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Genetic polymorphism of the nsp2 gene in North American type-Porcine reproductive and respiratory syndrome virus

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Abstract

We determined the complete nucleotide sequence of EDRD-1, a Japanese strain of the North American type-Porcine reproductive and respiratory syndrome virus (PRRSV), and identified a novel 117-base deletion and 108-base insertion previously reported in the nsp2 gene of the SP strain, which contains the largest genome among PRRSV strains. Based on genetic analysis of the partial nsp2 gene in 30 additional Japanese isolates and 50 strains from various countries, we classified North American-type PRRSVs into three nsp2-types, represented by EDRD-1, which contains the 117-base deletion and 108-base insertion; prototypic VR-2332, which does not contain the deletion and insertion; and SP, which contains only the 108-base insertion. The three nsp2-types were phylogenetically separated, suggesting that these structural changes only occurred at earlier stages of viral evolution. In the nsp2 genes, we identified an additional 19 deletions ranging from 3 to 378 bases and 2 insertions of 3 and 21 bases which were not common within each nsp2-type, suggesting that these changes occurred at later stages of viral evolution. In addition, our results suggest that the three nsp2-types can be rapidly differentiated by RT-PCR using their polymorphisms as natural tags.

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References

  1. Allende R, Lewis TL, Lu Z, Rock DL, Kutish GF, Ali A, Doster AR, Osorio FA (1999) North American and European porcine reproductive and respiratory syndrome viruses differ in non-structural protein coding regions. J Gen Virol 80:307–315

    PubMed  CAS  Google Scholar 

  2. Benfield DA, Collins JE, Dee SE, Halbur PG, Joo HS, Lager KM, Mengeling WL, Murtaugh MP, Rossow K, Stevenson GW, Zimmerman JJ (1999) Porcine reproductive and respiratory syndrome, 8th edn. Iowa State Press, Iowa

    Google Scholar 

  3. Cavanagh D (1997) Nidovirales: a new order comprising Coronaviridae and Arteriviridae. Arch Virol 142:629–633

    PubMed  CAS  Google Scholar 

  4. de Lima M, Pattnaik AK, Flores EF, Osorio FA (2006) Serologic marker candidates identified among B-cell linear epitopes of Nsp2 and structural proteins of a North American strain of porcine reproductive and respiratory syndrome virus. Virology 353:410–421

    Article  PubMed  Google Scholar 

  5. Dea S, Gagnon CA, Mardassi H, Pirzadeh B, Rogan D (2000) Current knowledge on the structural proteins of porcine reproductive and respiratory syndrome (PRRS) virus: comparison of the North American and European isolates. Arch Virol 145:659–688

    Article  PubMed  CAS  Google Scholar 

  6. Fang Y, Kim DY, Ropp S, Steen P, Christopher-Hennings J, Nelson EA, Rowland RR (2004) Heterogeneity in Nsp2 of European-like porcine reproductive and respiratory syndrome viruses isolated in the United States. Virus Res 100:229–235

    Article  PubMed  CAS  Google Scholar 

  7. Fang Y, Schneider P, Zhang WP, Faaberg KS, Nelson EA, Rowland RR (2007) Diversity and evolution of a newly emerged North American Type 1 porcine arterivirus: analysis of isolates collected between 1999 and 2004. Arch Virol 152:1009–1017

    Article  PubMed  CAS  Google Scholar 

  8. Forsberg R, Oleksiewicz MB, Petersen AM, Hein J, Botner A, Storgaard T (2001) A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease. Virology 289:174–179

    Article  PubMed  CAS  Google Scholar 

  9. Forsberg R, Storgaard T, Nielsen HS, Oleksiewicz MB, Cordioli P, Sala G, Hein J, Botner A (2002) The genetic diversity of European type PRRSV is similar to that of the North American type but is geographically skewed within Europe. Virology 299:38–47

    Article  PubMed  CAS  Google Scholar 

  10. Forsberg R (2005) Divergence time of porcine reproductive and respiratory syndrome virus subtypes. Mol Biol Evol 22:2131–2134

    Article  PubMed  CAS  Google Scholar 

  11. Gao ZQ, Guo X, Yang HC (2004) Genomic characterization of two Chinese isolates of porcine respiratory and reproductive syndrome virus. Arch Virol 149:1341–1351

