Causative agent of the mystery Swine disease, vaccine compositions and diagnostic kits

Abstract

Composition of matter comprising the causative agent of Mystery Swine Disease, Lelystad Agent, in a live, attenuated, dead, or recombinant form, or a part or component of it. Vaccine compositions and diagnostic kits based thereon. Recombinant nucleic acid comprising a Lelystad Agent-specific nucleotide sequence. Peptides comprising a Lelystad Agent-specific amino acid sequence. Lelystad Agent-specific antibodies.

Description

TECHNICAL FIELD

[0002] The invention relates to the isolation, characterization and utilization of the causative agent of the Mystery Swine Disease (MSD). The invention utilizes the discovery of the agent causing the disease and the determination of its genome organization, the genomic nucleotide sequence and the proteins encoded by the genome, for providing protection against and diagnosis of infections, in particular, protection against and diagnosis of MSD infections, and for providing vaccine compositions and diagnostic kits, either for use with MSD or with other pathogen-caused diseases.

BACKGROUND

[0003] In the winter and early spring of 1991, the Dutch pig industry was struck by a sudden outbreak of a new disease among breeding sows. Most sows showed anorexia, some aborted late in gestation (around day 110), showed stillbirths or gave birth to mummified fetuses and some had fever. Occasionally, sows with bluish ears were found, therefore, the disease was commonly named “Abortus Blauw”. The disease in the sows was often accompanied by respiratory distress and death of their young piglets and often by respiratory disease and growth retardation of older piglets and fattening pigs.

[0004] The cause of this epizootic was not known, but the symptoms resembled those of a similar disease occurring in Germany since late 1990, and resembled those of the so-called “Mystery Swine Disease” as seen since 1987 in the mid-west of the United States of America and in Canada (Hill, 1990). Various other names have been used for the disease; in Germany it is known as “Seuchenhafter Spätabort der Schweine” and in North America it is also known as “Mystery Pig Disease”, “Mysterious Reproductive Syndrome”, and “Swine Infertility and Respiratory Syndrome”. In North America, Loula (1990) described the general clinical signs as:

[0005] 1) off feed, sick animals of all ages;

[0006] 2) abortions, stillbirths, weak pigs, mummies;

[0007] 3) post-farrowing respiratory problems; and

[0008] 4) breeding problems.

[0009] No causative agent has as yet been identified, but encephalomyocarditis virus (“EMCV”), porcine parvo virus (“PPV”), pseudorabies virus (“PRV”), swine influenza virus (“SIV”), bovine viral diarrhea virus (“BVDV”), hog cholera virus (“HCV”), porcine entero viruses (“PEV”), an influenza-like virus, chlamidiae, leptospirae, have all been named as a possible cause (Loula, 1990; Mengeling and Lager, 1990; among others).

SUMMARY OF THE INVENTION

[0010] The invention provides a composition of matter comprising isolated Lelystad Agent which is the causative agent of Mystery Swine Disease, the Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Collection Nationale de Cultures De Microorganismes (C.N.C.M.) 25, rue du Docteur Roux, 75724 -Paris Cedex 15, France, deposit number I-1102. The words “essentially corresponding” refer to variations that occur in nature and to artificial variations of Lelystad Agent, particularly those which still allow detection by techniques like hybridization, PCR and ELISA, using Lelystad Agent-specific materials, such as Lelystad Agent-specific DNA or antibodies.

[0011] The composition of matter may comprise live, killed, or attenuated isolated Lelystad Agent; a recombinant vector derived from Lelystad Agent; an isolated part or component of Lelystad Agent; isolated or synthetic protein (poly)peptide, or nucleic acid derived from Lelystad Agent; recombinant nucleic acid which comprises a nucleotide sequence derived from the genome of Lelystad Agent; a (poly)peptide having an amino acid sequence derived from a protein of Lelystad Agent, the (poly)peptide being produced by a cell capable of producing it due to genetic engineering with appropriate recombinant DNA; an isolated or synthetic antibody which specifically recognizes a part or component of Lelystad Agent; or a recombinant vector which contains nucleic acid comprising a nucleotide sequence coding for a protein or antigenic peptide derived from Lelystad Agent.

[0012] On the DNA level, the invention specifically provides a recombinant nucleic acid, more specifically recombinant DNA, which comprises a Lelystad Agent-specific nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) which includes FIGS. 1a ; through 1q. Preferably, the Lelystad Agent-specific nucleotide sequence is selected from any one of the ORFs (Open Reading Frames) shown in FIG. 1 (SEQ ID NO: 1).

[0013] On the peptide/protein level, the invention specifically provides a peptide comprising a Lelystad Agent-specific amino acid sequence shown in FIG. 1 (SEQ ID NO: 1).

[0014] The invention further provides a vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against Mystery Swine Disease, comprising Lelystad Agent, either live, killed, or attenuated; or a recombinant vector which contains nucleic acid comprising a nucleotide sequence coding for a protein or antigenic peptide derived from Lelystad Agent; an antigenic part or component of Lelystad Agent; a protein or antigenic polypeptide derived from, or a peptide mimicking an antigenic component of, Lelystad Agent; and a suitable carrier or adjuvant.

[0015] The invention also provides a vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against a disease caused by a pathogen, comprising a recombinant vector derived from Lelystad Agent, the nucleic acid of the recombinant vector comprising a nucleotide sequence coding for a protein or antigenic peptide derived from the pathogen, and a suitable carrier or adjuvant.

[0016] The invention further provides a diagnostic kit for detecting nucleic acid from Lelystad Agent in a sample, in particular a biological sample such as blood or blood serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising a nucleic acid probe or primer which comprises a nucleotide sequence derived from the genome of Lelystad Agent, and suitable detection means of a nucleic acid detection assay.

[0017] The invention also provides a diagnostic kit for detecting antigen from Lelystad Agent in a sample, in particular a biological sample such as blood or blood serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising an antibody which specifically recognizes a part or component of Lelystad Agent, and suitable detection means of an antigen detection assay.

[0018] The invention also provides a diagnostic kit for detecting an antibody which specifically recognizes Lelystad Agent in a sample, in particular a biological sample such as blood or blood serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising Lelystad Agent; an antigenic part or component of Lelystad Agent; a protein or antigenic polypeptide derived from Lelystad Agent; or a peptide mimicking an antigenic component of Lelystad Agent; and suitable detection means of an antibody detection assay.

[0019] The invention also relates to a process for diagnosing whether an animal, in particular a mammal, more in particular a pig or swine, is contaminated with the causative agent of Mystery Swine Disease, comprising preparing a sample, in particular a biological sample such as blood or blood serum, sputum, saliva, or tissue, derived from the animal, and examining whether it contains Lelystad Agent nucleic acid, Lelystad Agent antigen, or antibody specifically recognizing Lelystad Agent, the Lelystad Agent being the causative agent of Mystery Swine Disease and essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

DETAILED DESCRIPTION OF THE INVENTION

[0020] The invention is a result of combined efforts of the Central Veterinary Institute (CVI) and the Regional Animal Health Services (RAHS) in the Netherlands in trying to find the cause of the new disease MSD. Farms with pigs affected by the new disease were visited by field veterinarians of the RAHS. Sick pigs, specimens of sick pigs, and sow sera taken at the time of the acute and convalescent phase of the disease were sent for virus isolation to the RAHS and the CVI. Paired sera of affected sows were tested for antibodies against ten known pig-viruses. Three different viruses, encephalomyocarditis virus, porcine entero virus type 2, porcine entero virus type 7, and an unknown agent, Lelystad Agent (LA), were isolated. Sows which had reportedly been struck with the disease mainly seroconverted to LA, and rarely to any of the other virus isolates or the known viral pathogens. In order to reproduce MSD experimentally, eight pregnant sows were inoculated intranasally with LA at day 84 of gestation. One sow gave birth to seven dead and four live but very weak piglets at day 109 of gestation; the four live piglets died one day after birth. Another sow gave birth at day 116 to three mummified fetuses, six dead piglets and three live piglets; two of the live piglets died within one day. A third sow gave birth at day 117 to two mummified fetuses, eight dead and seven live piglets. The other sows farrowed around day 115 and had less severe reproductive losses. The mean number of live piglets from all eight sows at birth was 7.3 and the mean number of dead piglets at birth was 4.6. Antibodies directed against LA were detected in 10 out of 42 serum samples collected before the pigs had sucked. LA was isolated from three piglets that died shortly after birth. These results justify the conclusion that LA is the causal agent of mystery swine disease.

[0021] LA grows with a cytopathic affect in pig lung macrophages and can be identified by staining in an immuno-peroxidase-monolayer assay (IPMA) with post-infection sera of pigs c 829 and b 822, or with any of the other post-infection sera of the SPF pigs listed in table 5. Antibodies to LA can be identified by indirect staining procedures in IPMA. LA did not grow in any other cell system tested. LA was not neutralized by homologous sera, or by sera directed against a set of known viruses (Table 3). LA did not haemagglutinate with the red blood cells tested. LA is smaller then 200 nm since it passes through a filter with pores of this size. LA is sensitive to chloroform. The above results show that Lelystad Agent is not yet identified as belonging to a certain virus group or other microbiological species. It has been deposited Jun. 5, 1991 under number I-1102 at Institute Pasteur, France.

[0022] The genome organization, nucleotide sequences, and polypeptides derived therefrom, of LA have now been found. These data together with those of others (see below) justify classification of LA (hereafter also called Lelystad Virus or LV) as a member of a new virus family, the Arteriviridae. As prototype virus of this new family we propose Equine Arteritis Virus (EAV), the first member of the new family of which data regarding the replication strategy of the genome and genome organization became available (de Vries et al., 1990, and references therein). On the basis of a comparison of our sequence data with those available for Lactate Dehydrogenase-Elevating Virus (LDV; Godeny et al., 1990), we propose that LDV is also a member of the Arteriviridae.

[0023] Given the genome organization and translation strategy of Arteriviridae, it seems appropriate to place this new virus family into the superfamily of coronaviruses (Snijder et al., 1990a).

[0024] Arteriviruses have in common that their primary target cells in respective hosts are macrophages. Replication of LDV has been shown to be restricted to macrophages in its host, the mouse; whereas this strict propensity for macrophages has not been resolved yet for EAV and LV.

[0025] Arteriviruses are spherical enveloped particles having a diameter of 45-60 nm and containing an icosahedral nucleocapsid (Brinton-Darnell and Plagemann, 1975; Horzinek et al., 1971; Hyllseth, 1973).

[0026] The genome of Arteriviridae consists of a positive stranded polyadenylated RNA molecule with a size of about 12-13 kilobases (kb) (Brinton-Darnell and Plageman, 1975; van der Zeijst et al., 1975). EAV replicates via a 3′ nested set of six subgenomic mRNAs, ranging in size from 0.8 to 3.6 kb, which are composed of a leader sequence, derived from the 5′ end of the genomic RNA, which is joined to the 3′ terminal body sequences (de Vries et al., 1990).

