identical among the APVs. The latter observation is consistent with the finding that antigenic cross-reactivity among APV-A, APV-B and APV-C occurs at the M protein and not the N protein (Lwamba et al., Avian Dis. 46: 725-729 (2002)). The M, M2, F and L proteins were the other proteins showing greater than 80% aa identity between APV-CO and the HMPVs. Among the membrane glycoproteins, F and SH proteins were more conserved within APV-C strains than the G protein.







TABLE 5







Comparison of the putative ORFs of APV/CO with other


pneumoviruses.











Complete



Protein Length (aa)
Genome
















Virus
N
P
M
F
M2
SH
G
L
Length (nt)





APV-C
394
294
254
537
184
175
585
2005
14150


APV-A
391 
278
254
538
186
174
391
2004
13373


APV-B
391
279
254
538
186
175
414
—
—


APV-D
—
—
—
—
—
—
389
—
—


HMPV-00-1
394
294
254
539
187
183
236
2005
13378†


CAN97-83
394
294
254
539
187
179
219
2005
13335


CAN98-75
394
294
254
539
187
177
236
2005
13280


RSV-A
391
241
256
574
194
 64
298
2165
15225


RSV-B
391
241
256
574
195
 65
299
2166
15191


BRSV
391
241
256
574
186
 81
257
2162
15140


PVM
393
295
257
537
176
 92
396
—
—





—: Sequence not available


†Sequences at the termini are primer-based sequences


RSV: Respiratory syncytial virus;


BRSV: Bovine respiratory syncytial virus;


