Genomic evolution of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) isolates revealed by deep sequencing

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Brar, Manreetpal Singh ^a   Shi, Mang ^b   Hui, Raymond Kin Hi ^a   Leung, Frederick Chi Ching ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTERIVIRUS; ARTICLE; CODON; CONTROLLED STUDY; DELETION MUTANT; ENDEMIC DISEASE; GENE DELETION; GENE FREQUENCY; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; GEOGRAPHIC ORIGIN; HONG KONG; HUMAN; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; STRAIN DIFFERENCE; STRUCTURAL GENOMICS; STRUCTURAL HOMOLOGY; VIRUS GENOME; VIRUS ISOLATION; VIRUS STRAIN; ANIMAL; CLASSIFICATION; EVOLUTION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SWINE; VIROLOGY;

MESSENGER RNA;

ANIMALS; BIOLOGICAL EVOLUTION; GENOME, VIRAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PHYLOGENY; PORCINE REPRODUCTIVE AND RESPIRATORY SYNDROME; PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SWINE;

EID: 84899125164     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0088807     Document Type: Article

References (50)

1. Nodelijk G (2002) Porcine reproductive and respiratory syndrome (PRRS) with special reference to clinical aspects and diagnosis: a review. Veterinary quarterly 24: 96-100.
2. Hill H (1990) Overview and history of mystery swine disease (swine infertility/respiratory syndrome). PrOf Mystery Swine Dis Committee: 29-31.
3. Paton D (1995) Porcine reproductive and respiratory syndrome (blue-eared pig disease). Reviews in Medical Microbiology 6: 119.
4. Edwards S, Robertson I, Wilesmith J, Ryan J, Kilner C, et al. (1992) PRRS ("blue-eared pig disease") in Great Britain. AASP Newsletter 4: 32-36.
5. Plana J, Vayreda M, Vilarrasa J, Bastons M, Rosell R, et al. (1992) Porcine epidemic abortion and respiratory syndrome (mystery swine disease). Isolation in Spain of the causative agent and experimental reproduction of the disease. Veterinary microbiology 33: 203-211.
6. Wensvoort G, Terpstra C, Pol J, Ter Laak E, Bloemraad M, et al. (1991) Mystery swine disease in The Netherlands: the isolation of Lelystad virus. The Veterinary Quarterly 13: 121.
7. Baoqing G (1996) Isolation and Identification of Porcine Reproductory and Respiratory Syndrome (PRRS) Virus from aborted fetuses suspected of PRRS [J]. Chinese Journal of Preventive Veterinary Medicine 2: 1-5.
8. Kweon CH, Kwon BJ, Lee HJ (1994) Isolation of porcine reproductive and respiratory syndrome virus (PRRSV) in Korea. Korean J Vet Res 34: 77-83.
9. Shimizu M, Yamada S, Murakami Y, Morozumi T, Kobayashi H, et al. (1994) Isolation of porcine reproductive and respiratory syndrome (PRRS) virus from Heko-Heko disease of pigs. The Journal of veterinary medical science/the Japanese Society of Veterinary Science 56: 389.
10. Damrongwatanapokin S, Arsayuth K, Kongkrong C, Parchariyanon S, Pinyochon W, et al. (1996) Serological studies and isolation of porcine reproductive and respiratory syndrome (PRRS) virus in Thailand. J Thai Vet Med Assoc 47: 19-30.
11. Neumann EJ, Kliebenstein JB, Johnson CD, Mabry JW, Bush EJ, et al. (2005) Assessment of the economic impact of porcine reproductive and respiratory syndrome on swine production in the United States. Journal of the American Veterinary Medical Association 227: 385-392. (Pubitemid 41098522)
12. Murtaugh M, Elam M, Kakach L (1995) Comparison of the structural protein coding sequences of the VR-2332 and Lelystad virus strains of the PRRS virus. Archives of virology 140: 1451-1460.
13. Nelsen CJ, Murtaugh MP, Faaberg KS (1999) Porcine reproductive and respiratory syndrome virus comparison: divergent evolution on two continents. Journal of virology 73: 270.
14. Dea S, Gagnon C, 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. Archives of virology 145: 659-688. (Pubitemid 30306142)
15. Kim WI, Yoon KJ (2008) Molecular assessment of the role of envelope-associated structural proteins in cross neutralization among different PRRS viruses. Virus genes 37: 380-391.
16. Magar R, Larochelle R, Dea S, Gagnon C, Nelson E, et al. (1995) Antigenic comparison of Canadian and US isolates of porcine reproductive and respiratory syndrome virus using monoclonal antibodies to the nucleocapsid protein. Canadian Journal of Veterinary Research 59: 232.
17. Shi M, Lam TTY, Hon CC, Hui RKH, Faaberg KS, et al. (2010) Molecular epidemiology of PRRSV: a phylogenetic perspective. Virus Research.
18. Shi M, Lam TTY, Hon CC, Murtaugh MP, Davies PR, et al. (2010) Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses. Journal of virology 84: 8700.
19. Han J, Wang Y, Faaberg KS (2006) Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus. Virus Research 122: 175-182. (Pubitemid 44637246)
20. Tian K, Yu X, Zhao T, Feng Y, Cao Z, et al. (2007) Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark. PLoS One 2: e526.