[0027] Here we show that the genome organization and replication strategy of LV is similar to that of EAV, coronaviruses and toroviruses, whereas the genome sizes of the latter viruses are completely different from those of LV and EAV.

[0028] The genome of LV consists of a genomic RNA molecule of about 14.5 to 15.5 kb in length (estimated on a neutral agarose gel), which replicates via a 3′ nested set of subgenomic RNAs. The subgenomic RNAs consist of a leader sequence, the length of which is yet unknown, which is derived from the 5′ end of the genomic RNA and which is fused to the body sequences derived from the 3′ end of the genomic RNA (FIG. 2).

[0029] The nucleotide sequence of the genomic RNA of LV was determined from overlapping cDNA clones. A consecutive sequence of 15,088 bp was obtained covering nearly the complete genome of LV (FIG. 1, SEQ ID NO: 1). In this sequence 8 open reading frames (ORFs) were identified: ORF 1A, ORF 1B, and ORFs 2 to 7.

[0030] ORF 1A and ORF 1B are predicted to encode the viral replicase or polymerase (SEQ ID NO: 2 and SEQ ID NO: 3), whereas ORFs 2 to 6 are predicted to encode structural viral membrane (envelope) associated proteins (SEQ ID NOS: 4-8). ORF 7 is predicted to encode the structural viral nucleocapsid protein (SEQ ID NO: 9).

[0031] Because the products of ORF 6 and ORF 7 of LV (SEQ ID NO: 8 and SEQ ID NO: 9) show a significant similarity with VpX and Vp1 of LDV, respectively, it is predicted that the sequences of ORFs 6 and 7 will also be highly conserved among antigenic variants of LV.

[0032] The complete nucleotide sequence of FIG. 1 (SEQ ID NO: 1) and all the sequences and protein products encoded by ORFs 1 to 7 (SEQ ID NOS: 1-9) and possible other ORFs located in the sequence of FIG. 1 (SEQ ID NO: 1) are especially suited for vaccine development, in whatever sense, and for the development of diagnostic tools, in whatever sense. All possible modes are well known to persons skilled in the art.

[0033] Since it is now possible to unambiguously identify LA, the causal agent of MSD, it can now be tested whether pigs are infected with LA or not. Such diagnostic tests have, until now, been unavailable.

[0034] The test can be performed by virus isolation in macrophages, or other cell culture systems in which LA might grow, and staining the infected cultures with antibodies directed against LA (such as post-infection sera c 829 or b 822), but it is also feasible to develop and employ other types of diagnostic tests.

[0035] For instance, it is possible to use direct or indirect immunohistological staining techniques, i.e., with antibodies directed to LA that are labeled with fluorescent compounds such as isothiocyanate, or labeled with enzymes such as horseradish peroxidase. These techniques can be used to detect LA antigen in tissue sections or other samples from pigs suspected to have MSD. The antibodies needed for these tests can be c 829 or b 822 or other polyclonal antibodies directed against LA, but monoclonal antibodies directed against LA can also be used.

[0036] Furthermore, since the nature and organization of the genome of LA and the nucleotide sequence of this genome have been determined, LA-specific nucleotide sequences can be identified and used to develop oligonucleotide sequences that can be used as probes or primers in diagnostic techniques such as hybridization, polymerase chain reaction, or any other techniques that are developed to specifically detect nucleotide acid sequences.

[0037] It is also possible to test for antibodies directed against LA. Table 5 shows that experimentally infected pigs rapidly develop antibodies against LA, and table 4 shows that pigs in the field also have strong antibody responses against LA. Thus, it can now also be determined whether pigs have been infected with LA in the past. Such testing is of utmost importance in determining whether pigs or pig herds or pig populations or pigs in whole regions or countries are free of LA. The test can be done by using the IPMA as described, but it is also feasible to develop and employ other types of diagnostic tests for the detection of antibodies directed against LA.

[0038] LA-specific proteins, polypeptides, and peptides, or peptide sequences mimicking antigenic components of LA, can be used in such tests. Such proteins can be derived from the LA itself, but it is also possible to make such proteins by recombinant DNA or peptide synthesis techniques. These tests can use specific polyclonal and/or monoclonal antibodies directed against LA or specific components of LA, and/or use cell systems infected with LA or cell systems expressing LA antigen. The antibodies can be used, for example, as a means for immobilizing the LA antigen (a solid surface is coated with the antibody whereafter the LA antigen is bound by the antibody) which leads to a higher specificity of the test, or can be used in a competitive assay (labeled antibody and unknown antibody in the sample compete for available LA antigen).

[0039] Furthermore, the above described diagnostic possibilities can be applied to test whether other animals, such as mammals, birds, insects or fish, or plants, or other living creatures, can be, or are, or have been infected with LA or related agents.

[0040] Since LA has now been identified as the causal agent of MSD, it is possible to make a vaccine to protect pigs against this disease. Such a vaccine can simply be made by growing LA in pig lung macrophage cultures, or in other cell systems in which LA grows. LA can then be purified or not, and killed by established techniques, such as inactivation with formaline or ultra-violet light. The inactivated LA can then be combined with adjuvantia, such as Freund's adjuvans or aluminum hydroxide or others, and this composition can then be injected in pigs.

[0041] Dead vaccines can also be made with LA protein preparations derived from LA infected cultures, or derived from cell systems expressing specifically LA protein through DNA recombinant techniques. Such subunits of LA would then be treated as above, and this would result in a subunit vaccine.

[0042] Vaccines using even smaller components of LA, such as polypeptides, peptides, or peptides mimicking antigenic components of LA, are also feasible for use as dead vaccine.

[0043] Dead vaccines against MSD can also be made by recombinant DNA techniques through which the genome of LA, or parts thereof, is incorporated in vector systems such as vaccinia virus, herpesvirus, pseudorabies virus, adeno virus, baculo virus or other suitable vector systems that can so express LA antigen in appropriate cells systems. LA antigen from these systems can then be used to develop a vaccine as above, and pigs, vaccinated with such products would develop protective immune responses against LA.

[0044] Vaccines against MSD can also be based on live preparations of LA. Since only young piglets and pregnant sows seem to be seriously affected by infection with LA, it is possible to use unattenuated LA, grown in pig lung macrophages, as vaccine for older piglets, or breeding gilts. In this way, sows can be protected against MSD before they get pregnant, which results in protection against abortions and stillbirth, and against congenital infections of piglets. Also the maternal antibody that these vaccinated sows give to their offspring would protect their offspring against the disease.

[0045] Attenuated vaccines (modified-live-vaccines) against MSD can be made by serially passaging LA in pig lung macrophages, in lung macrophages of other species, or in other cell systems, or in other animals, such as rabbits, until it has lost its pathogenicity.

[0046] Live vaccines against MSD can also be made by recombinant DNA techniques through which the genome of LA, or parts thereof, is incorporated in vector systems such as vaccinia virus, herpesvirus, pseudorabies virus, adeno virus or other suitable vector systems that can so express LA antigen. Pigs vaccinated with such live vector systems would then develop protective immune responses against LA.

[0047] Lelystad Agent itself would be specifically suited to use as a live vector system. Foreign genes could be inserted in the genome of LA and could be expressing the corresponding protein during the infection of the macrophages. This cell, which is an antigen-presenting cell, would process the foreign antigen and present it to B-lymphocytes and T-lymphocytes which will respond with the appropriate immune response.

[0048] Since LA seems to be very cell specific and possibly also very species specific, this vector system might be a very safe system, which does not harm other cells or species.

BRIEF DESCRIPTION OF THE DRAWINGS

[0049] FIG. 1 (SEQ ID NO: 1) shows the nucleotide sequence of the LV genome. The deduced amino acid sequence of the identified ORFs (SEQ ID NOS: 2-9) are shown. The methionines encoded by the (putative) ATG start sites are indicated in bold and putative N-glycosylation sites are underlined. Differences in the nucleotide and amino acid sequence, as identified by sequencing different cDNA clones, are shown. The nucleotide sequence of primer 25, which has been used in hybridization experiments (see FIG. 2 and section “results”), is underlined.

[0050] FIG. 2 shows the organization of the LV genome. The cDNA clones, which have been used for the determination of the nucleotide sequence, are indicated in the upper part of the figure. The parts of the clones, which were sequenced, are indicated in black. In the lower part of the FIG. the ORFs, identified in the nucleotide sequence, and the subgenomic set of mRNAs, encoding these ORFs are shown. The dashed lines in the ORFs represent alternative initiation sites (ATGs) of these ORFs. The leader sequence of the genomic and subgenomic RNAs is indicated by a solid box.

[0051] FIG. 3 shows the growth characteristics of LA:

[0052] empty squares—titre of cell-free virus;

[0053] solid squares—titre of cell-associated virus;

[0054] solid line—percentage cytopathic effect (CPE).

MATERIALS AND METHODS

[0055] Sample Collection

[0056] Samples and pigs were collected from farms where a herd epizootic of MSD seemed to occur. Important criteria for selecting the farm as being affected with MSD were: sows that were off feed, the occurrence of stillbirth and abortion, weak offspring, respiratory disease and death among young piglets. Samples from four groups of pigs have been investigated:

[0057] (1) tissue samples and an oral swab from affected piglets from the field (Table 1A);

[0058] (2) blood samples and oral swabs from affected sows in the field (Tables 1B and 4);

[0059] (3) tissue samples, nasal swabs and blood samples collected from specific-pathogen-free (SPF) pigs experimentally infected by contact with affected sows from the field; or

[0060] (4) tissue samples, nasal swabs and blood samples collected from specific-pathogen-free (SPF) pigs experimentally infected by inoculation with blood samples of affected sows from the field (Tables 2 and 5).

[0061] Sample Preparation

[0062] Samples for virus isolation were obtained from piglets and sows which on clinical grounds were suspected to have MSD, and from experimentally infected SPF pigs, sows and their piglets.

[0063] Tissue samples were cut on a cryostat microtome and sections were submitted for direct immunofluorescence testing (IFT) with conjugates directed against various pig pathogens.

[0064] 10% Suspensions of tissues samples were prepared in Hank's BSS supplemented with antibiotics, and oral and nasal swabs were soaked in Hank's BSS supplemented with antibiotics. After one hour at room temperature, the suspensions were clarified for 10 min at 6000 g and the supernatant was stored at −70° C. for further use. Leucocyte fractions were isolated from EDTA or heparin blood as described earlier (Wensvoort and Terpstra, 1988) and stored at −70° C. Plasma and serum for virus isolation were stored at −70° C.

