Restriction enzyme screen for differentiating porcine reproductive and respiratory syndrome virus strains

Abstract

A test based on restriction enzyme analysis identifies and differentiates strains of porcine reproductive and respiratory syndrome virus (PRRSV). Amplified cDNA from the ORF 5 region of the viral genome has been targeted for identification of unique restriction sites that allow for the differentiation of the vaccine strain from field strains, and for differentiation of field strains from each other through the use of selected restriction enzymes. This assay is useful for both clinical diagnosis of PRRSV field strains in vaccinated pigs as well as for epidemiological studies in the evaluation of the source and transmission of PRRS field viruses.

Description

BACKGROUND OF THE INVENTION

1. Field of the Invention

This invention relates to a differential test for distinguishing strains of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) from one another and for differentiating field stains from the currently used vaccine strain.

Porcine reproductive and respiratory syndrome (PRRS) was first reported in North America in 1987 (Keffaber, 1989) and emerged in Europe in late 1990 (Wensvoort et al., 1991). Recently, PRRS has gained world-wide attention because of its economic impact on the swine industry. The disease is characterized by reproductive failure in pregnant sows and respiratory problems in pigs of all ages (Loula, 1991). The causative agent of PRRS is a small (50-60 nm) positive-stranded RNA enveloped virus. The genome is a polyadenylated RNA molecule of about 15 kb and contains eight open reading frames (ORFs). Viral proteins are expressed by six subgenomic mRNAs which are transcribed from the negative strand using a body sequence derived from the 5' end of the viral genome (Meulenberg et al., 1995). The virus replicase is most likely encoded by ORFs 1a/1b by a -1 frameshift (Conzelmann et al., 1993). Open reading frames 2 to 4 encode for putative structural proteins (Van Nieuwstadt, 1995). ORF 5 encodes for a envelope (E) glycoprotein of approximately 25 kDa. A non-glycosylated membrane (M) protein of 18 kDa is encoded by ORF 6 and the nucleocapsid (N) protein of 15 kDa is encoded by ORF 7 (Meulenberg et al., 1995; Conzelmann et al., 1993).

Morphologically and morphogenetically, PRRSV resembles equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), and simian hemorrhagic fever virus (SHFV) (Conzelmann et al., 1993; Meulenberg et al., 1993; Plagemann and Moennig, 1991; Snijder and Spaan, 1995). As a result of common features shared by these viruses, they have been tentatively grouped into a new virus family, Arteriviridae (Conzelmann et al., 1993; Meulenberg et al., 1993, Plagemann and Moennig, 1992).

2. Description of the Prior Art

Although the clinical features of PRRS in the United States and in Europe appear similar, several recent studies have indicated phenotypic, antigenic, and genetic differences exist among PRRSV isolates (Bautista et al., 1993; Meng et al., 1994; Wensvoort et al., 1992). The amino acid sequences of ORF 2 through ORF 7 of North American isolates share only 55-79% homology with those of European descent (Meulenberg et al., 1995). It is believed that the glycosylated structural envelope protein E, encoded by ORF 5, is partially responsible for these serological variations among isolates of PRRSV (Meulenberg et al., 1995). Protein E is the counterpart of G.sub.L of EAV (de Vries et al., 1992) and VP-3 of LDV (Gogeny et al., 1993). Both (G.sub.L and E) proteins contain a large internal hydrophobic region which has been thought to anchor these proteins in the membrane (Meulenberg et al., 1995). The existence of neutralizing epitopes in VP-3 of LDV (Harty and Plagemann, 1988) and G.sub.L of EAV (Balasuriya et al., 1995) was demonstrated using monoclonal antibodies and sequencing escape mutants. More recent studies indicate that protein E plays a role in inducing neutralizing antibodies (Persch et al., 1995).

A modified-live-virus vaccine strain RespPRRS.RTM. of PRRSV is currently used in the United States for the prevention of the respiratory facet of the syndrome. Although the vaccine strain is attenuated, it, like virulent field strains of PRRSV, has the ability to persist for at least several weeks in a vaccinated pig. Consequently, the source of PRRSV isolated from diagnostic samples is sometimes in question and it would be highly desirable to have a positive assay for identifying the source.

SUMMARY OF THE INVENTION

We have now discovered that ORF 5 can be targeted in a restriction enzyme analysis for distinguishing vaccine strain RespPRRS.RTM. of PRRSV from virulent field strains and also for distinguishing field strains from one another. The reading frame is first converted to a double stranded DNA, amplified, and then cut with restriction enzymes in conserved regions which collectively have sufficient variability among strains to permit generation of a unique fragment profile for each strain of PRRSV.

In accordance with this discovery, it is an object of the invention to provide a tool for distinguishing vaccine strain RespPRRS.RTM. from wild-type field strains.

It is also an object of the invention to provide a tool for epidemiological studies in the evaluation of the source and transmission of field strains of PRRSV.

It is also an object of the invention to provide a sensitive, reliable, and rapid assay for PRRSV suitable for large-scale herd screening.

A further object of the invention is to provide a diagnostic basis for designing an effective control program for PRRS in swine herds.

Other objects and advantages of this invention will become readily apparent from the ensuing description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the aligned ORF 5 sequences for field strain VR 2332 and vaccine strain RespPRRS.RTM. of PRRSV as well as the consensus sequence for these strains.

FIG. 2 shows the aligned ORF 5 nucleotide sequences for the 22 field strains and strain RespPRRS.RTM. of PRRSV sequenced in conjunction with the invention, and for strain VR 2332 (previously sequenced by others) as compared to the consensus sequence.

FIG. 3 is a computer generated schematic diagram of Mlu I, Sfc I, Hinc II and Sac II ORF 5 cDNA fragments for PRRSV field strain NADC-8 (F) and vaccine strain RespPRRS.RTM. (V).

DETAILED DESCRIPTION OF THE INVENTION

The primary points of novelty regarding the identification and distinction of individual strains of PRRSV in accordance with this invention include: (1) identification of a segment of the viral genome that is sufficiently variable among strains to allow differentiation, yet stable enough so that there is a low probability of mutational changes during repeated in vitro or in vivo passages of a particular strain; (2) selection of a universal set of primers that allows for reverse transcription (RT) and polymerase chain reaction (PCR) amplification of this segment; and (3) identification of unique restriction sites that allow for the differentiation of vaccine strains from field strains, and field strains from one another.

Insofar as currently known, ORF 5 is the only region of the PRRSV genome that has the proper combination of nucleotide variability among strains of PRRSV (exemplified by those listed in Table I) together with long term stability to allow for restriction enzyme differentiation. On the other hand, the stability of the ORF 5 nucleotide sequence of a particular strain is indicated (FIG. 1) by the fact that there are only two base differences (positions 38 and 451) between vaccine strain RespPRRS.RTM. (indicated in the figure as "resp.PRRS"), which was attenuated by repeated serial passages in cell culture, and its presumed parental strain VR 2332. These two strains (which could be considered variations of the same strain) are indistinguishable on the basis of restriction patterns associated with any of the 77 restriction enzymes reported in Table II.