PVM: Pneumonia virus of mice






Example 5
Development of a Reverse Genetics System for Production of Infectious APV/CO from Cloned cDNA
A cDNA that will transcribe the antigenomic (positive-strand) APV RNA in cells expressing the viral N, P, L and M2-1 proteins is constructed. Although synthesis of antigenomic RNA is not an absolute requirement, this approach has generally been used for recovery of negative-strand RNA viruses. The rationale for using the antigenomic RNA was that, unlike the genomic RNA, it would not be able to hybridize to the N, P, M2-1 and L mRNAs supplied to form RNP and initiate the first round of transcription.
A cDNA clone encoding the entire antigenome of APV/CO is constructed from cDNA fragments that are synthesized by RT-PCR from virion-derived genomic RNA (FIG. 8). Genomic RNA is extracted from purified APV/CO using TRIzol reagent according to the manufacturer's instructions (Invitrogen Corporation). RT is carried out using Superscript II RT (Invitrogen) and PCR is accomplished using proofreading Pfu DNA polymerase (Stratagene). The number of PCR cycles is limited to twenty to further minimize misincorporation of nucleotides. The leader end is constructed to join the promoter for T7 RNA polymerase that includes three transcribed G residues for optimal activity. The presence of these non-viral G residues has been shown not to interfere with the rescue of other paramyxoviruses (Collins et al., PNAS (USA) 92:11563-11567 (1995); and Whelan et al., PNAS (USA) 92:8388-8392 (1995)). To generate a nearly exact 3′ end, the trailer end is constructed to join hepatitis delta virus (HDV) antigenome ribosome sequence followed by tandem terminators of T7 transcription (Pringle, Arch. Virol. 143:203-210 (1998)).
pBR322 is used as the plasmid vector to assemble APV cDNA fragments since large-size inserts are more stable in this low copy number plasmid. Analysis of the complete genome sequence of APV/CO will identify unique restriction sites that are present in the APV genome but are absent in the pBR322 vector. Some of these restriction sites are chosen to assemble the cDNA fragments. Although the APV minigenome has been shown not to obey the “rule of six” (Randhawa et al., J. Virol. 71:9849-9854 (1997)), the exact number of nucleotides present in the genome of APV/CO is maintained in the full-length cDNA. Two unique restriction site markers are introduced into M-F and F-M2 intergenic regions of the antigenomic cDNA by incorporating changes into oligonucleotide primers used in RT-PCR. This facilitates assembly and are used as sequence markers to identify the recombinant virus.
Initially, each cDNA fragment is cloned separately and the correct sequence is confirmed by DNA sequencing. All the APV cDNA fragments are then ligated successively to form the full-length APV cDNA. If a cDNA fragment is found to contain misincorporation of nucleotide(s), it is recloned and resequenced. Alternatively, smaller fragments are joined using other unique restriction sites. DH10B cells (Invitrogen Corporation) are used to carry the full-length APV cDNA clone. These cells cause minimum rearrangement of large size plasmids. Also, the cells are grown at 30° C. to further reduce rearrangement.
Cloning of the cDNA fragments bearing the open reading frames of N, P, and M2-1 genes in pTM-1 plasmid is discussed below. The remaining L gene cDNA fragment is cloned into pTM-1 vector. The cloned gene is sequenced to entirety. The Vero cells are used for transfection experiments because these cells are highly permissive for APV and vaccinia virus. In addition, these cells can be transfected efficiently by Lipofectamine method (Invitrogenv Corporation). The cells are transfected under the transfection conditions that were used to rescue infectious human and bovine respiratory syncytial viruses (Collins et al., PNAS (USA) 92:11563-11567 (1995), Yunus et al., Virus Genes 23:157-164 (2001)).
Briefly, confluent monolayers of Vero cells in six-well dishes are infected with 1 focus-forming unit per cell of recombinant vaccinia virus strain MVA that expresses T7 RNA polymerase (MVA-T7). The MVA strain is a host-range mutant that grows permissively in avian cell; whereas, in mammalian cells, the virus expresses T7 RNA polymerase, but there is no production of infectious virus due to a block at a later stage in virion maturation (Pringle, Arch. Virol. 143:1449-1459 (1998)). A mixture of four plasmids containing the APV N, P, L, and M2 (ORFI) under the control of the T7 promoter (0.4. 0.3, 0.2, and 0.1*g per well, respectively) and a fifth plasmid [p(+)APV] encoding the full-length APV antigenome (1*g) are transfected with Lipofectamine as recommended by the supplier (Invitrogen Corporation). Cells are incubated in a CO2-incubator at 32° C. Twelve hours later, the medium is replaced with optiMEM medium (Invitrogen Corporation) containing 2% bovine fetal serum and 40*g of cytosine arabinoside per ml to inhibit the replication of vaccinia virus. After 3 days, clarified medium supernatants are passaged onto fresh Vero cells and overlaid with methylcellulose for staining with antiserum to APV by horseradish peroxidase method (36) or 1% agarose for plaque isolation. Control transfections include cells that received the support plasmids but no p(+)APV and cells that received p(+)APV, but no support plasmids. Different transfection methods are tested to achieve the highest level of APV recovery. Several APV-like plaques are picked from plates that have been overlaid with metylcellulose. Each plaque is further purified by two plaque-to-plaque isolations. Stocks of each plaque isolate are made in Vero cells for characterization. A schematic of the transfection procedure is shown in FIG. 8.