[0065] Serum for serology was obtained from sows suspected to be in the acute phase of MSD, a paired serum was taken 3-9 weeks later. Furthermore, sera were taken from the experimentally infected SPF pigs at regular intervals and colostrum and serum was taken from experimentally infected sows and their piglets. Sera for serology were stored at −20° C.

[0066] Cells

[0067] Pig lung macrophages were obtained from lungs of 5-6 weeks old SPF pigs or from lungs of adult SPF sows from the Central Veterinary Institute's own herd. The lungs were washed five to eight times with phosphate buffered saline (PBS). Each aliquot of washing fluid was collected and centrifuged for 10 min at 300 g. The resulting cell pellet was washed again in PBS and resuspended in cell culture medium (160 ml medium 199, supplemented with 20 ml 2.95% tryptose phosphate, 20 ml fetal bovine serum (FBS), and 4.5 ml 1.4% sodium bicarbonate) to a concentration of 4×107cells/ml. The cell suspension was then slowly mixed with an equal volume of DMSO mix (6.7 ml of above medium, 1.3 ml FBS, 2 ml dimethylsulfoxide 97%), aliquoted in 2 ml ampoules and stored in liquid nitrogen.

[0068] Macrophages from one ampoule were prepared for cell culture by washing twice in Earle's MEM, and resuspended in 30 ml growth medium (Earle's MEM, supplemented with 10% FBS, 200 U/ml penicillin, 0.2 mg/ml streptomycine, 100 U/ml mycostatin, and 0.3 mg/ml glutamine). PK-15 cells (American Type Culture Collection, CCL33) and SK-6 cells (Kasza et al., 1972) were grown as described by Wensvoort et al. (1989). Secondary porcine kidney (PK2) cells were grown in Earle's MEM, supplemented with 10% FBS and the above antibiotics. All cells were grown in a cell culture cabinet at 37° C. and 5% CO2.

[0069] Virus Isolation Procedures

[0070] Virus isolation was performed according to established techniques using PK2, PK-15 and SK-6 cells, and pig lung macrophages. The former three cells were grown in 25 ml flasks (Greiner), and inoculated with the test sample when monolayers had reached 70-80% confluency. Macrophages were seeded in 100 μl aliquots in 96-well microtiter plates (Greiner) or in larger volumes in appropriate flasks, and inoculated with the test sample within one hour after seeding. The cultures were observed daily for cytopathic effects (CPE), and frozen at −70° C. when 50-70% CPE was reached or after five to ten days of culture. Further passages were made with freeze-thawed material of passage level 1 and 2 or higher. Some samples were also inoculated into nine to twelve day old embryonated hen eggs. Allantoic fluid was subinoculated two times using an incubation interval of three days and the harvest of the third passage was examined by haemagglutination at 4° C. using chicken red blood cells, and by an ELISA specifically detecting nucleoprotein of influenza A viruses (De Boer et al., 1990).

[0071] Serology

[0072] Sera were tested in haemagglutinating inhibition tests (HAI) to study the development of antibody against haemagglutinating encephalitis virus (HEV), and swine influenza viruses H1N1 and H3N2 according to the protocol of Masurel (1976). Starting dilutions of the sera in HAI were 1:9, after which the sera were diluted twofold.

[0073] Sera were tested in established enzyme-linked immuno-sorbent assays (ELISA) for antibodies against the glycoprotein gI of pseudorabies virus (PRV; Van Oirschot et al., 1988), porcine parvo virus (PPV; Westenbrink et al., 1989), bovine viral diarrhea virus (BVDV; Westenbrink et al., 1986), and hog cholera virus (HCV; Wensvoort et al., 1988). Starting dilutions in the ELISA's were 1:5, after which the sera were diluted twofold.

[0074] Sera were tested for neutralizing antibodies against 30-300 TCID50 of encephalomyocarditis viruses (EMCV), porcine enteroviruses (PEV), and Lelystad Agent (LA) according to the protocol of Terpstra (1978). Starting dilutions of the sera in the serum neutralization tests (SNT) were 1:5, after which the sera were diluted twofold.

[0075] Sera were tested for binding with LA in an immuno-peroxidase-monolayer assay (IPMA). Lelystad Agent (LA; code: CDI-NL-2.91) was seeded in microtiter plates by adding 50 ml growth medium containing 100 TCID50 LA to the wells of a microtiter plate containing freshly seeded lung macrophages. The cells were grown for two days and then fixed as described (Wensvoort, 1986). The test sera were diluted 1:10 in 0.15 M NaCl, 0.05% Tween 80, 4% horse serum, or diluted further in fourfold steps, added to the wells and then incubated for one hour at 37° C. Sheep-anti-pig immunoglobulins (Ig) conjugated to horse radish peroxidase (HRPO, DAKO) were diluted in the same buffer and used in a second incubation for one hour at 37° C., after which the plates were stained as described (Wensvoort et al., 1986). An intense red staining of the cytoplasm of infected macrophages indicated binding of the sera to LA.

[0076] Virus Identification Procedures

[0077] The identity of cytopathic isolates was studied by determining the buoyant density in CsCl, by estimating particle. size in negatively stained preparations through electron microscopy, by determining the sensitivity of the isolate to chloroform and by neutralizing the CPE of the isolate with sera with known specificity (Table 3). Whenever an isolate was specifically neutralized by a serum directed against a known virus, the isolate was considered to be a representative of this known virus.

[0078] Isolates that showed CPE on macrophage cultures were also studied by staining in IPMA with post-infection sera of pigs c 829 or b 822. The isolates were reinoculated on macrophage cultures and fixed at day 2 after inoculation before the isolate showed CPE. Whenever an isolate showed reactivity in IPMA with the post-infection sera of pigs c 829 or b 822, the isolate was considered to be a representative of the Lelystad Agent. Representatives of the other isolates grown in macrophages or uninfected macrophages were also stained with these sera to check the specificity of the sera.

[0079] Further Identification of Lelystad Agent

[0080] Lelystad Agent was further studied by haemagglutination at 4° C. and 37° C. with chicken, guinea pig, pig, sheep, or human O red blood cells. SIV, subtype H3N2, was used as positive control in the haemagglutination studies.

[0081] The binding of pig antisera specifically directed against pseudorabies virus (PRV), transmissible gastroenteritis virus (TGE), porcine epidemic diarrhea virus (PED), haemagglutinating encephalitis virus (HEV), African swine fever virus (ASFV), hog cholera virus (HCV) and swine influenza virus (SIV) type H1N1 and H3N2, of bovine antisera specifically directed against bovine herpes viruses type 1 and 4 (BHV 1 and 4), malignant catarrhal fever (MCF), parainfluenza virus 3 (PI3), bovine respiratory syncitial virus (BRSV) and bovine leukemia virus (BLV), and of avian antisera specifically directed against avian leukemia virus (ALV) and infectious bronchitis virus (IBV) was studied with species-Ig-specific HRPO conjugates in an IPMA on LA infected and uninfected pig lung macrophages as described above.

[0082] We also tested in IPMA antisera of various species directed against mumps virus, Sendai virus, canine distemper virus, rinderpest virus, measles virus, pneumonia virus of mice, bovine respiratory syncytial virus, rabies virus, foamy virus, maedi-visna virus, bovine and murine leukemia virus, human, feline and simian immunodeficiency virus, lymphocytic choriomeningitis virus, feline infectious peritonitis virus, mouse hepatitis virus, Breda virus, Hantaan virus, Nairobi sheep disease virus, Eastern, Western and Venezuelan equine encephalomyelitis virus, rubellavirus, equine arteritis virus, lactic dehydrogenase virus, yellow fever virus, tick-born encephalitis virus and hepatitis C virus.

[0083] LA was blindly passaged in PK2, PK- 15, and SK-6 cells, and in embryonated hen eggs. After two passages, the material was inoculated again into pig lung macrophage cultures for reisolation of LA.

[0084] LA was titrated in pig lung macrophages prior to and after passing through a 0.2 micron filter (Schleicher and Schuell). The LA was detected in IPMA and by its CPE. Titres were calculated according to Reed and Muench (1938).

[0085] We further prepared pig antisera directed against LA. Two SPF pigs (21 and 23) were infected intranasally with 105TCID50 of a fifth cell culture passage of LA. Two other SPF pigs (25 and 29) were infected intranasally with a fresh suspension of the lungs of an LA-infected SPF piglet containing 105 TCID50 LA. Blood samples were taken at 0, 14, 28, and 42 days post-infection (dpi).

[0086] We further grew LA in porcine alveolar macrophages to determine its growth pattern over time. Porcine alveolar macrophages were seeded in F25 flasks (Greiner), infected with LA with a multiplicity of infection of 0.01 TCID50 per cell. At 8, 16,24, 32,40,48, 56, and 64 h after infection, one flask was examined and the percentage of CPE in relation to a noninfected control culture was determined. The culture medium was then harvested and replaced with an equal volume of phosphate-buffered saline. The medium and the flask were stored at −70° C. After all cultures had been harvested, the LA titres were determined and expressed as log TCID50 ml−1.

[0087] The morphology of LA was studied by electronmicroscopy. LA was cultured as above. After 48 h, the cultures were freeze-thawed and centrifuged for 10 min at 6000.times.g. An amount of 30 ml supernatant was then mixed with 0.3 ml LA-specific pig serum and incubated for 1.5 h at 37° C. After centrifugation for 30 min at 125,000× g, the resulting pellet was suspended in 1% Seakem agarose ME in phosphate-buffered saline at 40° C. After coagulation, the agarose block was immersed in 0.8% glutaraldehyde and 0.8% osmiumtetroxide (Hirsch et al., 1968) in veronal/acetate buffer, pH 7.4 (230 mOsm/kg H2O), and fixed by microwave irradiation. This procedure was repeated once with fresh fixative. The sample was washed with water, immersed in 1% uranyl acetate, and stained by microwave irradiation. Throughout all steps, the sample was kept at 0° C. and the microwave (Samsung RE211D) was set at defrost for 5 min. Thin sections were prepared with standard techniques, stained with lead citrate (Venable et al., 1965), and examined in a Philips CM 10 electron microscope.

[0088] We further continued isolating LA from sera of pigs originating from cases of MSD. Serum samples originated from the Netherlands (field case the Netherlands 2), Germany (field cases Germany 1 and Germany 2; courtesy Drs. Berner, Müinchen and Nienhoff, Münster), and the United States [experimental case United States 1 (experiment performed with ATCC VR-2332; courtesy Drs. Collins, St. Paul and Chladek, St. Joseph), and field cases United States 2 and United States 3; courtesy Drs. van Alstine, West Lafayette and Slife, Galesburg]. All samples were sent to the “Centraal Diergeneeskundig Instituut, Lelystad” for LA diagnosis. All samples were used for virus isolation on porcine alveolar macrophages as described. Cytophatic isolates were passaged three times and identified as LA by specific immunostaining with anti-LA post infection sera b 822 and c 829.

