WO2004110370A2 - Etiologic agnet for sow infertility syndrome - Google Patents

Abstract

Methods and materials are provided for isolating swine pestivirus-like virus and for detecting swine pestivirus-like virus infection in animals.

Description

ETIOLOGIC AGENT FOR SOW INFERTILITY SYNDROME

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority under 35 U.S.C. § 119(e) of U.S. Application No. 60/475,632, filed June 3, 2003, which is hereby incorporated by reference.

TECHNICAL FIELD

This invention relates to the etiologic agent for sow infertility syndrome, and more particularly to swine pestivirus-like virus and methods of reducing the risk of infection of swine pestivirus-like virus.

BACKGROUND Reproductive failure is a significant economic problem in swine production, particularly in terms of securing food supply. Although both infectious and noninfectious causes can result in reproductive problems, infectious disease receives more attention because of its greater economic consequence. Decreases in production (i.e., number of piglets produced from each sow) due to abortion, stillbirths, and neonatal death can be compensated for by breeding more sows at one time. Loss of sows due to death, however, can cause significant economic hardship to producers and significantly reduce production of pigs.

Since at least 1992, pork producers and swine practitioners have reported disease outbreaks characterized by early infertility, commonly referred to as "sow infertility syndrome" or "growth depression syndrome." Producers typically have observed an acute decline in farrowing rate followed by up to two years of sub-optimal farrowing performance. Herds may eventually return to pre-outbreak reproductive performance levels. An increased incidence of sow deaths has been observed in herds that have undergone infertility problems. Sow deaths may occur after the animals display signs of a neurological disorder and respiratory distress.

SUMMARY

The invention is based on the identification and characterization of a new virus, classified as a swine pestivirus-like virus, that can infect sows and young pigs. The virus is enveloped and contains an RNA genome. Phylogenetic analysis indicates that it is separate and distinct from existing pestiviruses, but likely derived from a common ancestor. The invention provides methods and materials for reducing the risk of swine pestivirus-like virus infection and for detecting the presence of the virus. In one aspect, the invention features isolated swine pestivirus-like viruses that include a nucleic acid having at least 65% sequence identity (e.g., at least 75%, 85%, or 95% sequence identity) to the nucleotide sequence set forth in SEQ ID NOS:1, 2, 3, 4, 5, or 6, and host cells that include such viruses. In some embodiments, the virus is attenuated and is effective to elicit an immune response upon administration to an animal. The invention also features compositions that include attenuated swine-pestivirus like viruses and a pharmaceutically acceptable carrier, and methods for reducing the risk of swine pestivirus-like infection in pigs by administering such compositions to the pigs. The composition can be administered intramuscularly, intranasally, or subcutaneously.

In another aspect, the invention features a method for detecting a swine pestivirus- like virus infection in an animal. The method includes contacting a biological sample from the animal with an antibody having specific binding affinity for the virus, wherein the virus, if present, binds to the antibody, to form an antibody- virus complex; and detecting the presence or absence of the antibody- virus complex, wherein the presence of the antibody- virus complex indicates the presence of the infection. In yet another aspect, the invention features isolated nucleic acids selected from the group consisting of i) a nucleic acid having the nucleotide sequence set forth in SEQ ID NOS:1, 2, 3, 4, 5, or 6; ii) a fragment of the nucleic acid of i), wherein the fragment of the nucleotide sequence set forth in SEQ ID NOS: 1, 2, or 3 contains at least 12 consecutive nucleotides of the nucleotide sequence of nucleotides 1-144, 163-218, or 236-351 of SEQ ID NO:1, nucleotides 1-163, 182-237, or 255-370 of SEQ ID NO:2, or nucleotides 1-175, 194-249, or 267-388 of SEQ ID NO:3; iii) a fragment of the nucleic acid of i), wherein the fragment of the nucleotide sequence of SEQ ID NOS: 1, 2 or 3 contains at least 32 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NOS: 1, 2, or 3; iv) a nucleic acid complementary to the nucleic acid of i), ii), or iii); v) a nucleic acid having at least 65% sequence identity to the nucleic acid of i), ii), iii), or iv); and vi) a fragment of the nucleic acid of i), wherein the fragment is at least 20 nucleotides in length. Diagnostic kits for detecting the presence of a swine pestivirus-like virus infection can include such nucleic acids.

The invention also features methods for detecting a swine pestivirus-like virus infection in an animal that includes providing a biological sample from the animal; and detecting the presence or absence of a swine pestivirus-like virus nucleic acid in the sample, wherein the presence of the nucleic acid indicates the presence of the infection.

The invention also features an antibody having specific binding affinity for a swine pestivirus-like virus, wherein the virus includes a nucleic acid having at least 65% sequence identity to the nucleotide sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6, and diagnostic test kits for detecting the presence of a swine pestivirus-like virus infection that include such an antibody.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the drawings and detailed description, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 is a sequence alignment of a portion of the NS5b gene from three viral isolates (SEQ ID NOS: 1, 2, and 3).

FIG. 2 is the sequence of a portion of the 5' NCR from the P60467 viral isolate (SEQ ID NO:4). FIG. 3 is a sequence alignment of a portion of the 3' NCRs from the KJY96 and P60467 (SEQ ID NOS:5 and 6, respectively).

FIG. 4 is a schematic depicting the phylo genetic relation of the virus with pestiviruses. Lines represent the distance corresponding with the sequence divergence from a common ancestor.

DETAILED DESCRIPTION

In general, the invention provides methods and materials for reducing the risk of swine pestivirus-like virus infection in pigs and for detecting the presence of such infections in animals. Swine pestivirus-like virus is the etiologic agent that infects sows and, on occasion, their offspring, to result in "sow infertility syndrome," "growth depression syndrome," or "head-banging syndrome." Clinical signs of swine pestivirus- like virus infection can include early abortion (usually after 30 days of gestation, but before 50 days); restlessness; and dyspnea, particularly after exercise. Neurological symptoms also can be present including posterior weakness, paresis, ataxia, lameness, head pressing or banging, and aggressive behavior. Affected animals may have an elevated body temperature. The majority of affected animals typically die within several days of showing clinical signs. Some animals, however, die suddenly without exhibiting clinical signs.

Swine Pestivirus-Like Virus

As described herein, a swine pestivirus-like virus can be isolated from infected tissues, e.g., serum, tonsil, lymph nodes, or brain, of affected animals. In particular, tissue can be homogenized in a suitable buffer (e.g., Earle's balanced solution) and filtered through a membrane (e.g., 0.22 μm membrane filter). The resulting material can be used to inoculate a host cell such as kidney cells derived from monkey, rabbit, pig, cattle, sheep, goat, dog, cat, or hamster. In addition, other cells originating from pigs (e.g., macrophage or testicle), cattle (turbinate), and horse (skin) are susceptible to swine- pestivirus like virus. Kidney cells (e.g., rabbit kidney cells such as RK-13 and buffalo green monkey kidney cells (BGM)) are particularly useful for supporting productive infection of the virus and level of progeny virus yield. Inoculated host cells can be cultured in a suitable growth medium until cytopathic effect is observed, which typically occurs after at least 12 hours (e.g., 24 hours, 2 days, or 5 days) in culture. Virions can be recovered from the conditioned cell medium. For example, 10³ to 10⁵ tissue culture infectious dose (TCID₅₀) per 100 μl of medium can be recovered. If no cytopathic effect is observed, cells can be harvested and lysed (e.g., by freeze-thawing), and virions recovered from the cell lysate. The virus also can be propagated by inoculating a host or host cell with a suspension containing infected cells or cell lines.

Swine pestivirus-like viruses of the invention include a nucleic acid having at least 65% (e.g., at least 70, 75, 80, 85, 90, 95, 98, or 99%) identity to the nucleotide sequence set forth in SEQ ID NO:1, 2, 3, 4, 5, or 6. SEQ ID NO:1 contains a 375 bp fragment from the NS5b polymerase gene from the ISUYP60467 isolate (see FIG. 1). SEQ ID NOS:2 and 3 contain fragments of the NS5b polymerase gene from the ISUYP56892 and KJY96 isolates, respectively (see FIG. 1). SEQ ID NO:4 is a portion of the 5' NCR of the P60467 isolate (see FIG. 2). SEQ ID NOS:5 and 6 are portions of the 3' NCR of the KJY96 and P60467 isolates, respectively (see FIG. 3). Percent sequence identity is calculated by determining the number of matched positions in aligned nucleic acid sequences, dividing the number of matched positions by the total number of aligned nucleotides, and multiplying by 100. A matched position refers to a position in which identical nucleotides occur at the same position in aligned nucleic acid sequences. Percent sequence identity also can be determined for any amino acid sequence. To determine percent sequence identity, a target nucleic acid or amino acid sequence is compared to the identified nucleic acid or amino acid sequence using the BLAST 2 Sequences (B12seq) program from the stand-alone version of BLASTZ containing BLASTN version 2.0.14 and BLASTP version 2.0.14. This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (www.fr.com/blast) or the U.S. government's National Center for Biotechnology Information web site (www.ncbi.nlm.nih.gov). Instructions explaining how to use the B12seq program can be found in the readme file accompanying BLASTZ.

B12seq performs a comparison between two sequences using either the BLASTN or BLASTP algorithm. BLASTN is used to compare nucleic acid sequences, while BLASTP is used to compare amino acid sequences. To compare two nucleic acid sequences, the options are set as follows: -i is set to a file containing the first nucleic acid sequence to be compared (e.g., C:\seql.txt); -j is set to a file containing the second nucleic acid sequence to be compared (e.g., C:\seq2.txt); -p is set to blastn; -o is set to any desired file name (e.g., C:\output.txt); -q is set to -1; -r is set to 2; and all other options are left at their default setting. The following command will generate an output file containing a comparison between two sequences: C:\B12seq -i c:\seql.txt -j c:\seq2.txt -p blastn -o c:\output.txt -q -1 -r 2. If the target sequence shares homology with any portion of the identified sequence, then the designated output file will present those regions of homology as aligned sequences. If the target sequence does not share homology with any portion of the identified sequence, then the designated output file will not present aligned sequences.

