Evolutionary Dynamics of a Highly Pathogenic Type 2 Porcine Reproductive and Respiratory Syndrome Virus: Analyses of Envelope Protein-Coding Genes

Transboundary and Emerging Diseases

Volumn 62, Issue 4, 2015, Pages 411-420

  Nguyen, V G ^a,b   Kim, H K ^c   Moon, H J ^d   Park, S J ^e   Chung, H C ^a   Choi, M K ^a   Park, B K ^a  

^a Seoul National University   (South Korea)

^b VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE   (Viet Nam)

^c Institute for Basic Science   (South Korea)

^d Green Cross Veterinary Products Co LTD   (South Korea)

^e Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

Author keywords

Envelope protein coding genes; Evolutionary dynamics; Highly pathogenic type 2 PRRSV

Indexed keywords

CODON; VIRUS ENVELOPE PROTEIN;

ANIMAL; BAYES THEOREM; CHINA; CODON; GENETICS; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; PATHOGENICITY; PHYLOGENY; PIG; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS; STATISTICAL MODEL; VIROLOGY;

ANIMALS; BAYES THEOREM; CHINA; CODON; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; SWINE; VIRAL ENVELOPE PROTEINS;

EID: 84934436387     PISSN: 18651674     EISSN: 18651682     Source Type: Journal    
DOI: 10.1111/tbed.12154     Document Type: Article

References (46)