FIG. 2 clearly depicts variations in the ORF 5 nucleotide sequences for strain RespPRRS.RTM. of PRRSV sequenced in conjunction with the invention and for 23 field strains of PRRSV, including 22 field strains sequenced in conjunction with the invention and VR 2332 (the sequence of which was previously reported in the literature). The consensus sequence for the 24 strains is also given in the figure. The position and frequency of these variations are sufficient to permit differentiation of every field strain (except presumed parental strain VR 2332) from the vaccine strain using a singular enzyme, either Mlu I or Sfc I (see Tables I and II). Assaying with both enzymes provides confirmation. As best shown in Table I, a high degree of assurance can be obtained by comparing the combined fragment patterns from Mlu I, Sfc I, Hinc II, and Sac II. All 23 of the field strains in Table I can be differentiated from one another by means of an appropriate combination of six or fewer restriction enzymes selected by reference to Table II. In Table II, the PRRSV strains are shown across the top and 77 enzymes which were evaluated for purposes of the invention are indicated on the left. The last column represents the cut sites for both strain RespPRRS.RTM. and its presumed parental strain VR 2332. Even though there are two base differences between the ORF 5 of these two strains, the cutting sites in the respective ORF 5 cDNAs are the same for all of the 77 enzymes shown in the table. The numbers shown in the table cells represent the size of the resultant fragments obtained by cutting a 716 bp amplified DNA including the ORF 5. Multiple fragment sizes are listed in order from 5' to 3'. The symbol "xxx" indicates that the particular enzyme does not cleave anywhere within the 716 bp fragment.

Given that the PRRSV genome is RNA, the region coding for ORF 5 must first be reverse transcribed by methods known in the art to produce double stranded cDNA. By means of PCR or any other like process, the coding region is then amplified to the extent necessary for the subsequent restriction enzyme analysis. Primers are preferably selected from nearby flanking regions upstream and downstream from the reading frame.

EXAMPLE 1

Cell and Virus Propagation

MARC-145 cells (Kim et al., 1993, herein incorporated by reference) were cultured in Eagle's minimum essential medium (MEM), supplemented with 5% fetal bovine serum (FES) and antibiotics. Twenty-two field stains of PRRSV isolated from Canada, Guatemala, and the United States as well as vaccine strain RespPRRS.RTM. of PRRSV were propagated and then cloned by three rounds of end point dilutions on MARC-145.

RNA Extraction and Reverse Transcriptase Polymerase Chain Reaction

Viral RNA was isolated from 22 field strains and vaccine strain RespPRRS.RTM. of PRRSV (see Table I) using a standard guanidinium isothiocyanate method (Sambrook et al., 1989, herein incorporated by reference). Single tube reverse transcriptase polymerase chain reactions (RT-PCR) as described by Sellner et al. (1992, herein incorporated by reference) with slight modifications were conducted on RNA isolated from each of the 23 strains in a Perkin-Elmer 4800.RTM.. Primers were designed based on the nucleotide sequence of field strain VR 2385 (Meng et al., 1995; Morozov et al., 1995, both herein incorporated by reference) and synthesized by Integrated DNA Technologies, Inc. (Coralville, Iowa). The sense primer was 5'-CCATTCTGTTGGCAATTTGA-3' (SEQ ID NO:25) and the anti-sense primer was 5'-GGCATATATCATCACTGGCG-3'(SEQ ID NO:26). In SEQ ID NO:27 (which is similar to SEQ ID NO:23 for ORF 5 of vaccine virus RespPRRS but additionally shows the immediate flanking regions), the sense primer extends from nucleotide 1 through nucleotide 20 and the antisense primer is the complement to the nucleotide sequence extending from nucleotide 716 to 697. A 716 bp piece encompassing ORF 5, with flanking regions of ORF 4 and ORF 6, was generated for all strains and the fragments were purified using a GENECLEAN.RTM. kit (Bio 101).

Sequencing

Double stranded nucleotide sequencing (Tabor and Richardson, 1987, herein incorporated by reference) with Taq polymerase and fluorescently labelled dideoxynucleotides (Applied Biosystems International, Prism System) as described in Sanger et al. (1977, herein incorporated by reference) was performed in triplicate on both strands for analysis with an Applied Biosystems 373A.RTM. automated sequencer. The same primer set as described above was used for sequencing. Nucleotide sequence editing and alignments were performed using Intelligenetics, GENEWORKS.RTM. version 2.2 software.

Analysis

To determine the rate of possible drift of ORF 5 sequence, four PRRSV strains of U.S. origin: NADC-8, NADC-9, 41572-2, and 18310-A were repeatedly passed on MARC-145 cells. NADC-8, NADC-9, and 41572-2 encountered 61 passages, and 18310 encountered 31 passages. RT-PCR was performed and the subsequent product was sequenced as described above.

Sequencing of the four selected strains passed in vitro revealed: 6 nucleotide and 4 amino acid substitutions (2,110,136,194 a.a.) for NADC-8; 2 nucleotide and 1 amino acid substitution (59 a.a.) for NADC-9; 2 nucleotide and 2 amino acid substitutions (3, 34 a.a.) for strain 41572-2; and 4 nucleotide and 2 amino acid substitutions (3,194 a.a.) for strain 18310-A (data not shown). However, none of these changes affected restriction patterns of any of these four strains.

Comparison of Sequences

The complete ORF 5 gene sequence for each of 22 PRRSV field strains and for the vaccine strain RespPRRS.RTM. was determined. The sequences for the field strains are shown in the SEQUENCE LISTING as SEQ ID NOs:1-22, that for field strain VR 2332 (previously published) is shown as SEQ ID NO:24, and that for vaccine strain RespPRRS.RTM. is shown as SEQ ID NO:23. These sequences were aligned and compared (FIG. 2) to the consensus sequence for all 24 strains. Alignment analysis indicates the same initiation and termination sites exist for all 24 strains. Regions of high and low variability are also apparent. Insertions and deletions were found to be nonexistent on the nucleotide level.

EXAMPLE 2

To differentiate the vaccine strain RespPRRS.RTM. and the presumed parental field strain VR 2332 from the 22 remaining (field) strains shown in Table I, it was necessary to select one or more appropriate restriction enzymes. The selection was based on a comparison of the ORF 5 sequence data for these strains in conjunction with the known cut sites for the enzymes as summarized in Table II. Using this technique, enzymes Mlu I, Sfc I, Hinc II and Sac II were initially selected. The enzymes Mlu I and Sfc I cut only the vaccine strain RespPRRS.RTM. and field strain VR 2332, and do not cut any of the other 22 PRRSV strains shown in Tables I and II. The restriction enzymes Hinc II and Sac II cut most of the PRRSV strains tested giving various gel patterns. Only strains 4 and 9 have a Hinc II gel pattern identical to the RespPRRS.RTM./VR 2332 gel pattern. A second gel analysis with Sac II differentiates the vaccine strain and VR 2332 from PRRSV field strains 4 and 9. The combined results with the 4 restriction enzymes give a high degree of assurance of the RespPRRS.RTM./VR 2332 genotype.

Restriction enzymes Mlu I and Sfc I are particularly valuable for differentiation because these enzymes cut only strain RespPRRS.RTM./VR 2332 and none of the other 22 strains of PRRSV. Mlu I recognizes the 6 base pair sequence A'CGCGT. For the other 22 PRRSV strains, there are two base differences, namely, guanines at positions 409 and 411; both need to occur in order to create a functional Mlu I site. Since two bases need to change for the other strains of PRRSV, the Mlu I pattern is a strong marker for the RespPRRS.RTM./VR 2332 genotype. Also Sfc I only cuts the RespPRRS.RTM./VR 2332 PCR-amplified DNA fragment. However, 9 of the 22 other strains of PRRSV require only a single nucleotide change, in the localized 6-nucleotide cutting site, to create a functional Sfc I site. Therefore, mutations resulting in Sfc I cutting are potentially more frequent than those for Mlu I cutting. As a safeguard against erroneous identification resulting from such mutations, it is advisable to conduct the assay with additional enzymes.