Once aligned, a length is determined by counting the number of consecutive nucleotides from the target sequence presented in alignment with sequence from the identified sequence starting with any matched position and ending with any other matched position. A matched position is any position where an identical nucleotide is presented in both the target and identified sequence. Gaps presented in the target sequence are not counted since gaps are not nucleotides. Likewise, gaps presented in the identified sequence are not counted since target sequence nucleotides are counted, not nucleotides from the identified sequence. The percent identity over a particular length is determined by counting the number of matched positions over that length and dividing that number by the length followed by multiplying the resulting value by 100. For example, if (1) a 100 nucleotide target sequence is compared to the sequence set forth in SEQ ID NO:1, (2) the B12seq program presents 85 nucleotides from the target sequence aligned with a region of the sequence set forth in SEQ ID NO: 1 where the first and last nucleotides of that 85 nucleotide region are matches, and (3) the number of matches over those 85 aligned nucleotides is 75, then the 100 nucleotide target sequence contains a length of 85 and a percent identity over that length of 88 (i.e., 75 ÷ 85 x 100 = 88).

It will be appreciated that different regions within a single nucleic acid target sequence that aligns with an identified sequence can each have their own percent identity. It is noted that the percent identity value is rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2. It also is noted that the length value will always be an integer.

Swine Pestivirus-Like Virus Nucleic Acids

Isolated nucleic acids of the invention are nucleic acid molecules that exist as separate molecules (e.g., a chemically synthesized nucleic acid, or a fragment produced by PCR or restriction endonuclease treatment) independent of other sequences as well as DNA that is incorporated into a vector, an autonomously replicating plasmid, a virus, or into the genomic DNA of a prokaryote or eukaryote. In addition, an isolated nucleic acid can include an engineered nucleic acid such as a DNA molecule that is part of a hybrid or fusion nucleic acid. A nucleic acid existing among hundreds to millions of other nucleic acids within, for example, cDNA libraries or genomic libraries, or gel slices containing a genomic DNA restriction digest, is not to be considered an isolated nucleic acid. As used herein, the term "nucleic acid" refers to both RNA and DNA, including synthetic (e.g., chemically synthesized) DNA or nucleic acid analogs. The nucleic acid can be double-stranded or single-stranded, and can be complementary to a sequence set forth in SEQ ID NO:1, 2, 3, 4, 5, or 6. Nucleic acid analogs can be modified at the base moiety, sugar moiety, or phosphate backbone to improve, for example, stability, hybridization, or solubility of a nucleic acid. Modifications at the base moiety include deoxyuridine for deoxythymidine, and 5-methyl-2'-deoxycytidine and 5-bromo-2'- deoxycytidine for deoxycytidine. Modifications of the sugar moiety can include modification of the 2' hydroxyl of the ribose sugar to form 2'-O-methyl or 2'-O-allyl sugars. The deoxyribose phosphate backbone can be modified to produce morpholino nucleic acids, in which each base moiety is linked to a six-membered, morpholino ring, or peptide nucleic acids, in which the deoxyphosphate backbone is replaced by a pseudopeptide backbone and the four bases are retained. See, for example, Summerton and Weller (1997) Antisense Nucleic Acid Drug Dev. 7:187-195; and Hyrup et al. (1996) Bioorgan. Med. Chem. 4:5-23. In addition, the deoxyphosphate backbone can be replaced with, for example, a phosphorothioate or phosphorodithioate backbone, a phosphoroamidite, or an alkyl phosphotriester backbone. Isolated swine pestivirus-like virus nucleic acids are at least 10 nucleotides in length (e.g., 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, 200, 300, 400, or more nucleotides in length). In particular, a nucleic acid of the invention can have the sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6 or a sequence having at least 65% identity to the sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6. hi other embodiments, a nucleic acid is a fragment of such nucleic acids. For example, a suitable fragment can contain at least 12 consecutive nucleotides of nucleotides 1-144, 163-218, or 236-351 of SEQ ID NO:1; nucleotides 1-163, 182-237, or 255-370 of SEQ ID NO:2; or nucleotides 1-175, 194-249, or 267-388 of SEQ ID NO:3. hi other embodiments, suitable fragments contain at least 20 (e.g., 30, 32, 35, or 40) consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NOS:1, 2, 3, 4, 5, or 6. Nucleic acid molecules of the invention are useful for diagnostic purposes (e.g., as probes or primers).

Isolated nucleic acid molecules of the invention can be produced by standard techniques, including, without limitation, common molecular cloning and chemical nucleic acid synthesis techniques. For example, polymerase chain reaction (PCR) techniques can be used. PCR refers to a procedure or technique in which target nucleic acids are enzymatically amplified. Sequence information from the ends of the region of interest or beyond typically is employed to design oligonucleotide primers that are identical in sequence to opposite strands of the template to be amplified. PCR can be used to amplify specific sequences from DNA as well as RNA, including sequences from total genomic DNA or total cellular RNA. Primers typically are 15 to 50 nucleotides in length, but can range from 10 nucleotides to hundreds of nucleotides in length. For example, a primer can be 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, or 45 nucleotides in length. A primer can be purified from a restriction digest by conventional methods, or can be chemically synthesized. Primers typically are single- stranded for maximum efficiency in amplification, but a primer can be double-stranded. Double-stranded primers are first denatured (e.g., treated with heat) to separate the strands before use in amplification. General PCR techniques are described, for example in PCR Primer: A Laboratory Manual, ed. by Dieffenbach and Dveksler, Cold Spring Harbor Laboratory Press, 1995. When using RNA as a source of template, reverse transcriptase can be used to synthesize a complementary DNA (cDNA) strand. Ligase chain reaction, strand displacement amplification, self-sustained sequence replication or nucleic acid sequence-based amplification also can be used to obtain isolated nucleic acids. See, for example, Lewis Genetic Engineering News 12(9):1 (1992); Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA. 87:1874-1878; and Weiss (1991) Science 254:1292. Isolated nucleic acids of the invention also can be chemically synthesized, either as a single nucleic acid molecule (e.g., using automated DNA synthesis in the 3' to 5' direction using phosphoramidite technology) or as a series of oligonucleotides. For example, one or more pairs of long oligonucleotides (e.g., >100 nucleotides) can be synthesized that contain the desired sequence, with each pair containing a short segment of complementarity (e.g., about 15 nucleotides) such that a duplex is formed when the oligonucleotide pair is annealed. DNA polymerase is used to extend the oligonucleotides, resulting in a single, double-stranded nucleic acid molecule per oligonucleotide pair, which then can be ligated into a vector.

Isolated nucleic acids of the invention also can be obtained by mutagenesis. For example, the sequences depicted in FIGS. 1, 2 or 3 can be mutated using standard techniques such as, for example, oligonucleotide-directed mutagenesis and/or site- directed mutagenesis through PCR. See, Short Protocols in Molecular Biology, Chapter 8, Green Publishing Associates and John Wiley & Sons, Edited by Ausubel et al, 1992. Examples of positions to be modified can be identified from the sequence alignments of FIGS. 1 and 3, or sequence alignments with known pestiviruses.

Vectors and Host Cells

The invention also provides vectors containing nucleic acids such as those described above. As used herein, a "vector" is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. The vectors of the invention can be expression vectors. An "expression vector" is a vector that includes one or more expression control sequences, and an "expression control sequence" is a DNA sequence that controls and regulates the transcription and/or translation of another DNA sequence. In the expression vectors of the invention, the nucleic acid is operably linked to one or more expression control sequences. As used herein, "operably linked" means incorporated into a genetic construct so that expression control sequences effectively control expression of a coding sequence of interest. Examples of expression control sequences include promoters, enhancers, and transcription terminating regions. A promoter is an expression control sequence composed of a region of a DNA molecule, typically within 100 nucleotides upstream of the point at which transcription starts (generally near the initiation site for RNA polymerase II). To bring a coding sequence under the control of a promoter, it is necessary to position the translation initiation site of the translational reading frame of the polypeptide between one and about fifty nucleotides downstream of the promoter. Enhancers provide expression specificity in terms of time, location, and level. Unlike promoters, enhancers can function when located at various distances from the transcription site. An enhancer also can be located downstream from the transcription initiation site. A coding sequence is "operably linked" and "under the control" of expression control sequences in a cell when RNA polymerase is able to transcribe the coding sequence into mRNA, which then can be translated into the protein encoded by the coding sequence.

Suitable expression vectors include, without limitation, plasmids and viral vectors derived from, for example, bacteriophage, baculoviruses, tobacco mosaic virus, herpes viruses, cytomegalovirus, retroviruses, poxviruses, adenoviruses, and adeno-associated viruses. Numerous vectors and expression systems are commercially available from such corporations as Novagen (Madison, WI), Clontech (Palo Alto, CA), Stratagene (La Jolla, CA), and Invitrogen/Life Technologies (Carlsbad, CA).

An expression vector can include a tag sequence designed to facilitate subsequent manipulation of the expressed nucleic acid sequence (e.g., purification or localization). Tag' sequences, such as green fluorescent protein (GFP), glutathione S-transferase (GST), polyhistidine, c-myc, hemagglutinin, or Flag™ tag (Kodak, New Haven, CT) sequences typically are expressed as a fusion with the encoded polypeptide. Such tags can be inserted anywhere within the polypeptide including at either the carboxyl or amino terminus.

