Canine coronavirus S gene and uses therefor

FIELD OF THE INVENTION

[0002] The present invention relates generally to canine coronavirus infections, and specifically to proteins useful in prophylaxis, therapy, and diagnosis of these infections in canines.

BACKGROUND OF THE INVENTION

[0003] The coronaviruses are a large family of mammalian and avian pathogens which were first described in 1968. They are the causative agents of several diseases including encephalitis, hepatitis, peritonitis and gastroenteritis. Enteric coronaviruses have been detected in the feces of man, pigs, calves, cats, mice, chickens and dogs.

[0004] Canine coronavirus (CCV) enteritis was first isolated from dogs suffering an acute gastroenteritis, as reported by Binn et al., Proc. 78th Ann. Mta. U.S. Animal Health Assoc., Roanoke VA, pp. 359-366 (1974). The disease became prevalent during the 1970s. CCV gastroenteritis appears to be primarily transmitted through fecal contamination from infected dogs via the oral route, leading ultimately to replication of the virus in the epithelial cells of the small intestine. Virus can be recovered from the feces of an infected dog between 3 and 14 days after infection.

[0005] CCV gastroenteritis is characterized by a mild depression, anorexia and loose stool from which the dog usually recovers. The onset of the disease is often sudden, accompanied by such symptoms as diarrhea, vomiting, excreted blood in stools, and dehydration. Deaths have occurred within as little as 24 to 36 hours after onset of clinical signs. Most dogs appear afebrile but elevated body temperature is seen in some cases. Often CCV will occur with a canine parvovirus infection and this coinfection can be fatal.

[0006] Serologically the disease is closely related to transmissible gastroenteritis virus of swine (TGEV). Although canine coronavirus does not infect pigs, transmissible gastroenteritis virus produces a subclinical infection in dogs. However, unlike the feline infectious peritonitis coronavirus (FIPV), previous exposure to CCV does not predispose dogs to enhanced disease; and antigen-antibody complexes, if formed, are not associated with disease pathology.

[0007] There remains a need in the art for compositions useful in diagnosing, treating and preventing infections with canine coronaviruses.

SUMMARY OF THE INVENTION

[0008] In one aspect the present invention provides the complete nucleotide sequence of the CCV S gene, strain 1-71, SEQ ID NO: 1. The S gene or fragments thereof may be useful in diagnostic compositions for CCV infection.

[0009] In another aspect the present invention provides a CCV S (or spike) protein characterized by the amino acid sequence of a CCV S protein, SEQ ID NO: 2, and peptide fragments thereof. These proteins may be optionally fused or linked to other fusion proteins or molecules.

[0010] Thus, in another aspect, the present invention provides a vaccine composition containing an effective immunogenic amount of at least one CCV S protein or an immunogenic fragment thereof.

[0011] In still another aspect, the invention provides a method of vaccinating an animal against infection with a coronavirus by administering an effective amount of a vaccine composition of this invention.

[0012] In yet a further aspect, the present invention provides a pharmaceutical composition for the treatment of CCV infection comprising a therapeutically effective amount of a CCV S peptide or protein of the invention and a pharmaceutically effective carrier.

[0013] Still another aspect of this invention is an antibody directed to CCV, which antibody is capable of distinguishing between CCV and other canine viruses. These antibodies may also be employed as diagnostic or therapeutic reagents.

[0014] In yet another aspect, a diagnostic reagent of the present invention comprises a CCV S protein or fragment thereof. In another aspect, the present invention provides a diagnostic reagent which comprises a nucleotide sequence which encodes a CCV S protein or fragment of the invention, and/or a nucleotide sequence which flanks the coding region, or fragments thereof. These protein and nucleotide sequences are optionally associated with detectable labels. Such diagnostic reagents may be used to assay for the presence of CCV in dogs using standard assay formats and can form components of a diagnostic kit.

[0015] In a further aspect, the invention provides a method of using a diagnostic reagent of this invention to identify dogs which are uninfected or which have been previously exposed to CCV. The diagnostic method can differentiate exposure to CCV from exposure to other related coronaviruses, allow the identification of dogs which have been vaccinated against these diseases, and allow one to distinguish between different strains of CCV, or to identify dogs at advanced stages of CCV infection.

[0016] In yet a further aspect, the invention provides a method for the production of a recombinant CCV protein comprising culturing a selected host cell, e.g., a mammalian cell or viral vector, transformed with a DNA sequence encoding a selected CCV S protein or fragment thereof in operative association with regulatory sequences capable of regulating the expression of said protein.

[0017] Another aspect of the invention is a recombinant DNA molecule comprising a DNA sequence coding for a selected portion of a canine coronavirus S protein, the DNA sequences in operative association with regulatory sequences capable of directing the expression thereof in host cells.

[0018] Other aspects and advantages of the present invention are described further in the following detailed description of the preferred embodiments thereof.

DETAILED DESCRIPTION OF THE INVENTION

[0019] The present invention provides novel isolated canine coronavirus (CCV) S proteins and fragments thereof, as well as isolated nucleotide sequences encoding the proteins or fragments. These proteins and fragments are useful for diagnostic, vaccinal and therapeutic compositions as well as methods for using these compositions in the diagnosis, prophylaxis and treatment of CCV-related and other coronavirus-related conditions.

[0020] I. Definitions

[0021] As defined herein, an amino acid fragment is any amino acid sequence from at least about 8 amino acids in length up to about the full-length CCV S gene protein. A nucleotide fragment defines a nucleotide sequence which encodes from at least about 8 amino acids in length up to about the full-length CCV S gene protein.

[0022] The term “region” refers to all or a portion of a gene or protein, which may contain one or more fragments as defined above.

[0023] The term “immunogenic” refers to any S gene protein or fragment thereof, any molecule, protein, peptide, carbohydrate, virus, region or portion thereof which is capable of eliciting a protective immune response in a host, e.g., an animal, into which it is introduced.