21. Halbur PG, Bush E (1997) Update on abortion storms and sow mortality. Swine Health Prod 5: 73.
22. Lauring AS, Andino R (2010) Quasispecies theory and the behavior of RNA viruses. PLoS Pathogens 6: e1001005.
23. Murtaugh MP, Yuan S, Nelson EA, Faaberg KS (2002) Genetic interaction between porcine reproductive and respiratory syndrome virus (PRRSV) strains in cell culture and in animals. Journal of Swine Health and Production 10: 15-22.
24. van Vugt JJFA, Storgaard T, Oleksiewicz MB, Bøtner A (2001) High frequency RNA recombination in porcine reproductive and respiratory syndrome virus occurs preferentially between parental sequences with high similarity. Journal of general virology 82: 2615-2620. (Pubitemid 32998639)
25. Yuan S, Nelsen CJ, Murtaugh MP, Schmitt BJ, Faaberg KS (1999) Recombination between North American strains of porcine reproductive and respiratory syndrome virus. Virus Research 61: 87-98. (Pubitemid 29276874)
26. Zhou Z, Ni J, Cao Z, Han X, Xia Y, et al. (2011) The epidemic status and genetic diversity of 14 highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) isolates from China in 2009. Veterinary microbiology 150: 257-269.
27. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32: 1792-1797.
28. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution 28: 2731-2739.
29. Team RC (2008) R: A language and environment for statistical computing. R Foundation Statistical Computing.
30. Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome research 19: 1639-1645.
31. Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562-563.
32. Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265: 218-225. (Pubitemid 30022217)
33. Martin D, Posada D, Crandall K, Williamson C (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Research & Human Retroviruses 21: 98-102. (Pubitemid 40179806)
34. Smith JM (1992) Analyzing the mosaic structure of genes. Journal of Molecular Evolution 34: 126-129.
35. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proceedings of the National Academy of Sciences 98: 13757-13762. (Pubitemid 33115971)
36. Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
37. Holmes EC, Worobey M, Rambaut A (1999) Phylogenetic evidence for recombination in dengue virus. Molecular biology and evolution 16: 405-409. (Pubitemid 29119977)
38. Boni MF, Posada D, Feldman MW (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035-1047. (Pubitemid 46961105)
39. Martin DP, Lemey P, Lott M, Moulton V, Posada D, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.
40. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS One 7: e46688.
41. Bromberg Y, Rost B (2007) SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic acids research 35: 3823-3835. (Pubitemid 47244674)
42. Opriessnig T, Halbur P, Yoon KJ, Pogranichniy R, Harmon K, et al. (2002) Comparison of molecular and biological characteristics of a modified live porcine reproductive and respiratory syndrome virus (PRRSV) vaccine (ingelvac PRRS MLV), the parent strain of the vaccine (ATCC VR2332), ATCC VR2385, and two recent field isolates of PRRSV. Journal of virology 76: 11837-11844. (Pubitemid 35304284)
43. Duan X, Nauwynck H, Pensaert M (1997) Effects of origin and state of differentiation and activation of monocytes/macrophages on their susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV). Archives of virology 142: 2483-2497. (Pubitemid 28017268)
44. Nielsen HS, Oleksiewicz MB, Forsberg R, Stadejek T, Bøtner A, et al. (2001) Reversion of a live porcine reproductive and respiratory syndrome virus vaccine investigated by parallel mutations. Journal of general virology 82: 1263-1272. (Pubitemid 32519757)
45. Storgaard T, Oleksiewicz M, Bøtner A (1999) Examination of the selective pressures on a live PRRS vaccine virus. Archives of virology 144: 2389-2401. (Pubitemid 30057177)
46. Fang Y, Kim D-Y, Ropp S, Steen P, Christopher-Hennings J, et al. (2004) Heterogeneity in Nsp2 of European-like porcine reproductive and respiratory syndrome viruses isolated in the United States. Virus Research 100: 229-235. (Pubitemid 38293047)
47. Yoshii M, Okinaga T, Miyazaki A, Kato K, Ikeda H, et al. (2008) Genetic polymorphism of the nsp2 gene in North American type-Porcine reproductive and respiratory syndrome virus. Archives of virology 153: 1323-1334.
48. Roongtham K, Suparlark NNA, Alongkorn A, Roongroje T (2010) NSP2 gene variation of the North American genotype of the Thai PRRSV in central Thailand. Virology Journal 7.
49. Han J, Wang Y, Faaberg KS (2006) Complete genome analysis of RFLP 184 isolates of porcine reproductive and respiratory syndrome virus. Virus Research 122: 175-182. (Pubitemid 44637246)
50. Zhou L, Zhang J, Zeng J, Yin S, Li Y, et al. (2009) 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. Journal of virology 83: 5156-5167.