The invention also provides host cells containing vectors of the invention. The term "host cell" is intended to include prokaryotic and eukaryotic cells into which a recombinant expression vector can be introduced. As used herein, "transformed" and "transfected" encompass the introduction of a nucleic acid molecule (e.g., a vector) into a cell by one of a number of techniques. Although not limited to a particular technique, a number of these techniques are well established within the art. Prokaryotic cells can be transformed with nucleic acids by, for example, electroporation or calcium chloride mediated transformation. Nucleic acids can be transfected into mammalian cells by techniques including, for example, calcium phosphate co-precipitation, DEAE-dextran- mediated transfection, lipofection, electroporation, or microinjection. Suitable methods for transforming and transfecting host cells are found in Sambrook et al., Molecular Cloning: A Laboratory Manual (2^nd edition), Cold Spring Harbor Laboratory, NY (1989), and reagents for transformation and/or transfection are commercially available (e.g., Lipofectin (Invitrogen/Life Technologies); Fugene (Roche, Indianapolis, IN); and SuperFect (Qiagen, Valencia, CA)).

Swine Pestivirus-Like Virus Compositions Compositions of the invention can include swine pestivirus-like virus, or an antigenic polypeptide thereof, and in particular, attenuated or inactivated swine pestivirus-like virus. Typically, a composition will contain between about 10² and about 10⁶ viral particles. Attenuated swine pestivirus-like virus can be prepared by repeated passaging of the virus. For example, host cells can be infected with a virulent strain of the swine pestivirus-like virus and cultured as described above, and the conditioned cell medium collected. The conditioned cell medium can be used to infect fresh host cells to start the next passage. Culture conditions of the host cells, including culture temperature, pH of the medium, and/or chemical composition of the medium can be altered to aid in the attenuation of the virus. For example, the culture temperature can be lowered or the pH of the medium can be reduced. Typically, attenuated swine pestivirus-like virus is obtained after 3 to 6 passages. Replication behavior in cell culture can be used to assess virulency. Animal trials also can be used to determine if the virus is attenuated.

Swine pestivirus-like virus can be inactivated using techniques known in the art. For example, the virus can be chemically inactivated with formaldehyde or alkylating agents such as ethylene oxide, ethyleneimine, acetylethyleneimine, or β-propiolactone. Routine purification methods can be used to remove traces of the inactivating chemicals, including immunological procedures, affinity chromatography, gel filtration, size- exclusion, and/or ion exchange chromatography. Alternatively, virus can be physically inactivated using heat or radiation.

Compositions of the invention can include various pharmaceutically acceptable carriers or excipients. For example, compositions can include buffers, stabilizers (e.g., albumin), diluents, preservatives, and solubilizers, and also can be formulated to facilitate sustained release. Diluents can include water, saline, dextrose, ethanol, glycerol, and the like. Additives for isotonicity can include sodium chloride, dextrose, mannitol, sorbitol, and lactose. Compositions can be formulated for particular routes of administration, including, for example, oral, intranasal, intramuscular, intra-lymph node, intradermal, intraperitoneal, or subcutaneous administration, or for a combination of routes.

In some embodiments, compositions can include an adjuvant. Suitable adjuvants can be selected based, for example, on route of administration and number of planned administrations. Non-limiting examples of adjuvants include mineral oil adjuvants such as Freund's complete and incomplete adjuvant, and Montanide incomplete seppic adjuvant (ISA, available from Seppic, Inc., Paris, France); oil-in-water emulsion adjuvants such as the Ribi adjuvant system (RAS); TiterMax®, and syntax adjuvant formulation containing muramyl dipeptide; or aluminum salt adjuvants.

Methods of Reducing Risk of Infection with Swine Pestivirus-like Virus

The compositions of the invention are generally useful for inducing immune responses in subjects (e.g., as prophylactic vaccines or immune response-stimulating therapeutics). For example, the compositions of the invention can be used as vaccines against swine pestivirus-like virus. The term "prophylaxis," as used herein, refers to the complete prevention of the symptoms of a disease, a delay in onset of the symptoms of a disease, or a lessening in the severity of subsequently developed disease symptoms. Typically, the compositions are administered to pigs, although such compositions can be administered to any species in which swine pestivirus-like virus infects and causes disease. In one embodiment, the attenuated or inactivated swine pestivirus-like virus itself is administered to the subject. In another embodiment, a vaccine containing the attenuated or inactivated swine pestivirus-like virus and an adjuvant is administered to the subject. Generally, the composition to be administered can be formulated as described above and administered orally, transdermally, intravenously, subcutaneously, intramuscularly, intraocularly, intraperitoneally, intrarectally, intravaginally, intranasally, intragastrically, intratracheally, intrapulmonarily, or any combination thereof. For example, the composition can be administered intranasally, subcutaneously, or intramuscularly. In some embodiments, the composition can be delivered directly to an appropriate lymphoid tissue (e.g., spleen, lymph node, or mucosal-associated lymphoid tissue (MALT)). Alternatively, the composition can be administered via the food and/or water supply of the subject or multiple subjects (e.g., a herd of pigs). If desired, booster immunizations may be given once or several times (e.g., 2, 3, 4, 8, or 12 times) at various intervals (e.g., spaced one week apart).

Suitable doses of the composition elicit an immune response in the subject but do not cause the subject to develop severe clinical signs of the particular viral infection. The dose required to elicit an immune response depends on the route of administration, the nature of the composition, the subject's size, weight, surface area, age, and sex, other drugs being administered, and the judgment of the attending practitioner or veterinarian. Wide variations in the needed dose are to be expected in view of the variety of compositions that can be produced, the variety of subjects to which the composition can be administered, and the differing efficiencies of various routes of administration. For example, oral administration would be expected to require higher doses than administration by intravenous injection. Variations in these dose levels can be adjusted using standard empirical routines for optimization, as is well understood in the art. Encapsulation of the composition in a suitable delivery vehicle (e.g., polymeric microparticles or implantable devices) may increase the efficiency of delivery, particularly for oral delivery.

To determine if an immune response was induced in the subject, a biological sample from the subject can be examined to determine if it contains detectable amounts of antibodies having specific binding affinity for one or more antigens of the particular organism the subject was vaccinated against. The biological sample can be blood (e.g., serum), a mucosal sample (e.g., saliva or gastric and bronchoalveolar lavages), or meat juice or meat exudate (i.e., the liquid that escapes from extra- and intracellular spaces when muscle tissues are frozen and thawed). Methods for detecting antibodies, including IgG, IgM, and IgA, are known, and can include, for example, indirect fluorescent antibody tests, serum virus neutralization tests, gel immunodiffusion tests, complement fixation tests, enzyme-linked immunosorbent assays, (ELISA) or Western immunoblotting. In addition, in vivo skin tests can be performed on the subjects. Such assays test for antibodies specific for the organism of interest. If antibodies are detected, the subject is considered to be seropositive.

Vaccinated subjects also can be tested for resistance to infection by the relevant organism. After immunization (as indicated above), the test subjects can be challenged with a single dose or various doses of the virus. The test subjects can be observed for pathologic symptoms familiar to those in the art, e.g., restlessness, dyspnea after exercise, neurological signs such as posterior weakness, paresis, ataxia, lameness, head pressing or banging, aggressive behavior, morbidity, and/or mortality. Alternatively, they may be euthanized at various time points, and their tissues (e.g., lung, brain, spleen, kidney or intestine) may be assayed for relative levels of the virus using standard methods. The data obtained with the test subjects can be compared to those obtained with a control group of subjects, e.g., subjects that were exposed to the diluent in which the swine pestivirus-like virus was suspended (e.g., physiological saline) or adjuvant without the virus if adjuvant was used for immunization. Increased resistance of the test subjects to infection relative to the control groups would indicate that the test compound is an effective vaccine. Thus, in some embodiments, a vaccinated subject is resistant to an infection upon challenge. That is, the subject does not develop severe clinical signs of the infection after being challenged with a virulent form of the virus. Li other embodiments, a vaccinated subject exhibits an altered course of the infection, hi still other embodiments, overall mortality from a particular microorganism in a group of subjects (e.g., a group of animals such as a herd of pigs) may be reduced.

Production ofAnti Swine Pestivirus-Like Virus Antibodies The invention also features antibodies having specific binding affinity for swine pestivirus-like virus or an antigenic polypeptide thereof. "Antibody" or "antibodies" includes intact molecules as well as fragments thereof that are capable of binding to swine pestivirus-like virus or a swine pestivirus-like virus antigenic polypeptide. Thus, the terms "antibody" and "antibodies" include polyclonal antibodies, monoclonal antibodies, chimeric antibodies, single chain Fv antibody fragments, Fab fragments, and F(ab)₂ fragments. Such antibodies can be used in immunoassays in liquid phase or bound to a solid phase. For example, the antibodies provided herein can be used in competitive and non-competitive immunoassays in either a direct or indirect format. Examples of such immunoassays include the radioimmunoassay (RIA) and the sandwich (immunometric) assay. The antibodies provided herein can be prepared using any method. For example, swine pestivirus-like virus, isolated as described above, or an antigenic polypeptide thereof, can be used as an immunogen to elicit an immune response in an animal (e.g., a pig) such that specific antibodies are produced. The immunogen can be conjugated to a carrier polypeptide, if desired. Commonly used carriers that are chemically coupled to an immunizing polypeptide include, without limitation, keyhole limpet hemocyanin (KLH), thyroglobulin, bovine serum albumin (BSA), and tetanus toxoid.