[0024] The term “antigenic” refers only to the ability of a molecule, protein, peptide, carbohydrate, virus, region or portion thereof to elicit antibody formation in a host (not necessarily protective).

[0025] As used herein, the term “epitope” refers to a region of a protein which is involved in its immunogenicity, and can include regions which induce B cell and/or T cell responses.

[0026] As used herein, the term “B cell site or T cell site” defines a region of the protein which is a site for B cell or T cell binding. Preferably this term refers to sites which are involved in the immunogenicity of the protein.

[0027] II. Sources of CCV Sequences

[0028] The examples below specifically refer to newly identified spike gene sequences from canine coronavirus (CCV) strain 1-71. This strain is deposited with the American Type Culture Collection (ATCC), 12301 Parklawn Drive, Rockville, Maryland under Accession No. VR-809. Particularly disclosed are nucleotide and amino acid sequences, SEQ ID NO: 1 and 2, respectively, of the CCV S gene.

[0029] The present invention is not limited to the particular CCV strain employed in the examples. Other CCV strains have been described, e.g., strain CCV-TN449 [ATCC 2068]. Utilizing the teachings of this invention, analogous fragments of other canine coronavirus strains can be identified and used in the compositions of this invention.

[0030] IIl. CCV Nucleotide and Amino Acid Sequences of the Invention.

[0031] The inventors have identified and selected nucleotide and protein sequences of CCV strain 1-71 which have been determined to be of interest for use as vaccinal, therapeutic and/or diagnostic compositions. For example, selected peptide and nucleotide sequences present primarily in the variable N terminal region of the CCV S protein and gene are characterized by representing areas of homology between FIPV, TGEV, feline enteric coronavirus (FECV) and other coronavirus strains.

[0032] Peptide fragments obtained from this heterogeneous N terminal of the S protein are useful fragments for diagnostic compositions and kits for distinguishing between infection with CCV strain 1-71 from other CCV infections, and for distinguishing between infection with CCV and other coronavirus identified above in a vaccinated or infected dog, as well as for use in vaccine and therapeutic agents.

[0033] Additionally, the amino terminal sequences of CCV S protein include peptide sequences which are B cell sites and thus useful in vaccinal or therapeutic compositions, or for generating antibodies to CCV, in assays for the detection of CCV antibodies in dogs.

[0034] In addition, certain peptide fragments of the CCV S protein are believed to represent T cell sites, and thus are useful in vaccinal or therapeutic compositions.

[0035] Other suitable CCV amino acid regions for pharmaceutical or diagnostic use are located within other regions of the CCV S protein SEQ ID NO: 2. These amino acid and nucleotide fragments of the CCV S protein and its nucleotide sequence discussed above are specifically reported below in Tables I and II. Table II also reports the respective homologies of, certain of these desired fragments to wild-type FIPV, i.e., FIPV WSU 1146. The CCV S nucleotide fragments in Tables I and II can be useful for diagnostic probes, PCR primers, or for use in recombinant production of relevant S protein fragments for use in therapeutic or vaccinal compositions. Other suitable fragments may also be identified for such use.

1TABLE ICCV Amino AcidsB cell sitesT cell sitesSEQ ID NOS:50-250 3375-425 4450-470 5550-600 6650-700 7770-850 8900-1025 91150-1225101250-14521140-471263-8113187-19114241-27415335-34116395-42817468-49418846-86019916-95220977-992211068-1145221366-139123

[0036]

2

TABLE II

Amino Acid Sequences

CCV 1-71
% Homology CCV 1-71
SEQ ID NOS.

Amino Acid
Nucleotides
to WT FIPV WSU 1146
AA Nucl.

1113-1236
3337-3708
100
25 and 24

540-599
1618-1797
93.3
27 and 26

342-388
1024-1164
93.6
29 and 28

137-153
409-459
64.7
31 and 30

375-388
1123-1164
85.7
33 and 32

1424-1440
4270-4320
94.1
35 and 34

1407-1420
4219-4260
85.7
37 and 36

1342-1406
4024-4218
96.9
39 and 38

398-652
1192-1956
93.3
41 and 40

128-555
382-1665
89.5
43 and 42

447-628
1339-1884
91.8
45 and 44

[0037] IV. Modified Sequences of the Invention.

[0038] In addition to the amino acid sequences and corresponding nucleotide sequences of the specifically- recited embodiments of CCV S proteins of this invention, the invention also encompasses other DNA and amino acid sequences of CCV S proteins. Such other nucleic acid sequences include those sequences capable of hybridizing to SEQ ID NO: 1 under conditions of at least 85% stringency, i.e. having at least 85% homology to the sequence of SEQ ID NO: 1, more preferably at least 90% homology, and most preferably at least 95% homology. Such homologous sequences are characterized by encoding a CCV S gene protein related to strain 1-71.

[0039] Further, allelic variations (naturally-occurring base changes in the species population which may or may not result in an amino acid change) of DNA sequences encoding the various S amino acid or DNA sequences from the illustrated CCV are also included in the present invention, as well as analogs or derivatives thereof. Similarly, DNA sequences which code for protein sequences of the invention but which differ in codon sequence due to the degeneracies of the genetic code or variations in the DNA sequence encoding these proteins which are caused by point mutations or by induced modifications to enhance the activity, half- life or production of the peptide encoded thereby are also encompassed in the invention.

[0040] Variations in the amino acid sequences of this invention may typically include analogs that differ by only 1 to about 4 codon changes. Other examples of analogs include polypeptides with minor amino acid variations from the natural amino acid sequence of S gene proteins and/or the fusion partner; in particular, conservative amino acid replacements. Conservative replacements are those that take place within a family of amino acids that are related in their side chains. Genetically encoded amino acids are generally divided into four families: (1) acidic=aspartate, glutamate; (2) basic=lysine, arginine, histidine; (3) non-polar=alanine, valine, leucine, isoleucine, praline, phenylalanine, methionine, tryptophan; and (4) uncharged polar=glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. For example, it is reasonable to expect that an isolated replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar conservative replacement of an amino acid with a structurally related amino acid will not have a significant effect on its activity, especially if the replacement does not involve an amino acid at an epitope of the polypeptides of this invention.