[0089] We also studied the antigenic relationships of isolates NL1 (the first LA isolate; code CDI-NL-2.91), NL2, GE1, GE2, US1, US2, and US3. The isolates were grown in macrophages as above and were tested in IPMA with a set of field sera and two sets of experimental sera. The sera were also tested in IPMA with uninfected macrophages.

[0090] The field sera were: Two sera positive for LV (TH-187 and TO-36) were selected from a set of LA-positive Dutch field sera. Twenty-two sera were selected from field sera sent from abroad to Lelystad for serological diagnosis. The sera originated from Germany (BE-352, BE-392 and NI-f2; courtesy Dr. Bemer, München and Dr. Nienhoff, Münster), the United Kingdom (PA-141615, PA-141617 and PA-142440; courtesy Dr. Paton, Weybridge), Belgium (PE-1960; courtesy Prof. Pensaert, Gent), France (EA-2975 and EA-2985; courtesy Dr. Albina, Ploufragan), the United States (SL-441, SL-451, AL-RP9577, AL-P10814/33, AL-4994A, AL-7525, JC-MN41, JC-MN44 and JC-MN45; courtesy Dr. Slife, Galesburg, Dr. van Alstine, West Lafayette, and Dr. Collins, St. Paul), and Canada (RB-16, RB- 19, RB-22 and RB-23; courtesy Dr. Robinson, Quebec).

[0091] The experimental sera were: The above described set of sera of pigs 21, 23, 25, and 29, taken at dpi 0, 14, 28, and 42. A set of experimental sera (obtained by courtesy of Drs. Chladek, St. Joseph, and Collins, St. Paul) that originated from four six-month-old gilts that were challenged intranasally with 105.1TCID50 of the isolate ATCC VR-2332. Blood samples were taken from gilt 2B at 0, 20, 36, and 63 dpi; from gilt 9G at 0, 30, 44, and 68 dpi; from gilt 16W at 0, 25, 40, and 64 dpi; and from gilt 16Y at 0, 36, and 64 dpi.

[0092] To study by radio-immunoprecipitation assay (RIP; de Mazancourt et al., 1986) the proteins of LA in infected porcine alveolar macrophages, we grew LA-infected and uninfected macrophages for 16 hours in the presence of labeling medium containing 35S-Cysteine. Then the labeled cells were precipitated according to standard methods with 42 dpi post-infection sera of pig b 822 and pig 23 and with serum MN 8 which was obtained 26 days after infecting a sow with the isolate ATCC VR-2332 (courtesy Dr. Collins, St. Paul). The precipitated proteins were analyzed by electrophoresis in a 12% SDS-PAGE gel and visualized by fluorography.

[0093] To characterize the genome of LA, we extracted nuclear DNA and cytoplasmatic RNA from macrophage cultures that were infected with LA and grown for 24 h or were left uninfected. The cell culture medium was discarded, and the cells were washed twice with phosphate-buffered saline. DNA was extracted as described (Strauss, 1987). The cytoplasmic RNA was extracted as described (Favaloro et al., 1980), purified by centrifugation through a 5.7 M CsCl cushion (Setzer et al., 1980), treated with RNase-free DNase (Pharmacia), and analyzed in a 0.8% neutral agarose gel (Moormann and Hulst, 1988).

[0094] Cloning and Sequencing

[0095] To clone LV RNA, intracellular RNA of LV-infected porcine lung alveolar macrophages (10 μg) was incubated with 10 mM methylmercury hydroxide for 10 minutes at room temperature. The denatured RNA was incubated at 42° C. with 50 mM Tris-HCI, pH 7.8, 10 mM MgCl2, 70 mM KCl, 0.5 mM dATP, dCTP, dGTP and dTTP, 0.6 μg calf thymus oligonucleotide primers pd(N)6 (Pharmacia) and 300 units of Moloney murine leukemia virus reverse transcriptase (Bethesda Research Laboratories) in a total volume of 100μl 20 mM EDTA was added after 1 hr; the reaction mixture was then extracted with phenol/chloroform, passed through a Sephadex G50 column and precipitated with ethanol.

[0096] For synthesis of the second cDNA strand, DNA polymerase I (Boehringer) and RNase H (Pharmacia) were used (Gübler and Hoffinan, 1983). To generate blunt ends at the termini, double-stranded cDNA was incubated with T4 DNA polymerase (Pharmacia) in a reaction mixture which contained 0.05 mM deoxynucleotide-triphosphates. Subsequently, cDNA was fractionated in a 0.8% neutral agarose gel (Moormann and Hulst, 1988). Fragments of 1 to 4 kb were electroeluted, ligated into the Smal site of pGEM-4Z (Promega), and used for transformation of Escherichia coli strain DH5α (Hanahan, 1985). Colony filters were hybridized with a 32P-labeled single-stranded cDNA probe. The probe was reverse transcribed from LV RNA which had been fractionated in a neutral agarose gel (Moormann and Hulst, 1988). Before use, the single stranded DNA probe was incubated with cytoplasmic RNA from mock-infected lung alveolar macrophages.

[0097] The relationship between LV cDNA clones was determined by restriction enzyme analysis and by hybridization of Southern blots of the digested DNA with nick-translated cDNA probes (Sambrook et al., 1989).

[0098] To obtain the 3′ end of the viral genome, we constructed a second cDNA library, using oligo (dT)12-18 and a 3′ LV-specific oligonucleotide that was complementary to the minus-strand viral genome as a primer in the first-strand reaction. The reaction conditions for first- and second-strand synthesis were identical to those described above. This library was screened with virus-specific 3′ end oligonucleotide probes.

[0099] Most (>95%) of the cDNA sequences were determined with an Automated Laser Fluorescent A.L.F.™. DNA sequencer from Pharmacia LKB. Fluorescent oligonucleotide primer directed sequencing was performed on double-stranded DNA using the AutoRead™. Sequencing Kit (Pharmacia) essentially according to procedures C and D described in the Autoread™ Sequencing Kit protocol. Fluorescent primers were prepared with FluorePrime™. (Pharmacia). The remaining part of the sequence was determined via double-stranded DNA sequencing using oligonucleotide primers in conjunction with a T7 polymerase based sequencing kit (Pharmacia) and α-32S-dATP (Amersham). Sequence data were analyzed using the sequence analysis programs PCGENE (Intelligenetics, Inc, Mountain View, U.S.A.) and FASTA (Pearson and Lipman, 1988).

[0100] Experimental Reproduction of MSD

[0101] Fourteen conventionally reared pregnant sows that were pregnant for 10-11 weeks were tested for antibody against LA in the IPMA. All were negative. Then two groups of four sows were formed and brought to the CVI. At week 12 of gestation, these sows were inoculated intranasally with 2 ml LA (passage level 3, titre 104.8 TCID50 /ml). Serum and EDTA blood samples were taken at day 10 after inoculation. Food intake, rectal temperature, and other clinical symptoms were observed daily. At farrowing, the date of birth and the number of dead and living piglets per sow were recorded, and samples were taken for virus isolation and serology.

Results

[0102] Immunofluorescence

[0103] Tissue sections of pigs with MSD were stained in an IFT with FITC-conjugates directed against African swine fever virus, hog cholera virus, pseudorabies virus, porcine parvo virus, porcine influenza virus, encephalomyocarditis virus and Chlamydia psittaci. The sections were stained, examined by fluorescent microscopy and all were found negative.

[0104] Virus Isolation from Piglets from MSD Affected Farms

[0105] Cytopathic isolates were detected in macrophage cultures inoculated with tissue samples of MSD affected, two-to-ten day old piglets. Sixteen out of 19 piglets originating from five different farms were positive (Table 1A). These isolates all reacted in IPMA with the post-infection serum of pig c 829, whereas non-inoculated control cultures did not react. The isolates, therefore, were representatives of LA. One time a cytopathic isolate was detected in an SK-6 cell culture inoculated with a suspension of an oral swab from a piglet from a sixth farm (farm VE) (Table 1A). This isolate showed characteristics of the picoma viridae and was neutralized by serum specific for PEV 2, therefore, the isolate was identified as PEV 2 (Table 3). PK2, PK-15 cells and hen eggs inoculated with samples from this group remained negative throughout.

[0106] Virus Isolation from Sows from MSD Affected Farms

[0107] Cytopathic isolates were detected in macrophage cultures inoculated with samples of MSD affected sows. 41 out of 63 sows originating from 11 farms were positive (Table 1B). These isolates all reacted in IPMA with the post-infection serum of pig b 822 and were, therefore, representatives of LA. On one occasion a cytopathic isolate was detected in a PK2 cell culture inoculated with a suspension of a leucocyte fraction of a sow from farm HU (Table 1B). This isolate showed characteristics of the picoma viridae and was neutralized by serum specific for EMCV, therefore, the isolate was identified as EMCV (Table 3). SK-6, PK-15 cells and hen eggs inoculated with samples from this group remained negative.

[0108] Virus Isolation from SPF Pigs Kept in Contact with MSD Affected Sows

[0109] Cytopathic isolates were detected in macrophage cultures inoculated with samples of SPF pigs kept in contact with MSD affected sows. Four of the 12 pigs were positive (Table 2). These isolates all reacted in IPMA with the post-infection serum of pig c 829 and of pig b 822 and were, therefore, representatives of LA. Cytopathic isolates were also detected in PK2, PK-15 and SK-6 cell cultures inoculated with samples of these SPF pigs. Seven of the 12 pigs were positive (Table 2), these isolates were all neutralized by serum directed against PEV 7. One of these seven isolates was studied further and other characteristics also identified the isolate as PEV 7 (Table 3).

[0110] Virus Isolation from SPF Pigs Inoculated with Blood of MSD Affected Sows

[0111] Cytopathic isolates were detected in macrophage cultures inoculated with samples of SPF pigs inoculated with blood of MSD affected sows. Two out of the eight pigs were positive (Table 2). These isolates all reacted in IPMA with the post-infection serum of pig c 829 and of pig b 822 and were, therefore, representatives of LA. PK2, SK-6 and PK-15 cells inoculated with samples from this group remained negative.

[0112] Summarizing, four groups of pigs were tested for the presence of agents that could be associated with mystery swine disease (MSD).

[0113] In group one, MSD affected piglets, the Lelystad Agent (LA) was isolated from 16 out of 20 piglets; one time PEV 2 was isolated.

[0114] In group two, MSD affected sows, the Lelystad Agent was isolated from 41 out of 63 sows; one time EMCV was isolated. Furthermore, 123 out of 165 MSD affected sows seroconverted to the Lelystad Agent, as tested in the IPMA. Such massive seroconversion was not demonstrated against any of the other viral pathogens tested.

