Observation of high recombination occurrence of Porcine Reproductive and Respiratory Syndrome Virus in field condition

Virus Research

Volumn 194, Issue , 2014, Pages 159-166

  Franzo, Giovanni ^a   Cecchinato, Mattia ^a   Martini, Marco ^a   Ceglie, Letizia ^b   Gigli, Alessandra ^b   Drigo, Michele ^a  

^a Production and Health   (Italy)

^b ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLE VENEZIE   (Italy)

Author keywords

Italy; ORF5; ORF7; PRRSV; Recombination

Indexed keywords

ARTERIVIRUS; ARTICLE; COMPUTER MODEL; EVOLUTION; EXPERIMENTAL STUDY; FIELD STUDY; GENBANK; GENE SEQUENCE; GENETIC RECOMBINATION; GEOGRAPHY; IN VITRO STUDY; ITALY; NONHUMAN; PHYSICAL CHEMISTRY; PROGENY; VIRUS STRAIN; ANIMAL; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; OPEN READING FRAME; PIG; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS; VIROLOGY;

PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS;

VIRUS RNA;

ANIMALS; GENETIC VARIATION; ITALY; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; RECOMBINATION, GENETIC; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 84920555095     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2014.08.005     Document Type: Article

References (63)

1. Anisimova M., Gil M., Dufayard J.-F., Dessimoz C., Gascuel O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst. Biol. 2011, 60:685-699.
2. Ansari I.H., Kwon B., Osorio F.A., Pattnaik A.K. Influence of N-linked glycosylation of porcine reproductive and respiratory syndrome virus GP5 on virus infectivity, antigenicity, and ability to induce neutralizing antibodies. J. Virol. 2006, 80:3994.
3. Balka G., Hornyák A., Bálint A., Kiss I., Kecskeméti S., Bakonyi T., Rusvai M. Genetic diversity of porcine reproductive and respiratory syndrome virus strains circulating in Hungarian swine herds. Vet. Microbiol. 2008, 127:128.
4. Bielejec F., Rambaut A., Suchard M.A., Lemey P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 2011, 27:2910-2912.
5. Chen N., Yu X., Wang L., Wu J., Zhou Z., Ni J., Li X., Zhai X., Tian K. Two natural recombinant highly pathogenic porcine reproductive and respiratory syndrome viruses with different pathogenicities. Virus Genes 2013, 46:473-478.
6. Cho J.G., Dee S.A. Porcine reproductive and respiratory syndrome virus. Theriogenology 2006, 66:655-662.
7. Darriba D., Taboada G.L., Doallo R., Posada D. JModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 2012, 9:772.
8. Darwich L., Díaz I., Mateu E. Certainties, doubts and hypotheses in porcine reproductive and respiratory syndrome virus immunobiology. Virus Res. 2010, 154:123-132.
9. Díaz I., Pujols J., Ganges L., Gimeno M., Darwich L., Domingo M., Mateu E. In silico prediction and ex vivo evaluation of potential T-cell epitopes in glycoproteins 4 and 5 and nucleocapsid protein of genotype-I (European) of porcine reproductive and respiratory syndrome virus. Vaccine 2009, 27:5603.
10. Dokland T. The structural biology of PRRSV. Virus Res. 2010, 154:86.
11. Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29:1969.
12. Fang Y., Schneider P., Zhang W.P., Faaberg K.S., Nelson E.A., Rowland R.R.R. Diversity and evolution of a newly emerged North American Type 1 porcine arterivirus: analysis of isolates collected between 1999 and 2004. Arch. Virol. 2007, 152:1009-1017.
13. Firth A.E., Zevenhoven-Dobbe J.C., Wills N.M., Go Y.Y., Balasuriya U.B., Atkins J.F., Snijder E.J., Posthuma C.C. Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production. J. Gen. Virol. 2011, 92:1097-1106.
14. Forsberg R., Storgaard T., Nielsen H.S., Oleksiewicz M.B., Cordioli P., Sala G., Hein J., Bøtner A. The genetic diversity of European type PRRSV is similar to that of the North American type but is geographically skewed within Europe. Virology 2002, 299:38-47.
15. Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
16. Gupta R., Jung E., Brunak S. Prediction of N-glycosylation sites in human proteins 2004, Available from:. http://www.cbs.dtu.dk/services/NetNGlyc/.
