title: Emergence of mosaic recombinant strains potentially associated with vaccine JXA1-R and predominant circulating strains of porcine reproductive and respiratory syndrome virus in different provinces of China.
abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) has caused several outbreaks in China since 2006. However, the genetic diversity of PRRSV in China has greatly increased by rapid evolution or recombination events. Modified live-attenuated vaccines are widely used to control this disease worldwide. Although the risk and inefficacy of the vaccine has been reported, the genetic diversity between epidemic field strains and vaccine strains in China has not been completely elucidated.
  
  
  
  A total of 293 clinical samples were collected from 72 pig farms in 16 provinces of China in 2015 for PRRSV detection. A total of 28 infected samples collected from 24 pig farms in nine provinces were further selected for immunohistochemical analysis and whole genome sequencing of PRRSV. Phylogenetic analysis and recombination screening were performed with the full genome sequences of the 28 strains and other 623 reference sequences of PRRSV.
  
  
  
  Of 293 clinical samples, 117 (39.93%) were positive for PRRSV by RT-PCR. Phylogenetic results showed that the 28 strains were nested into sublineage 10.5 (classic highly pathogenic [HP]-PRRSV), sublineage 10.6 (HP-PRRSV-like strains and related recombinants), sublineage 10.7 (potential vaccine JXA1-R-like strains), and lineage 9 (NADC30-like strains and recombinants of NADC30-like strains), respectively, suggesting that multiple subgenotypes of PRRSV currently circulate in China. Recombination analyses showed that nine of 28 isolates and one isolate from other laboratory were potential complicated recombinants between the vaccine JXA1-R-like strains and predominant circulating strains.
  
  
  
  These results indicated an increase in recombination rates of PRRSV under current vaccination pressure and a more pressing situation for PRRSV eradication and control in China.
authors.affiliation: Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.|College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.|Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Huajian
authors.initials: H
authors.lastname: Zhao
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China.
authors.forename: Qinggong
authors.initials: Q
authors.lastname: Han
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wu
authors.affiliation: College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.|Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Shen
authors.affiliation: Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China. jiangp@njau.edu.cn.
authors.forename: Ping
authors.initials: P
authors.lastname: Jiang
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D014644:Genetic Variation; D007150:Immunohistochemistry; D017720:Molecular Epidemiology; D010802:Phylogeny; D019318:Porcine Reproductive and Respiratory Syndrome / Q000453:epidemiology / Q000821:virology*; D019316:Porcine respiratory and reproductive syndrome virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013552:Swine; D014765:Viral Vaccines / Q000235:genetics*
chemical_list: D014765:Viral Vaccines
keywords: PRRSV; Predominant circulating strains; Recombination; Vaccine JXA1-R