A typical gel electrophoresis test, in which vaccine strain RespPRRS.RTM. and strain NADC 8 are compared after digestion with Mlu I, Sfc I, Hinc II and Sac II, is represented by FIG. 3. The Mlu I and Sfc I gel patterns of strain NADC 8 are the same for all 22 PRRSV strains and distinct from strain RespPRRS.RTM./VR 2332 gel pattern. For restriction enzymes Hinc II and Sac II, strain NADC-8 gel patterns are also distinct from strain RespPRRS.RTM./VR 2332 patterns, but similar to other PRRSV strains. However, all of the PRRSV strains in Table II can be differentiated one from another by appropriate selection of restriction enzymes. No more than 6 restriction enzymes would be needed for differentiating the strains reported in Table II.

EXAMPLE 3

The constancy of the restriction enzyme pattern within ORF 5 during persistent infection of pigs with PRRSV was evaluated for the purpose of assessing the validity of the assay described in Example 2. Virus stability upon PRRSV replication in vivo was studied in four individual gilts, in penmates, and in gilt-piglet relationships. The results are shown in Table III, below. In each of evaluations Nos. 1-3, the virus was passaged in vivo in a gilt for a period of 7 weeks. After this time, virus was isolated from a sample taken by lung lavage wherein the alveolar macrophages, which are believed to be the primary cells for virus replication in vivo, are flushed from the lung. In each case, the recovered strain was characterized by the same RE pattern as the exposure strain (RespPRRS.RTM.). In evaluation No. 4, the same results were obtained for strain NADC-8. In evaluation Nos. 5 and 6, a pig was exposed to strain NADC-8, and 8 weeks later brought into contact with a second pig which thereafter shared the same pen. After 3 weeks, the RE pattern of the strain recovered from the second pig was identical to that of Strain NADC-8 used to infect the first pig. In evaluation No. 7, a pregnant gilt was infected with strain RespPRRS.RTM. eight weeks prior to farrowing. The RE pattern of the PRRSV recovered 5 weeks later from one of her piglets was the same as the original strain RespPRRS.RTM..

It is understood that the foregoing detailed description is given merely by way of illustration and that modifications and variations may be made therein without departing from the spirit and scope of the invention.