17. Gustiananda M. Immunoinformatics analysis of H5N1 proteome for designing an epitope-derived vaccine and predicting the prevalence of pre-existing cellular-mediated immunity toward bird flu virus in Indonesian population. Immunome Res. 2011, 7:1.
18. Holmes E.C. The Evolution and Emergence of RNA Viruses 2009, Oxford University Press, USA.
19. Kass E.R., Raftery E.A. Bayes factors. J. Am. Stat. Assoc. 1995, 90:773-795.
20. Kim W.-I., Kim J.-J., Cha S.-H., Wu W.-H., Cooper V., Evans R., Choi E.-J., Yoon K.-J. Significance of genetic variation of PRRSV ORF5 in virus neutralization and molecular determinants corresponding to cross neutralization among PRRS viruses. Vet. Microbiol. 2013, 162:10-22.
21. Korber B., LaBute M., Yusim K. Immunoinformatics comes of age. PLoS Comput. Biol. 2006, 2:0484.
22. Lai M.M.C. Recombination in large RNA viruses: coronaviruses. Semin. Virol. 1996, 7:381.
23. Larsen J.E., Lund O., Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res. 2006, 2:2.
24. Lemey P., Rambaut A., Drummond A.J., Suchard M.A. Bayesian phylogeography finds its roots. PLoS Comput. Biol. 2009, 5:e1000520.
25. Li B., Fang L., Xu Z., Liu S., Gao J., Jiang Y., Chen H., Xiao S. Recombination in vaccine and circulating strains of porcine reproductive and respiratory syndrome viruses. Emerg. Infect. Dis. 2009, 15:2032-2035.
26. Liu D., Zhou R., Zhang J., Zhou L., Jiang Q., Guo X., Ge X., Yang H. Recombination analyses between two strains of porcine reproductive and respiratory syndrome virus in vivo. Virus Res. 2011, 155:473-486.
27. Maddison W., Maddison P.D.R. Mesquite: a modular system for evolutionary analysis 2011.
28. Martin D.P., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26:2462-2463.
29. Martínez-Lobo F.J., Díez-Fuertes F., Simarro I., Castro J.M., Prieto C. Porcine reproductive and respiratory syndrome virus isolates differ in their susceptibility to neutralization. Vaccine 2011, 29:6928-6940.
30. Mateu E., Diaz I. The challenge of PRRS immunology. Vet. J. 2008, 177:345-351.
31. Mateu E., Díaz I., Darwich L., Casal J., Martín M., Pujols J. Evolution of ORF5 of Spanish porcine reproductive and respiratory syndrome virus strains from 1991 to 2005. Virus Res. 2006, 115:198-206.
32. Mengeling W.L. The potential role of genetic recombination in the evolution of new strains of porcine reproductive and respiratory syndrome virus (PRRSV). J. Swine Health Prod. 2002, 10:273-275.
33. Meulenberg J.J. PRRSV, the virus. Vet. Res. 2000, 31:11-21.
34. Murtaugh M.P., Stadejek T., Abrahante J.E., Lam T.T., Leung F.C. The ever-expanding diversity of porcine reproductive and respiratory syndrome virus. Virus Res. 2010, 154:18-30.
35. Murtaugh M.P., Yuan S., Faaberg K.S. Appearance of novel PRRSV isolates by recombination in the natural environment. Adv. Exp. Med. Biol. 2001, 494:31-36.
36. Neumann E.J., Kliebenstein J.B., Johnson C.D., Mabry J.W., Bush E.J., Seitzinger A.H., Green A.L., Zimmerman J.J. Assessment of the economic impact of porcine reproductive and respiratory syndrome on swine production in the United States. J. Am. Vet. Med. Assoc. 2005, 227:385-392.
37. Nielsen M., Lund O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics 2009, 10:296. 10.1186/1471-2105-10-296.
38. Nieuwenhuis N., Duinhof T.F., van Nes A. Economic analysis of outbreaks of porcine reproductive and respiratory syndrome virus in nine sow herds. Vet. Rec. 2012, 170:225.
39. Oleksiewicz M.B., Bøtner A., Madsen K.G., Storgaard T. Sensitive detection and typing of porcine reproductive and respiratory syndrome virus by RT-PCR amplification of whole viral genes. Vet. Microbiol. 1998, 64:7-22.
40. Pasternak A.O., Spaan W.J.M., Snijder E.J. Nidovirus transcription: how to make sense. . .?. J. Gen. Virol. 2006, 87:1403-1421.
41. Penn O., Privman E., Ashkenazy H., Landan G., Graur D., Pupko T. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 2010, 38:W23-W28.
42. Persia D., Pacciarini M., Cordioli P.S. Evaluation of three RT-PCR assays for the detection of porcine and respiratory syndrome virus (PRRSV) in diagnostic samples. Proceedings of the 10th International Symposium of Veterinary Laboratory Diagnosticians and OIE Seminar on Biotechnologies 2001, 440-441.