[0041] V. Fusion Proteins.

[0042] If desired, the CCV S proteins and peptide fragments, e.g. those identified in Tables I and II, can be produced in the form of fusion proteins as defined below. Such a fusion protein may contain either a full-length Ccv S protein or an immunogenic fragment thereof. Suitable fragments include those contained within SEQ ID NO: 2 and the amino acids fragments of Tables I and II. Other suitable fragments can be determined by one of skill in the art by analogy to the sequences provided herein.

[0043] Proteins or peptides may be selected to form fusion proteins with the selected S protein or peptide sequence based on a number of considerations. The fusion partner may be a preferred signal sequence, a sequence which is characterized by enhanced secretion in a selected host cell system, or a sequence which enhances the stability or presentation of the S-derived peptide. Such exemplary fusion partners include, without limitation, ubiquitin and a mating factor for yeast expression systems, and beta-galactosidase and influenza NS-1 protein for bacterial systems. One of skill in the art can readily select an appropriate fusion partner for a selected expression system. The present invention is not limited to the use of any particular fusion partner.

[0044] The CCV S protein or fragments thereof can optionally be fused to each other or to the fusion partner through a conventional linker sequence, i.e., containing about 2 to 50 amino acids, and more preferably, about 2 to about 20 amino acids in length. This optional linker may provide space between the two linked sequences. Alternatively, this linker sequence may encode, if desired, a polypeptide which is selectively cleavable or digestible by conventional chemical or enzymatic methods. For example, the selected cleavage site may be an enzymatic cleavage site, including sites for cleavage by a proteolytic enzyme, such as enterokinase, factor Xa, trypsin, collagenase and thrombin. Alternatively, the cleavage site in the linker may be a site capable of being cleaved upon exposure to a selected chemical, e.g., cyanogen bromide or hydroxylamine. The cleavage site, if inserted into a linker useful in the fused sequences of this invention, does not limit this invention. Any desired cleavage site, of which many are known in the art, may be used for this purpose.

[0045] VI. Production of sequences of Invention

[0046] The CCV S gene protein of the invention and amino acid regions, fragments thereof and their corresponding nucleotide sequences, as well as other proteins described herein, e.g. fusion partners, may be produced by conventional methods. These proteins or fragments and the nucleotide sequences may be prepared by chemical synthesis techniques [Merrifield, J.A.C.S., 85:2149-2154 (1963)]. Preferably, however, they are prepared by known recombinant DNA techniques by cloning and expressing within a host microorganism or cell a DNA fragment carrying a coding sequence for the selected protein. See, e.g., Sambrook et al, “Molecular Cloning. A Laboratory Manual”, 2nd edit., Cold Spring Harbor Laboratory, New York (1989). Such techniques are discussed below in the Examples.

[0047] According to cloning techniques, a selected gene fragment of this invention can be cloned into a selected expression vector. Vectors for use in the method of producing S protein proteins comprise a novel S gene DNA sequence (or a fragment thereof) of the invention and selected regulatory sequences in operative association with the DNA coding sequence, and capable of directing the replication and expression of the peptide in a selected host cell.

[0048] Vectors, e.g., polynucleotide molecules, of the invention may be designed for expression of CCV S proteins and/or fusion proteins in bacterial, mammalian, fungal or insect cells or in selected viruses. Suitable vectors are known to one skilled in the art by resort to known publications or suppliers.

[0049] The resulting DNA molecules or vectors containing nucleotide sequences encoding the canine coronavirus S peptides or fragments thereof and/or encoding the fusion proteins are then introduced into host cells and expression of the heterologous protein induced.

[0050] Additional expression systems may include the known viral expression systems, e.g., vaccinia, fowlpox, swine pox. It is understood additionally, that the design of the expression vector will depend on the choice of host cell. A variety of suitable expression systems in any of the below-identified host cells are known to those skilled in the art and may be readily selected without undue effort.

[0051] Suitable cells or cell lines for use in expressing the S protein or peptides of this invention can be eukaryotic or prokaryotic. A preferred expression system includes mammalian cells, such as Chinese Hamster ovary cells (CHO) or COS-l cells. The selection of other suitable mammalian host cells and methods for transformation, culture, amplification, screening and product production and purification are known in the art. See, e.g., Gething and Sambrook, Nature, 293:620-625 (1981), or alternatively, Kaufman et al, Mol. Cell. Biol., (7):1750-1759 (1985) or Howley et al, U. S. Pat. No. 4,419,446. Also desirable are insect cell systems, such as the baculovirus or Drosophila systems. The selection of other suitable host cells and methods for transformation, culture, amplification, screening and product production and purification can be performed by one of skill in the art by reference to known techniques. See, e.g., Gething and Sambrook, Nature, 293:620-625 (1981).

[0052] After the transformed host cells are conventionally cultured for suitable times and under suitable culture conditions known to those skilled in the art, the cells may be lysed. It may also be possible, depending on the construct employed, that the recombinant proteins are secreted extracellularly and obtained from the culture medium. Cell lysates or culture medium are then screened for the presence of CCV S protein or peptide which are recognized by antibodies, preferably monoclonal antibodies (MAbs), to a peptide antigenic site from CCV.

[0053] Similarly, the fusion proteins may be produced by resort to chemical synthesis techniques, or preferably, recombinant methods, as described above. The selected primer sets used in the PCR reaction described in the Examples below may be designed to produce PCR amplified fragments containing restriction endonuclease cleavage site sequences for introduction of a canine coronavirus S gene fragment in a specific orientation into a selected expression vector to produce fusion proteins of the invention. The vector may contain a desired protein or fragment thereof to which the S gene fragment is fused in frame to produce a fusion protein.