    Article  PubMed  CAS  Google Scholar 

  12. Goldberg TL, Hahn EC, Weigel RM, Scherba G (2000) Genetic, geographical and temporal variation of porcine reproductive and respiratory syndrome virus in Illinois. J Gen Virol 81:171–179

    PubMed  CAS  Google Scholar 

  13. Han J, Wang Y, Faaberg KS (2006) Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus. Virus Res 122:175–182

    Article  PubMed  CAS  Google Scholar 

  14. Han J, Liu G, Wang Y, Faaberg KS (2007) Identification of nonessential regions of the nsp2 replicase protein of porcine reproductive and respiratory syndrome virus strain VR-2332 for replication in cell culture. J Virol 81:9878–9890

    Article  PubMed  CAS  Google Scholar 

  15. Hanada K, Suzuki Y, Nakane T, Hirose O, Gojobori T (2005) The origin and evolution of porcine reproductive and respiratory syndrome viruses. Mol Biol Evol 22:1024–1031

    Article  PubMed  CAS  Google Scholar 

  16. Kapur V, Elam MR, Pawlovich TM, Murtaugh MP (1996) Genetic variation in porcine reproductive and respiratory syndrome virus isolates in the midwestern United States. J Gen Virol 77:1271–1276

    Article  PubMed  CAS  Google Scholar 

  17. Keffaber KK (1989) Reproductive failure of unknown etiology. Am Assoc Swine Pract Newsl 1:1–9

    Google Scholar 

  18. Kim DY, Calvert JG, Chang KO, Horlen K, Kerrigan M, Rowland RR (2007) Expression and stability of foreign tags inserted into nsp2 of porcine reproductive and respiratory syndrome virus (PRRSV). Virus Res 128:106–114

    Article  PubMed  CAS  Google Scholar 

  19. Kim HS, Kwang J, Yoon IJ, Joo HS, Frey ML (1993) Enhanced replication of porcine reproductive and respiratory syndrome (PRRS) virus in a homogeneous subpopulation of MA-104 cell line. Arch Virol 133:477–483

    Article  PubMed  CAS  Google Scholar 

  20. Kuwahara H, Nunoya T, Tajima M, Kato A, Samejima T (1994) An outbreak of porcine reproductive and respiratory syndrome in Japan. J Vet Med Sci 56:901–909

    PubMed  CAS  Google Scholar 

  21. Labarque G, Van Reeth K, Nauwynck H, Drexler C, Van Gucht S, Pensaert M (2004) Impact of genetic diversity of European-type porcine reproductive and respiratory syndrome virus strains on vaccine efficacy. Vaccine 22:4183–4190

    Article  PubMed  CAS  Google Scholar 

  22. Li Y, Wang X, Bo K, Tang B, Yang B, Jiang W, Jiang P (2007) Emergence of a highly pathogenic porcine reproductive and respiratory syndrome virus in the Mid-Eastern region of China. Vet J 174:577–584

    Article  PubMed  CAS  Google Scholar 

  23. Mateu E, Martin M, Vidal D (2003) Genetic diversity and phylogenetic analysis of glycoprotein 5 of European-type porcine reproductive and respiratory virus strains in Spain. J Gen Virol 84:529–534

    Article  PubMed  CAS  Google Scholar 

  24. Mengeling WL, Lager KM, Vorwald AC (1995) Diagnosis of porcine reproductive and respiratory syndrome. J Vet Diagn Invest 7:3–16

    PubMed  CAS  Google Scholar 

  25. Meulenberg JJ, Hulst MM, de Meijer EJ, Moonen PL, den Besten A, de Kluyver EP, Wensvoort G, Moormann RJ (1993) Lelystad virus, the causative agent of porcine endemic abortion and respiratory syndrome (PEARS), is related to LDV and EAV. Virology 192:62–72

    Article  PubMed  CAS  Google Scholar 

  26. Murakami Y, Kato A, Tsuda T, Morozumi T, Miura Y, Sugimura T (1994) Isolation and serological characterization of porcine reproductive and respiratory syndrome (PRRS) viruses from pigs with reproductive and respiratory disorders in Japan. J Vet Med Sci 56:891–894