TABLE I__________________________________________________________________________Restriction Enzyme Analysis of PRRSV Isolates Restricted Enzyme.sup.aStrains ID Origin Year MluI SfcI HincII SacII__________________________________________________________________________1 46448 IA 1989 -- -- 219 242 46907 KY 1991 -- -- -- 243 1205-D MO 1992 -- -- -- 244 10654 IA 1992 -- -- 360 --5 30093-A IL 1992 -- -- 219 246 34075 NE 1992 -- -- 88,219 247 49138 TX 1992 -- -- 88,219 248 5556 MI 1993 -- -- -- 24,5559 22805 KS 1992 -- -- 360 55510 5591 NC 1993 -- -- 219 2411 14622 AR 1993 -- -- 88 24,55512 19950-E MN 1993 -- -- 88,219 2413 26948-2 VA 1993 -- -- 88 24,55514 41572-2 NE 1993 -- -- 88,219 24,55515 42928 IL 1993 -- -- 88,219 2416 32983-LG NC 1993 -- -- 88,219 2417 30352-3 MI 1993 -- -- -- 24,55518 47324-2 Canada 1993 -- -- 88 24,55519 18310-A PA 1994 -- -- 88 2420 24901 Guatemala 1994 -- -- 88,219 24NADC-8 (IA)-92 IA 1992 -- -- 219 24,555NADC-9 (IA)-93 IA 1993 -- -- 219 24,555RespPRRS .RTM. -- MN.sup.b 408 116 360 24VR 2332 -- MN 408 116 360 24__________________________________________________________________________ .sup.a The designated cut sites are for the 603 bp ORF 5 .sup.b Presumed to originate from strain VR 2332. TABLE II - ENZYME #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 Acc I 318 318 318 318 318 xxx xxx 318 318 318 318 318 Aha II xxx 268 268 118 xxx xxx xxx xxx xxx xxx xxx xxx Alu I multi(4) multi(4) multi(4) multi(4) multi(5) 136/176 136/176 136/176/198 multi(4) 136/176 136/176 136/176 Apa LI xxx xxx xxx xxx xxx 268 268 xxx xxx 268 xxx 268 Apo I 140/204 xxx 204 xxx 140/204 204 204 204 xxx 204 204 204 Bal I xxx 309 309 xxx xxx 585 xxx 309 xxx xxx 309 xxx Bsn I 267 267 267 267 267 xxx xxx 267 267 xxx xxx xxx Bbv 145/368 145/368 145/368 145/368 145/368 145/368 145/368 142/145/368 145/368 145 145/368 multi(5) Bfa I 195/280 195/199 195 195/445 195/280/378 306/465/629 465/629 195/199/629 195/445 629 xxx 280/465/629 Bse HI xxx 268 268 118 xxx xxx xxx xxx xxx xxx xxx xxx Bsa JI 49/376/580 49/376/580 49/376/580 49/376/580 49/580 muiti(4) 49/580 49/376/560 49/376/580 49/580 49/376/580 49/376/580 Bsi EI 498 498 498 498 498 498 498 xxx 498 498 498 498 Bal I xxx xxx xxx xxx xxx xxx 325 xxx xxx xxx xxx 331 Bsm AI 263 263 263 263 263 xxx 216 263 263 xxx 263 xxx Bsp 1286I 272/377 377 377 112/272/377 272/377 112/272/377 112/272/377 272/377 112/272/377 112/272/377 112/272 112/272/377 Bsr FI xxx 324 324 xxx xxx 324 xxx xxx xxx xxx xxx xxx Bsr I 216 xxx xxx xxx 216 xxx 195 xxx xxx xxx xxx xxx Bst EII xxx xxx xxx xxx xxx 540 xxx 496 xxx xxx xxx 540 Bst WI 378/428 378/428 378/428 378/428 306/428 378/428 428 378 378/428 428 378/428 378/428 Bst UI 51/366 muiti(4) 51/65/366 65/366 51/366 51/366 51/65/366 multi(4) 65/582 muiti(4) multi(4) 51/65/366 Cfr 10I xxx 324 324 xxx xxx 324 xxx xxx xxx xxx xxx xxx Cla I xxx xxx xxx 550 xxx xxx xxx xxx xxx xxx xxx xxx Dde I 351/472/628 351/472/628 351/472/628 351/172/628 351/472/628 xxx 472 351/472 351/472/628 472 351/472/628 199/472 Dpn I 549 549 549 549/553 549 xxx 549 549 553 497/549 549 549 Dpn II 547 xxx 547 547/551 547 xxx 547 547 551 495/547 547 547 Eas I xxx 307 307 xxx xxx 583 xxx 307 xxx 379 307 xxx Ear I 510 xxx xxx 510 510 xxx xxx xxx 510 xxx xxx xxx Eco 47III xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Esp 3I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Fnu 4HI 134/382 134/382 134/382 134/382 134/382 134/382 134/382 multi(4) 134/382/583 134/382 134/382/583 muiti(5) Fok I xxx xxx xxx xxx xxx xxx xxx 610 xxx xxx 610 xxx Hae II 121/434 121/271/434 121/271/434 434 121/434 434 434 121/434 434 434 434 434 Hae III xxx 309 309 xxx 304 585 541 309 xxx 381/541 309 xxx Hga I 173 173 173 126/173 173 173 173 173 173 173 173 173 Hgi AI xxx xxx xxx 112 xxx 112/272 112/272/377 xxx 112 112/272/377 112 112/272 Hhe I 110/120/433 multi(4) muLti(4) 433 110/120/433 433 433 110/120/433 433 433 375/433 433 Hinc II 247 xxx xxx 388 247 116/247 116/247 xxx 388 247 116 116/247 Hinf I 248/481 248/481 248/481 248/481 248/481 248/481 248/481 248/481 248/481 248/481 248/481 248/481 ENZYME #13 #14 #15 #16 #17 #18 #19 #20 NADC-8 NADC-9 REF:V2332 Acc I 318 xxx xxx 318 318 318 xxx xxx xxx xxx 318 Aha II xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Alu I 136/176 136/176 138/176 136/176 136/175 136/176 136/176 136/176 multi(4) muti(4) multi(4) Apa LI 268 268 268 268 xxx xxx 268 268 xxx xxx xxx Apo I 204 204 204 xxx 204 204 204 204 140/204 140/204/601 204 Bal I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Bsn I xxx xxx xxx xxx 267 267 xxx xxx 257 267 267 Bbv I multi(4) multi(4) 145/368 multi(7) 145/368 145/368 145/368 muLti(4) 145/368 145/368 145/368 Bfa I 465/629 280/629 629 280/465/629 xxx 280 629 629 195/280 195/280 195 Bse HI xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Bsa JI 49/376/580 multi(4) 49/376/580 49/376/580 49/580 muiti(4) 49/580 49/580 49/376/580 49/376/580 49/376/580 Bsi EI 498 498 498 498 xxx 498 498 xxx 498 498 498 Bal I xxx xxx xxx xxx xxx xxx 325 325 xxx xxx xxx Bsm AI xxx xxx 216 xxx 263 xxx 216/630 216 263 263 263 Bsp 1286I 112/272/377 112/272/377 112/272/371 112/272/377 272/377 112/272 112/272/377 112/272/377 272/377 272/377 112/272/377 Bsr FI xxx 324 324 xxx xxx xxx xxx xxx xxx xxx xxx Bsr I xxx xxx xxx xxx xxx xxx 195 xxx 216 216 xxx Bst EII 308 540 xxx xxx 496 xxx 540 540 540 540 xxx Bst WI 378/428 378/428 98/378/428 378/428 428 378/428 428 428 378/428 378/428 378/428 Bst UI multi(4) multi(4) 51/65/366 51/65/366 multi(4) multi(4) 51/65 51/65/366 51/366/582 51/366/582 multi(4) Cfr 10I xxx 324 324 xxx xxx xxx xxx xxx xxx xxx xxx Cla I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Dde I 351/472 xxx 472 47Z 351/472/628 351/628 472 472 351/472/628 351/472/628 351/472/628 Dpn I 549 549 497/549 549 549 xxx 549 549 549 549 549 Dpn II 547 547 495/547 547 547 xxx 547 547 547 547 547 Eas I xxx xxx xxx xxx 307 xxx xxx xxx xxx xxx xxx Ear I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Eco 47III xxx xxx xxx xxx xxx xxx xxx xxx xxx 109 xxx Esp 3I xxx xxx xxx xxx xxx xxx 630 xxx xxx xxx xxx Fnu 4HI multi(5) multi(5) 134/382 multi(7) 134/382/583 134/382/583 134/382 multi(4) 134/362/583 134/382/583 134/382 Fok I xxx xxx xxx xxx 610 xxx xxx xxx xxx xxx xxx Hae II 434 434 130/434 434 121/434 434 434 434 121/434 121/434 434 Hae III xxx xxx 541 xxx 309 xxx xxx 55 xxx xxx xxx Hga I 173 173 