First, is ascertained that the recovered virus is APV. A plaque neutralization test is performed using hyperimmune serum against wild-type APV/CO. Methyl cellulose overlay and neutral red staining is used in the plaque assay. Wild-type APV/CO is used as a positive control and wild-type vaccinia virus is used as a negative control. The size of the plaques derived from recovered APV is compared with those of the wild-type APV/CO.
To verify that the two sequence markers inserted into the full-length cDNA are present in the recovered APV, reverse transcription of genomic RNA purified from wild-type and recombinant APV, using primers from upstream of each restriction site, is carried out. The reverse transcription products are amplified by PCR using an additional primer downstream of each restriction site. The presence of the sequence marker in the recombinant virus is verified by digestion of the PCR products with appropriate restriction enzymes. The PCR products representing the recombinant APV contain the expected restriction sites, while those representing the wild-type APV do not contain the restriction sites. To further confirm the sequence markers, the PCR products are cloned and sequenced. This confirms that the recovered APV was produced from cDNA clones and was not a laboratory contamination of wild-type APV/CO.
The replication behavior of the recovered APV is compared to that of the wild-type APV/CO. Briefly, Vero cell monolayers in 25-cm2 culture flasks are infected with 2 PFU either virus per cell. One flask every 12 hours is transferred to −70° C. The samples are subsequently thawed and titrated in parallel by plaque assay. Only 2 PFU of APV per cell are used because APV does not grow to high titer. This will indicate any differences in the replication behavior between the recombinant and wild-type APV.
Example 6
Construction of Expression Plasmids
cDNA fragments bearing the open reading frames of N, P and M2-1 genes were generated by RT-PCR from APV/CO genomic RNA using primers based on published nucleotide sequence of these genes. The cDNA fragment were cloned in an expression plasmid (pT<−1) which has an encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) downstream of the T7 RNA polymerase promoter and makes use of the translation start codon contained in Nco I site of IRES. The cloned genes were sequenced to their entirely and were found to be correct. Correct expression also has been obtained for these genes using TNT T7 coupled reticulocyte lysate system (Promega).
Example 7
Generation of Recombinant APV with Mutations in the Fusion Protein Cleavage Site and Evaluation of the Pathogenecity of Mutant APV in Turkeys
The amino acid sequence at the F protein cleavage site has been thought to be a major determinant of paramyxovirus virulence (Nagai et al., Virol. 72:494-508 (1976)). Cleavage of the precursor protein F0 to F1 and F2 by host cell proteases is required for progeny viruses to become infective (Collins et al., in Fields Virology, Fields et al., eds., Lippincott-Raven, Philadelphia, Pa., pp. 1205-1241 (1996)). In closely-related NDV, the virulent strains have multibasic residues Arg-Gln-Lys-Arg (SEQ ID NO:19) at the cleavage site, which are substrates for proteases found in most tissues. The F0 protein of antivirulent NDV strains has dibasic residues Arg-Gln-Gly-Arg (SEQ ID NO:20) at the cleavage site, which are cleaved by proteases found only in the respiratory tract. Therefore, the avirulent NDV strains replicate only in the respiratory tract and do not spread to other tissues. The APV US isolates have an F protein cleavage site sequence of Arg-Lys-Ala-Arg (SEQ ID NO:21), which is similar to the multibasic residues found at the cleavage site of virulent NDV strains. Therefore, one can mutate the F protein cleavage site sequence of APV/CO to Arg-Gln-Gly-Arg (SEQ ID NO:20), which are present at the F protein cleavage sites of avirulent NDV strains LaSota and B1. This particular mutant APV may replicate only in limited tissues and not cause disease in turkeys.
Mutations are introduced into APV F gene cDNA fragments separately and then assembled into the full-length cDNA. The two unique restriction sites introduced in M-F and F-M2 intergenic regions will be used to replace the wild-type F gene fragment with an F gene fragment that contains mutations at the cleavage site. The F protein cleavage site mutant will be generated by sequential PCR mutagenesis (Byrappa et al., Genome Res. 5:404-407 (1995)). All PCR amplifications are carried out using proofreading Pfu DNA polymerase. The mutated fragment is sequenced in its entirety to confirm that the correct mutations were present. The wild-type gene fragment in the full-length cDNA clone is then replaced with the mutated F gene fragment and sequenced again to reconfirm the mutations in the full-length cDNA. The strategy for construction is shown in FIG. 8.