The preparation of polyclonal antibodies is well-known to those skilled in the art (e.g., Green et al, Production of Polyclonal Antis era, hi: Immunochemical Protocols (Manson, ed.), pages 1-5 (Humana Press 1992) and Coligan et al, Production of Polyclonal Antisera in Rabbits, Rats, Mice and Hamsters, In: Current Protocols in Immunology, section 2.4.1 (1992)). hi addition, various techniques common in the immunology arts can be used to purify and/or concentrate polyclonal antibodies, as well as monoclonal antibodies (Coligan, et al, Unit 9, Current Protocols in Immunology, Wiley Interscience, 1994). Monoclonal antibodies can be prepared using standard hybridoma technology. In particular, monoclonal antibodies can be obtained by any technique that provides for the production of antibody molecules by continuous cell lines in culture such as described by Kohler et al., Nature, 256:495 (1975), the human B-cell hybridoma technique of Kosbor et al., Immunology Today. 4:72 (1983) and/or Cole et al., Proc. Natl. Acad. Sci. USA. 80:2026 (1983), and the EBV-hybridoma technique of Cole et al., "Monoclonal

Antibodies and Cancer Therapy," Alan R. Liss, Inc. pp. 77-96 (1983). Such antibodies can be of any immunoglobulin class including IgM, IgG, IgE, IgA, IgD, and any subclass thereof. A hybridoma producing monoclonal antibodies can be cultivated in vitro or in vivo. Monoclonal antibodies can be isolated using know techniques, including, without limitation, affinity chromatography with Protein-A Sepharose, size-exclusion chromatography, and ion-exchange chromatography (Coligan et ah, sections 2.7.1-2.7.12 and sections 2.9.1-2.9.3; Barnes et al, Purification of Immunoglobulin G (IgG), In: Methods in Molecular Biology, Vol. 10, pages 79-104 (Humana Press 1992)).

In addition, methods of in vitro and in vivo multiplication of monoclonal antibodies are well-known to those skilled in the art. Multiplication in vitro can be carried out in suitable culture media such as Dulbecco's Modified Eagle Medium (MEM) or RPMI 1640 medium, optionally replenished by mammalian serum such as fetal calf serum, or trace elements and growth-sustaining supplements such as normal mouse peritoneal exudate cells, spleen cells, and bone marrow macrophages. Production in vitro provides relatively pure antibody preparations and allows scale-up to yield large amounts of the desired antibodies. Large scale hybridoma cultivation can be carried out by homogenous suspension culture in an airlift reactor, in a continuous stirrer reactor, or in immobilized or entrapped cell culture. Multiplication in vivo may be carried out by injecting cell clones into mammals histocompatible with the parent cells (e.g., osyngeneic mice) to cause growth of antibody-producing tumors. Optionally, the animals are primed with a hydrocarbon, especially oils such as pristane (tetramethylpentadecane) prior to injection. After one to three weeks, the desired monoclonal antibody is recovered from the body fluid of the animal.

Antibody fragments can be prepared by proteolytic hydrolysis of an intact antibody or by the expression of a nucleic acid encoding the fragment. Antibody fragments can be obtained by pepsin or papain digestion of intact antibodies by conventional methods. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab')₂. This fragment can be further cleaved using a thiol reducing agent, and optionally, a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab' monovalent fragments. Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab' fragments and an Fc fragment directly. These methods are described, for example, by Goldenberg (U.S. Patent Nos. 4,036,945 and 4,331,647) and others (Nisonhoff et al., Arch. Biochem. Biophys. 89:230 (1960); Porter, Biochem. J. 73:119 (1959); Edelman et al., Methods in Enzymology, Vol. 1, page 422 (Academic Press 1967); and Coligan et al. at sections 2.8.1-2.8.10 and 2.10.1-2.10.4). Once produced, antibodies or fragments thereof are tested for recognition of swine pestivirus-like virus by standard immunoassay methods including, for example, ELISA or RIA. See, Short Protocols in Molecular Biology. Chapter 11, Ausubel et al., (eds.), Green Publishing Associates and John Wiley & Sons (1992).

Antibody Based Methods for Detecting Swine Pestivirus-like Virus Infection

Antibodies of the invention can be used to detect swine pestivirus-like virus infection. Li general, a biological sample is obtained from the animal (e.g., pig) to be tested then contacted with an antibody having specific binding affinity for the virus. Suitable biological samples include blood, serum, bodily fluids (e.g., nasal secretions or semen), scrapings (e.g., oropharygneal scrapings), lavages (e.g., bronchioalveolar lavage), or tissue samples (e.g., secondary lymphoid tissues, brain, kidney, lung, liver, intestinal tissues, or reproductive organs), including biopsies. Secondary lymphoid tissues and fetal thoracic fluid are particularly useful samples for detecting swine pestivirus-like virus in a fetus. Detecting the presence of antibody- virus or antibody-polypeptide complexes is indicative of a swine pestivirus-like virus infection. In general, such complexes can be detected using an indicator molecule having specific binding affinity for the complex. As used herein, an "indicator molecule" is any molecule that allows the presence of a given polypeptide, antibody, antibody-polypeptide complex, or antibody-virus complex to be visualized, either with the naked eye or an appropriate instrument. Typically, the indicator molecule is an antibody having specific binding affinity for antibodies from the species from which the antibody was obtained, e.g., an anti-pig IgG antibody.

Indicator molecules can be detected either directly or indirectly by standard methodologies. See, e.g., Current Protocols in Immunology, Chapters 2 and 8, Coligan et al., (eds.), John Wiley & Sons (1996). For direct detection, the indicator molecule or the antibody can be labeled with a radioisotope, fluorochrome, other non-radioactive label, or any other suitable chromophore. For indirect detection methods, enzymes such as horseradish peroxidase (HRP) and alkaline phosphatase (AP) can be attached to the indicator molecule, and the presence of the complexes can be detected using standard assays for HRP or AP. Alternatively, the indicator molecule can be attached to avidin or streptavidin, and the presence of a complex can be detected with biotin conjugated to, for example, a fluorochrome, or vice versa. Thus, assay formats for detecting antibody complexes can include ELISAs such as competitive ELISAS, RIAs, fluorescence assays, chemiluminescent assays, immunoblot assays (Western blots), particulate-based assays, and other known techniques. hi some embodiments, complexes are formed in solution. Such complexes can be detected by imrnunoprecipitation. See, e.g., Short Protocols in Molecular Biology, Chapter 10, Section VI, Ausubel et al., (eds.), Green Publishing Associates and John Wiley & Sons (1992).

Nucleic Acid Based Methods for Detecting Swine Pestivirus-like Virus Infection

In general, nucleic acid based methods of detecting swine pestivirus-like virus include detecting the presence or absence of a swine pestivirus-like virus nucleic acid in a biological sample (e.g., blood, plasma, serum, bodily secretions and excretions, brain, kidney, lung, secondary lymphoid organs, intestinal tissues, or reproductive organs) from a subject. The presence of a swine pestivirus-like nucleic acid indicates the presence of the infection. The presence of a swine pestivirus-like virus can be detected using nucleic acid hybridization, with or without an amplification step. Any one of a number of clinical diagnostic techniques can be used to detect swine pestivirus-like virus nucleic acid. Hybridization can be performed on a solid substrate such as a nylon membrane (e.g., a macroarray) or a microarray (e.g., a microchip) or in solution (e.g., ORIGEN technology). Nucleic acid based methods of detecting swine pestivirus-like virus can include an amplification step using, for example, PCR. Template nucleic acid need not be purified for PCR; it can be a minor fraction of a complex mixture, such as a cell lysate. Template DNA or RNA can be extracted from a biological sample using routine techniques. Once a PCR amplification product is generated, it can be detected by, for example, hybridization using FRET technology. FRET technology (see, for example, U.S. Patent Nos. 4,996,143, 5,565,322, 5,849,489, and 6,162,603) is based on the concept that when a donor fluorescent moiety and a corresponding acceptor fluorescent moiety are positioned within a certain distance of each other, energy transfer taking place between the two fluorescent moieties can be visualized or otherwise detected and quantitated. Two oligonucleotide probes, each containing a fluorescent moiety, can hybridize to an amplification product at particular positions determined by the complementarity of the oligonucleotide probes to the target nucleic acid sequence. Upon hybridization of the oligonucleotide probes to the amplification product at the appropriate positions, a FRET signal is generated. Hybridization temperatures and times can range from about 35⁰C to about 65°C for about 10 seconds to about 1 minute. Detection of FRET can occur in realtime, such that the increase in an amplification product after each cycle of a PCR assay is detected and, in some embodiments, quantified.

Fluorescent analysis and quantification can be carried out using, for example, a photon counting epifluorescent microscope system (containing the appropriate dichroic mirror and filters for monitoring fluorescent emission in a particular range of wavelengths), a photon counting photomultiplier system, or a fluorometer. Excitation to initiate energy transfer can be carried out with an argon ion laser, a high intensity mercury arc lamp, a fiber optic light source, or another high intensity light source appropriately filtered for excitation in the desired range. Fluorescent moieties can be, for example, a donor moiety and a corresponding acceptor moiety. As used herein with respect to donor and corresponding acceptor fluorescent moieties, "corresponding" refers to an acceptor fluorescent moiety having an emission spectrum that overlaps the excitation spectrum of the donor fluorescent moiety. The wavelength maximum of the emission spectrum of an acceptor fluorescent moiety typically should be at least 100 nm greater than the wavelength maximum of the excitation spectrum of the donor fluorescent moiety, such that efficient non-radiative energy transfer can be produced there between.

Fluorescent donor and corresponding acceptor moieties are generally chosen for (a) high efficiency Forster energy transfer; (b) a large final Stokes shift (>100 nm); (c) shift of the emission as far as possible into the red portion of the visible spectrum (>600 nm); and (d) shift of the emission to a higher wavelength than the Raman water fluorescent emission produced by excitation at the donor excitation wavelength. For example, a donor fluorescent moiety can be chosen with an excitation maximum near a laser line (for example, Helium-Cadmium 442 nm or Argon 488 nm), a high extinction coefficient, a high quantum yield, and a good overlap of its fluorescent emission with the excitation spectrum of the corresponding acceptor fluorescent moiety. A corresponding acceptor fluorescent moiety can be chosen that has a high extinction coefficient, a high quantum yield, a good overlap of its excitation with the emission of the donor fluorescent moiety, and emission in the red part of the visible spectrum (>600 nm).