[0054] The crude cell lysates containing the CCV S protein or peptides or fusion proteins can be used directly as vaccinal components, therapeutic compositions or diagnostic reagents. Alternatively, the CCV S peptides can be purified from the crude lysate or medium by conventional means.

[0055] VII. Vaccine Compositions

[0056] The CCV S proteins and immunogenic fragments of. this invention may be incorporated in a vaccine composition. Such a vaccine composition may contain an immunogenic amount of one or more selected CCV S peptides or proteins, e.g., encoded by the complete S gene sequence of CCV or partial sequences thereof, and prepared according to the method of the present invention, together with a carrier suitable for administration as a vaccine composition for prophylactic treatment of CCV infections. The protein may be in the form of a fusion protein as above-described. Alternatively, the CCV S gene or fragment may be incorporated into a live vector, e.g., adenovirus, vaccinia virus and the like. The expression of vaccinal proteins in such live vectors are well-known to those in the art [See, e.g., U. S. Pat. No. 4,920,209]. It is preferable that the protein employed in the vaccine composition induces protective immune responses against more than one strain of CCV.

[0057] A vaccine composition according to the invention may optionally contain other immunogenic components. Particularly desirable are vaccine compositions containing other canine antigens, e.g., canine distemper, Borrelia burgdorferi, canine Bordetella, rabies, canine parvovirus, Leptosporidia sp., canine rotavirus, canine parainfluenza virus and canine adenovirus.

[0058] In another embodiment, the CCV S proteins may be used in a combination vaccine directed to related coronaviruses. Other suitable coronaviruses which can be used in such a combination vaccine include a feline coronavirus, such as FIPV or FECV. For example, a CCV S peptide or protein of the present invention may be employed as an additional antigen in the temperature sensitive FIPV vaccine described in detail in co-owned, co-pending U. S. patent application Ser. No. 07/428,796 filed Oct. 30, 1989, incorporated by reference herein. Alternatively, the CCV S protein or peptide or a fragment thereof could be used in a vaccine composition containing other coronavirus S proteins or fragments thereof, particularly those described in co-pending, co-owned U.S. patent application Ser. No. 07/698,927 (and its corresponding published PCT Application No. W092/08487).

[0059] The preparation of a pharmaceutically acceptable vaccine composition, having appropriate pH isotonicity, stability and other conventional characteristics is within the skill of the art. Thus such vaccines may optimally contain other conventional components, such as adjuvants and/or carriers, e.g. aqueous suspensions of aluminum and magnesium hydroxides, liposomes and the like.

[0060] The vaccine composition may be employed to vaccinate animals against the clinical symptoms associated with CCV. The vaccines according to the present invention can be administered by an appropriate route, e.g., by the oral, intranasal, subcutaneous, intraperitoneal or intramuscular routes. The presently preferred methods of administration are the subcutaneous and intranasal routes.

[0061] The amount of the CCV S peptide or protein of the invention present in each vaccine dose is selected with regard to consideration of the animal's age, weight, sex, general physical condition and the like. The amount required to induce an immunoprotective response in the animal without significant adverse side effects may vary depending upon the recombinant protein employed as immunogen and the optional presence of an adjuvant. Generally, it is expected that each dose will comprise between about 0.05-5000 micrograms of protein per mL, and preferably 0.05-100 micrograms per mL of a sterile solution of an immunogenic amount of a protein or peptide of this invention. Initial doses may be optionally followed by repeated boosts, where desirable.

[0062] Another vaccine agent of the present invention is an anti-sense RNA sequence generated to the S gene of CCV strain 1-71 [SEQ ID NO: 1] [S. T. Crooke et al, Biotech., 10:882-886 (Aug. 1992)]. This sequence may easily be generated by one of skill in the art either synthetically or recombinantly. Under appropriate delivery, such an anti-sense RNA sequence when administered to an infected animal should be capable of binding to the RNA of the virus, thereby preventing viral replication in the cell.

[0063] VIll. Pharmaceutical Compositions

[0064] The invention also provides a pharmaceutical composition comprising one or more CCV S peptides or proteins prepared according to the present invention and a pharmaceutically effective carrier. Suitable pharmaceutically effective carriers for internal administration are known to-those skilled in the art. One selected carrier is sterile saline. The pharmaceutical composition can be adapted for administration by any appropriate route, but is designed preferentially for administration by injection or intranasal administration.

[0065] IX. Antibodies of the Invention

[0066] The present invention also encompasses the development of an antibody to one or more epitopes in the above identified amino acid sequences derived from the CCV S protein, which epitope is distinct from those of other CCV strains or other coronaviruses, e.g. FIPV, TGEV or FECV. The antibody can be developed employing as an antigenic substance, a peptide of Table I or II. Alternatively, other regions of the CCV strain 1-71 S protein SEQ ID NO: 2 may be employed in the development of an antibody according to conventional techniques.

[0067] In one embodiment, the antibody is capable of identifying or binding to a CCV antigenic site encoded by SEQ ID NO: 1 or a fragment thereof. Such an antibody may be used in a diagnostic screening test, e.g., as a hybridization probe, or as a therapeutic agent.

[0068] Antibodies which bind CCV peptides from the regions identified above or to other regions capable of distinguishing between CCV, TGEV, FIPV, FECV, and other coronaviruses for use in the assays of this invention may be polyclonal. However, it is desirable for purposes of increased target specificity to utilize MAbs, both in the assays of this invention and as potential therapeutic and prophylactic agents. Additionally, synthetically designed MAbs may be made by known genetic engineering techniques [W. D. Huse et al, Science, 24:1275-1281 (1989)] and employed in the methods described herein. For purposes of simplicity the term MAb(s) will be used throughout this specification; however, it should be understood that certain polyclonal antibodies, particularly high titer polyclonal antibodies and recombinant antibodies, may also be employed.