1. Allende, R., T. L. Lewis, Z. Lu, D. L. Rock, G. F. Kutish, A. Ali, A. R. Doster, and F. A. Osorio, 1999: North American and European porcine reproductive and respiratory syndrome viruses differ in non-structural protein coding regions. J. Gen. Virol. 80, 307-315.
2. Allende, R., G. F. Kutish, W. Laegreid, Z. Lu, T. L. Lewis, D. L. Rock, J. Friesen, J. A. Galeota, A. R. Doster, and F. A. Osorio, 2000: Mutations in the genome of porcine reproductive and respiratory syndrome virus responsible for the attenuation phenotype. Arch. Virol. 145, 1149-1161.
3. An, T. Q., Z. J. Tian, Y. J. Zhou, Y. Xiao, J. M. Peng, J. Chen, Y. F. Jiang, X. F. Hao, and G. Z. Tong, 2011: Comparative genomic analysis of five pairs of virulent parental/attenuated vaccine strains of PRRSV. Vet. Microbiol. 149, 104-112.
4. Cancel-Tirado, S. M., R. B. Evans, and K. J. Yoon, 2004: Monoclonal antibody analysis of porcine reproductive and respiratory syndrome virus epitopes associated with antibody-dependent enhancement and neutralization of virus infection. Vet. Immunol. Immunopathol. 102, 249-262.
5. Chand, R. J., B. R. Trible, and R. R. R. Rowland, 2012: Pathogenesis of porcine reproductive and respiratory syndrome virus. Curr. Opin. Virol. 2, 256-263.
6. Das, P. B., P. X. Dinh, I. H. Ansari, M. de Lima, F. A. Osorio, and A. K. Pattnaik, 2010: The minor envelope glycoproteins GP2a and GP4 of porcine reproductive and respiratory syndrome virus interact with the receptor CD163. J. Virol. 84, 1731-1740.
7. Delisle, B., C. A. Gagnon, M. È. Lambert, and S. D'Allaire, 2012: Porcine reproductive and respiratory syndrome virus diversity of Eastern Canada swine herds in a large sequence dataset reveals two hypervariable regions under positive selection. Infect. Genet. Evol. 12, 1111-1119.
8. Drummond, A., and A. Rambaut, 2007: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214.
9. Duffy, S., L. A. Shackelton, and E. C. Holmes, 2008: Rates of evolutionary change in viruses: patterns and determinants. Nat. Rev. Genet. 9, 267-276.
10. Gray, R., J. Parker, P. Lemey, M. Salemi, A. Katzourakis, and O. Pybus, 2011: The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evol. Biol. 11, 131.
11. Grebennikova, T. V., D. F. Clouser, A. C. Vorwald, M. I. Musienko, W. L. Mengeling, K. M. Lager, R. D. Wesley, S. F. Biketov, A. D. Zaberezhny, T. I. Aliper, and E. A. Nepoklonov, 2004: Genomic characterization of virulent, attenuated, and revertant passages of a North American porcine reproductive and respiratory syndrome virus strain. Virology 321, 383-390.
12. Guindon, S., J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel, 2010: New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321.
13. Guo, B., K. M. Lager, J. N. Henningson, L. C. Miller, S. N. Schlink, M. A. Kappes, M. E. Jr Kehrli, S. L. Brockmeier, T. L. Nicholson, H.-C. Yang, and K. S. Faaberg, 2013: Experimental infection of United States swine with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus. Virology 435, 372-384.
14. Johnson, C. R., T. F. Griggs, J. Gnanandarajah, and M. P. Murtaugh, 2011: Novel structural protein in porcine reproductive and respiratory syndrome virus encoded by an alternative ORF5 present in all arteriviruses. J. Gen. Virol. 92, 1107-1116.
15. Kass, R. E., and A. E. Raftery, 1995: Bayes factors. J. Am. Stat. Assoc. 90, 773-795.
16. Kim, W. I., J. J. Kim, S. H. Cha, W. H. Wu, V. Cooper, R. Evans, E. J. Choi, and K. J. Yoon, 2013: Significance of genetic variation of PRRSV ORF5 in virus neutralization and molecular determinants corresponding to cross neutralization among PRRS viruses. Vet. Microbiol. 162, 10-22.
17. Kosakovsky Pond, S. L., S. D. W. Frost, Z. Grossman, M. B. Gravenor, D. D. Richman, and A. J. L. Brown, 2006: Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput. Biol. 2, e62.
18. Kumar, S., A. Skjaeveland, R. Orr, P. Enger, T. Ruden, B. H. Mevik, F. Burki, A. Botnen, and K. Shalchian- Tabrizi, 2009: AIR: a batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics 10, 357.
19. Lee, C., and D. Yoo, 2006: The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties. Virology 355, 30-43.
20. Lemey, P., S. L. Kosakovsky Pond, A. J. Drummond, O. G. Pybus, B. Shapiro, H. Barroso, N. Taveira, and A. Rambaut, 2007: Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput. Biol. 3, e29.
21. Leng, C. L., T. Q. An, J. Z. Chen, D. Q. Gong, J. M. Peng, Y. Q. Yang, J. Wu, J. J. Guo, D. Y. Li, Y. Zhang, Z. X. Meng, Y. Q. Wu, Z. J. Tian, and G. Z. Tong, 2012a: Highly pathogenic porcine reproductive and respiratory syndrome virus GP5 B antigenic region is not a neutralizing antigenic region. Vet. Microbiol. 159, 273-281.
22. Leng, X., Z. Li, M. Xia, X. Li, F. Wang, W. Wang, X. Zhang, and H. Wu, 2012b: Mutations in the genome of the highly pathogenic porcine reproductive and respiratory syndrome virus potentially related to attenuation. Vet. Microbiol. 157, 50-60.
23. Li, B., L. Fang, X. Guo, J. Gao, T. Song, J. Bi, K. He, H. Chen, and S. Xiao, 2011: Epidemiology and evolutionary characteristics of the porcine reproductive and respiratory syndrome virus in China between 2006 and 2010. J. Clin. Microbiol. 49, 3175-3183.
24. de Lima, M., I. H. Ansari, P. B. Das, B. J. Ku, F. J. Martinez-Lobo, A. K. Pattnaik, and F. A. Osorio, 2009: GP3 is a structural component of the PRRSV type II (US) virion. Virology 390, 31-36.