[0115] In group three, SPF pigs kept in contact with MSD affected sows, LA was isolated from four of the 12 pigs; PEV 7 was isolated from seven pigs. All 12 pigs seroconverted to LA and PEV 7.

[0116] In group four, SPF pigs inoculated with blood of MSD affected sows, the LA was isolated from two pigs. All eight pigs seroconverted to LA.

[0117] Serology of Sows from MSD Affected Farms

[0118] Paired sera from sows affected with MSD were tested against a variety of viral pathogens and against the isolates obtained during this study (Table 4). An overwhelming antibody response directed against LA was measured in the IPMA (75% of the sows seroconverted, in 23 out of the 26 farms seroconversion was found), whereas with none of the other viral pathogens a clear pattern of seroconversion was found. Neutralizing antibody directed against LA was not detected.

[0119] Serology of SPF Pigs Kept in Contact with MSD Affected Sows

[0120] All eight SPF pigs showed an antibody response in the IPMA against LA (Table 5). None of these sera were positive in the IPMA performed on uninfected macrophages. None of these sera were positive in the SNT for LA. The sera taken two weeks after contact had all high neutralizing antibody titres (>1280) against PEV 7, whereas the pre-infection sera were negative (<10), indicating that all pigs had also been infected with PEV 7.

[0121] Serology of SPF Pigs Inoculated with Blood of MSD Affected Sows

[0122] All eight SPF pigs showed an antibodyresponse in the IPMA against LA (Table 5). None of these sera were positive in the IPMA performed on uninfected macrophages. None of these sera were positive in the SNT for LA. The pre- and two weeks post-inoculation sera were negative (<10) against PEV 7.

[0123] Further Identification of Lelystad Agent

[0124] LA did not haemagglutinate with chicken, guinea pig, pig, sheep, or human O red blood cells.

[0125] LA did not react in IPMA with sera directed against PRV, TGE, PED, ASFV, etc.

[0126] After two blind passages, LA did not grow in PK2, PK-15, or SK-6 cells, or in embryonated hen eggs, inoculated through the allantoic route.

[0127] LA was still infectious after it was filtered through a 0.2 micron filter, titres before and after filitration were 105.05 and 105.3 TCID50 as detected by IPMA.

[0128] Growth curve of LA (see FIG. 3). Maximum titres of cell-free virus were approximately 105.5TCID50 ml−1 from 32-48 h after inoculation. After that time the macrophages he cytopathic effect of LA.

[0129] Electronmicroscopy. Clusters of spherical LA particles were found. The particles measured 45-55 nm in diameter and contained a 30-35 nm nucleocapsid that was surrounded by a lipid bilayer membrane. LA particles were not found in infected cultures that were treated with negative serum or in negative control preparations.

[0130] Isolates from the Netherlands, Germany, and the United States. All seven isolates were isolated in porcine alveolar macrophages and passaged three to five times. All isolates caused a cytopathic effect in macrophages and could be specifically immunostained with anti-LA sera b 822 and the 42 dpi serum 23. The isolates were named NL2, GE1, GE 2, US1, US2, and US3.

[0131] Antigenic relationships ofisolates NL1, NL2, GE1, GE2, US 1, US2, and US3. None of the field sera reacted in IPMA with uninfected macrophages but all sera contained antibodies directed against one or more of the seven isolates (Table 7). None of the experimental sera reacted in IPMA with uninfected macrophages, and none of the 0 dpi experimental sera reacted with any of the seven isolates in IPMA (Table 8). All seven LA isolates reacted with all or most of the sera from the set of experimental sera of pigs 21, 23, 25, and 29, taken after 0 dpi. Only the isolates US1, US2, and US3 reacted with all or most of the sera from the set of experimental sera of gilts 2B, 9G, 16W, and 16Y, taken after 0 dpi.

[0132] Radioimmunoprecipitation studies. Seven LA-specific proteins were detected in LA-infected macrophages but not in uninfected macrophages precipitated with the 42 dpi sera of pigs b 822 and 23. The proteins had estimated molecular weights of 65, 39, 35, 26, 19, 16, and 15 kilodalton. Only two of these LA-specific proteins, of 16 and 15 kilodalton, were also precipitated by the 26 dpi serum MN8.

[0133] Sequence and Organization of the Genome of LV

[0134] The nature of the genome of LV was determined by analyzing DNA and RNA from infected porcine lung alveolar macrophages. No LV-specific DNA was detected. However, we did detect LV-specific RNA. In a 0.8% neutral agarose gel, LV RNA migrated slightly slower than a preparation of hog cholera virus RNA of 12.3 kb (Moormann et al., 1990) did. Although no accurate size determination can be performed in neutral agarose gels, it was estimated that the LV-specific RNA is about 14.5 to 15.5 kb in length.

[0135] To determine the complexity of the LV-specific RNAs in infected cells and to establish the nucleotide sequence of the genome of LV, we prepared cDNA from RNA of LV-infected porcine lung alveolar macrophages and selected and mapped LV-specific cDNA clones as described under Materials and Methods. The specificity of the cDNA clones was reconfirmed by hybridizing specific clones, located throughout the overlapping cDNA sequence, to Northern blots carrying RNA of LV-infected and uninfected macrophages. Remarkably, some of the cDNA clones hybridized with the 14.5 to 15.5 kb RNA detected in infected macrophages only, whereas others hybridized with the 14.5 to 15.5 kb RNA as well as with a panel of 4 or 5 RNAs of lower molecular weight (estimated size, 1 to 4 kb). The latter clones were all clustered at one end of the cDNA map and covered about 4 kb of DNA. These data suggested that the genome organization of LV may be similar to that of coronaviridae (Spaan et al., 1988), Berne virus (BEV; Snijder et al., 1990b), a torovirus, and EAV (de Vries et al., 1990), i.e., besides a genomic RNA there are subgenomic mRNAs which form a nested set which is located at the 3′ end of the genome. This assumption was confirmed when sequences of the cDNA clones became available and specific primers could be selected to probe the blots with. A compilation of the hybridization data obtained with cDNA clones and specific primers, which were hybridized to Northern blots carrying the RNA of LV-infected and uninfected macrophages, is shown in FIG. 2. Clones 12 and 20 which are located in the 5′ part and the centre of the sequence, respectively, hybridize to the 14.5 to 15.5 kb genomic RNA detected in LV-infected cells only. Clones 41 and 39, however, recognize the 14.5 to 15.5 kb genomic RNA and a set of 4 and 5 RNAs of lower molecular weight, respectively. The most instructive and conclusive hybridization pattern, however, was obtained with primer 25, which is located at the ultimate 5′ end in the LV sequence (compare FIG. 1). Primer 25 hybridized to a panel of 7 RNAs, with an estimated molecular weight ranging in size from 0.7 to 3.3 kb (subgenomic mRNAs), as well as the genomic RNA. The most likely explanation for the hybridization pattern of primer 25 is that 5′ end genomic sequences, the length of which is yet unknown, fuse with the body of the mRNAs which are transcribed from the 3′ end of the genome. In fact, the hybridization pattern obtained with primer 25 suggests that 5′ end genomic sequences function as a so called “leader sequence” in subgenomic mRNAs. Such a transcription pattern is a hallmark of replication of coronaviridae (Spaan et al., 1988), and of EAV (de Vries et al., 1990).

[0136] The only remarkable discrepancy between LV and EAV which could be extracted from the above data is that the genome size of LV is about 2.5 kb larger than that of EAV.

[0137] The consensus nucleotide sequence of overlapping cDNA clones is shown in FIG. 1 (SEQ ID NO: 1). The length of the sequence is 15,088 basepairs, which is in good agreement with the estimated size of the genomic LV RNA.

[0138] Since the LV cDNA library was made by random priming of the reverse transcriptase reaction with calf thymus pd(N) 6 primers, no cDNA clones were obtained which started with a poly-A stretch at their 3′ end. To clone the 3′ end of the viral genome, we constructed a second cDNA library, using oligo (dT) and primer 39U183R in the reverse transcriptase reaction. Primer 39U183R is complementary to LV minus-strand RNA, which is likely present in a preparation of RNA isolated from LV-infected cells. This library was screened with virus-specific probes (nick-translated cDNA clone 119 and oligonucleotide 119R64R), resulting in the isolation of five additional cDNA clones (e.g., cDNA clone 151, FIG. 2). Sequencing of these cDNA clones revealed that LV contains a 3′ poly(A) tail. The length of the poly(A) tail varied between the various cDNA clones, but its maximum length was twenty nucleotides. Besides clone 25 and 155 (FIG. 2), four additional cDNA clones were isolated at the 5′ end of the genome, which were only two to three nucleotides shorter than the ultimate 5′ nucleotide shown in FIG. 1 (SEQ ID NO: 1). Given this finding and given the way cDNA was synthesized, we assume to be very close to the 5′ end of the sequence of LV genomic RNA.

[0139] Nearly 75% of the genomic sequence of LV encodes ORF 1A and ORF 1B. ORF 1A probably initiates at the first AUG (nucleotide position 212, FIG. 1) encountered in the LV sequence. The C-terminus of ORF 1A overlaps the putative N-terminus of ORF 1 B over a small distance of 16 nucleotides. It thus seems that translation of ORF 1B proceeds via ribosomal frameshifling, a hallmark of the mode of translation of the polymerase or replicase gene of coronaviruses (Boursnell et al., 1987; Bredenbeek et al. 1990) and the torovirus BEV (Snijder et al., 1990a). The characteristic RNA pseudoknot structure which is predicted to be formed at the site of the ribosomal frameshifting is also found at this location in the sequence of LV (results not shown).

[0140] ORF 1B encodes an amino acid sequence (SEQ ID NO: 3) of nearly 1400 residues which is much smaller than ORF 1B of the coronaviruses MHV and IBV (about 3,700 amino acid residues; Bredenbeek et al., 1990; Boursnell et al., 1987) and BEV (about 2,300 amino acid residues; Snijder et al., 1990a). Characteristic features of the ORF 1B product (SEQ ID NO: 3) of members of the superfamily of coronaviridae, like the replicase motif and the Zinc finger domain, can also be found in ORF 1B of LV (results not shown).

[0141] Whereas ORF 1A and ORF 1B encode the viral polymerase (SEQ ID NO:2 and SEQ ID NO:3) and, therefore, are considered to encode a non-structural viral protein, ORFs 2 to 7 are believed to encode structural viral proteins (SEQ ID NOS:4-9).

[0142] The products of ORFs 2 to 6 (SEQ ID NOS:4-8) all show features reminiscent of membrane (envelope) associated proteins. ORF 2 encodes a protein (SEQ ID NO:4) of 249 amino acids containing two predicted N-linked glycosylation sites (Table 9). At the N-terminus a hydrophobic sequence, which may function as a so-called signal sequence, is identified. The C-terminus also ends with a hydrophobic sequence, which in this case may function as a transmembrane region, which anchors the ORF 2 product (SEQ ID NO:4) in the viral envelope membrane.