Recovery of the mutant APV strains is carried out as described above. Recovered viruses are biologically cloned by plaque purification before amplification and analysis. If a problem should arise in recovery of the mutant virus due to inefficient cleavage of the F protein, then acetylated trypsin (0.01 mg/ml) is added to the medium to facilitate growth. If necessary, trypsin is also added to the overlay medium in the plaque assay. To confirm the presence of the mutation in the genome of the recovered virus, the region of the F protein containing the cleavage site is amplified by RT-PCR, cloned into TA cloning vector and sequenced. The stability of the mutations is also examined after several passages (at least 15 passages).
To compare the viral proteins synthesized by the wild-type and mutant viruses, Vero cells are infected with a multiplicity of infection of 2 PFU and labeled by incubation with [35S] methionine from 12 to 15 hours post infection. APV-specific proteins are immunoprecipitated from infected cell lysates using polyclonal APV antiserum. Total and immunoprecipitated proteins are analyzed by SDS-PAGE. The uncleaved FO (68,000 Da) and the cleaved FI (53,000 Da) and F (1 5,000 Da) forms of the fusion protein of wild-type and mutant viruses are analyzed. If necessary, the F proteins are also characterized by Western blot analysis.
To study the pathogenicity and persistence of APV, sixty 2-week-old turkey poults are allotted equally to four groups. Each bird in Group I is inoculated with 0.2 ml of 105 TCID50 of APV/CO wild-type virus through the oculonasal route. The birds in Groups II and III are inoculated with the same amount of virus via the oculonasal route, with recombinant APV and “F” cleavage site mutant APV respectively. Birds in Group IV are kept as uninfected controls. Three poults from each group are euthanized at 1, 7, 14, 21 and 28 days post-inoculation (PI). The birds are observed daily for clinical signs. A score of 0-6 is used to describe the clinical signs (Cook et al., Avian Pathol. 18:511-522 (1989)) as follows: 0=no clinical signs, 1=unilateral nasal discharge, 2=bilateral nasal discharge, 3=unilateral watery eyes, 4=bilateral watery eyes, 5=moderate sinus swelling, 6=severe sinus swelling. Swabs and sections from sinuses, harderian glands, trachea and lungs are collected at necropsy for virus isolation and viral RNA detection. Blood is collected from euthanized poults on days 14, 21 and 28 PI for serologic examination.
To study the tissue distribution of wild-type, recombinant and mutant APV in turkey poults, sixty 2-week-old turkey poults are allotted to four groups equally. Each bird in Groups I to III are inoculated with 0.2 ml of 105 TCID50 of the respective APV strains (APV wild-type, recombinant APV and mutant APV). Birds in Group IV are kept as uninfected controls. Three poults are euthanized at 3, 5, 7, 14 and 21 days PI. Sections from sinuses, harderian glands, trachea, lungs, thymus, bursae, liver, spleen, ileum, jejunum, brain and bone marrow are collected for virus isolation, viral RNA detection and histopathology. Blood is collected from euthanized birds at 3, 5, 7, 14 and 21 days PI for serologic examination.
Virus isolation is attempted from 1:10 diluted sample supernatants in 9- to 11-day-old chicken embryos inoculated via the allantoic route (Cook, Rev. Sci. Tech. Off. Int. Epiz 19:602-612 (2000)). For viral RNA detection, the total viral RNA is extracted from the samples using TRIzol (Invitrogon) reagent, and RT-PCR is conducted using primers specific for the M gene of APV. For serologic estimation of APV antibodies, an indirect ELISA employing homologous, purified APV viruses and virus neutralization tests in Vero cells is performed, essentially as described earlier by O'Loan et al., J. Virol. Meth. 25:271-282 (1989). For histological evaluation of the tissues, the sections from sinuses and tissues are fixed in 10% neutral buffered formaldehyde, processed through graded alcohols, and embedded in paraffin. Four to five micrometer thick sections are out and stained by hematoxylin and eosin before analyzing the histological changes.
It will be clear that the invention may be practiced otherwise than as particularly described in the foregoing description and examples.
Numerous modifications and variations of the present invention are possible in light of the above teachings and, therefore, are within the scope of the appended claims.
The entire disclosure of all publications (including patents, patent applications, journal articles, laboratory manuals, books, or other documents) cited herein are hereby incorporated by reference.

## Claims

1. A live-attenuated avian pneumovirus containing one or more attenuating mutations in the F protein cleavage site, wherein the sequence of the mutated F protein cleavage site is Arg-Gln-Gly-Arg (SEQ ID NO:20).

2. The avian pneumovirus of claim 1 wherein the avian pneumovirus is strain Colorado (AVP/CO).