25. Liu, K., T. J. Warnow, M. T. Holder, S. M. Nelesen, J. Yu, A. P. Stamatakis, and C. R. Linder, 2012: SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst. Biol. 61, 90-106.
26. Mardassi, H., B. Massie, and S. Dea, 1996: Intracellular synthesis, processing, and transport of proteins encoded by ORFs 5 to 7 of porcine reproductive and respiratory syndrome virus. Virology 221, 98-112.
27. Murtaugh, M. P., T. Stadejek, J. E. Abrahante, T. T. Y. Lam, and F. C. C. Leung, 2010: The ever-expanding diversity of porcine reproductive and respiratory syndrome virus. Virus Res. 154, 18-30.
28. van Nieuwstadt, A. P., J. J. Meulenberg, A. van Essen-Zanbergen, A. Petersen-den Besten, R. J. Bende, R. J. Moormann, and G. Wensvoort, 1996: Proteins encoded by open reading frames 3 and 4 of the genome of Lelystad virus (Arteriviridae) are structural proteins of the virion. J. Virol. 70, 4767-4772.
29. Pond, S. L. K., S. D. W. Frost, and S. V. Muse, 2005: HyPhy: hypothesis testing using phylogenies. Bioinformatics 21, 676-679.
30. Shapiro, B., A. Rambaut, and A. J. Drummond, 2006: Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 23, 7-9.
31. Shi, M., T. T. Lam, C. C. Hon, M. P. Murtaugh, P. R. Davies, R. K. Hui, J. Li, L. T. Wong, C. W. Yip, J. W. Jiang, and F. C. Leung, 2010: Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses. J. Virol. 84, 8700-8711.
32. Snijder, E. J., and J. J. Meulenberg, 1998: The molecular biology of arteriviruses. J. Gen. Virol. 79, 961-979.
33. Song, J., D. Shen, J. Cui, and B. Zhao, 2010: Accelerated evolution of PRRSV during recent outbreaks in China. Virus Genes 41, 241-245.
34. Stadejek, T., A. Stankevicius, T. Storgaard, M. B. Oleksiewicz, S. Belak, T. W. Drew, and Z. Pejsak, 2002: Identification of radically different variants of porcine reproductive and respiratory syndrome virus in Eastern Europe: towards a common ancestor for European and American viruses. J. Gen. Virol. 83, 1861-1873.
35. Sun, L., Y. Li, R. Liu, X. Wang, F. Gao, T. Lin, T. Huang, H. Yao, G. Tong, H. Fan, Z. Wei, and S. Yuan, 2013: Porcine reproductive and respiratory syndrome virus ORF5a protein is essential for virus viability. Virus Res. 171, 178-185.
36. Tian, K., X. Yu, T. Zhao, Y. Feng, Z. Cao, C. Wang, Y. Hu, X. Chen, D. Hu, X. Tian, D. Liu, S. Zhang, X. Deng, Y. Ding, L. Yang, Y. Zhang, H. Xiao, M. Qiao, B. Wang, L. Hou, X. Wang, X. Yang, L. Kang, M. Sun, P. Jin, S. Wang, Y. Kitamura, J. Yan, and G. F. Gao, 2007: Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in china and molecular dissection of the unique hallmark. PLoS ONE 2, e526.
37. Vu, H. L. X., B. Kwon, K.-J. Yoon, W. W. Laegreid, A. K. Pattnaik, and F. A. Osorio, 2011: Immune evasion of porcine reproductive and respiratory syndrome virus through glycan shielding involves both glycoprotein 5 as well as glycoprotein 3. J. Virol. 85, 5555-5564.
38. Wei, Z., T. Lin, L. Sun, Y. Li, X. Wang, F. Gao, R. Liu, C. Chen, G. Tong, and S. Yuan, 2012: N-linked glycosylation of GP5 of porcine reproductive and respiratory syndrome virus is critically important for virus replication in vivo. J. Virol. 86, 9941-9951.
39. Welch, S. K., R. Jolie, D. S. Pearce, W. D. Koertje, E. Fuog, S. L. Shields, D. Yoo, and J. G. Calvert, 2004: Construction and evaluation of genetically engineered replication-defective porcine reproductive and respiratory syndrome virus vaccine candidates. Vet. Immunol. Immunopathol. 102, 277-290.
40. Wissink, E. H. J., M. V. Kroese, H. A. R. van Wijk, F. A. M. Rijsewijk, J. J. M. Meulenberg, and P. J. M. Rottier, 2005: Envelope protein requirements for the assembly of infectious virions of porcine reproductive and respiratory syndrome virus. J. Virol. 79, 12495-12506.
41. Wu, W.-H., Y. Fang, R. Farwell, M. Steffen-Bien, R. R. R. Rowland, J. Christopher-Hennings, and E. A. Nelson, 2001: A 10-kDa structural protein of porcine reproductive and respiratory syndrome virus encoded by ORF2b. Virology 287, 183-191.
42. Yu, X., N. Chen, L. Wang, J. Wu, Z. Zhou, J. Ni, X. Li, X. Zhai, J. Shi, and K. Tian, 2012: New genomic characteristics of highly pathogenic porcine reproductive and respiratory syndrome viruses do not lead to significant changes in pathogenicity. Vet. Microbiol. 158, 291-299.
43. Yu, X., N. Chen, X. Deng, Z. Cao, W. Han, D. Hu, J. Wu, S. Zhang, B. Wang, X. Gu, and K. Tian, 2013: Genomic sequencing reveals mutations potentially related to the overattenuation of a highly pathogenic porcine reproductive and respiratory syndrome virus. Clin. Vaccine Immunol. 20, 613-619.
44. Zhou, Y.-J., T.-Q. An, Y.-X. He, J.-X. Liu, H.-J. Qiu, Y.-F. Wang, and G. Tong, 2006: Antigenic structure analysis of glycosylated protein 3 of porcine reproductive and respiratory syndrome virus. Virus Res. 118, 98-104.
45. Zhou, L., S. Chen, J. Zhang, J. Zeng, X. Guo, X. Ge, D. Zhang, and H. Yang, 2009a: Molecular variation analysis of porcine reproductive and respiratory syndrome virus in China. Virus Res. 145, 97-105.
46. Zhou, L., J. Zhang, J. Zeng, S. Yin, Y. Li, L. Zheng, X. Guo, X. Ge, and H. Yang, 2009b: The 30-amino-acid deletion in the Nsp2 of highly pathogenic porcine reproductive and respiratory syndrome virus emerging in China is not related to its virulence. J. Virol. 83, 5156-5167.