173 173 173 173 173 173 173 173 173 Hgi AI 112/272 112/272 112/272 112/272 xxx 112 112/272/377 112/272/377 xxx xxx 112 Hhe I 433 433 129/433 433 110/120/433 375/433 433 433 110/120/433 110/120/433 433 Hinc II 116 116/247 116/247 116/247 xxx 116 116 116/247 247 247 388 Hinf I 481 248/481 248/461 248/481 248/481 248/481 248/481 248/481 248/481 248/481 248/481 ENZYME #1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 Hind PI 108/118/431 multi(4) multi(4) 431 108/118/431 431 431 108/118/4 31 431 431 373/431 431 Hpa II 325 325 325 325 325 325 325 325 xxx 325 325 325 Hph I xxx xxx xxx 266 xxx 266/534 266 47/490 xxx 266 xxx 534 Kas I xxx 267 267 xxx xxx xxx xxx xxx xxx xxx xxx xxx Mae I 195/280 195/199 195 195/445 195/280/378 306/465/629 465/629 195/199/629 195/445 629 xxx 280/465/629 Mae III 308 593 593 308 308 308/540 308 496 308 308/333 593 308/540 Mbo I 547 547 547 547/551 547 xxx 547 547 551 495/547 547 547 Mbo II 425/453/527 324/425/453 324/425/453 425/453/527 425/453/52 7 324/425/453 425 227/453 453/527 425 425/453 425 Mlu I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Mnl I multi(4) 282/523/564 282/523/564 282/453/527 multi(4) 523/564 471/523/564 282/523/564 282/510/523 523/564 282/523/564 523/564 Msc I xxx 309 309 xxx xxx 585 xxx 309 xxx xxx 309 xxx Mse I xxx xxx xxx xxx xxx 594 594 xxx xxx 594 xxx 387/594 Msp I 325 325 325 325 325 325 325 325 325 325 325 325 Mun I 66 xxx xxx 147/298 66 xxx xxx xxx 147/298 xxx xxx xxx Nar I xxx 268 268 xxx xxx xxx xxx xxx xxx xxx xxx xxx Nci I 326 xxx xxx 326 326 xxx 326 326 326 326 xxx 326 Nhe I 194 194 194 194 194 xxx xxx 194 194 xxx xxx xxx Nle III 425/442 425/442 425/442 425/442 425/442 425/442 425/442 425/430/442 425/442 425/442 425 425 Nle IV 269/578 269/578 269/578 269/578 269/578 578 578 269/578 269/578 578 578 578 Nru I xxx 65 65 65 xxx xxx 65 65 65 65 65 65 Nsp BII 51/149 51/149/609 51/149/609 609 51/149 51/609 51 51/582/609 582/609 51/609 51/582/609 51/609 Nsp HI 425 425 425 425 425 425 425 425 425 425 425 425 Ple I 242/475 242/475 242/475 242/475 242/475 242/475 242/475 242/415 242/475 242/475 242/475 242/475 Pvu I xxx xxx xxx xxx xxx xxx xxx xxx xxx 498 xxx xxx Pvu II 149 149 149 xxx 149 xxx xxx xxx xxx xxx xxx xxx Rsa I 443 443 443 443 443 443 443 443 443 443 443 443 Sac II 52 52 52 xxx 52 52 52 52/583 583 52 52/583 52 Sau 3aI 547 547 547 547/551 547 xxx 547 547 551 495/547 547 547 Sau 96I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Scr FI 326/378/428 378/428 378/428 326/378/428 306/326/428 378/428 326/428 326/378 326/378/428 326/428 378/428 326/378/428 Sec I 49/376/580 49/376/580 49/376/580 49/376/580 49/580 multi(4) 49/580 49/376/580 49/376/560 49/580 49/376/580 49/376/580 Sfa NI 367 367 367 367 367 367 367 30/367 367 367 367 367 Sfc I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Sfi I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Sty I xxx xxx xxx xxx xxx 472 xxx xxx xxx xxx xxx xxx Taq I 535/550 535/550 535/550 550 535/550 550 535/550 535/550 535 535/550 535/550 535/550 535/550 Tth 111I 297 297 xxx xxx 297 297 xxx 297 xxx 297 297 297 Xba I xxx xxx xxx xxx xxx 464 xxx xxx xxx xxx xxx 464 Xcm I 461 461 461 461 xxx xxx xxx 461 461 461 461 xxx ENZYME #13 #14 #15 #16 #17 #18 #19 #20 NADC-8 NADC-9 REF:V2332 Hind PI 431 431 127/431 431 108/118/431 373/431 431 431 108/118/431 108/118/431 431 Hpa II 325/609 325 325 325 325 xxx 325 325 325 325 325 Hph I 598 534 266 xxx 47/490 xxx 266/534 47/286/534 534 534 xxx Kas I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Mae I 465/529 280/629 629 280/465/829 xxx 280 629 629 195/280 195/280 195 Mae III 308 308/540 308 308 496 308 308/540 308/540 308/540/593 308/540/593 308 Mbo I 547 547 495/547 547 547 xxx 547 547 547 547 547 Mbo II 324/425 425 425 425 425/453 324/425/453 425 425 425/453 425/453 453 Mlu I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx 436 Mnl I 333/523/564 523/564 523/564 523/564 282/523/564 523/584 523/564 486/523/564 282/523/564 282/523/564 282/523/564 Msc I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Mse I 594 387/594 566 387/594 xxx xxx 594 594 xxx xxx xxx Msp I 325/609 325 325 325 325 xxx 325 325 325 325 325 Mun I xxx xxx xxx xxx xxx xxx xxx xxx 66 66 xxx Nar I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Nci I 326 xxx xxx 326 326 xxx 326 326 xxx 326 326 Nhe I xxx xxx xxx xxx xxx xxx xxx xxx 194 194 194 Nle III 425/442 425/442 425/442 425/442 425/442 425/442 425 425 425/442 425/442 425 Nle IV 578 578 578 578 269/578 269/578 578 578 269/578 269/578 269/578 Nru I 65 65 65 65 65 65 65 65 xxx xxx 65 Nsp BII 51/582 51/582/609 51/609 51/609 51/582/609 multi(4) 51/609 51/609 multi(4) 51/149/582 51/149/609 Nsp HI 425 425 425 425 425 425 425 425 425 425 425 Ple I 475 242/475 242/475 242/475 242/475 242/475 242/475 242/475 242/475 242/475 242/475 Pvu I xxx xxx 498 xxx xxx xxx xxx xxx xxx xxx xxx Pvu II xxx xxx xxx xxx xxx xxx xxx xxx 149 149 149 Rsa I 185 443 443 443 443 443 443 443 443 443 443 Sac II 52/583 52/583 52 52 52/583 52/583 52 52 52/583 52/583 52 Sau 3aI 547 547 495/547 547 547 xxx 547 547 547 547 547 Sau 96I xxx xxx xxx xxx xxx xxx xxx 53 xxx xxx xxx Scr FI 326/378/428 378/428 98/378/428 326/378/428 326/428 378/428 326/428 326/428 378/428 326/378/426 326/378/428 Sec I 49/376/580 multi(4) 49/376/480 49/376/580 49/580 multi(4) 49/580 49/580 49/376/580 49/376/580 49/376/580 Sfa NI 367 367 367 367 367 367 367 367 367 367 367 Sfc I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx 144 Sfi I xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx xxx Sty I xxx 472 xxx xxx xxx 472 xxx xxx xxx xxx xxx Taq I 535/550 535/550 535/550 535/550 535/550 535/550 535/550 535/550 535/550 529/535/550 535/550 Tth 111I 297 297 297 297 297 xxx xxx xxx 297 297 297 Xba I 464 xxx xxx 464 xxx Xxx xxx xxx xxx xxx xxx Xcm I xxx 461 461 xxx 461 461 461 461 461 46t 461 TABLE III__________________________________________________________________________Restriction Enzyme Pattern after PRRSV Replication in vivo Sample Duration of PRRSV StrainNo. Type Source Infection Exposure Recovered__________________________________________________________________________1 Lung-Lavage Gilt 7 wks RespPRRS .RTM. RespPRRS .RTM. 2 " " " " " 3 " " " " " 4 " " " NADC-8 NADC-8 5 " Pig-Pig 8 + 3 " " 6 " " 8 + 3 " " 7 " Gilt-Piglet 8 + 5 RespPRRS .RTM. RespPRRS .RTM.__________________________________________________________________________

