The online version of this article (doi:10.1186/s12985-017-0735-3) contains supplementary material, which is available to authorized users.
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.
Additional file 1: Table S1. Primers used in generating overlapping amplicons spanning PRRSV genomes. (DOCX 13 kb)12985_2017_735_MOESM1_ESM.docx
Additional file 2: Table S2. Homology between the 28 isolates sequenced in this study. (DOCX 19 kb)12985_2017_735_MOESM2_ESM.docx
Additional file 3: Table S3. Sequence identity of the JXA1-R-like strains with JXA1 derivatives and representative strains. (DOCX 20 kb)12985_2017_735_MOESM3_ESM.docx
Additional file 4: Figure S1. Comparisons of partial ORF1a, ORF1b, and GP4 deduced amino acid sequences. *Unique and identical amino acids among the JXA1 derivatives. (PDF 491 kb)12985_2017_735_MOESM4_ESM.pdf
Additional file 5: Figure S2. Phylogenetic analysis of parental regions of putative 10 recombinant strains. The parental vaccine JXA1-R group (sublineage 10.7) is shown in red, the 2009–2010 HP-PRRSV-like group (sublineage 10.6) is shown in deep sky blue, and the NADC30-like strain (lineage 9) is shown in green. Putative recombinant strains are labeled with black triangles (▲). (PDF 502 kb)12985_2017_735_MOESM5_ESM.pdf
Additional file 6: Figure S3. Morbidity and mortality rates among farms with pigs infected with recombinant JXA1-R-like strains. (PDF 87 kb)12985_2017_735_MOESM6_ESM.pdf
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- 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
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