[0069] A MAb may be generated by the well-known Kohler and Milstein techniques and modifications thereof and directed to one or more of the amino acid residue regions identified above, or to other CCV S peptides or epitopes containing differences between CCV strain 1-71 and other coronaviruses. For example, a fragment of SEQ ID NO: 2 which represents an antigenic site, which differs from that of FIPV, may be presented as an antigen in conventional techniques for developing MAbs. One of skill in the art may generate any number of MAbs by using fragments of the amino acid residue regions identified herein as an immunogen and employing these teachings.

[0070] For diagnostic purposes, the antibodies (as well as the diagnostic probes) may be associated with individual labels. Where more than one antibody is employed in a diagnostic method, the labels are desirably interactive to produce a detectable signal. Most desirably, the label is detectable visually., e.g. calorimetrically. Detectable labels for attachment to antibodies useful in the diagnostic assays of this invention may also be easily selected by one skilled in the art of diagnostic assays, amont which include, without limitation, horseradish peroxidase (HRP) or alkaline phosphatase (AP), hexokinase in conjunction with glucose-6-phosphate dehydrogenase, and NAD oxidoreductase with luciferase and substrates NADH and FMN or peroxidase with luminol and substrate peroxide. These and other appropriate label systems and methods for coupling them to antibodies or peptides are known to those of skill in the art.

[0071] Antibodies may also be used therapeutically as targeting agents to deliver virus-toxic or infected cell- toxic agents to infected cells. Rather than being associated with labels for diagnostic uses, a therapeutic agent employs the antibody linked to an agent or ligand capable of disabling the replicating mechanism of the virus or of destroying the virally-infected cell. The identity of the toxic ligand does not limit the present invention. It is expected that preferred antibodies to peptides encoded by the S genes identified herein may be screened for the ability to internalize into the infected cell and deliver the ligand into the cell.

[0072] X. Diagnostic Reagents and Assays

[0073] The nucleotide sequences, amino acid fragments and antibodies described above may be employed as diagnostic reagents for use in a variety of diagnostic methods according to this invention.

A. PCR Diagnostic Assays.

[0074] For example, these sequences can be utilized in a diagnostic method employing the polymerase chain reaction (PCR) technique to identify the presence of a CCV or CCV-like virus and in therapy of infected animals.

[0075] In addition to those sequences identified above, the oligonucleotide sequences that were designed to prime CDNA synthesis at specific sites within the CCV S gene, as described in detail below in Example 3 [SEQ ID NO: 46-50], may also be employed as diagnostic reagents according to this invention. These sequences, as well as the below-described optimized conditions for the PCR amplification of CCV fragments therefrom, may also be employed in a diagnostic method.

[0076] The PCR technique is known to those of skill in the art of genetic engineering and is described in detail in Example 4 [see, e.g., R. K. Saiki et al, Science, 230:1350-1354 (1985)], which is incorporated herein by reference. Briefly described, PCR employs two oligonucleotide primers which are complementary to the opposite strands of a double stranded nucleic acid of interest whose strands are oriented such that when they are extended by DNA polymerase, synthesis occurs across the region which separates the oligonucleotides. By repeated cycles of heat denaturation, annealing of the primers to their complementary sequences and extension of the annealed primers with a temperature stable DNA polymerase, millions of copies of the target gene sequence are generated. The template for the reaction is total RNA, which is isolated from CCV infected cells. DNA fragments generated by PCR were amplified from CDNA which had been synthesized from this RNA. Other strains of CCV or CCV-related sequences may also provide PCR templates in a similar manner.

[0077] In one diagnostic method, for example, heterogenous CCV gene sequences of this invention are useful as reagents in diagnostic assays to detect and distinguish the presence of specific viruses from each other, e.g., to distinguish one canine coronavirus strain from another or one species of coronavirus from another by means of conventional assay formats. For example, using protocols similar to those used for forensic purposes, tissue or blood samples from a dog suspected to be infected with CCV would be subjected to PCR amplification with a selected CCV-specific set of primers, such as those DNA sequences disclosed herein. Amplification of DNA from a sample tissue or biological fluid of the animal suspected of infection using nucleotide sequences as primers specific for regions of the CCV viral gene sequences could correlate to the presence of CCV. Absence of CCV in the sample would result in no amplification. Similarly, the selection of specific sets of S gene primers would allow the identification of a particular strain of CCV as well. Thus, appropriate treatments may be selected for the infected animal.

[0078] Example 3 provides oligonucleotide primers which permitted the synthesis of regions of the CCV S gene. The nucleotide sequence of the S gene of CCV provides desirable sequences for hybridization probes and PCR primers, for example, the sequences between nucleotide base pairs 900 to about 1600 [SEQ ID NO: 55] and about 2500 to about 3900 [SEQ ID NO: 56] of SEQ ID NO: 1. Smaller or larger DNA fragments in these regions may also be employed as PCR primers or hybridization probes. It is desirable to have PCR primer sequences between 15 to 30 bases in length, with an intervening sequence of at least 100 bases to as large as 5000 bases there between, according to conventional PCR technology. However, it is possible that larger or smaller sequence lengths may be useful based upon modifications to the PCR technology. In general, in order to achieve satisfactory discrimination, a hybridization or oligonucleotide probe made up of one or more of these sequences would consist of between 15 and 50 bases in length based on current technology.

B. Conventional Assay Formats

[0079] The CCV S proteins or peptide fragments may also be employed in standard diagnostic assays which rely on S protein immunogens as targets for sera recognition. The diagnostic assays may be any conventionally employed assay, e.g., a sandwich ELISA assay, a Western blot, a Southern blot and the like. Because a wide variety of diagnostic methods exist and are conventionally known which can be adapted to the use of the nucleotide and amino acid sequences described herein, it should be understood that the nature of the diagnostic assay does not limit the use of the sequences of this invention.

[0080] For example, the amino acid sequences encoded by CCV S gene sequences, such as those appearing in Tables I and II above, which may be amplified by PCR, provide peptides useful in such diagnostic assays as ELISA or Western assay, or as antigens for the screening of sera or development of antibodies.