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Bautista E M, Goyal S M, Collins J E (1993) Serologic survey for Lelystad and VR-2332 strains of porcine respiratory and reproductive syndrome (PRRS) virus in US swine herds. J Vet Diagn Invest 5:621-614.

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Meulenberg J J M, Hulst M M, De Meijer E J, Moonen P L J M, Den Besten A, De Kluyver E P, Wensvoort G, Moormann R J M (1993) Lelystad virus, the causative agent of porcine epidemic abortion and respiratory syndrome (PEARS), is related to LVD and EAV. Virology 192:62-72.

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Wensvoort G, Terpstra C, Pol J M A, ter Laak E A, Bloemraad M, de Kluyver E P, Kragten C, Van Buiten K L, den Besten A, Wagenaar F, Broekhuijsen J M, Moonen P L J M, Zetsstra T, de Boer E A, Tibben H J, de Jong M F, van't Veld P, Groenland G J R, van Gennep J A, Voets M T, Verheijden J H M, Braamskamp J (1991) Mystery swine disease in the Netherlands: the isolation of Lelystad virus. Vet. Q. 13:121-130.

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__________________________________________________________________________# SEQUENCE LISTING - - - - (1) GENERAL INFORMATION: - - (iii) NUMBER OF SEQUENCES: 27 - - - - (2) INFORMATION FOR SEQ ID NO:1: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 46448(IA) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: - - ATGTTGGGTA AATGCTTGAC CGCGGGCTGT TGCTCGCAAT TGCTTTTTTG GT -#GGTGTATC 60 - - GTGCCGTCTT GTTTTGTTGC GCTCGTCAGC GCCAACGGGA ACAGCAGCTC AA -#ATTTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ATAAATTT 180 - - GACTGGGCAG TGGAGTGTTT TGTCATTTTT CCCGTGTTGA CTCACATTGT CT -#CTTATGGT 240 - - GCCCTCACTA CTAGCCATTT CCTTGACACA GTCGGTCTGG TCACTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGTT TGCGAAGAAT TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTCATC 480 - - ATAGAGAAGA GGGGTAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTATAACC AAAGTTTCAG CAGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:2: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 46907(KY) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCCT GTTTTGTTGC GCTCGTCAGC GCCAACAGCA ACAGCAGCTC CC -#ATTTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#GTAGATTT 180 - - GATTGGGCAG TGGAGTGTTT TGTCATCTTT CCTGTGCTGA CTCACATTGT CT -#CCTATGGC 240 - - GCCCTCACTA CCAGCCATTT CCTTGACACA GTCGGTCTGG CCACTGTGTC TA -#CCGCCGGT 300 - - TTTCTTCGCG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - TTTTGCTTCG TCATTAGATT GGCGAAGAAT TGCATGTCCT GGCGCTATTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA TACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTCATC 480 - - ATAGAGAAAA AGGGTAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA GA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTGTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:3: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 1205-D(MO) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCCT GTTTTGTTGC GCTCGTCAGC GCCAACAGCA ACAGCAGCTC TC -#ATTTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ATAAATTT 180 - - GATTGGGCAG TGGAATGTTT TGTCATCTTT CCTGTGCTGA CTCACATTGT CT -#CCTATGGC 240 - - GCCCTCACTA CCAGCCATTT CCTTGACACA TTCGGTCTGG CCACTGTGTC TA -#CCGCCGGT 300 - - TTTCTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - TTTTGCTTCG TCATTAGATT TGCGAAGAAT TGCATGTCCT GGCGCTATTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA TACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTCATC 480 - - ATAGAGAAAA AGGGTAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA GA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTGTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:4: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 10654(IA) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCAAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCTT GTCTTGTTGC GCTCGTCAGC GCCAACGGGA ACAGCAGCTC AA -#ATTTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ATAAATTT 180 - - GACTGGGCAG TGGAGTGTTT TGTCATTTTT CCCGTGTTGA CTCACATTGT CT -#CTTACGGT 240 - - GCCCTCACTA CTAGCCATTT CCTTGACACA GTCGGCCTGG TCACTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT AG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGTT TGCGAAGAAT TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACTAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTCATC 480 - - ATAGAGAAGA GGGGTAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCCA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTATAACC AGAGTTTCAG CAGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:5: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 30093-A(IL) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCAAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCTT GTCTTGTTGC GCTCGTCAGC GCCAACGGGA ACAGCAGCTC AA -#ATTTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ATAAATTT 180 - - GACTGGGCAG TGGAGTGTTT TGTCATTTTT CCCGTGTTGA CTCACATTGT CT -#CTTACGGT 240 - - GCCCTCACTA CTAGCCATTT CCTTGACACA GTCGGCCTGG TCACTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT AG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGTT TGCGAAGAAT TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACTAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTCATC 480 - - ATAGAGAAGA GGGGTAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCCA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTATAACC AGAGTTTCAG CAGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:6: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 34075(NE) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTTGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT TTTTTGCTGT GCTCGTCAAC GCCAACAGCA CCAGCAGCTC CC -#ATTTGCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGGC TA -#ATAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTTATTTTT CCCGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACCA CCAGCCATTT CCTTGACACA GTCGGTCTAG TTACTGTGTC CA -#CCGCCGGT 300 - - TTTCTTCACG GGCGGTATGT CTTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - GTTTGCTTCG GCATTAGGTT TGCGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTAGA CACCAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTCATC 480 - - ATAGAGAAAA GGGGTAAGGT TGAGGTCGCA GGTCACCTAA TCGACCTCCA AA -#GAGTTGTG 540 - - CCTGATGGTT CCGTGGCCAC TCCTTTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:7: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 49138(TX) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGTCAAC GCCAACAGCA ACAGCAGCTC TC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ACTGGCTGGC TA -#ACAAATTT 180 - - GATTGGGCAG TGGAGACTTT TGTCATCTTT CCCGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACCA CCAGCCATTT CCTTGACACA GTTGGTCTGG TTACTGTGTC CA -#CCGCCGGG 300 - - TTTTATCACG GGCGGTATGT CTTGAGTAGC ATCTACGCGG TCTGTGCTCT GG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGTT TGCGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TCCTCCTAGA TACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTTATC 480 - - ATAGAGAAAG GGGGTAAGGT TGAGGTCGAA GGCCACCTGA TCGACCTCCA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC TCCTTTAACC AGAGTTTCAG CAGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:8: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and Respiratory Virus (B) STRAIN: 5556(MI) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8: - - ATGTTGGTGA GATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCCT GTTTTGTTGC GCTCGTCAGC GCCAACATAA GCAGCAGCTC TC -#ATTCACAG 120 - - TTGATTTACA ACCTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#GTAAATTT 180 - - GATTGGGCAG TGGAGTGCTT TGTCATCTTC CCTGTGCTGA CTCACATTGT CT -#CCTATGGT 240 - - GCCCTCACTA CCAGCCATTT TCTTGACACA GTCGGTCTGG CCACTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - ATTTGCTTCG TCATCAGGTT TGTGAAAAAT TGCATGTCAT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC AC -#CTGTCATC 480 - - ATAGAGAAAA AGGGTAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA GA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC CCCTATAACC AGAGTTTCAG CGGAACAATG GG -#GTCATCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:9: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 22805(KS) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9: - - ATGTTGGGGA AATGCTTGAC CGTGGGCTGT TGCTCGCGAT TGCCTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGCCAAC GCTCACGGCA ACAGCAGCTC TC -#ATCTGCAA 120 - - TTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TG -#ATAGATTT 180 - - GATTGGGCAG TGGAGAGCTT TGTCATCTTT CCTGTTTTGA CTCACATTGT CT -#CCTATGGT 240 - - GCCCTCACTA CCAGCCATTT CCTTGACACA ATTGCTTTAG TCACTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACA GGCGGTATGT CCTGAGTAGC ATCTACGCAG TCTGTGCCCT GG -#CTGCGTTG 360 - - ACTTGCTTCG TCATTAGGTT TGTAAAGAAT TGCATGTCCT GGCGCTACTC AT -#GTACTAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTCATC 480 - - ATAGAGAAGA GGGGCAAGGT TGAGGTCGAA GGTCATCTGA TTGATCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC CCCTATAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:10: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 5591(NC) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10: - - ATGTTGGGGA AATGCTTGAC CGCGGATTGT TGCTCGCGAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GGTTTGCTGT GCTCGGCAAC GCCAACAGCA CCAGCAGCTC TC -#ACTTACAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGTTGGC TA -#ACAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTTATTTTT CCCGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACCA CCAGCCATTT CCTTGACACA GTCGGTCTGG TTACTGTGTC TA -#CCGCCGGG 300 - - TTTTGTCACG GGCGGTATGT CTTGAGTAGC ATCTACGCGG TCTGTGCTCT GG -#CCGCGTTG 360 - - ATTTGTTTCG TCATCAGGTT TGCGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TCCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGATC GC -#CTGTCATC 480 - - ATAGAGAAAG GGGGTAAGGT TGAGGTCGAA GGCCATCTGA TCGACCTCCA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTTTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:11: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 14622(AR) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTCTTT GT -#GGTTTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGTCAAC GCCAACAGCA ACAGCAGCTC TC -#ATTCACAG 120 - - TTGATTTATA ACCTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGGC TA -#ATAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTCATCTTT CCTGTGCTGA CTCACATTGT CT -#CTTATAGT 240 - - GCCCTCACTA CCAGCCATTT CCTTGACACA GTCGGTCTGG CCACTGTGTC TA -#CCGCCGGA 300 - - TTTGTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGCGCCCT GG -#CTGCGTTG 360 - - ATTTGCTTCA TCATCAGGTT TGCGAAGAAT TGCATGTCCT GGCGCTACTC TT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTCATC 480 - - ATAGAGAAAA GGGGCAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA GA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC CCCTGTAACC AAAGTTTCAG CGGAACAATG GG -#GTCATCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:12: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 19950-E(MN) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGTCAAC GCCAACAGCA GCAGCAGCTC TC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGGC TG -#AGAAATTT 180 - - GATTGGGCGG TGGAAAGTTT TGTCATTTTT CCCGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACTA CTAGCCATTT TCTTGACACA GTCGGTCTGG TTACTGTGTC TA -#CCGCCGGG 300 - - TTTTGGCACG GGCGGTATGT CTTGAGCAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTA 360 - - ATTTGCTTTG TCATTAGGCT TGCGAAGAAC TGCATGTCCT GGCGCTACTC TT -#GTACCAGA 420 - - TATACTAACT TCCTTCTAGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTTATC 480 - - ATAGAGAAAG GGGGTAAGGT TGAGGTCGAA GGTCACCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTTTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:13: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 26948-2(VA) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCCTTTTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGGTGT GCTCGTCAAC GCCAACAGCA GCAGCAGCTC TC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGTACAG ATTGGCTGGC AG -#GAAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTCATTTTT CCCGTGCTGA