Representative donor fluorescent moieties that can be used with various acceptor fluorescent moieties in FRET technology include fluorescein, Lucifer Yellow, B- phycoerythrin, 9-acridineisothiocyanate, Lucifer Yellow VS, 4-acetamido-4'-isothio- cyanatostilbene-2,2'-disulfonic acid, 7-diethylamino-3-(4'-isothiocyanatophenyl)-4- methylcoumarin, succinimdyl 1-pyrenebutyrate, and 4-acetamido-4'- isothiocyanatostilbene-2,2'-disulfonic acid derivatives. Representative acceptor fluorescent moieties, depending upon the donor fluorescent moiety used, include LC™- Red 640, LC™-Red 705, Cy5, Cy5.5, Lissamine rhodamine B sulfonyl chloride, tetramethyl rhodamine isothiocyanate, rhodamine x isothiocyanate, erythrosine isothiocyanate, fluorescein, diethylenetriamine pentaacetate, and other chelates of Lanthanide ions (e.g., Europium, or Terbium). Donor and acceptor fluorescent moieties can be obtained from, for example, Molecular Probes, Inc. (Eugene, OR) or Sigma Chemical Co. (St. Louis, MO).

Donor and acceptor fluorescent moieties can be attached to probe oligonucleotides via linker arms. The length of each linker arm is important, as the linker arms will affect the distance between the donor and acceptor fluorescent moieties. The length of a linker arm for the purpose of the present invention is the distance in Angstroms (A) from the nucleotide base to the fluorescent moiety, hi general, a linker arm is from about 10 to about 25 A in length. The linker arm may be of the kind described, for example, in WO 84/03285. WO 84/03285 also discloses methods for attaching linker arms to a particular nucleotide base, as well as methods for attaching fluorescent moieties to a linker arm. An acceptor fluorescent moiety such as an LC™-Red 640-NHS-ester can be combined with C6-Phosphoramidites (available from ABI (Foster City, CA) or Glen Research (Sterling, VA)) to produce, for example, LC™-Red 640-Phosphoramidite. Linkers frequently used to couple a donor fluorescent moiety such as fluorescein to an oligonucleotide include thiourea linkers (FITC-derived, for example, fluorescein-CPG's from Glen Research or ChemGene (Ashland, MA)), amide-linkers (fluorescein-NHS- ester-derived, such as fiuorescein-CPG from BioGenex (San Ramon, CA)), or 3'-amino- CPG' s that require coupling of a fluorescein-NHS -ester after oligonucleotide synthesis.

Using commercially available real-time PCR instrumentation (e.g., LightCycler™, Roche Molecular Biochemicals, Indianapolis, IN)₃ PCR amplification, detection, and quantification of an amplification product can be combined in a single closed cuvette with dramatically reduced cycling time. Since detection and quantification occur concurrently with amplification, real-time PCR methods obviate the need for manipulation of the amplification product, and diminish the risk of cross-contamination between amplification products. Real-time PCR greatly reduces turn-around time and is an attractive alternative to conventional PCR techniques in the clinical laboratory or in the field.

Control samples can be included within each thermocycler run. Positive control samples can amplify a nucleic acid control template (e.g., a nucleic acid other than a target nucleic acid) using, for example, control primers and control probes. Positive control samples also can amplify, for example, a plasmid construct containing a control nucleic acid template. Such a plasmid control can be amplified internally (e.g., within the sample) or in a separate sample run side-by-side with the test samples. Each thermocycler run also should include a negative control that, for example, lacks the target template DNA. Such controls are indicators of the success or failure of the amplification, hybridization and/or FRET reaction. Therefore, control reactions can readily determine, for example, the ability of primers to anneal with sequence-specificity and to initiate elongation, as well as the ability of probes to hybridize with sequence-specificity and for FRET to occur.

Another FRET format utilizes TaqMan^® technology to detect the presence or absence of an amplification product, and hence, the presence or absence of swine pestivirus-like virus. TaqMan^® technology utilizes one single-stranded hybridization probe labeled with two fluorescent moieties. When a first fluorescent moiety is excited with light of a suitable wavelength, the absorbed energy is transferred to a second fluorescent moiety according to the principles of FRET. The second fluorescent moiety is generally a quencher molecule. During the annealing step of the PCR reaction, the labeled hybridization probe binds to the target DNA (i.e., the amplification product) and is degraded by the 5' to 3' exonuclease activity of the Taq Polymerase during the subsequent elongation phase. As a result, the excited fluorescent moiety and the quencher moiety become spatially separated from one another. As a consequence, upon excitation of the first fluorescent moiety in the absence of the quencher, the fluorescence emission from the first fluorescent moiety can be detected. By way of example, an ABI PRISM^® 7700 Sequence Detection System (Applied Biosystems, Foster City, CA) uses TaqMan^® technology, and is suitable for performing the methods described herein for detecting swine pestivirus-like virus. Information on PCR amplification and detection using an ABI PRISM^® 7700 system can be found at the website of Applied Biosystems. Molecular beacons in conjunction with FRET also can be used to detect the presence of an amplification product using the real-time PCR methods of the invention. Molecular beacon technology uses a hybridization probe labeled with a first fluorescent moiety and a second fluorescent moiety. The second fluorescent moiety is generally a quencher, and the fluorescent labels are typically located at each end of the probe. Molecular beacon technology uses a probe oligonucleotide having sequences that permit secondary structure formation (e.g., a hairpin). As a result of secondary structure formation within the probe, both fluorescent moieties are in spatial proximity when the probe is in solution. After hybridization to the target nucleic acids (i.e., amplification products), the secondary structure of the probe is disrupted and the fluorescent moieties become separated from one another such that after excitation with light of a suitable wavelength, the emission of the first fluorescent moiety can be detected.

As an alternative to FRET, amplification product can be detected using, for example, a fluorescent DNA binding dye (e.g., SYBRGreenl^® or SYBRGold^® (Molecular Probes)). Upon interaction with an amplification product, such DNA binding dyes emit a fluorescent signal after excitation with light at a suitable wavelength. A double-stranded DNA binding dye such as a nucleic acid intercalating dye also can be used. When double-stranded DNA binding dyes are used, a melting curve analysis usually is performed for confirmation of the presence of the amplification product.

Articles of Manufacture

Compositions, nucleic acids, or antibodies described herein can be combined with packaging materials and sold as articles of manufacture or kits (e.g., diagnostic kits). Components and methods for producing articles of manufactures are well known. The articles of manufacture may combine one or more components described herein. In addition, the articles of manufacture may further include sterile water, pharmaceutical carriers, buffers, indicator molecules, and/or other useful reagents for detecting swine pestivirus-like virus infection. Instructions describing how a vaccine is effective for preventing the incidence of infection, preventing the occurrence of the clinical signs of an infection, ameliorating the clinical signs of an infection, lowering the risk of the clinical signs of an infection, lowering the occurrence of the clinical signs of an infection and/or reducing the spread of infections may be included in such kits, hi addition, instructions can be included that describe how a nucleic acid or antibody can be used to detect swine pestivirus-like virus infection. The compositions may be provided in a pre-packaged form in quantities sufficient for a single administration (e.g., for a single pig) or for a pre- specified number of animals in, for example, sealed ampoules, capsules, or cartridges. The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Methods and Materials

Sample Collection. Serum, blood, and tissues, including brain, secondary lymphoid tissues, lung, kidney, and liver, were collected from affected sows and tested as described below. Secondary lymphoid tissues included tonsil, regional lymph nodes, and spleen. Buffy coat cells were isolated from EDTA treated blood and tested as described below. Tissues were tested after a 10-20% (w/v) homogenate was made in Earle's balanced salt solution and filter-sterilized through 0.22 μm membrane filters.

Virus Isolation. Virus isolation was attempted using various cell lines and a few primary cells of porcine origin. All cell lines and primary cells were confirmed to be free of bovine viral diarrhea virus (BVDV) and border disease virus (BDV) prior to and during the experiments.

Cells were prepared in 48-well plates and 25-cm² TC flasks and grown in Minimum Essential Medium (MEM) supplemented with 10% (v/v) BVDV-free fetal bovine serum or 5% (v/v) horse serum (Sigma Chemical Co., St. Louis, MO), 2OmM L- glutamine (Gibco/BRL Life Science, Grand Island, NY), and an antibiotic-antimycotic mixture (Sigma Chemical Co., St. Louis, MO). After confluent monolayers were formed, samples (0.25 ml/well and 1 ml/flask) were added to each cell flask in duplicate or triplicate. After incubating for one-hour at 37°C, cells were rinsed with fresh growth medium and incubated further in a humid 37°C incubator with 5% CO₂ supply.

Inoculated cells then were observed daily for cytopathic effect (CPE) until 7 days post inoculation (PI). When CPE was evident in more than 70% of cell monolayers, cell culture medium was harvested and inoculated onto freshly prepared cells in duplicate. If no CPE was evident by 5 days PI, cells were subjected to 2 cycles of freeze- thawing at -7O⁰C and 35°C, respectively, and then cell lysate was inoculated to freshly prepared cells in the same manner as above.