43. Pesch S., Meyer C., Ohlinger V.F. New insights into the genetic diversity of European porcine reproductive and respiratory syndrome virus (PRRSV). Vet. Microbiol. 2005, 107:31-48.
44. Pesente P., Rebonato V., Sandri G., Giovanardi D., Ruffoni L.S., Torriani S. Phylogenetic analysis of ORF5 and ORF7 sequences of porcine reproductive and respiratory syndrome virus (PRRSV) from PRRS-positive Italian farms: a showcase for PRRSV epidemiology and its consequences on farm management. Vet. Microbiol. 2006, 114:214-224.
45. Plagemann P. GP5 ectodomain epitope of porcine reproductive and respiratory syndrome virus, strain Lelystad virus. Virus Res. 2004, 102:225-230.
46. Shi M., Holmes E.C., Brar M.S., Leung F.C. Recombination is associated with an outbreak of novel highly pathogenic porcine reproductive and respiratory syndrome viruses in china. J. Virol. 2013, 87:10904-10907.
47. Shi M., Lam T.T., Hon C.C., Hui R.K., Faaberg K.S., Wennblom T., Murtaugh M.P., Stadejek T., Leung F.C. Molecular epidemiology of PRRSV: a phylogenetic perspective. Virus Res. 2010, 154:7-17.
48. Shi M., Lam T.T., Hon C.C., Murtaugh M.P., Davies P.R., Hui R.K., Li J., Wong L.T., Yip C.-W., Jiang J.-W., Leung F.C. Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses. J. Virol. 2010, 84:8700-8711.
49. Shimodaira H., Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2002, 17:1246.
50. Silvestro D., Michalak I. RaxmlGUI: a graphical front-end for RAxML. Organ. Divers. Evol. 2012, 12:335.
51. Simon-Loriere E., Holmes E.C. Why do RNA viruses recombine?. Nat. Rev. Microbiol. 2011, 9:617-626.
52. Stadejek T., Oleksiewicz M.B., Potapchuk D., Podgórska K. Porcine reproductive and respiratory syndrome virus strains of exceptional diversity in eastern Europe support the definition of new genetic subtypes. J. Gen. Virol. 2006, 87:1835-1841.
53. Stadejek T., Oleksiewicz M.B., Scherbakov A.V., Timina A.M., Krabbe J.S., Chabros K., Potapchuk D. Definition of subtypes in the European genotype of porcine reproductive and respiratory syndrome virus: nucleocapsid characteristics and geographical distribution in Europe. Arch. Virol. 2008, 153:1479-1488.
54. Stadejek T., Stankevicius A., Murtaugh M.P., Oleksiewicz M.B. Molecular evolution of PRRSV in Europe: current state of play. Vet. Microbiol. 2013, 165:21-28.
55. Stranzl T., Larsen M.V., Lundegaard C., Nielsen M. NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics 2010, 62:357.
56. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
57. van Vugt J., Storgaard T., Oleksiewicz M.B., Bøtner A. High frequency RNA recombination in porcine reproductive and respiratory syndrome virus occurs preferentially between parental sequences with high similarity. J. Gen. Virol. 2001, 82:2615-2620.
58. Vanhee M., Van Breedam W., Costers S., Geldhof M., Noppe Y., Nauwynck H. Characterization of antigenic regions in the porcine reproductive and respiratory syndrome virus by the use of peptide-specific serum antibodies. Vaccine 2011, 29:4794-4804.
59. Vu H.L.X., Kwon B., Yoon K., Laegreid J., Pattnaik W.W., Osorio A.K.F.A. Immune evasion of porcine reproductive and respiratory syndrome virus through glycan shielding involves both glycoprotein 5 as well as glycoprotein 3. J. Virol. 2011, 85:5555-5564.
60. Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.C., Williams K.L., Appel R.D., Hochstrasser D.F. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. (Clifton, N.J.) 1999, 112:531.
61. Yoon S.H., Kim H., Park B., Kim H. Tracing the genetic history of porcine reproductive and respiratory syndrome viruses derived from the complete ORF 5-7 sequences: a Bayesian coalescent approach. Arch. Virol. 2012, 157:2143-2151.
62. Yoshii M., Okinaga T., Miyazaki A., Kato K., Ikeda H., Tsunemitsu H. Genetic polymorphism of the nsp2 gene in North American type-porcine reproductive and respiratory syndrome virus. Arch. Virol. 2008, 153:1323-1334.
63. Yuan S.S., Nelsen C.J., Murtaugh M.P., Schmitt B.J., Faaberg K.S. Recombination between North American strains of porcine reproductive and respiratory syndrome virus. Virus Res. 1999, 61:87-98.