Genetic Evoulution And Recombination Hotspot Analysis Based On Partial Full-Length Genomes Of PRRSV

Porcine reproductive and respiratory syndrome(PRRS)is an important infectious disease caused by PRRS virus.Due to the lack of proofreading function of RNA-dependent RNA polymerase(RdRp)of the virus,and the bases in the genome of the virus are prone to mutation.Since PRRSV was first isolated in 1991,PRRSV has been mutated continuously,which makes the genetic diversity of PRRSV very complicated.In order to understand the genetic variation of North-American type(NA-type)PRRSV in China,12 NA-type PRRSV strains were isolated and determined from PRRSV infection materials in 9 provinces during 2014-2018.The whole genome sequences were analyzed,and the recombination phenomenon was found in most of the strains.In order to further discover the recombination regularity and genetic variation characteristics of NA-type PRRSV,the complete genome sequence of NA-type PRRSVs(strain sequenced=138,GenBank sequence=713)were analyzed for genetic evolution,recombination,and NSP2 insertion and deletion(Indel)polymorphism.It was found that:(1)During 2014-2018,Chinese NA-type PRRSVs can be divided into three Lineage(L),namely L1,L3,and L8,and US NA-type PRRSVs can be divided into L1,L5,L7,and L8.Evolutionary dynamics analysis showed that the genetic diversity of NADC30-like PRRSVs was decreasing,and the diversity of NADC34-like PRRSVs was relatively stable.(2)NSP2 can be divided into 5 deletion patterns according to the positions of insertions and deletions.(3)The hotspots of recombination of NA-type PRRSV strains in China and the United States between 2014 and 2018 were distributed in NSP9 and GP2-GP3.From 1991-2013 to 2014-2018,major parents of recombinants showed a trend from complex to single.The major parents of Chinese recombinants showed a transition from L8 to L1.However,the major parents of US recombinants remained L1.(4)Recombination breakpoints within the lineages were distributed throughout the genome.At the same time,the genetic variation of European-type(EU-type)PRRSV was analyzed in this study.The sequence of the strain includes three genome sequenced and all EU-type PRRSVs during 1991-2018 from GenBank(n = 88).The results showed that:(1)HL85 strain had a continuous deletion of 11 amino acids in the overlapping region of ORF3 and ORF4.(2)High-frequency recombination regions of EU-type PRRSVs were concentrated in NSP2 and GP2-GP4.(3)The number of NSP2 deleted strains was large(61/91),ranging from 1-148 amino acid(aa),of which there were three main deletions patterns.(4)Phylogenetic analysis shows that most EU-type PRRSVs in China may be related to the three import of overseas strains.This study conducted genetic evolution analysis of the complete genome sequence of NA-type PRRSVs(n = 851)during 1991-2018 and the complete genome sequence of EU-type PRRSVs(n = 91)during 1991-2018.The high-frequent recombination region NSP9 and GP2-GP3 in NA-type PRRSVs,high-frequent recombination region NSP2 and GP2-GP4 in EU-type PRRSVs,and complex insertion and deletion diversity of NSP2 were found.The results of this study provide an important reference for further understanding of the genetic variation and recombination characteristics of PRRSV.