Cells inoculated with cell-culture material were monitored daily for CPE for another 5 days PI. At the time when CPE was evident, or 7 days PI if no CPE was observed, one set of cells were fixed by immerging them in 80% aqueous acetone and used for immunofluorescence microscopy using fluorescent isothiocynate (FITC)-labeled antibodies (USDA National Veterinary Services Laboratories, Ames, IA; Rural Technologies, Inc., Brookings, SD; DBA American Bioresearch, Inc., Seymour, TN) raised against the following known swine viral pathogens: porcine reproductive and respiratory syndrome virus (PRRSV), PRRSV Lelystad strain, pseudorabies virus (PRV), porcine cytomegalovirus (PCMV), porcine circovirus type 2 (PCV2), porcine parvovirus (PPV), encephalomyocarditis virus (EMCV), porcine enterovirus (PEV), transmissible gastroenteritis virus (TGEV), hemagglutinating encephalomyelitis virus (HEV), Hl and H3 swine influenza virus (SIV), porcine reoviras, rabies virus, and BVDV.

In addition, sera collected from animals that had survived the course of natural infection also were tested. For pig and bovine sera, anti-porcine IgG (H+L) and anti- bovine IgG (H+L) conjugated with FITC (Kirkegaard and Perry Laboratories, Inc., Gaithersburg, MD) was used as secondary antibody to visualize specific antigen:antibody complex.

Another set of cells were subjected to freeze-thawing and the resulting cell lysates were tested using PCR based tests for the following known swine viral pathogens: PRRSV, PCV type 1 and 2, group 1 PEV, Influenza A Virus, PPV, porcine reovirus type 1, 2 and 3, PCMV, PRV, TGEV, porcine respiratory coronavirus, porcine epidemic diarrhea virus, Japanese encephalitis B virus, classical swine fever virus, porcine endogenous retrovirus (PERV), porcine lymphotropic herpesvirus type 1 (PLHV-I), swine hepatitis E virus (sHEV), BVDV, West Nile virus (WNV), and members of alpha Togavirus. A multiplex PCR was used for detecting PCV2 DNA as previously described. See,

Pogranichnyy et al., 2000, Viral Immunol. 13:143-153. APCR assay described by Ellis et al. (1999, J. Vet. Diagn. Invest.. 11:3-14) was employed for detecting PPV DNA. Reverse transcription (RT)-PCR assays were used for detecting RNA of PRRSV (Yoon et al., 1999, Vet. Res.. 30:629-638), PEV (ZeIl et al., 2000, J. Virol. Methods. 88:205-218), CSFV (Wirz et al., 1993, J. Clin. Microbiol. 31:1148-11541 JEV and WNV

(Scaramozzino et al., 2001, J. Clin. Microbiol.. 39:1922-1927), BVDV (Ridpath and Bolin, 1998, MoI. Cell. Probes. 12:1010-106), PERV (Akiyoshi et al., 1998, J. Virol.. 72:4503-4507), and alpha-togaviruses (Powers et al., 2001, J. Virol. 75:10118-10131). SIV or TGEV/PRCV was detected using multiplex RT-PCR assays established in ISU- VDL (Hartman, 1997, 78^th Conference of Research Workers in Animal Disease. Abstract #84;Harmon and Yoon, 1999, Swine Research Reports, pp. 180-182, Cooperative Extension Service, Iowa State University, Ames, Iowa).

Electron Microscopy. To assess morphological characteristics of the viral isolate, cells inoculated with virus material were examined by thin-section positive-staining electron microscopy. Cell culture fluid containing the viral isolate was inoculated onto freshly prepared MARC-145 (CL ISUVDL33, clone of MA104, African green monkey), and BGM (CL ISUVDL44, buffalo green monkey kidney) cells. Inoculated cells were incubated at 37⁰C in a humid 5% CO₂ atmosphere for up to 120 hours PI. At 48 and 120 hours PI respectively, the cells were harvested using a cell scraper and pelleted by low- speed centrifugation. Each cell pellet was fixed in 2% glutaraldehyde (w/v) and 2% paraformaldehyde (w/v) in 0.05M phosphate-buffered saline (PBS, pH 7.2) for 48 hours at 4⁰C. Samples were rinsed once in PBS followed by 2 washes in 0.1 M cacodylate buffer (pH 7.2) and then fixed in 1% osmium tetroxidate in 0.1 M cacodylate buffer for 1 hour at ambient temperature. The samples then were dehydrated in the graded ethanol series, cleared with ultrapure acetone, infiltrated and embedded using a modified EPON epoxy resin (Embed 812, Electron Microscopy Science, Fort Washington, PA). Resin blocks were polymerized for 48 hours at 7O⁰C. Thick and ultra-thin sections were made using a Reichert Ultracut S ultramicrotome (Leeds Precision Instruments, Minneapolis, MN). Ultra-thin sections were collected onto copper grids and counterstained with 5% uranyl acetate in 100% methanol for 15 min followed by Sato's lead stain for 10 min. Images were captured using a JEOL 1200EX scanning and transmission electron microscope (Japan Electro Optic Laboratories, Akishima, Japan).

Histopathology and fluorescent antibody (^"FA) examination of frozen tissue sections. Tissues were fixed by immersing in 10% neutral buffered formalin immediately after collection. Fixed tissues were processed, embedded in paraffin, and sectioned according to the standard protocol established in the Veterinary Diagnostic Laboratory (VDL) of Iowa State University. Sections then were stained with hematoxylin and eosin for microscopic examination.

The FA test was performed on sections of rapidly frozen tissues (brain, tonsil, kidney, lymph nodes) from clinically affected animals submitted to VDL to detect viral antigens. Thin sections of each tissue were obtained using a cryostat and microtome. Sections were attached to prepared glass slides and fixed by immersing in cold 100% acetone. Fixed tissue sections were then stained with a field bovine serum composite containing neutralizing antibody against BVDV. The bovine serum was diluted 1:80 in the 0.01M phosphate-buffered saline (PBS) at pH 7.4 and used. Slides flooded with the antiserum were then incubated at 37°C for one hour in a humid condition and then rinsed with PBS three times. The antigen-antibody reaction in tissues was visualized by staining tissue sections with optimally diluted goat anti-bovine IgG (H+L) conjugated with FITC (Kirkegaard and Perry Laboratories, Inc., Gaithersburg, MD). Swine sera collected from naturally or experimentally infected pigs were used in the same manner but FITC-labeled antiporcine IgG (H+L) was used instead of anti-bovine conjugate. Slides were then observed under a fluorescence microscope. Example 1 Isolation and Characterization of a Pestivirus-Like Virus

A cytolytic viral agent, which was filtered through a 0.22 μm membrane filter, was repeatedly isolated from serum, tonsil, lymph nodes, and brain from affected adult animals and designated ISU-KJY96 and later ISUYP604671. Cell lines (CL) ISUVDLIl (BT cells, cow turbinate), ISUVDL13b (RK-13 cells, rabbit kidney), ISUVDL22 (Vero, African green monkey kidney), ISUVDL33 (MARC-145 clone of MA104, African green monkey), ISUVDL44 (BGM, buffalo green monkey kidney), ISUVDL55 (ED cells, equine horse skin), ISUVDL66 (BHK, hamster kidney), ISUVDL77b (ST, pig testis), ISUVDL88 (FrCK, feline kidney), ISUVDL99 (PK-15, pig kidney), ISUVDL1152 (MDBK, cow kidney), ISUVDL1156 (RK-I, rabbit kidney), and ISUVDL2659 (MDCK, dog kidney), and cell cultures (CC) ISUVDLlOy (PAM, porcine alveolar macrophage) and CC ISUVDLIlOm (PSM, porcine synovial macrophages from joint) were permissive to the viral agent and supported productive infection of the virus. Other isolates were obtained in a similar matter.

CPE by the virus was evident initially in permissive cells within 24 hours after inoculation and was observed in 100% of the cells by 2 days PI. Cytopathology was characterized by cell rounding, death or lysis, and detachment of the cells, resulting in many rounded, apoptotic cells floating in the medium. Visible CPE, however, disappeared after second passages of the isolate in cell culture. Of the cell lines tested, BGM and RK- 13 was the best at continuously supporting productive infection of the virus and the level of progeny virus yield.

Morphologically, the virus was enveloped and was approximately 50 nm in diameter. The virion contained an icosahedral core and acquired its envelope by budding through the endoplasmic reticulum of infected cells. Overall, the virus resembled members of the families Flavivirida, Togaviridae, and Arterivmdae. National Veterinary Services Laboratories (NVSL) examined virus material submitted using negative-staining EM and reported that virions similar to Pestivirus were observed in the material. The virus was determined to contain RNA genome. The virus did not agglutinate erythrocytes of chicken, guinea pig, or pigs. The virus was completed inactivated by storing at 56°C for one hour. Detergents also will have a detrimental effect on virus infectivity.

Bi indirect fluorescent antibody tests, the viral agent did not react with antibody to any known swine viral agents including PRRSV (both VR2332 and Lelsytad virus), PRV, SIV (both HlNl and H3N2), TGEV, PPV, PCV (both type 1 and 2), porcine reovirus, EMCV, PEV, HEV, PCMV, and rabies virus. The virus was recognized specifically, however, by a composite of sera from clinically affected animals in the field and by antiserum raised against the viral agent in a pregnant sow (Sow 80) that was inoculated with virus culture material (ISU-KJY96) at early-to-mid gestation and that showed some degrees of clinical affects by the virus. The viral agent also was reactive in some degree to the antiserum raised against BVDV.

Using PCR techniques, the viral agent was determined not to be PRRSV (both North American and European genotypes), PCVl, PCV2, PEV group I, influenza A virus, TGEV, porcine respiratory coronavirus (PRCV), porcine epidemic diarrhea virus (PEDV), PPV, sHEV, CSFV, BVDV, WNV, PERV, PLHV- 1 , JEV, or an alpha-Togavirus. Based on its cross-reactivity with BVDV and its morphological similarity to flaviviruses, the agent was tentatively classified as a swine pestivirus-like virus. Cross reactivity among pestiviruses has been described (Wensvoort et al., 1989, Vet. Microbiol, 20:291-306; and Terpstra, 1981, Res. Vet. Sci.. 30:185-191). In affected animals, the virus could be detected in various tissues using an immunoassay. Secondary lymphoid tissues showed extensive fluorescence staining for the virus, hi particular, virus could be directly detected in tonsil, lymph nodes, spleen, and kidney.

