Surveillance And Genetic Analysis Of PRRSV In Different Regions Of Guangxi From 2015 To 2019

Porcine reproductive and respiratory syndrome(PRRS)has become a widespread epidemic in the world.Due to the characteristics of its high incidence,rapid transmission,and difficulty in control,PRRS has created a huge economic loss for the global pig industry.The diversity of PRRSV has become more complex since porcine reproductive and respiratory syndrome virus(PRRSV)was isolated for the first time in mainland China in 1996.In order to understand the prevalence and genetic variation of PRRSV in Guangxi province,545 samples of clinical samples were collected from different pig farms of Guangxi province from 2015 to 2019.PRRSV was detected by RT-PCR,and ORF5 and Nsp2 were sequenced,compared and analyzed for genetic evolution.The results of RT-PCR showed that among 545 clinical samples collected,167 positive PRRSVs were detected with a positive rate of 30.6%.Phylogenetic tree based on ORF5 and Nsp2 showed that all PRRSV strains in this study belonged to the American type PRRSV,clustering into four lineages.Among 115 PRRSV strains,5 of 115 belonged to NADC30-like PRRSV(Lineage 1),3 of 115 belonged to QYYZ-like PRRSV(Lineage 3),1 of 115 belonged to VR-2332-like PRRSV(Lineage 5)and 106 of 115 belonged to HP-PRRSV-like(Lineage 8)strains.Nucleotide and amino acid identity analysis of ORF5 showed that the nucleotide identity of the ORF5 gene with the reference strains was 80.1%-99.2%,and the amino acid homology was 81.6%-98.6%;The number of glycosylation sites of 115 GP5 sequences were 3 ～ 5,of which 9 PRRSV strains contained 3 N-glycosylation sites;7 strains contained 5N-glycosylation sites;The pattern of N-glycosylation site of most strains is similar to JXA1 and CH-1a.The PRRSV strains GXNN1835,GXNN1836,GXNN1839 and GXNN1843 which grouped in lineage 1 have a glycosylation site at N43;GXNN1811f also has a Glycosylation site at the position of N59.The nucleotide identity of nsp2 is 71.3% ～ 99.2% and the amino acid identity is 62.9% ～ 98.6% compared with the reference strains.Sequence comparison results showed that most strains had a deletion of 1 + 29 amino acids the Nsp2 gene,which is considered as the genetic hallmark of HP-PRRSV strains.The strains grouped in Lineage 1 had 131 amino acids deletion in Nsp2,which is similar with aa deletion pattern seen in NADC30 strain.In addition,the strain GXGL1905 a had an additional 19 amino acids upstream of the deletion of1 + 29 amino acids.The whole genome of the NADC30-like strain GXNN1839 was amplified,sequenced and used for genetic evolution analysis and recombination analysis.The comparison results showed that the nucleotide identity of GXNN1839 with NADC30,VR-2332,QYYZ,CH-1a,JXA1,and LV were 92.2%,84.5%,81.9%,83.9%,82.9%,and 59.8%,respectively.The results of recombination analysis showed that GXNN1839 was a natural recombination between the strains of lineage 5(VR-2332-like)and lineage 1(NADC30-like).The recombination sites occurred at nsp9(7872nt-8162nt)and ORF2-4(12587nt-13282nt).In summary,PRRSV is highly prevalent in Guangxi from 2015 to 2019.The main prevalent genotype is HP-PRRSV like strains.The NADC30-like PRRSV(Lineage 1)and QYYZ-like PRRSV(Lineage 3)also circulating in the field.The emergence of recombinant PRRSV expands the diversity of PRRSV strains.The results of this study lay a foundation for the prevention and control of PRRSV in Guangxi province.