A fast and robust method for full genome sequencing of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Type 1 and Type 2

Journal of Virological Methods

Volumn 193, Issue 2, 2013, Pages 697-705

  Kvisgaard, Lise K ^a   Hjulsager, Charlotte K ^a   Fahnøe, Ulrik ^a   Breum, Solvej Ø ^a   Ait Ali, Tahar ^b   Larsen, Lars E ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Full genome sequencing; Illumina HiSeq2000; Ion Torrent PGM sequencer; Next generation sequencing; PRRSV; Roche 454 FLX

Indexed keywords

VIRUS RNA;

ANALYZER; ANIMAL CELL; ARTERIVIRUS; ARTICLE; CELL CULTURE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS 1; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME VIRUS 2; PRIORITY JOURNAL; PROCESS DEVELOPMENT; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; VALIDATION STUDY; VIRUS GENOME;

FULL GENOME SEQUENCING; ILLUMINA HISEQ2000; ION TORRENT PGM SEQUENCER; NEXT GENERATION SEQUENCING; PRRSV; ROCHE 454 FLX;

ANIMALS; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SWINE; VIROLOGY;

EID: 84882998892     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2013.07.019     Document Type: Article

References (31)

1. Allende R., Lewis T.L., Lu Z., Rock D.L., Kutish G.F., Ali A., Doster A.R., Osorio F.A. North American and European porcine reproductive and respiratory syndrome viruses differ in non-structural protein coding regions. Journal of General Virology 1999, 80(Pt 2):307-315.
2. An T.Q., Tian Z.J., Xiao Y., Li R., Peng J.M., Wei T.C., Zhang Y., Zhou Y.J., Tong G.Z. Origin of highly pathogenic porcine reproductive and respiratory syndrome virus, China. Emerging Infectious Diseases 2010, 16:365-367.
3. 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. Journal of Virology 2006, 80:3994-4004.
4. Balka G., Hornyak A., Balint A., Benyeda Z., Rusvai M. Development of a one-step real-time quantitative PCR assay based on primer-probe energy transfer for the detection of porcine reproductive and respiratory syndrome virus. Journal of Virological Methods 2009, 158:41-45.
5. Benfield D.A., Nelson E., Collins J.E., Harris L., Goyal S.M., Robison D., Christianson W.T., Morrison R.B., Gorcyca D., Chladek D. Characterization of swine infertility and respiratory syndrome (SIRS) virus (isolate ATCC VR-2332). Journal of Veterinary Diagnostic Investigation 1992, 4:127-133.
6. Cavanagh D. Nidovirales: a new order comprising Coronaviridae and Arteriviridae. Archives of Virology 1997, 142:629-633.
7. Collins J.E., Benfield D.A., Christianson W.T., Harris L., Hennings J.C., Shaw D.P., Goyal S.M., McCullough S., Morrison R.B., Joo H.S. Isolation of swine infertility and respiratory syndrome virus (isolate ATCC VR-2332) in North America and experimental reproduction of the disease in gnotobiotic pigs. Journal of Veterinary Diagnostic Investigation 1992, 4:117-126.
8. Darwich L., Gimeno M., Sibila M., Diaz I., de la Torre E., Dotti S., Kuzemtseva L., Martin M., Pujols J., Mateu E. Genetic and immunobiological diversities of porcine reproductive and respiratory syndrome genotype I strains. Veterinary Microbiology 2011, 150:49-62.
9. Diaz I., Darwich L., Pappaterra G., Pujols J., Mateu E. Different European-type vaccines against porcine reproductive and respiratory syndrome virus have different immunological properties and confer different protection to pigs. Virology 2006, 351:249-259.
10. Fang Y., Rowland R.R., Roof M., Lunney J.K., Christopher-Hennings J., Nelson E.A. A full-length cDNA infectious clone of North American type 1 porcine reproductive and respiratory syndrome virus: expression of green fluorescent protein in the Nsp2 region. Journal of Virology 2006, 80:11447-11455.
11. 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. Journal of General Virology 2011, 92:1097-1106.
12. Glenn T.C. Field guide to next-generation DNA sequencers. Molecular Ecology Resources 2011, 11:759-769.
13. Jackova A., Vlasakova M., Leskova V., Vilcek S. Identification of a new unusual length polymorphism of the nucleocapsid protein in porcine reproductive and respiratory syndrome virus. Virus Genes 2012, 45:590-592.