Example 2 Sequence Analysis of the Pestivirus-like virus

As the virus was reactive to anti-BVD virus antibody, several PCR assays for pestiviruses that particularly targeted the polymerase gene (NS5b) and 5' and 3¹ non- coding regions (NCRs) were developed. These regions were selected because of the conserved nature among pestiviruses. Primers for the polymerase gene and 5' NCR were adapted from published information (Hofmann et al., 1994, Arch. Virol., 139:217- 229;Vilcek et al., 1994, Arch. Virol., 136:309-323; and Bjorklund et al., 1999, Virus Genes, 19:189-195). The following primers for 3' NCRs were designed in our laboratory based on sequence information available from GenBank for CSF viruses and BVD viruses: CS3endlF 5'-GACCCGCCAGGAC-S' (SEQ ID NO:7) and CS3end2R 5'- AAAAATGAGTGTAGTGTGGTAAC-3 ' (SEQ ID NO:8).

Viral RNA was extracted from serum or tissue homogenates as well as cell culture material using the QIAamp Tissue Kit (Qiagen, Santa Clarita, CA), as recommended by the manufacturer. Eight μl of each extract were used as the template for amplification. Reverse transcription was performed at 37⁰C for 60 min, followed by 35 cycles of denaturation at 94°C for 15 min, annealing at 53⁰C for 30 sec, and extension at 72°C for 30 sec. Reference BVDV was used as positive control for the assay to validate results. PCR products and primers were sequenced by the Iowa State University Nucleic Acid Facility. PCR products were obtained from three isolates of the virus (ISUYP60467, ISU-KJY96, and 56892-02tn). The NS 5b sequence from the three isolates of the virus was compared to the corresponding sequence from BVDV type I and the following classic swine fever virus strains (CSFV): Kaernten 933-LY (GenBank Accession No. AFl 82849); SP2087 (GenBank Accession No. AFl 82850); Behring (GenBank Accession No. AFl 82869); EWS 1053 (GenBank Accession No. AFl 82870); Kanagawa (GenBank Accession No. AFl 82903); and Congenital tremor (GenBank Accession No. AFl 82935); Steiermark (GenBank Accession No. AFl 82852); SP4165 (GenBank Accession No. AFl 82851); 1185 (GenBank Accession No. AFl 82853); 1466 (GenBank Accession No. AFl 82854); 1822 (GenBank Accession No. AFl 82856); Bassevelde (GenBank Accession No. AF182857); EVHOO (GenBank Accession No. AF182858); EV1136 (GenBank Accession No. AF182859); EV1192 (GenBank Accession No. AF182860); Wuhan (GenBank

Accession No. AFl 82862 andAF182863); IBRS2 (GenBank Accession No. AFl 82861); 518/94 (GenBank Accession No. AF182864); Alfort/M (GenBank Accession No. AF182866); and Atzbull (GenBank Accession No. AF182868). The sequences were aligned using sequence analysis software (DNAstar®, DNASTAR Inc., Madison, WI) according to the Jotun Hein method and the following parameters: gap penalty 11 ; gap length penalty 3 for multiple alignment; and Ktuple 6 for pair-wise alignment. The NS5b sequence from the three isolates had 97 to 99.2% identity to each other (see FIG. 1), but less than 40% identity (31 to 38% identity) to the NS5b sequence from BVDV type I or any of the classic swine fever virus strains.

The 5' NCRs of the virus were compared to those of known pestiviruses, including BVDV type I and II (GenBank Accession Nos. AF502399, NC002032, AF220247, and AF268278); CSFV strains Brescia (GenBank Accession No. AF091661), 39 (China) (GenBank Accession No. AF407339), Alfort 187 (GenBank Accession No. X87939); and BDV strains C413 (GenBank Accession No. AF002227) and X1818 (GenBank Accession No. AF037405). The 5¹ NCR of the P60467 isolate of the virus exhibited 56-59% identity with the other pestiviruses. The sequence of a portion of the 5' NCR of P60467 is shown in FIG. 2. Similarly, when the 3' NCRs of the KJY96 and P60467 isolates of the virus were compared with the sequence of the pestiviruses to which the 5' NCR was compared, the 3' NCRs had 26.2 to 46.6% identity. The KJY96 and P60467 isolates had 98.3% identity with each other (FIG. 3). The Clustal W method was used to construct a phylogenetic relationship of the virus to other pestiviruses using parameters discussed above. Phylogenetic analysis demonstrated that the newly identified virus was on its own genetic branch that was separated and distinct from existing pestiviruses and yet may have derived from a common ancestor (FIG. 4). Comparisons with sequences deposited in GenBank did not demonstrate any close genetic relatedness with other viral agents known to be present in and pathogenic to pigs or cattle.

Example 3 Response of Adult Female Pigs to Infection with the Virus To evaluate pathogenicity of the newly identified viral agent in pigs, several pilot animal studies were conducted. In one study, three pregnant sows (#80, #94 and #96) at 56 to 71 days of gestation were purchased from a closed specific-pathogen free (SPF) herd and used for the study. Two of the sows (#80 and #94) were injected intramuscularly with either homogenate of tissues collected from an affected sow plus serum from the same animal or cell culture material containing the viral agent (ISU-KJY96). The remaining animal (sow #96) served as an un-inoculated control. All animals were kept individually in separate rooms for 4 weeks after inoculation. During that period, the animals were monitored daily for any change in behavior and rectal temperature as well as overt clinical signs. Sera also were collected periodically from all pigs and stored frozen for virus assays. At the end of 4 weeks PI, the animals were euthanized. Tissues (lung, tonsil, spleen, lymph nodes, kidney, brain) and serum were collected from each animal for virus assays and serology. The sera were also submitted to USDA National Veterinary Services Laboratories, Ames, IA, for purity check (i.e., a complete panel of serology testing).

One (sow #80) of two pigs inoculated with virus material (ISU-KJY96) had an elevated body temperature and looked pale (i.e., anemic) for a few days. At day 7 PI, clinical pathology was run to measure packed cell volume. Sow 80 was 36% while sow 94 (inoculated animal) and sow 96 (control) were 45% and 42%, respectively. Sow 80 also showed "head pressing" and aggressive behavior as evident by the presence of trauma around ears and legs during the first 7 days after inoculation; its hind limbs appeared to be weaker, suggesting that the central nerve system (CNS) of the animal was affected. Sow 80 also transiently suffered from dyspnea.

Both challenged animals were restless and lost appetite for 7 to 10 days after inoculation. No other clinical abnormalities including abortion were observed. The control animal remained unchanged in behaviors and appearance. No viral agent was detected in sera collected from all animals prior to inoculation and on the day of challenge. Viremia was detected in serum samples collected from both inoculated sows on 4 days. The inoculated animals were still viremic at day 21 PI.

No significant gross and microscopic lesions were observed in organs and tissues collected from inoculated sows at the termination of study (i.e., 4 weeks PI) except lungs from both sows had a very mild multifocal, lymphocytic pneumonia. In contrast, it was noted that piglets from inoculated sows had petichiae on most, if not all, of serosa. Hemorrhagic lesion was also observed on the surface of the liver, heart and lung. No hemorrhagic lesion was observed in any of piglets from the control sow (#96).

Both inoculated animals developed antibody to ISU-KJY96 as measured by IFA test while the control sow remained seronegative throughout the study. All animals were serongative for ISUKJY96 on the day of challenge. Sera collected from these animals at the end of study were negative for antibodies against PRRSV, PRV, HEV, MCFV, CSFV, BVDV (type 1 and 2), SIV, EMCV, TGEV, PRCV and PEV group 1. One of two inoculated sows and the control were seropositive for PPV.

The study was repeated with another three pregnant sows (#37, #42, #71) at 71 to 79 days of gestation in the same manner as described above with two exceptions. In this later study, blood samples were collected in EDTA for clinical pathology (C BC, blood chemistry). AU animals were euthanized at 10 days PI.

Inoculated sows (#42 and #71) were off-feed, slightly cyanotic, depressed and restless while the control sow (#37) remained clinical normal throughout the observation period. In contrast to the first run, no fever and aggressive behavior was observed in any of the animals.

Inoculated animals were viremic by 2 days PI and remained viremic during the study period (10 days). Total white blood cell count dropped significantly by day 5 PI, returned to normal at day 7 PI, and then decreased again. Leukopenia was due to a decrease in lymphocytes. No significant change was observed in neutrophils and monocytes.

At termination (i.e., 10 days PI), no significant gross and microscopic lesions were observed in the control sow (#37) or any of her fetuses (n=8). In contrast, mild pneumonic lesions were observed in the lung from one (#42) of two inoculated sows. Necrotic lesions were also found on the middle and horn area of the uterus from Sow 42. Sow 71 had focal hemorrhagic lesion and mild fibrinoid degeneration of small arteries in the parenchyma (pon). Fetuses from the inoculated sows had mild to moderate hemorrhagic lesion on serosa of most of internal organs, more severely liver, heart and lung.

Example 4

Response of Young Swine to Infection with the Virus Two- to 3-weeks-old caesarian-derived-colostrum-deprived (CDCD) piglets (n=40) were purchased from a commercial source and used to evaluate clinical effect of the new virus on young swine. Animals were placed in three groups. One group (n=15) was inoculated with cell culture material containing the viral agent (ISU-KJY96) via intranasal and intramuscular routes. Another group (n=15) was inoculated through the same routes with serum from sow #80 that had been experimentally infected with tissue homogenate determined to contain the virus. The remaining group (n=10) was inoculated with normal cell culture medium plus serum from the control animal in the previous study and served as sham control. All animals were monitored first 2 weeks after inoculation for change in rectal temperature and clinical signs. One pig per group was necropsied on days 0, 2, 5, 7, 9, 12 and 14 PI. Tissues (brain, tonsil, lung, spleen, kidney, lymph nodes) were collected from each pig for both virus assays and histopathology. Animals were bled at-2, O₅ 2, 5, 7, 9, 12 , 16, 21, 28 and 30 days PI to collect whole blood and serum. At the termination of study, all live animals were euthanized and necropsied.