[0081] For example, the sequences between about amino acid 1 to about 250 [SEQ ID NO: 57], about 450 to about 650 [SEQ ID NO: 58], and about 900 to about 1150 [SEQ ID NO: 59] of the CCV strain 1-71 S gene protein SEQ ID NO: 2, are anticipated to be useful as such antigens. Such peptides can optionally also be used in the design of synthetic peptide coupled to a carrier for diagnostic uses, e.g., antibody detection in sera. Suitable carriers include ovalbumin, keyhole limpet hemocyanin, bovine serum albumin, sepharose beads and polydextran beads.

[0082] Such peptide antigens and antibodies to these peptides would react positively with tissue or serum samples of dogs infected with CCV, but negatively with non-CCV infected dogs. These antibodies are discussed in more detail below.

[0083] For example, the invention provides a method of using the full length CCV S protein or fragments thereof as diagnostic agents for identifying the presence or absence of antibodies in previously exposed, naive or vaccinated dogs, respectively, as well as for differentiating exposure to CCV from other related coronaviruses. Other S peptides or fusion proteins which show differential reactivity to CCV and other coronavirus sera may also be useful as CCV-specific reagents in ELISA-based screening assays to detect CCV exposure in dogs. Similarly, an S protein or peptide which contains epitopes recognized only by sera from CCV infected dogs or by sera from CCV positive dogs could be employed to distinguish or differentiate among coronavirus infections.

[0084] As one assay format, the reactivity of affinity purified CCV S proteins or peptides fragments to canine biological fluids or cells can be assayed by Western blot. The assay is preferably employed on sera, but may also be adapted to be performed on other appropriate fluids or cells, for example, macrophages or white blood cells. In the Western blot technique, the purified protein, separated by a preparative SDS polyacrylamide gel, is transferred to nitrocellulose and cut into multiple strips. The strips are then probed with dog sera from uninfected or infected dogs. Binding of the dog sera to the protein is detected by incubation with alkaline phosphatase tagged goat anti-dog IgG followed by the enzyme substrate BCIP/NBT. Color development is stopped by washing the strip in water.

[0085] CCV S protein or fragments thereof may also be used in an ELISA based assay for detecting CCV disease. A typical ELISA protocol would involve the adherence of antigen (e.g., a S protein) to the well of a 96-well tray. The serum to be tested is then added. If the serum contains antibody to the antigen, it will bind. Specificity of the reaction is determined by the antigen absorbed to the plate. With the S protein, only sera from those dogs infected with CCV would bind to the plate; sera from naive or uninfected dogs would not bind.

[0086] Similarly, a CCV S protein or peptide which contained epitopes recognized only by sera from CCV-infected dogs or by sera from CCV-positive dogs could be employed to distinguish coronavirus infections. After the primary antibody is bound, an enzyme-labeled antibody directed against the globulin of the animal whose serum is tested is added. Substrate is then added. The enzyme linked to antibody bound to the well will convert the substrate to a visible form. The amount of color measured is proportional to the amount of antibody in the test material. In this manner, dogs infected with CCV can be identified and treated, or dogs naive to the virus can be protected by vaccination.

[0087] When used as diagnostic reagents, the primers, probes, peptide antigens, nucleotide sequence encoding or flanking a CCV S protein or fragment of the invention, and antibodies of this invention may be optionally associated with detectable labels or label systems known to those skilled in the art. Such labelled diagnostic reagents may be used to assay for the presence of CCV in dogs in hybridization assays or in the PCR technique as described above.

C. Diagnostic Kits

[0088] The assay methods, PCR primers, CCV S nucleotide sequences [SEQ ID NO: 1], S proteins and peptides, and antibodies described herein may be efficiently utilized in the assembly of a diagnostic kit, which may be used by veterinarians or laboratories. The kit is useful in distinguishing between CCV infected animals and vaccinated animals, as well as non-exposed dogs, and between CCV- infected animals and animals infected with serologically related viruses, such as other CCV or FIPV, TGEV, and FECV. Such a diagnostic kit contains the components necessary to practice the assays described above.

[0089] Thus, the kit may contain a sufficient amount of at least one CCV S protein, fusion protein or peptide fragment, at least one CCV S gene nucleotide sequence or PCR primer pair of this invention, a MAb directed to a first epitope on the CCV S protein (which MAb may be labeled), optional additional components of a detectable labelling system, vials for containing the serum samples, protein samples and the like, and a second MAb conjugated to the second enzyme, which in proximity to the first enzyme, produces a visible product. Other conventional components of such diagnostic kits may also be included.

[0090] Alternatively, a kit may contain a selected CCV S protein or peptide, a MAb directed against a selected CCV S peptide fragment bound to a solid surface and associated with a first enzyme, a different MAb associated with a second enzyme, and a sufficient amount of the substrate for the first enzyme, which, when added to the serum and MAbs, provides the reactant for the second enzyme, resulting in the color change.

[0091] Other known assay formats will indicate the inclusion of additional components for a diagnostic kit according to this invention.

[0092] The following examples illustrate the embodiments of this invention and do not limit the scope of the present invention.

Example 1-Isolation of CCV

[0093] Canine coronavirus strain 1-71 was isolated in 1971 from military dogs suffering from a viral gastroenteritis by Binn et al., Proceeding 78th Annual Meeting U.S. Animal Health Association, October 1974, p. 359-366. The initial isolate from the feces of the infected dog was grown in tissue culture on the PrDKTCA72 dog cell line [ATCC No. CRL 1542]. The coronavirus strain used in this study was received from the ATCC (ATCC #VR-809, CCV Strain 1-71, Frozen lot#4, Passage 7/PDK, 17 May 1988) and passaged five times on PrDKTCA72.

Example 2-RNA purification

[0094] After the fifth passage the infected cells were processed for RNA isolation by infecting a 1700 cc2 roller bottle with a CCV inoculum. The inoculum was prepared by diluting 2.5 μl of infected fluids from a confluent monolayer into 13.0 mls of media. One ml of this material was used to infect a roller bottle and the cells were grown until they demonstrated a pronounced cytopathic effect at 48 hours. The infected monolayers were harvested and total cytoplasmic RNA was extracted using the guanidinium thiocyanate procedure as described in Chirgwin et al., Biochem., 18:5294 (1979).