    PubMed  CAS  Google Scholar 

  27. Nelsen CJ, Murtaugh MP, Faaberg KS (1999) Porcine reproductive and respiratory syndrome virus comparison: divergent evolution on two continents. J Virol 73:270–280

    PubMed  CAS  Google Scholar 

  28. Nielsen HS, Oleksiewicz MB, Forsberg R, Stadejek T, Botner A, Storgaard T (2001) Reversion of a live porcine reproductive and respiratory syndrome virus vaccine investigated by parallel mutations. J Gen Virol 82:1263–1272

    PubMed  CAS  Google Scholar 

  29. Oleksiewicz MB, Botner A, Toft P, Normann P, Storgaard T (2001) Epitope mapping porcine reproductive and respiratory syndrome virus by phage display: the nsp2 fragment of the replicase polyprotein contains a cluster of B-cell epitopes. J Virol 75:3277–3290

    Article  PubMed  CAS  Google Scholar 

  30. Opriessnig T, Pallares FJ, Nilubol D, Vincent AL, Thacker EL, Vaughn EM, Roof M, Halbur PG (2005) Genomic homology of ORF 5 gene sequence between modified live vaccine virus and porcine reproductive and respiratory syndrome virus challenge isolates is not predictive of vaccine efficacy. J Swine Health Prod 13(5):246–253

    Google Scholar 

  31. Parvin JD, Wang LH (1984) Mechanisms for the generation of src-deletion mutants and recovered sarcoma viruses: identification of viral sequences involved in src deletions and in recombination with c-src sequences. Virology 138:236–245

    Article  PubMed  CAS  Google Scholar 

  32. Paton DJ, Brown IH, Edwards S, Wensvoort G (1991) ‘Blue ear’ disease of pigs. Vet Rec 128:617

    PubMed  CAS  Google Scholar 

  33. Pedersen KW, van der Meer Y, Roos N, Snijder EJ (1999) Open reading frame 1a-encoded subunits of the arterivirus replicase induce endoplasmic reticulum-derived double-membrane vesicles which carry the viral replication complex. J Virol 73:2016–2026

    PubMed  CAS  Google Scholar 

  34. Ropp SL, Wees CE, Fang Y, Nelson EA, Rossow KD, Bien M, Arndt B, Preszler S, Steen P, Christopher-Hennings J, Collins JE, Benfield DA, Faaberg KS (2004) Characterization of emerging European-like porcine reproductive and respiratory syndrome virus isolates in the United States. J Virol 78:3684–3703

    Article  PubMed  CAS  Google Scholar 

  35. Shen S, Kwang J, Liu W, Liu DX (2000) Determination of the complete nucleotide sequence of a vaccine strain of porcine reproductive and respiratory syndrome virus and identification of the Nsp2 gene with a unique insertion. Arch Virol 145:871–883

    Article  PubMed  CAS  Google Scholar 

  36. Snijder EJ, Meulenberg JJ (1998) The molecular biology of arteriviruses. J Gen Virol 79:961–979

    PubMed  CAS  Google Scholar 

  37. Snijder EJ, van Tol H, Roos N, Pedersen KW (2001) Non-structural proteins 2 and 3 interact to modify host cell membranes during the formation of the arterivirus replication complex. J Gen Virol 82:985–994

    PubMed  CAS  Google Scholar 

  38. Snijder EJ, Brinton MA, Faaberg KS, Godeny EK, Gorbalenya AE, MacLachlan NJ, Mengeling WL, Plagemann PG (2005) Family Arteriviridae. Elsevier Academic Press, California

    Google Scholar 

  39. Stadejek T, Oleksiewicz MB, Potapchuk D, Podgorska K (2006) Porcine reproductive and respiratory syndrome virus strains of exceptional diversity in eastern Europe support the definition of new genetic subtypes. J Gen Virol 87:1835–1841

    Article  PubMed  CAS  Google Scholar 

  40. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  41. Tian K, Yu X, Zhao T, Feng Y, Cao Z, Wang C, Hu Y, Chen X, Hu D, Tian X, Liu D, Zhang S, Deng X, Ding Y, Yang L, Zhang Y, Xiao H, Qiao M, Wang B, Hou L, Wang X, Yang X, Kang L, Sun M, Jin P, Wang S, Kitamura Y, Yan J, Gao GF (2007) Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark. PLoS ONE 2:e526