Control pigs remained clinically normal throughout the study. No change in behavior and appearance was observed in any of inoculated pigs. No clinical signs of respiratory or neurologic diseases were evident in the inoculated animals either. Some (n=23), but not all, of inoculated animals became viremic. Viremic animals developed antibody to ISU-KJY96; however, the level of IEA antibody was relatively low as compared to previous sow studies. No gross and microscopic lesions were observed in animals necropsied during the study and at the end of the study. The new virus could not be isolated from any of tissues collected.

Example 5

Response of Pregnant Animals to Infection with the Virus

Sows were purchased from a closed herd known to be free of PRV and PRRSV. Serologically, animals were positive for PPV, SIV, Leptospira sp., Mycoplasma hyopneumonia due to vaccinations. Selected sows were transferred to an animal holding facility with farrowing crates and bred through artificial insemination. Once pregnancy was confirmed by an ultrasound technique, five sows were selected for challenge with the newly isolated virus ISUYP604671 or original material to reproduce clinical signs observed in the field. Three pregnant sows at 30 days of gestation were inoculated intranasally, subcutaneous and intramuscularly with one of the following biological materials: a) cell culture fluid containing the agent (ISUYP604671); b) homogenate of tissues collected form a clinically affected sow; or c) serum collected from the clinically affected sow. AU inoculated animals were kept in the same room, but individually on farrowing crates for 30 days. The one remaining sow served as sham-inoculated control and was kept in a separate room. All animals were monitored for changes in behavior and reproductive problems. In addition, the sows were bled every seven days. At the termination of the study, all sows were euthanized, and various clinical specimens (brain, tonsil, lung, spleen, lymph nodes, kidney, liver, placenta, spinal cord, uterus fluid). If fetuses were present, they were collected from each sow for histopathology, virus isolation and/or serology.

During the 30-day observation period, all animals were normal in their behavior and no abortions were observed. At the termination of the study, the control sow appeared to be normal and no lesions were observed, hi contrast, two of sows inoculated with material containing virus ISUYP604671 showed some gross lesions, such as hemorrhages in inguinal lymph node, decolorization of uterus (green and brown) and possible embryonic death of fetuses. Microscopically, necrotic edema in the lymph node, mineralization plaques in uterus and necrotic debris in the lumen were observed, which supports the possibility of embryonic death and/or fetal reabsorption. In fact, one of the inoculated sows did not have any fetus at necropsy although no significant lesions were observed. Clinical signs and gross and microscopic lesions are summarized in Table 1. Virus was recovered from tissues (spleen, liver, jejunum, uterus) of inoculated sows, confirming virus replication in sows, particularly secondary lymphoid organs. In addition, the virus was also isolated from fetal tissues, indicating transplacental transmission of the virus.

TABLE l

Example 6 Buoyant density of Swine Pestivirus-Like Virus

The density of the swine pestivirus-like virus was determined using a method described by Horzinek (1966, J. Bacteriol., 92: 1723-6) with some modification. In brief, a continuous cesium chloride (CsCl) gradient was prepared in ultraclear nitrocellulose tubes (Beckman Fullerton, CA, USA) from two CsCl solutions at a concentration of 51 mg/ml and 472.4 mg/ml, respectively, in Tris-HCl buffer (pH 7.4) using a gradient delivery system (Model 475, Bio-Rad, Hercules, CA, USA). Each tube received a total of 10 ml CsCl linear gradient. On top of the gradient, 2 ml of each sample (tissue homogenate or cell culture supernatant) were overlaid and then centrifuged through the gradient using a SW41 swinging bucket in a ultracentrifuge (Optima LE-80K, Beckman, Fullerton, CA, USA) for 24hr at 39,000 RPM (i.e., 260,000 x g). All visible bands were collected using a syringe with a long needle. Each fraction was tested for the presence and titer of the swine pestivirus-like virus, which was confirmed by FA using convalescent serum or experimentally infected animals. Reflective index of each fraction was determined using a digital refractometer AR200 (Leica, Buffalo, NY, USA) and density was calculated based on tabulated reference provided by Beckman. Density of the swine pestivirus-like virus was determined to be 1.15 - 1.2 g/ml, which agrees with previous observations for CSFV (Horzinek, 1966, supra; Rumenapf et al, 1991, Arch. Virol. Suppl. 3:7-18). OTHER EMBODIMENTS

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

WHAT IS CLAIMED IS:

1. Isolated swine pestivirus-like virus, wherein said virus comprises a nucleic acid having at least 65% sequence identity to the nucleotide sequence set forth in SEQ ID NOS:1, 2, 3, 4, 5, or 6.

2. A host cell comprising the virus of claim 1.

3. An isolated attenuated swine pestivirus-like virus, wherein said virus is effective to elicit an immune response upon administration to an animal, and wherein said virus comprises a nucleic acid having at least 65% identity to the nucleotide sequence set forth in SEQ ID NOS:1, 2, 3, 4, 5, or 6.

4. A composition comprising the virus of claim 3 and a pharmaceutically acceptable carrier.

5. The composition of claim 4, said nucleic acid having at least 75% identity to the nucleotide sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6.

6. The composition of claim 4, said nucleic acid having at least 85% identity to the nucleotide sequence set forth in SEQ ID NOS:1, 2, 3, 4, 5, or 6.

7. The composition of claim 4, said nucleic acid having at least 95% identity to the nucleotide sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6.

8. A method for reducing the risk of swine pestivirus-like infection in a pig, said method comprising administering said composition of claim 4 to said pig.

9. The method of claim 8, wherein said composition is administered intramuscularly, intranasally, or subcutaneously.

10. A method for detecting a swine pestivirus-like virus infection in an animal, said virus comprising a nucleic acid having at least 65% sequence identity to the nucleotide sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6, said method comprising:

(a) contacting a biological sample from said animal with an antibody having specific binding affinity for said virus, wherein said virus, if present, binds to said antibody, to form an antibody-virus complex; and

(b) detecting the presence or absence of said antibody- virus complex, wherein the presence of said antibody- virus complex indicates the presence of said infection.

11. A method for detecting a swine pestivirus-like virus infection in an animal comprising:

(a) providing a biological sample from said animal; and

(b) detecting the presence or absence of a swine pestivirus-like virus nucleic acid in said sample, wherein the presence of said nucleic acid indicates the presence of said infection, and wherein said nucleic acid is selected from the group consisting of: i) a nucleic acid having the nucleotide sequence set forth in SEQ ID NOS:l, 2, 3, 4, 5, or 6; ii) a fragment of the nucleic acid of i), wherein said fragment of the nucleotide sequence of SEQ E) NOS: 1, 2, or 3 contains at least 12 consecutive nucleotides of the nucleotide sequence of nucleotides 1-144, 163-218, or 236-351 of SEQ ID NO:1, nucleotides 1-163, 182-237, or 255-370 of SEQ ID NO:2, or nucleotides 1-175, 194-249, or 267-388 of SEQ ID NO:3; iii) a fragment of the nucleic acid of i), wherein said fragment of the nucleotide sequence of SEQ ID NOS: 1, 2, or 3 contains at least 32 consecutive nucleotides of the nucleotide sequence set forth in SEQ ID NOS:l, 2, or 3; iv) a nucleic acid complementary to the nucleic acid of i), ii), or iϋ); v) a nucleic acid having at least 65% sequence identity to the nucleic acid of i), ii), iii), or iv); and vi) a fragment of the nucleic acid of i), wherein said fragment is at least 20 nucleotides in length.

12. An antibody having specific binding affinity for a swine pestivirus-like virus, said virus comprising a nucleic acid having at least 65% sequence identity to the nucleotide sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6.

13. A diagnostic kit for detecting the presence of a swine pestivirus-like virus infection, said virus comprising a nucleic acid having at least 65% sequence identity to the nucleotide sequence set forth in SEQ ID NOS: 1, 2, 3, 4, 5, or 6, said kit comprising an antibody having specific binding affinity for said virus.

14. An isolated nucleic acid selected from the group consisting of:

(a) a nucleic acid having the nucleotide sequence set forth in SEQ ID NOS:l, 2, 3, 4, 5, or 6;

(b) a fragment of the nucleic acid of (a), wherein said fragment of the nucleotide sequence of SEQ ID NOS: 1, 2, or 3 contains at least 12 consecutive nucleotides of the nucleotide sequence of nucleotides 1-144, 163-218, or 236-351 of SEQ ID NO:1, nucleotides 1-163, 182-237, or 255-370 of SEQ ID NO:2, or nucleotides 1-175, 194-249, or 267-388 of SEQ ID NO:3;

(c) a fragment of the nucleic acid of (a), wherein said fragment of the nucleotide sequence of SEQ ID NOS: 1, 2, or 3 contains at least 32 consecutive nucleotides of the nucleotide sequence set forth in SEQ TD NOS: 1, 2, or 3;

(d) a nucleic acid complementary to the nucleic acid of (a), (b), or (c);

(e) a nucleic acid having at least 65% sequence identity to the nucleic acid of (a), (b), (c), or (d); and

(f) a fragment of the nucleic acid of a), wherein said fragment is at least 20 nucleotides in length.

15. A diagnostic kit for detecting the presence of a swine pestivirus-like virus infection, said kit comprising said nucleic acid of claim 14.