CCCACATTGT TT -#CCTATGGT 240 - - GCACTTACTA CCAGCCATTT CCTTGACACA GTCGGTCTGG TTACCGTGTC TA -#CCGCCGGG 300 - - TTTCTTCACG GGAGGTATGT CCTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGCT TGCGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GCACCAGA 420 - - TATACCAACT TCCTTCTAGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTTATC 480 - - ATAGAAAAAA AAGGTAAGGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC TCCTTTAACC AGAGTTTCAC CGGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:14: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 41572-2(NE) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GGTTTGCTGT GCTCGTCAAC GCCAGCAGCA ACAGCAGCTC TC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGGC TA -#ATAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTCATCTTT CCTGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACTA CTAGCCATTT CCTTGACACA GTCGGTCTGG TTACTGTGTC CA -#CCGCCGGT 300 - - TTTTTTCACG GGCGGTATGT CTTGAGCAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTA 360 - - ATTTGCTTTG TCATTAGGCT TGCGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TCCTTCTGGA CACCAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTTATC 480 - - ATAGAGAAAA GGGGTAAGGT TGAGGTCGAA GGTCACCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCTAC CCCTTTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:15: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 42928(IL) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTCCT GGTTTGCTGT GCTCGTCAAC GCCAACAGCG CCAGCAGCTC TC -#ATTTGCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGTTGGC TG -#ACAAGTTT 180 - - GATTGGGCAG TGGAGACTTT TGTTCTTTAT CCCGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACCA CCAGCCATTT CCTTGACACA GTCGGTCTGG TTACTGTGTC CA -#CCGCCGGT 300 - - TTTGTTCACG GGCGGTATGT CTTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - AGTTGTTTTG TCATCAGGTT TGTGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TCCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGATC GC -#CTGTCATC 480 - - ATAGAGAAAG GGGGTAAGGT TGAGGTCGAA GGCCATCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTTTAACC AGAGTTTCAG CGGAACGATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:16: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 32983-LG(NC) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGC TGCTCGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGTCAAC GCCAACAGCA GCAGCAGCTC TC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGGC TG -#GGGAATTT 180 - - GATTGGGCGG TGGAAAGTTT TGTCATTTTT CCCGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACTA CTAGCCATTT TCTTGACACA GTCGGTCTGG TTACTGTGTC TA -#CCGCCGGG 300 - - TTTTTGCACG GGCGGTATGT CTTGAGCAGC ATCTACGCGG TTTGTGCCCT GG -#CTGCGTTA 360 - - ATTTGCTTTG TCATTAGGCT TGCGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACTAACT TCCTTCTAGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTTATC 480 - - ATAGAGAAAG GGGGTAAGGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTTTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:17: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 30352-3(MI) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17: - - ATGTTGGTGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCCT GTTTTGTTGC GCTCGTCAGC GCCAACGCCA ACAGCAGCTC CC -#ATTCACAG 120 - - TTGATTTACA ACCTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGTC TA -#ATAAATTT 180 - - GATTGGGCAG TGGAGTGTTT TGTCATCTTT CCTGTGCTGA CTCACATTGT CT -#CCTATGGT 240 - - GCCCTCACTA CCAGCCATTT CCTTGACACA GTCGGTCTGG CCGTTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT TG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGATT TGCGAAGAAT TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC AC -#CTGTCATC 480 - - ATAGAGAAAA GGGGTAAAGT TGAGGTCGAA GGTAATCTGA TCGACCTCAA GA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC CCCTATAACC AAAGTTTCAG CGGAACAATG GG -#GTCATCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:18: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 47324-2(CAN) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCCT GTTTTGTTGT GCTCGTCAAC GCCAACAACA GAAGCAGCTC CC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGGC TG -#ATAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTCATCTTT CCCGTTTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCCCTAACCA CTAGCCATTT TCTTGACACA GTTGGTCTGG TTACTGTGTC TA -#CCGCTGGT 300 - - TTTCTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGCGCCCT GG -#CTGCGTTG 360 - - ATTTGCTTTG TCATTAGGTT CGTGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - CATACCAACT TTCTTCTGGA TACCAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTCATC 480 - - ATAGAGAAAG GGGGTAAAGT TGAGGTCGAA GGTCATCTCA TCGACCTCAA GA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC CCCTATAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:19: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 18310-A(PA) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGTCAAC GCCAACAGCA ACAGCAGCTC TC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ACTGGCTGGC TA -#ACAAATTT 180 - - GATTGGGCAG TGGAGACTTT TGTCATTTTT CCCGTATTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACCA CCAGCCATTT CCTTGACACA GTTGGTCTGG TTACTGTGTC CA -#CCGCCGGG 300 - - TTTTATCACG GGCGGTATGT CTTGAGTAGC ATCTATGCGG TCTGTGCTCT GG -#CTGCGTTG 360 - - TTTTGCTTCG TCATTAGGCT TGCGAAGAAC TGCATGTCCT GGCGCTACTC TT -#GTACCAGA 420 - - TATACCAACT TCCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CCGTTATT 480 - - ATAGAGAAAG GGGGTAAGGT TGAGGTCGAA GGTCACCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTTTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCTC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:20: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 24901(GUA) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20: - - ATGTTGGTGA AATGCTTGAC CGCGGGCCGT TGCTCGCGAT TGCCTTTTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGTCAAC GCCAACAGCA GCAGCAGCTC TC -#ATTTTCAG 120 - - TTGATTTATA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTGGC TG -#ACAAATTT 180 - - GATTGGGCAG TAGAGACTTT TGTCATCTTT CCCGTGTTGA CTCACATTGT TT -#CCTATGGT 240 - - GCACTCACCA CCAGCCATTT CCTTGACACA GTTGGTCTGG TTACTGTGTC CA -#CCGCCGGG 300 - - TTTTATCACG GGCGGTATGT CTTGAGTAGC ATCTACGCGG TCTGTGCTCT GG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGCT TGCGAAGAAC TGCATGTCCT GGCGCTACTC TT -#GTACCAGA 420 - - TATACCAACT TCCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGAGGTC GC -#CCGTTATC 480 - - ATAGAGAAAG GGGGTAAGGT TGAGGTCGAA GGTCACCTGA TCGACCTCCA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTTTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCC 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:21: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: NADC-8(IA) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21: - - ATGTTGGGGA AATGCTTGAC CGCGGGCTGT TGCTCGCAAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGCCGTCTT GTTTTGTTGC GCTCGTCAGC GCCAACAGCA ACAGCAGCTC AA -#ATTTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ATAAATTT 180 - - GACTGGGCAG TGGAGTGTTT TGTCATCTTT CCTGTGTTGA CTCACATTGT CT -#CTTATGGT 240 - - GCCCTCACTA CTAGCCATTT CCTTGACACA GTCGGTCTGG TCACTGTGTC CA -#CCGCCGGA 300 - - TTTTTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGCT TGCGAAGAAT TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTCATC 480 - - ATAGAGAAAA GGGGCAAAGT TGAGGTCGAA GGTCACCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC CCCTGTAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:22: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: NADC-9(IA) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22: - - ATGTTGGTGA AATGCTTGAC CGCGGGCTGT TGCTCGCAAT TGCTTTTTTT GT -#GGTGTATC 60 - - GTGTCGTCCT GTTTTGTAGC GCTCGTCAGC GCCAACACGA CCAGCAGCTC AA -#ATTTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ATAAATTT 180 - - GACTGGGCAG TGGAGTGTTT TGTCATTTTT CCTGTGTTGA CTCACATTGT CT -#CTTATGGT 240 - - GCCCTCACTA CTAGCCATTT CCTTGACACA GTCGGTCTGG TCACTGTGTC CA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT TCTGAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - ATTTGCTTCG TCATTAGGCT TGCGAAGAAC TGCATGTCCT GGCGCTACTC AT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTCATC 480 - - GTAGAGAAAA GGGGCAAGGT CGAGGTCGAA GGTCACCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGCGGCAAC TCCTGTAACC AGAATTTCAT CAGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:23: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: RespPRRS - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:23: - - ATGTTGGAGA AATGCTTGAC CGCGGGCTGT TGCTCGCAAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGCCAAC GCCAGCAACG ACAGCAGCTC CC -#ATCTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ACAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTCATCTTT CCCGTTTTGA CTCACATTGT CT -#CCTATGGT 240 - - GCCCTCACTA CCAGCCATTT CCTTGACACA GTCGCTTTAG TCACTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT CCTAAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - ACTTGCTTCG TCATTAGGTT TGCAAAGAAT TGCATGTCCT GGCGCTACGC GT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC GGACTCTATC GTTGGCGGTC GC -#CTGTCATC 480 - - ATAGAGAAAA GGGGCAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTATAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:24: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 603 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: 2332(MN) - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24: - - ATGTTGGAGA AATGCTTGAC CGCGGGCTGT TGCTCGCGAT TGCTTTCTTT GT -#GGTGTATC 60 - - GTGCCGTTCT GTTTTGCTGT GCTCGCCAAC GCCAGCAACG ACAGCAGCTC CC -#ATCTACAG 120 - - CTGATTTACA ACTTGACGCT ATGTGAGCTG AATGGCACAG ATTGGCTAGC TA -#ACAAATTT 180 - - GATTGGGCAG TGGAGAGTTT TGTCATCTTT CCCGTTTTGA CTCACATTGT CT -#CCTATGGT 240 - - GCCCTCACTA CCAGCCATTT CCTTGACACA GTCGCTTTAG TCACTGTGTC TA -#CCGCCGGG 300 - - TTTGTTCACG GGCGGTATGT CCTAAGTAGC ATCTACGCGG TCTGTGCCCT GG -#CTGCGTTG 360 - - ACTTGCTTCG TCATTAGGTT TGCAAAGAAT TGCATGTCCT GGCGCTACGC GT -#GTACCAGA 420 - - TATACCAACT TTCTTCTGGA CACTAAGGGC AGACTCTATC GTTGGCGGTC GC -#CTGTCATC 480 - - ATAGAGAAAA GGGGCAAAGT TGAGGTCGAA GGTCATCTGA TCGACCTCAA AA -#GAGTTGTG 540 - - CTTGATGGTT CCGTGGCAAC CCCTATAACC AGAGTTTCAG CGGAACAATG GG -#GTCGTCCT 600 - - TAG - # - # - # 603 - - - - (2) INFORMATION FOR SEQ ID NO:25: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: YES - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:25: - - CCATTCTGTT GGCAATTTGA - # - # - # 20 - - - - (2) INFORMATION FOR SEQ ID NO:26: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: YES - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26: - - GGCATATATC ATCACTGGCG - # - # - # 20 - - - - (2) INFORMATION FOR SEQ ID NO:27: - - (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 716 base - #pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: double (D) TOPOLOGY: linear - - (ii) MOLECULE TYPE: cDNA - - (iii) HYPOTHETICAL: NO - - (iv) ANTI-SENSE: NO - - (vi) ORIGINAL SOURCE: (A) ORGANISM: Porcine R - #eproductive and RespiratorySyndrome Virus (B) STRAIN: RespPRRS - - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27: - - CCATTCTGTT GGCAATTTGA ATGTTTAAGT ATGTTGGAGA AATGCTTGAC CG -#CGGGCTGT 60 - - TGCTCGCAAT TGCTTTCTTT GTGGTGTATC GTGCCGTTCT GTTTTGCTGT GC -#TCGCCAAC 120 - - GCCAGCAACG ACAGCAGCTC CCATCTACAG CTGATTTACA ACTTGACGCT AT -#GTGAGCTG 180 - - AATGGCACAG ATTGGCTAGC TAACAAATTT GATTGGGCAG TGGAGAGTTT TG -#TCATCTTT 240 - - CCCGTTTTGA CTCACATTGT CTCCTATGGT GCCCTCACTA CCAGCCATTT CC -#TTGACACA 300 - - GTCGCTTTAG TCACTGTGTC TACCGCCGGG TTTGTTCACG GGCGGTATGT CC -#TAAGTAGC 360 - - ATCTACGCGG TCTGTGCCCT GGCTGCGTTG ACTTGCTTCG TCATTAGGTT TG -#CAAAGAAT 420 - - TGCATGTCCT GGCGCTACGC GTGTACCAGA TATACCAACT TTCTTCTGGA CA -#CTAAGGGC 480 - - GGACTCTATC GTTGGCGGTC GCCTGTCATC ATAGAGAAAA GGGGCAAAGT TG -#AGGTCGAA 540 - - GGTCATCTGA TCGACCTCAA AAGAGTTGTG CTTGATGGTT CCGTGGCAAC CC -#CTATAACC 600 - - AGAGTTTCAG CGGAACAATG GGGTCGTCCT TAGATGACTT CTGTCATGAT AG -#CACGGCTC 660 - - CAGAAAAGGT GCTTTTGGCG TTTTCTATTA CCTACACGCC AGTGATGATA TA - #TGCC 716__________________________________________________________________________