[0143] ORF 3 may initiate at the AUG starting at nucleotide position 12394 or at the AUG starting at nucleotide position 12556 and then encodes proteins (SEQ ID NO:5) of 265 and 211 amino acids, respectively. The protein of 265 residues contains seven putative N-linked glycosylation sites, whereas the protein of 211 residues contains four (Table 9). At the N-terminus of the protein (SEQ ID NO:5) of 265 residues a hydrophobic sequence is identified.

[0144] Judged by hydrophobicity analysis, the topology of the protein encoded by ORF 4 (SEQ ID NO:6) is similar to that encoded by ORF 2 (SEQ ID NO:4) if the product of ORF 4 (SEQ ID NO:6) initiates at the AUG starting at nucleotide position 12936. However, ORF 4 may also initiate at two other AUG codons (compare FIGS. 1 and 2) starting at positions 12981 and 13068 in the sequence respectively. Up to now it is unclear which start codon is used. Depending on the start codon used, ORF 4 may encode proteins (SEQ ID NO:6) of 183 amino acids containing four putative N-linked glycosylation sites, of 168 amino acids containing four putative N-linked glycosylation sites, or of 139 amino acids containing three putative N-linked glycosylation sites (Table 9).

[0145] ORF 5 is predicted to encode a protein (SEQ ID NO:7) of 201 amino acids having two putative N-linked glycosylation sites (Table 9). A characteristic feature of the ORF 5 product (SEQ ID NO:7) is the internal hydrophobic sequence between amino acid 108 to amino acid 132.

[0146] Analysis for membrane spanning segments andhydrophilicity of the product of ORF 6 (SEQ ID NO:8) shows that it contains three transmembrane spanning segments in the N-terminal 90 amino acids of its sequence. This remarkable feature is also a characteristic of the small envelope glycoprotein M or E1 of several coronaviruses, e.g., Infectious Bronchitis Virus (IBV; Boursnell et al., 1984) and Mouse Hepatitis Virus (MHV: Rottier et al., 1986). It is, therefore, predicted that the protein encoded by ORF 6 (SEQ ID NO:8) was a membrane topology analogous to that of the M or E1 protein of coronaviruses (Rottier et al., 1986). A second characteristic of the M or E1 protein is a so-called surface helix which is located immediately adjacent to the presumed third transmembrane region. This sequence of about 25 amino acids which is very well conserved among coronaviruses is also recognized, although much more degenerate, in LV. Yet we predict the product of LV ORF 6 (SEQ ID NO:8) to have an analogous membrane associated function as the coronavirus M or E1 protein. Furthermore, the protein encoded by ORF 6 (SEQ ID NO:8) showed a strong similarity (53% identical amino acids) with VpX (Godeny et al., 1990) of LDV.

[0147] The protein encoded by ORF 7 (SEQ ID NO:9) has a length of 128 amino acid residues (Table 9) which is 13 amino acids longer than Vp1 of LDV (Godeny et al., 1990). Yet a significant similarity (43% identical amino acids) was observed between the protein encoded by ORF 7 (SEQ ID NO:9) and Vp1. Another shared characteristic between the product of ORF 7 (SEQ ID NO:9) and Vp1 is the high concentration of basic residues (Arg, Lys and His) in the N-terminal half of the protein. Up to amino acid 55, the LV sequence contains 26% Arg, Lys and His. This finding is fully in line with the proposed function of the ORF 7 product (SEQ ID NO:9) or Vp1 (Godeny et al., 1990), namely encapsidation of the viral genomic RNA. On the basis of the above data, we propose the LV ORF 7 product (SEQ ID NO:9) to be the nucleocapsid protein N of the virus.

[0148] A schematic representation of the organization of the LV genome is shown in FIG. 2. The map of overlapping clones used to determine the sequence of LV is shown in the top panel. A linear compilation of this map indicating the 5′ and 3′ end of the nucleotide sequence of LV, shown in FIG. 1 (SEQ ID NO:1), including a division in kilobases, is shown below the map of cDNA clones and allows the positioning of these clones in the sequence. The position of the ORFs identified in the LV genome is indicated below the linear map of the LV sequence. The bottom panel shows the nested set of subgenomic mRNAs, and the position of these RNAs relative to the LV sequence.

[0149] In line with the translation strategy of coronavirus, torovirus and arterivirus subgenomic mRNAs, it is predicted that ORFs 1 to 6 are translated from the unique 5′ end of their genomic or mRNAs. This unique part of the mRNAs is considered to be that part of the RNA that is obtained when a lower molecular weight RNA is “subtracted” from the higher molecular weight RNA which is next in line. Although RNA 7 forms the 3′ end of all the other genomic and subgenomic RNAs, and thus does not have a unique region, it is believed that ORF 7 is only translated from this smallest sized mRNA. The “leader sequence” at the 5′ end of the subgenomic RNAs is indicated with a solid box. The length of this sequence is about 200 bases, but the precise site of fusion with the body of the genomic RNAs still has to be determined.

[0150] Experimental Reproduction of MSD

[0151] Eight pregnant sows were inoculated with LA and clinical signs of MSD such as inappetance and reproductive losses were reproduced in these sows. From day four to day 10-12 post-inoculation (p.i.), all sows showed a reluctance to eat. None of the sows had elevated body temperatures. Two sows had bluish ears at day 9 and 10 p.i. In Table 6 the day of birth and the number of living and dead piglets per sow is given. LA was isolated from 13 of the born piglets.

TABLE 1
Description and results of virus isolation of field samples.
A Samples of piglets suspected of infection with MSD.
	number	age
farm	of pigs	days	material used	results*
RB	5	2	lung, tonsil, and brains	5 × LA
DV	4	3	lung, brains,	3 × LA
			pools of kidney,
			spleen
TH	3	3-5	lung, pools of kidney, tonsil	3 × LA
DO	3	10	lung, tonsil	2 × LA
ZA	4	1	lung, tonsil	3 × LA
VE	1	?	oral swab	1 × PEV 2
TOTAL	20			16 × LA,
				1 × PEV 2
B Samples of sows suspected of infection with MSD.
	number
farm	of sows	material used	results
TH	2	plasma and leucocytes	1 × LA
HU	5	plasma and leucocytes	2 × LA, 1 × EMCV
TS	10	plasma and leucocytes	6 × LA
HK	5	plasma and leucocytes	2 × LA
LA	6	plasma and leucocytes	2 × LA
VL	6	serum and leucocytes	5 × LA
TA	15	serum	11 × LA
LO	4	plasma and leucocytes	2 × LA
JA	8	plasma and leucocytes	8 × LA
VD	1	plasma and leucocytes	1 × LA
VW	1	serum	1 × LA
TOTAL	63		41 × LA, 1 × EMCV
*Results are given as the number of pigs from which the isolation was made. Sometimes the isolate was detected in more than one sample per pig.
LA = Lelystad Agent
PEV 2 = porcine entero virus type 2
EMCV = encephalomyocarditis virus

[0152]

TABLE 2
Description and results of virus isolation of
samples of pigs with experimentally induced infections.
	sow	pig@	material used	results*
	A (LO) #	c 835	lung, tonsil	2 × LA
		c 836	nasal swabs	2 × PEV 7
		c 837	nasal swabs
	B (JA)	c 825	lung, tonsil
		c 821	nasal swabs	1 × PEV 7
		c 823	nasal swabs	4 × PEV 7
	C (JA)	c 833	lung, tonsil	1 × LA,
				1 × PEV 7
		c 832	nasal swabs	2 × PEV 7
		c 829	nasal swabs,
			plasma and	3 × LA,
			leucocytes	2 × PEV 7
	D (VD)	c 816	lung, tonsil
		c 813	nasal swabs	1 × LA
		c 815	nasal swabs	1 × PEV 7
	TOTAL isolates from contact pigs	7 × LA,
		13 × PEV 7
	A	b 809	nasal swabs
		b 817	nasal swabs
	B	b 818	nasal swabs, plasma	1 × LA
			and leucocytes
		b 820	nasal swabs
	C	b 822	nasal swabs
		b 826	nasal swabs
	D	b 830	nasal swabs	1 × LA
		b 834	nasal swabs
	TOTAL isolates from blood inoculated pigs	2 × LA
	@SPF pigs were either kept in contact (c) with a sow suspected to be infected with MSD, or were given 10 ml EDTA blood (b) of that sow intramuscularly at day 0 of the experiment. Groups of one sow and three SPF pigs (c) were kept in one pen, and all four of these groups were housed in one stable. At day 6, one SPF pig in each group was killed and tonsil and lungs were used for virus isolation. The four groups of SPF pigs inoculated with blood (b) were housed in four other pens in
	#a separate stable. EDTA blood for virus isolation from plasma and leucocytes was taken whenever a pig had fever.
	*Results are given as number of isolates per pig.
	LA = Lelystad Agent
	PEV 7 = procine entero virus type 7
	# In brackets the initials of the farm of origin of the sow are given.

[0153]

TABLE 3
Identification of viral isolates
	buoyant1	particle2		neutralized by4
origin and	density	size in	sens3 to	serum directed
cell culture	in CsCl	FM (nm)	chloroform	against (titre)
leucocytes	1.33 g/ml	28-30	not sens.	EMCV ( 1280)
sow farm HU
PK-15,
PK2, SK6
oral swab	ND	28-30	not sens.	PEV 2 (>1280)
piglet farm VE
SK6
nasal swabs,	ND	28-30	not sens.	PEV 7 (>1280)
tonsil
SPF pigs CVI
PK-15, PK2,
SK6
various	1.19 g/ml	pleomorf	sens.	none (all <5)
samples
various farms
pig lung
macrophages
1 Buoyant density in preformed linear gradients of CsCl in PBS was determined according to standard techniques (Brakke; 1967). Given is the density where the peak of infectivity was found.
2 Infected and noninfected cell cultures of the isolate under study were freeze-thawed. Cell lysates were centrifuged for 30 min at 130,000 g, the resulting pellet was negatively stained according to standard techniques (Brenner and Horne; 1959), and studied with a Philips CM 10 electron microscope. Given is the size of particles that were present in infected and not present in non-infected cultures.
3 Sensitivity to chloroform was determined according to standard techniques (Grist, Ross, and Bell; 1974).
4 Hundred to 300 TCID50 of isolates were mixed with varying dilutions of specific antisera and grown in the appropriate cell system until full CPE was observed. Sera with titres higher than 5 were retested, and sera which blocked with high titres the CPE were considered specific for the isolate. The isolates not sensitive to chloroform were tested with sera specifically directed against porcine
#entero viruses (PEV) 1 to 11 (courtesy Dr. Knowles, Pirbright, UK), against encephalomyocarditis virus (EMCV; courtesy Dr. Ahl, Tübingen, Germany), against porcine parvo virus, and against swine vesicular disease.
The isolate (code: CDI-NL-2.91) sensitive to chloroform was tested with antisera specifically directed against pseudorabies virus, bovine herpes virus 1, bovine herpes virus 4, malignant catarrhal virus, bovine viral diarrhea virus, hog cholera virus, swine influenza virus H1N1 and H3N2, parainfluenza 3 virus, bovine respiratory syncitial virus, transmissible gastroenteritis virus, porcine epidemic diarrhoea virus, haemagglutinating encephalitis virus, infectious bronchitis virus, bovine
#leukemia virus from the SPF-pigs (see Table 5).