    Article  PubMed  Google Scholar 

  42. Wensvoort G, Terpstra C, Pol JM, ter Laak EA, Bloemraad M, de Kluyver EP, Kragten C, van Buiten L, den Besten A, Fea Wagenaar (1991) Mystery swine disease in The Netherlands: the isolation of Lelystad virus. Vet Q 13:121–130

    PubMed  CAS  Google Scholar 

  43. Wu WH, Fang Y, Farwell R, Steffen-Bien M, Rowland RR, Christopher-Hennings J, Nelson EA (2001) A 10-kDa structural protein of porcine reproductive and respiratory syndrome virus encoded by ORF2b. Virology 287:183–191

    Article  PubMed  CAS  Google Scholar 

  44. Yan Y, Guo X, Ge X, Chen Y, Cha Z, Yang H (2007) Monoclonal antibody and porcine antisera recognized B-cell epitopes of Nsp2 protein of a Chinese strain of porcine reproductive and respiratory syndrome virus. Virus Res 126:207–215

    Article  PubMed  CAS  Google Scholar 

  45. Yoshii M, Kaku Y, Murakami Y, Shimizu M, Kato K, Ikeda H (2005) Genetic variation and geographic distribution of porcine reproductive and respiratory syndrome virus in Japan. Arch Virol 150:2313–2324

    Article  PubMed  CAS  Google Scholar 

  46. Ziebuhr J, Snijder EJ, Gorbalenya AE (2000) Virus-encoded proteinases and proteolytic processing in the Nidovirales. J Gen Virol 81:853–879

    PubMed  CAS  Google Scholar 

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Acknowledgments

We thank Dr. H. Kuwahara, Nippon Institute for Biological Science, and Dr. T. Saito, Tochigi Livestock Hygiene Service Center, for providing Japanese isolates Gu922 M and Jtg1, respectively. We also thank Dr. Y. Murakami, National Institute of Animal Health, for providing the EDRD-1 strain and the lung homogenate from which it had been isolated. We also thank Dr. Y. Kaku, National Institute of Health, and Dr. T. Sekizaki, Dr. M. Osaki, and Dr. I. Yamane, National Institute of Animal Health, and Dr. K. Tamura, Tokyo Metropolitan University, and Dr. N. Saito, National Institute of Genetics, for their helpful suggestion.

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Author notes

  1. Masaaki Yoshii

    Present address: Himeji Elsa Animal Hospital, Himeji, Hyogo, 670-0811, Japan

  2. Hidetoshi Ikeda

    Present address: Laboratory of Veterinary Public Health, School of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo, 180-8602, Japan

Authors and Affiliations

  1. Research Team for Viral Diseases, National Institute of Animal Health, Tsukuba, Ibaraki, 305-0856, Japan

    Masaaki Yoshii, Tatsuyuki Okinaga, Ayako Miyazaki & Hiroshi Tsunemitsu

  2. Research Team for Zoonotic Diseases, National Institute of Animal Health, Tsukuba, Ibaraki, Japan

    Kanako Kato & Hidetoshi Ikeda

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  1. Masaaki Yoshii
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  2. Tatsuyuki Okinaga
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Correspondence to Masaaki Yoshii.

Additional information

The GenBank/EMBL/DDBJ accession numbers of the sequences reported in this paper are AB288110–AB288139 and AB288356.

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705_2008_98_MOESM1_ESM.ppt

Amino acid alignment of the three nsp2-types in nsp2. Dots and hyphens represent identical amino acids and gapped positions, respectively. B-cell epitopes identified in NVSL97-7895 [1] and BJ-4 strains [2] are underlined. Shaded areas represent positions of possible deletion ranges. a Alignment of nsp2 aa positions 423-866 (based on the SP strain) in 31 Japanese isolates and 50 strains from other countries. b Alignment of nsp2 aa 297-444 (based on the SP strain) in Jnt1 and representative strains. (PPT 62 kb).

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Yoshii, M., Okinaga, T., Miyazaki, A. et al. Genetic polymorphism of the nsp2 gene in North American type-Porcine reproductive and respiratory syndrome virus . Arch Virol 153, 1323–1334 (2008). https://doi.org/10.1007/s00705-008-0098-6

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