Claims

1. A method for differentiating any one of a first North American strain of Porcine ReproductiVe and Respiratory Syndrome Virus (PRRSV) from any one of a second North American strain of said virus wherein said first and second North American strains are selected from the pool of all known North American strains of PRRSV comprising the steps:

a. reverse transcribing and amplifying the ORP 5 region of said first strain to produce an amplified cDNA of said region;

b. selecting from a matrix of ORF-5 restriction enzyme patterns for said known North American strains of PRRSV at least one restriction enzyme which yields a distinctive fragment profile from said cDNA as compared to a fragment profile of a corresponding cDNA from said second strain;

c. cleaving the ORF 5 cDNA of said first strain with said at least one restriction enzyme;

d. comparing the restriction enzyme fragment pattern resulting from step (c) with the restriction enzyme fragment pattern produced by digesting the cDNA from said second strain with the same enzyme used in step (c); and

e. differentiating said first North American strain of PRRSV from said second North American strain of PRRSV based on the comparing in step (d).

2. The method of claim 1 wherein one of said strains is the vaccine strain of PRRSV characterized by an ORF 5 having SEQ ID NO:23.

3. The method as described in claim 2 wherein said restriction enzyme is selected from the group consisting of Mlu I and Sfc I.

4. The method as described in claim 1 wherein said restriction enzyme is selected from the group consisting of Mlu I, Sfc I, Hinc II and Sac II.

5. The method of claim 1 wherein said reverse transcribing and amplifying in step (a) is conducted using a universal set of primers for all combinations of first and second strains of PRRSV selected from the set of all North American strains of PRRSV.

6. A kit for differentiating a first North American strain of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) from a second North American strain of said virus comprising a pair of primers for amplifying ORP 5 cDNA from said first strain and at least one first restriction enzyme which yields a distinctive fragment profile for the ORF 5 cDNA from each of said first and second strains, wherein said first restriction enzyme is selected from the group consisting of MIu I and Sfc I.

7. The kit of claim 6 wherein said primers have the sequence of SEQ ID NO:25 and SEQ ID NO:26.

8. The kit of claim 6 further comprising at least one second restriction enzyme selected from the group consisting of Hinc II and Sac II.

9. The kit of claim 8 comprising three of said restriction enzymes.