14. Johnson C.R., Griggs T.F., Gnanandarajah J., Murtaugh M.P. Novel structural protein in porcine reproductive and respiratory syndrome virus encoded by an alternative ORF5 present in all arteriviruses. Journal of General Virology 2011, 92:1107-1116.
15. Kim H.S., Kwang J., Yoon I.J., Joo H.S., Frey M.L. Enhanced replication of porcine reproductive and respiratory syndrome (PRRS) virus in a homogeneous subpopulation of MA-104 cell line. Archives of Virology 1993, 133:477-483.
16. Meulenberg J.J., Bos-de Ruijter J.N., van De Graaf R., Wensvoort G., Moormann R.J. Infectious transcripts from cloned genome-length cDNA of porcine reproductive and respiratory syndrome virus. Journal of Virology 1998, 72:380-387.
17. Nielsen H.S., Liu G., Nielsen J., Oleksiewicz M.B., Botner A., Storgaard T., Faaberg K.S. Generation of an infectious clone of VR-2332, a highly virulent North American-type isolate of porcine reproductive and respiratory syndrome virus. Journal of Virology 2003, 77:3702-3711.
18. Oleksiewicz M.B., Botner A., Normann P. Porcine B-cells recognize epitopes that are conserved between the structural proteins of American- and European-type porcine reproductive and respiratory syndrome virus. Journal of General Virology 2002, 83:1407-1418.
19. Ostrowski M., Galeota J.A., Jar A.M., Platt K.B., Osorio F.A., Lopez O.J. Identification of neutralizing and nonneutralizing epitopes in the porcine reproductive and respiratory syndrome virus GP5 ectodomain. Journal of Virology 2002, 76:4241-4250.
20. Rasmussen T.B., Reimann I., Hoffmann B., Depner K., Uttenthal A., Beer M. Direct recovery of infectious pestivirus from a full-length RT-PCR amplicon. Journal of Virological Methods 2008, 149:330-333.
21. Rasmussen T.B., Reimann I., Uttenthal A., Leifer I., Depner K., Schirrmeier H., Beer M. Generation of recombinant pestiviruses using a full-genome amplification strategy. Veterinary Microbiology 2010, 142:13-17.
22. Snijder E.J., Meulenberg J.J. The molecular biology of arteriviruses. Journal of General Virology 1998, 79(Pt 5):961-979.
23. Stadejek T., Stankevicius A., Storgaard T., Oleksiewicz M.B., Belak S., Drew T.W., Pejsak Z. Identification of radically different variants of porcine reproductive and respiratory syndrome virus in Eastern Europe: towards a common ancestor for European and American viruses. Journal of General Virology 2002, 83:1861-1873.
24. Stadejek T., Oleksiewicz M.B., Potapchuk D., Podgorska K. Porcine reproductive and respiratory syndrome virus strains of exceptional diversity in eastern Europe support the definition of new genetic subtypes. Journal of General Virology 2006, 87:1835-1841.
25. 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. Archives of Virology 2008, 153:1479-1488.
26. Terpstra C., Wensvoort G., Pol J.M. Experimental reproduction of porcine epidemic abortion and respiratory syndrome (mystery swine disease) by infection with Lelystad virus: Koch's postulates fulfilled. Veterinary Quarterly 1991, 13:131-136.
27. 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 G.F. Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark. PLoS One 2007, 2:e526.
28. Untergasser A., Nijveen H., Rao X., Bisseling T., Geurts R., Leunissen J.A. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Research 2007, 35:W71-W74.
29. Van Doorsselaere J., Geldhof M., Nauwynck H.J., Delputte P.L. Characterization of a circulating PRRSV strain by means of random PCR cloning and full genome sequencing. Virology Journal 2011, 8:160.
30. Wensvoort G., Terpstra C., Pol J.M., Ter Laak E.A., Bloemraad M., De Kluyver E.P., Kragten C., Van Buiten L., den Besten A., Wagenaar F. Mystery swine disease in The Netherlands: the isolation of Lelystad virus. Veterinary Quarterly 1991, 13:121-130.
31. Wu W.H., Fang Y., Farwell R., Steffen-Bien M., Rowland R.R., Christopher-Hennings J., Nelson E.A. A 10-kDa structural protein of porcine reproductive and respiratory syndrome virus encoded by ORF2b. Virology 2001, 287:183-191.