Example 3-Primers Used for PCR Amplification of CCV Snike Grene Fragments

[0095] The primers appearing below in Table III were synthesized conventionally by the phosphoramidite method and gel purified prior to use. Primer #3045 was based on an FECV S gene sequence; and primers #4920, 1923, 2443 and 2600 were based on WT FIPV WSU 1146 sequences.

3TABLE IIIAmplifiedClonedTopBottomS Gene RegionRegionPrimerPrimer1-362 aa1-352 aa#3045#4920352-1452 aa352-1452 aa#2600#19231-555 aa128-555 aa#3045#2443

[0096]

4

Primer #
DNA Sequence

1923
TAAATAGGCCTTTAGTGGACATGCACTTTTTCAATTGG

[SEQ ID NO:46]
StuI

2443
TTAGTAGGCCTGTCGAGGCTATCGGTTGACCATAACCAC

[SEQ ID NO:47]
StuI

2600
CAGATCCCGGGTGTACAATCTGGTATGGGTGCTACAG

[SEQ ID NO:48]
XmaI

2045
GTGCCCCCGGGTATGATTCTCCTCGTAACTTGCCTCTTG

[SEQ ID NO:49]
XmaI

4920
AGCACCCATACCAGATTGTACATCTGCAGTGAAATTAAGATTG

[SEQ ID NO:50]
PstI

Example 4-PCR Amplification of CCV S Gene

[0097] PCR amplified fragments of CCV S gene were generated using the following procedure. All PCR reagents were supplied by Perkin Elmer-Cetus, Norwalk, Conn. In a final reaction volume of 20 μl of 1X RT buffer (5X RT buffer: 250 mM Tris-HCl, pH 8.3, 375 mM KCl, 15 nM MgCl2,), the following components were assembled in RNAse-free siliconized 500 μl microcentrifuge tubes: 1.0 mM of each dNTP, 20 units of RNAsin [Promega Corp, Madison, Wis.], 2.5 picomoles of random hexamer oligonucleotides [Pharmacia, Milwaukee, Wis.], 100 picomoles/μl solution in TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 7.5), 200 units of reverse transcriptase [Superscript RT, Bethesda Research Labs, Gaithersburg, Md.] and 1.0 μg of respective RNA isolated as described above in Example 3. To avoid pipetting errors and contamination, all solutions were aliquoted from master mixes made with diethyl pyrocarbonate (DEPC) treated water and consisted of all of the reaction components except the RNA which was added last.

[0098] The mixture was incubated in a programmable thermal cycler [Perkin-Elmer Cetus, Norwalk, Conn.] at 21° C. for ten minutes followed by 42° C. for one hour then 95° C. for five minutes and finally held at 4° C. until PCR amplification.

[0099] Amplification of the cDNA was performed essentially according to the method of R. K. Saiki et al, Science, 230:1350-1354 (1985) using the Taq polymerase. Briefly, to the 20 μl cDNA- reaction mix from above was added 10.0 μl 10X PCR buffer, 1.0 μl of each upstream and downstream primer previously diluted in water to 30 picomoles per microliter and 2.5 units of Taq polymerase (Perkin-Elmer Cetus, Norwalk, Conn.). Final volume was made up to 100 μl using DEPC treated water and overlaid with 100 μl of mineral oil. As above, master mixes were prepared to avoid contamination. The reaction was performed in the Perkin-Elmer Cetus thermal cycler for one cycle by denaturing at 95° C. for 1 minute, annealing at 37° C. for 3 minutes followed by an extension at 72° C. for 40 minutes. This initial cycle increased the likelihood of first strand DNA synthesis. A standard PCR profile was then performed by a 95° C. for 1 minute denaturation, 37° C. for 3 minutes annealing, 72° C. for 3 minutes extension for 40 cycles. A final extension cycle was done by 95° C. for 1 minute denaturation, 37° C. for 2 minutes annealing, 72° C. for 15 minutes extension and held at 4° C. until analyzed.

[0100] PCR products were analyzed by electrophoresing 5.0 μl of the reaction on a 1.2% agarose gel for 16-17 hours. Bands were visualized by ethidium bromide staining the gel and fluorescence by UV irradiation at 256 nm. Photography using Polaroid type 55 film provided a negative that could be digitized for sample distance migration and comparison against markers run on each gel. The actual sizes of the bands were then calculated using the Beckman Microgenie software running on an IBM AT.

Example 5-Cloning of CCV Spike Gene Regions

[0101] Cloning procedures were performed substantially as described by Maniatis et al, cited above. Details of the clonings are provided in the following examples. Calf-alkaline phosphatase was from Bethesda Research Labs (Gaithersburg, Md.). Ligation products were transformed into E. coli host strain XL1 Blue [Stratagene Cloning Systems, La Jolla, Calif.]. pBluescript SK□M13-phagemid vector was also obtained from Stratagene Cloning Systems. All restriction enzymes were purchased from New England Biolabs (Beverly, Mass.) or Bethesda Research Labs (Gaithersburg, Md.) and used according to manufacturer's specifications. T4 DNA ligase was received from Boehringer Mannheim Biochemicals (Indianapolis, Ind.). Calf intestinal alkaline phosphatase was purchased from Bethesda Research Labs.

Example 6-CCV S Protein Fragment. A.A. 1-128 [SEQ ID NO: 51]

[0102] Five microliters (approximately 200 ng) of PCR-amplified DNA representing amino acids 1-362 [SEQ ID NO: 53] of the CCV spike gene were ligated to the pT7Blue T-Vector (Novagen, Madison, Wis.) as per the manufacturer's instructions. One microliter of the ligation mix was used to transform NovaBlue competent cells (Novagen) and transformation mixes were plated on LB plates supplemented with ampicillin, isopropylthio-β-galactoside (IPTG; Sigma Chemical Co., St. Louis, Mo.), and 5-bromo-4-chloro-3-indoylyl-βD-galactoside (X-gal; Sigma Chemical Co., St. Louis, Mo.). White colonies were picked and screened by restriction analysis of mini-prep DNA. Insert-bearing clones were identified and oriented with respect to vector by SmaI/PstI, StuI, and PstI digests. Clone #2964 contained a full-length 1-362 amino acid insert and was used to provide sequence analysis from 1-128 amino acids of the CCV S gene.