[0154]

TABLE 4
Results of serology of paired field sera taken from sows
suspected to have MSD. Sera were taken
in the acute phase of the disease and 3-9 weeks
later. Given is the number of sows which showed
a fourfold or higher rise in titre/number of sows tested.
	Intervali
Farm	in weeks	HAI HEV	H1N1	H3N2	ELISA PPV	PPV	BVDV	HCV
TH	3	0/6	0/6	0/6	0/6	0/6	0/5	0/6
RB	5	0/13	1/13	0/13	1/9	0/7	0/6	0/9
HU	4	0/5	0/5	3/5	0/5	0/5	0/5	0/5
TS	3	1/10	0/10	0/10	0/10	0/10	0/4	0/10
VL	3	0/5	0/5	0/5	0/5	1/5	0/5	0/5
JA	3	0/11	1/11	3/11	0/11	2/11	0/11	0/11
WE	4	1/6	1/6	1/6	3/7	3/7	0/7	0/7
GI	4	0/4	1/4	0/4	0/4	0/4	0/4	0/4
SE	5	0/8	0/8	0/8	0/8	0/6	0/3	0/8
KA	5	0/1	0/1	0/1	0/1	0/1	ND	0/1
HO	3	1/6	0/5	1/6	0/6	0/6	0/6	0/6
NY	4	0/5	1/5	1/5	0/3	0/4	0/2	0/4
JN	3	0/10	5/10	0/10	0/10	1/10	0/10	0/10
KOf	3	1/10	0/10	0/10	0/10	2/10	0/10	0/10
OE	9	ND	ND	ND	0/6	0/6	0/6	0/6
LO	6	ND	ND	ND	0/3	0/3	0/2	0/3
WI	4	ND	ND	ND	0/1	1/1	0/1	0/3
RR	3	ND	ND	ND	1/8	0/8	0/8	0/8
RY	4	ND	ND	ND	0/3	0/4	0/3	0/4
BE	5	ND	ND	ND	0/10	0/10	0/10	0/10
BU	3	ND	ND	ND	1/6	0/6	0/6	0/6
KR	3	ND	ND	ND	1/4	0/4	0/4	0/4
KW	5	ND	ND	ND	0/10	0/10	0/10	0/10
VR	5	ND	ND	ND	1/6	0/6	0/6	0/6
HU	4	ND	ND	ND	1/4	0/3	0/3	0/4
ME	3	ND	ND	ND	0/5	1/5	0/5	0/5
total negativen	19	41	29	97	16	140	165
total positivep	77	48	62	55	131	1	0
total sero-converteds	4	10	9	9	11	0	0
total tested	100	99	100	161	158	141	165
	Interval	SNT							IPMA
Farm	in weeks	EMCV	EMCVi	PEV2	PEV2i	PEV7	PEV7i	LA	LA
TH	3	0/6	0/6	0/5	0/5	0/6	0/5	0/6	6/6
RB	5	1/7	1/9	0/6	2/6	1/8	0/6	0/13	7/9
HU	4	ND	0/5	0/5	0/5	ND	0/5	0/5	5/5
TS	3	0/10	0/10	0/7	0/4	0/10	0/7	ND	10/10
VL	3	ND	ND	1/5	0/5	ND	0/5	ND	5/5
JA	3	0/11	0/11	0/11	0/11	1/11	2/11	0/5	8/11
WE	4	1/7	1/6	1/6	1/7	1/7	1/7	0/7	7/7
GI	4	0/4	0/4	0/4	0/4	0/4	0/4	0/4	4/4
SE	5	0/8	0/8	0/6	1/8	0/8	1/5	0/8	6/8
KA	5	0/1	0/1	0/1	0/1	0/1	0/1	0/1	0/1
HO	3	0/6	0/6	0/6	0/6	0/6	0/6	0/6	4/6
NY	4	0/4	0/4	0/2	0/2	0/4	0/3	0/4	4/4
JN	3	0/10	0/10	1/10	0/9	0/10	0/10	0/10	5/10
KOf	3	0/10	0/10	2/10	2/10	1/10	3/10	ND	8/10
OE	9	0/6	0/6	1/6	1/5	ND	1/6	ND	4/6
LO	6	0/3	0/3	0/3	0/3	0/3	0/3	ND	3/3
WI	4	ND	ND	0/1	0/1	ND	0/1	ND	0/3
RR	3	0/8	1/8	0/8	0/8	0/8	0/8	ND	8/8
RY	4	0/4	ND	0/4	0/1	ND	1/4	ND	1/4
BE	5	ND	ND	0/10	0/10	ND	1/10	ND	0/10
BU	3	ND	ND	0/6	0/6	ND	0/6	ND	6/6
KR	3	ND	ND	0/4	0/4	ND	0/4	ND	1/4
KW	5	ND	ND	0/10	0/10	ND	1/10	ND	10/10
VR	5	ND	ND	0/6	1/6	ND	0/6	ND	6/6
HU	4	ND	ND	0/3	0/4	ND	0/3	ND	3/4
ME	3	ND	ND	0/5	0/5	ND	0/5	ND	2/5
total neg.n	15	29	0	0	2	1	69	15
total pos.p	88	74	144	138	90	136	0	27
total sero-converteds	2	3	6	8	4	10	0	123
total tested	105	107	150	146	96	147	69	165
The sera were tested in haemagglutinating inhibition (HAI) tests for the detection of antibody against haemagglutinating encephalitis virus (HEV), and swine influenza viruses H1N1 and H3N2, in enzyme-linked-immuno sorbent assays (ELISA) for the detection of antibody against the glycoprotein gI of pseudorabies virus (PRV), against porcine parvo virus (PPV), bovine viral diarrhea virus (BVDV), and hog cholera virus (HCV).
The sera were tested in serum neutralization tests (SNT) for the detection of neutralizing antibody directed against encephalomyocarditis virus (EMCV), the isolated (i) EMCV, porcine entero viruses (PEV) 2 and 7 and the PEV isolates (i), and against the Lelystad Agent (LA), and were tested in an immuno-peroxidase-monolayer-assay (IPMA) for the detection of antibody directed against the Lelystad Agent (LA).
f fattening pigs.
i time between sampling of the first and second serum.
n total number of pigs of which the first serum was negative in the test under study, and of which the second serum was also negative or showed a less than fourfold rise in titre.
p total number of pigs of which the first serum was positive and of which the second serum showed a less than fourfold rise in titre.
s total number of pigs of which the second serum had a fourfold or higher titre than the first serum in the test under study.
ND = not done.

[0155]

TABLE 5
Development of antibody directed against
Lelystad Agent as measured by IPMA.
A contact pigs serum titres in IPMA
		Weeks post contact:
	Pig	0	2	3	4	5
	c 836	0	10	640	640	640
	c 837	0	10	640	640	640
	c 821	0	640	640	640	640
	c 823	0	160	2560	640	640
	c 829	0	160	640	10240	10240
	c 832	0	160	640	640	2560
	c 813	0	640	2560	2560	2560
	c 815	0	160	640	640	640
B blood inoculated pigs serum titres in IPMA
	Weeks post inoculation:
	Pig	0	2	3	4	6
	b 809	0	640	2560	2560	2560
	b 817	0	160	640	640	640
	b 818	0	160	640	640	640
	b 820	0	160	640	640	640
	b 822	0	640	2560	2560	10240
	b 826	0	640	640	640	10240
	b 830	0	640	640	640	2560
	b 834	0	160	640	2560	640
	See Table 2 for description of the experiment. All pigs were bled at regular intervals and all sera were tested in an immuno-peroxidase-monolayer-assay (IPMA) for the detection of antibody directed against the Lelystad Agent (LA).

[0156]

TABLE 6
Experimental reproduction of MSD.
		No. of piglets
	Length	at birth	No. of	LA1 in piglets
	of	alive	dead	deaths	born	died in
Sow	gestation	(Number Ab pos)2	week 1	dead	week 1
52	113	12 (5)	3 (2)	6	2	4
965	116	3 (0)	9 (3)	2	4
997	114	9 (0)	1 (0)	0
1305	116	7 (0)	2 (0)	1
134	109	4 (4)	7 (4)	4	3
941	117	7	10
1056	113	7 (1)	3 (0)	4
1065	115	9	2
1 LA was isolated from lung, liver, spleen, kidney, or ascitic fluids.
2 Antibodies directed against LA were detected in serum samples taken before the piglets had sucked, or were detected in ascitic fluids of piglets born dead.

[0157]

TABLE 7
Reactivity in IPMA of a collection of field sera from
Europe and North America tested with LA
isolates from the Netherlands (NL1 and NL2),
Germany (GE1 and GE2), and the United States
(US1, US2 and US3).
Isolates:		NL1	NL2	GE1	GE2	US1	US2	US3
Sera from:
The Netherlands
TH-187		3.5t	3.5	2.5	3.5	−	−	−
TO-36		3.5	3.0	2.5	3.0	−	1.0	−
Germany
BE-352		4.0	3.5	2.5	3.0	−	1.5	−
BE-392		3.5	3.5	2.5	2.5	1.5	1.5	0.5
NI-f2	2.5	1.5	2.0	2.5	−	−	−
United Kingdom
PA-141615		4.0	3.0	3.0	3.5	−	−	−
PA-141617		4.0	3.5	3.0	3.5	−	2.5	2.0
PA-142440		3.5	3.0	2.5	3.5	−	2.0	2.5
Belgium
PE-1960		4.5	4.5	3.0	4.0	1.5	−	−
France
EA-2975		4.0	3.5	3.0	3.0	2.0	−	−
EA-2985		3.5	3.0	3.0	2.5	−	−	−
United States
SL-441		3.5	1.5	2.5	2.5	3.5	3.5	3.0
SL-451		3.0	2.0	2.5	2.5	3.5	4.5	4.0
AL-RP9577		1.5	−	−	1.0	3.0	4.0	2.5
AL-P10814/33		0.5	2.5	−	−	2.5	3.5	3.0
AL-4094A		−	−	−	−	1.0	2.0	0.5
AL-7525		−	−	−	−	−	1.0	−
JC-MN41		−	−	−	−	1.0	3.5	1.0
JC-MN44		−	−	−	−	2.0	3.5	2.0
JC-MN45		−	−	−	−	2.0	3.5	2.5
Canada
RB-16		2.5	−	3.0	2.0	3.0	3.5	−
RB-19		1.0	−	1.0	−	2.5	1.5	−
RB-22		1.5	−	2.0	2.5	2.5	3.5	−
RB-23		−	−	−	−	−	3.0	−
t = titre expressed as negative log;
− = negative

