西南地区PRRSV分子流行病学调查及其类NADC30株基因组特征分析

Molecular epidemiological investigation of PRRSV and genomic characteristics analysis of NADC30-like isolates in southwest China

为了解我国西南地区猪繁殖与呼吸综合征病毒(PRRSV)流行株的遗传变异和分子流行病学情况。本研究采集2018年我国四川、重庆、贵州和云南4省共计41个猪场292份疑似PRRS患病保育猪病料样本(肺脏样本48份和血清样本244份),对其进行PRRSV ORF7基因的检测和流行株全基因组特征分析。结果显示PRRSV的检出率为44.18%(95%confidence interval(CI)=38.4%~50.1%,129/292)。通过RT-PCR检测129份阳性样本的NSP2基因,结果有64份样品检出该基因。经测序分析表明类NADC30病毒株、高致病性病毒株(HP-PRRSV)和经典株的检出率分别为70.3%(95%CI=57.6%~81.1%,45/64)、12.5%(95%CI=5.6%~23.2%,8/64)和17.2%(95%CI=8.9%~28.7%,11/64)。通过对7株病毒基因组同源性分析结果表明其均与类NADC30病毒株SD53-1603同源性最高,为95.6%~96.4%,与欧洲型病毒株LV同源性最低,为58.7%~59.5%;通过对7株PRRSV基因组进行遗传演化分析结果显示其均与类NADC30病毒株聚为一大支;重组分析结果显示其均未与任何病毒株发生基因重组。序列分析显示7株病毒株均在GP5蛋白发生了一个氨基酸(S/N33)的缺失,并且存在该缺失模式的病毒已经在我国其它地区存在和流行。本研究表明近年来我国西南地区类NADC30病毒株的感染率呈逐年上升趋势,并且已经成为西南地区PRRSV的优势流行株。提示规模化养殖场应更加注重生物安全,完善引种程序,避免引入新的类NADC30病毒株。

In order to investigate the prevalence and genetic characterization of porcine reproductive and respiratory syndrome virus(PRRSV)in northwest area.In this study,292 suspected PRRS specimens of nursery pigs(48 lung samples and 244 serum samples)were collected from 41 swine farms from Sichuan,Chongqing,Guizhou and Yunnan provinces of China during 2018.PRRSV ORF7 gene was detected,and the complete genome was sequenced and analyzed from the ORF7 positive samples.The results showed that based on the ORF7 gene detection,the positive rate of PRRSV was 44.18%(95% confidence interval(CI)=38.4%-50.1%,129/292).However,based on the NSP2 gene detection,only 64 samples(64/129)were PRRSV positive.Sequence analysis showed that 70.3%(95%CI=57.6%-81.1%,45/64)were closely related to NADC30-like PRRSV,12.5%(95%(CI)=5.6%-23.2%,8/64)were closely related to highly pathogenic PRRSV,and 17.2%(95%(CI)=8.9%-28.7%,11/64)were closely related to classical PRRSV.Furthermore,the genome lengths of 7 isolates obtained in this study displayed the highest homology with the NADC30-like isolate SD53-1603(95.6%-96.4% sequence identities),the lowest homology with the European virus strain LV(58.7%-59.5% sequence identities).Phylogenetic tree analysis of 7 PRRSV isolates showed that they clustered with NADC30-like strains.Recombination analysis results showed that none of the seven isolates happened to recombination.Besides,an amino acid(S/N33)deletion occurred in the GP5 protein,which is the common found in the other isolates that prevalent in other regions of China.These results demonstrated that the infection rate of NADC30-like strain had an increasing trend in recent years,which was the dominant epidemic isolates in southwest China.This study suggested that swine farms should emphasize the biological safety and candidate introducton to avoid new NADC30-like isolates.