Example 7-CCV S Protein Fragment. A.A. 128-555 [SEQ ID NO: 43]

[0103] 10 μl of PCR DNA encoding 1-555aa of the CCV spike protein was digested with SmaI/Stul for 4 hours at room temperature. DNA bands were isolated and purified from low-melting temperature agarose gels as described by Maniatis et al, cited above. Briefly, DNA fragments were visualized after staining with ethidium bromide, excised from the gel with a scalpel and transferred to microfuge tubes. Gel slices were incubated 5 min at 65° C., vortexed, and 5 volumes of 20 mM Tris, pH 8.0, 1 mM EDTA were added. Samples were incubated an additional 2 minutes at 65° C. and were then extracted once with phenol and again with phenol:chloroform. The DNA was precipitated with 1/10 volume 3 M NaOAc, pH 7.0, and 2.5 volumes of cold 95% EtOH overnight at −20° C. Insert DNAs were ligated to SK□M13-SmaI-digested, dephosphorylated vector [Stratagene] for 4 hours at room temperature. Insert-bearing clones were identified by XhoI/SstI and BglI digests of mini-prep DNA. Restriction enzyme and sequence analysis indicated that the cloned insert was short by −300bp due to the presence of a Stul site at amino acid #128 of the CCV spike gene. Therefore, these clones contained the CCV S protein spanning amino acids from about 128-555 [SEQ ID NO: 43].

Example 8-CCV S Protein Fragment. A.A. 352-1452 [SEQ ID NO: 52]

[0104] PCR-amplified DNA fragments encoding amino acids 352-1454 of the CCV spike protein were purified using Prime-Erase Quik Columns [Stratagene] according to the manufacturer's instructions. Column-purified DNAs were then digested with XMaI/EcoRV overnight at 15° C. and subsequently isolated and eluted from low-melting temperature agarose gels as described by Maniatis et al, cited above. Inserts were ligated overnight at 15° C. to SK□M13-XmaI/StuI digested, dephosphorylated vector [Stratagene]. Clones were identified and oriented with respect to vector by XhoI/SstI and PvuII digests of mini-prep DNAs, respectively.

Example 9-DNA SeMuencing

[0105] DNA sequence for the CCV S gene was determined from the individual clones #1775 (AA 352-1452; SEQ ID NO: 52), #2007 (AA 128-555; SEQ ID NO: 43) and #2964 (AA 1-362; SEQ ID NO: 53). Nested set deletions were prepared from each clone or internal primers synthesized to facilitate primer walking and the sequence determined from both strands [Lark Sequencing Technologies, Houston, Tex.]. The chain termination method performed as described in Sanger et al, Proc. Natl. Acad. Sci. USA, 74:5463-5467 (1977) was used to determine the sequence of all clones. The full length sequence of the CCV S gene was assembled from overlapping sequences of each of the three separate fragments by computer analysis.

[0106] DNA sequence analysis was performed using either Beckman Microgenie programs on an IBM Model PS/2 Model 70 or the University of Wisconsin GCG package of programs implemented on a DEC VAX cluster [Devereau et al., (1984)].

[0107] SEQ ID NO: 1 is the complete nucleotide sequence of the CCV strain 1-71 S gene. The amino acid [SEQ ID NO: 2] and nucleotide sequences [SEQ ID NO: 1] of CCV 1-71 total 1452 amino acids and 4356 base pairs. CCV 1-71 has a DNA homology of 90.8% to published FIPV strain WT WSU 1146, 93.2% identity with FIPV strain DF2 and 94.1% similarity with FECV. In comparison to WSU 1146, this CCV strain further contains two amino acid deletions at positions 11 and 12, and two amino acid insertions at positions 118 and 119. In comparison to the amino acid sequences of other coronavirus S genes, the amino acid sequence of CCV is 82.2% homologous to TGEV, 89.7% homologous to DF2-HP, 90.0% homologous to TS-BP, 92.9% homologous to TS, 93.2% homologous to DF2, and 94.1% homologous to FECV.

[0108] The canine coronavirus S gene encoding amino acids #225-1325 [SEQ ID NO: 54] has an overall homology to the published WT FIPV WSU 1146 strain at amino acids 352 to 1454 of 95.9%. The homology level is increased to 97.5% when the comparison is done under the amino acid similarity rules as proposed by M. O. Dayhoff, Atlas of Protein Sequence and Structure, Vol. 5, Supp. 3, Natl. Biomed. Res. Found., Washington, DC (1978). There are 42 amino acid differences between the CCV S gene and the published sequence of WSU 1146 strain within the CCV sequence of SEQ ID NO: 2. Other CCV fragment homologies with WT FIPV WSU 1146 are illustrated in Table II above.

[0109] Numerous modifications and variations of the present invention are included in the above-identified specification and are expected to be obvious to one of skill in the art. Such modifications and alterations to the compositions and processes of the present invention are believed to be encompassed in the scope of the claims appended hereto.

	Number	Date	Country
Parent	09494151	Jan 2000	US
Child	09972484	Oct 2001	US

	Number	Date	Country
Parent	08331625	Nov 1994	US
Child	09494151	Jan 2000	US

	Number	Date	Country
Parent	07880194	May 1992	US
Child	08331625	Nov 1994	US
Parent	07698927	May 1991	US
Child	07880194	May 1992	US
Parent	07613066	Nov 1990	US
Child	07698927	May 1991	US

Canine coronavirus S gene and uses therefor

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