[0158]

TABLE 8
Reactivity in IPMA of a collection of experimental sera
raised against LA and SIRSV tested with
LA isolates from the Netherlands (NL1 and NL2),
Germany (GE1 and GE2), and the United States
(US1, US2 and US3).
Isolates:	NL1	NL2	GE1	GE2	US1	US2	US3
Sera:
anti-LA:
21	14 dpi	2.5t	2.0	2.5	3.0	1.5	2.0	1.5
	28 dpi	4.0	3.5	3.5	4.0	−	2.5	1.5
	42 dpi	4.0	3.5	3.0	3.5	1.5	2.5	2.0
23	14 dpi	3.0	2.0	2.5	3.0	1.0	2.0	1.0
	28 dpi	3.5	3.5	3.5	4.0	1.5	2.0	2.0
	42 dpi	4.0	4.0	3.0	4.0	−	2.5	2.5
25	14 dpi	2.5	2.0	2.5	3.0	1.5	2.0	1.0
	28 dpi	4.0	3.5	4.0	3.5	−	1.5	2.0
	42 dpi	3.5	4.0	3.5	3.5	1.5	2.0	2.0
29	14 dpi	3.5	3.5	3.0	3.5	−	2.0	1.5
	28 dpi	3.5	3.5	3.0	3.5	−	2.5	2.0
	42 dpi	4.0	3.5	3.5	4.0	1.5	2.5	2.5
anti-
SIRSV:
2B	20 dpi	−	−	−	−	2.0	2.0	−
	36 dpi	−	−	−	−	1.5	2.0	−
	63 dpi	−	−	−	−	1.0	1.0	−
9G	30 dpi	−	−	−	−	2.5	3.0	−
	44 dpi	−	−	−	−	2.5	3.5	−
	68 dpi	−	−	−	−	2.0	3.5	1.5
16W	25 dpi	−	−	−	−	2.0	3.0	−
	40 dpi	−	−	−	−	2.0	3.0	−
	64 dpi	−	−	−	−	2.5	2.5	1.5
16Y	36 dpi	−	−	−	−	1.0	3.0	1.0
	64 dpi	−	−	−	−	2.5	3.0	−
t = titer expressed as negative log;
− = negative

[0159]

TABLE 9
Characteristics of the ORFs of Lelystad Virus.
			Calculated
		No. of	size of the	number of
	Nucleotides	amino	unmodified	glycosylation
ORF	(first-last)	acids	peptide (kDa)	sites
ORF1A	212-7399	2396	260.0	3 (SEQ ID NO: 2)
ORF1B	7384-11772	1463	161.8	3 (SEQ ID NO: 3)
ORF2	11786-12532	249	28.4	2 (SEQ ID NO: 4)
ORF3	12394-13188	265	30.6	7 (SEQ ID NO: 5)
	12556-13188	211	24.5	4
ORF4	12936-13484	183	20.0	4 (SEQ ID NO: 6)
	12981-13484	168	18.4	4
	13068-13484	139	15.4	3
ORF5	13484-14086	201	22.4	2 (SEQ ID NO: 7)
ORF6	14077-14595	173	18.9	2 (SEQ ID NO: 8)
ORF7	14588-14971	128	13.8	1 (SEQ ID NO: 9)

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Claims

1. Composition of matter comprising isolated Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

2. Composition of matter comprising killed isolated Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

3. Composition of matter comprising attenuated isolated Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

4. Composition of matter comprising a recombinant vector derived from Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

5. Composition of matter comprising an isolated part or component of Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

6. Composition of matter comprising isolated or synthetic protein, (poly)peptide, or nucleic acid derived from Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

7. Composition of matter comprising recombinant nucleic acid which comprises a nucleotide sequence derived from the genome of Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

8. Composition of matter comprising recombinant nucleic acid which comprises a Lelystad Agent-specific nucleotide sequence shown in FIG. 1.

9. Composition of matter comprising recombinant nucleic acid which comprises a Lelystad Agent-specific nucleotide sequence selected from anyone of the Open Reading Frames shown in FIG. 1.

10. Composition of matter comprising a (poly)peptide having an amino acid sequence derived from a protein of Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, the (poly)peptide being produced by a cell capable of producing it due to genetic engineering with appropriate recombinant DNA.

11. Composition of matter comprising a (poly)peptide comprising a Lelystad Agent-specific amino acid sequence shown in FIG. 1.

12. Composition of matter comprising an isolated or synthetic antibody which specifically recognizes a part or component of Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

13. Composition of matter comprising a recombinant vector which contains nucleic acid comprising a nucleotide sequence coding for a protein or antigenic peptide derived from Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

14. Vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against Mystery Swine Disease, comprising Lelystad Agent which is the causative agent of Mystery swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, and a suitable carrier or adjuvant.

15. Vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against Mystery Swine Disease, comprising killed Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, and a suitable carrier or adjuvant.

16. Vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against Mystery Swine Disease, comprising attenuated Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, and a suitable carrier or adjuvant.

17. Vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against Mystery Swine Disease, comprising a recombinant vector which contains nucleic acid comprising a nucleotide sequence coding for a protein or antigenic peptide derived from Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.9 1) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, and a suitable carrier or adjuvant.

18. Vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against Mystery Swine Disease, comprising an antigenic part or component of Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, and a suitable carrier or adjuvant.

19. Vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against Mystery Swine Disease, comprising a protein or antigenic polypeptide derived from, or a peptide mimicking an antigenic component of, Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, and a suitable carrier or adjuvant.

20. Vaccine composition for vaccinating animals, in particular mammals, more in particular pigs or swine, to protect them against a disease caused by a pathogen, comprising a recombinant vector derived from Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, the nucleic acid of the recombinant vector comprising a nucleotide sequence coding for a protein or antigenic peptide derived from the pathogen, and a suitable carrier or adjuvant.

21. Diagnostic kit for detecting nucleic acid from Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, in a sample, in particular a biological samples such as blood or blood serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising a nucleic acid probe or primer which comprises a nucleotide sequence derived from the genome of Lelystad Agent, and suitable detection means of a nucleic acid detection assay.

22. Diagnostic kit for detecting antigen from Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, in a sample, in particular a biological sample such as blood or blood serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising an antibody which specifically recognizes a part or component of Lelystad Agent, and suitable detection means of an antigen detection assay.

23. Diagnostic kit for detecting an antibody which specifically recognizes Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, in a sample, in particular a biological sample such as blood or blood serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising an antigenic part or component of Lelystad Agent, and suitable detection means of an antibody detection assay.

24. Diagnostic kit for detecting an antibody which specifically recognizes Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, in a sample, in particular a biological sample such as blood or blood serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising a protein or antigenic polypeptide derived from Lelystad Agent, or a peptide mimicking an antigenic component of Lelystad Agent, and suitable detection means of an antibody detection assay.

25. Diagnostic kit for detecting an antibody which specifically recognizes Lelystad Agent which is the causative agent of Mystery Swine Disease, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, in a sample, in particular a biological sample such as blond or blond serum, sputum, saliva, or tissue, derived from an animal, in particular a mammal, more in particular a pig or swine, comprising killed, live or attenuated Lelystad Agent, and suitable detection means of an antibody detection assay.

26. A process for diagnosing whether an animal, in particular a mammal, more in particular a pig or swine, is contaminated with the causative agent of Mystery Swine Disease, comprising preparing a sample, in particular a biological sample such as blond or blond serum, sputum, saliva, or tissue, derived from the animal, and examining whether it contains Lelystad Agent nucleic acid, Lelystad Agent antigen, or antibody specifically recognizing Lelystad Agent, said Lelystad Agent being the causative agent of Mystery Swine Disease and essentially corresponding to the isolate Lelystad Agent (CDI-NL-2.91) deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

27. A diagnostic kit for detecting nucleic acid from Lelystad Agent, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, in a biological sample, derived from an animal, said diagnostic kit comprising: a nucleic acid probe or primer which comprises a nucleotide sequence essentially corresponding to the genome of Lelystad Agent, and means for detecting nucleic acid.

28. The diagnostic kit of claim 27 wherein the means for detecting a nucleic acid comprises a hybridization of the nucleic acid probe or primer.

29. The diagnostic kit of claim 28 wherein the means for detecting a nucleic acid comprises polymerase chain reaction (“PCR”).

30. A diagnostic kit for detecting an antibody which specifically recognizes Lelystad Agent in a biological sample derived from an animal, said kit comprising an antigen selected from the group consisting of virus, protein, polypeptide, and peptide, said antigen immunoreactive with serum antibodies of a sow, said serum antibodies obtained by: a) intranasally inoculating a specific pathogen free sow with two milliliters of a virus essentially corresponding to the virus identified as deposit number I- 1102, deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France (at passage level 3, titer 104.8TCID50 / milliliter); and further comprising b) collecting serum antibodies from the thus inoculated sow after 25 to 33 days, and means for detecting said antibody.

31. A diagnostic kit for detecting an antibody which specifically recognizes Lelystad Agent, said Lelystad Agent essentially corresponding to the isolated Lelystad Agent deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102, in a sample derived from an animal said diagnostic kit comprising: a protein or antigenic polypeptide derived from Lelystad Agent, or a peptide mimicking an antigenic component of Lelystad Agent, and means for detecting an antibody reacting with said protein or antigenic polypeptide derived from Lelystad Agent, or a peptide mimicking an antigenic component of Lelystad Agent.

32. A diagnostic kit for detecting an antibody which specifically recognizes a causative agent of Mystery Swine Disease, said causative agent being at least partially antigenically cross-reactive with Lelystad Agent essentially corresponding to the isolated Lelystad Agent deposited Jun. 5, 1991 with the Institut Pasteur; Paris, France, deposit number I-1102, in a sample derived from an animal, said diagnostic kit comprising said causative agent, and means for detecting said antibody.

33. The diagnostic kit of claim 32 wherein the causative agent is live.

34. A process for detecting a causative agent of Mystery Swine Disease in an animal, comprising preparing a sample derived from the animal, and examining whether the sample contains Lelystad Agent nucleic acid, Lelystad Agent antigen, or antibody specifically recognizing Lelystad Agent, said Lelystad Agent essentially corresponding to the isolate Lelystad Agent deposited Jun. 5, 1991 with the Institut Pasteur, Paris, France, deposit number I-1102.

35. The process according to claim 34 wherein said sample is serum taken from the animal.