Molecular epidemiological investigation and recombination analysis of porcine reproductive and respiratory syndrome virus in Zhejiang Province(浙江省猪繁殖与呼吸综合征病毒的分子流行病学调查及重组分析)

To understand the molecular epidemiological characteristics and recombination dynamics of porcine reproductive and respiratory syndrome virus (PRRSV) in Zhejiang Province, 749 porcine clinical serum samples were collected from 40 swine farms from eight regions of Zhejiang Province in 2023. These samples were tested by real time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Partial positive samples were selected for amplification and sequencing analysis of the open reading frame 5 gene (ORF5), non-structural protein 2 gene (Nsp2), and whole genome. The results showed that the positive rate of PRRSV in all samples was 7.61% (57/749), the positive rate of swine farms was 35.00% (14/40), and the detection rate was relatively high in winter (11.04%). Phylogenetic analysis based on the ORF5 gene indicated that all 30 obtained PRRSV strains belonged to genotype 2, clustering into lineages L1.8 (NADC30-like), L3.5 (QYYZ-like), L8.7 (highly pathogenic PRRSV, HP-PRRSV), and L1.5 (NADC34-like). Alignment of the Nsp2 amino acid sequences from 28 obtained PRRSV strains showed that 25 strains had deletion patterns consistent with NADC30-like strains, whereas three strains had deletion patterns consistent with HP-PRRSV strains. Whole genome analysis of five recombinant strains showed that they all used NADC30-like strains as the backbone, with the recombinant fragments derived from HP-PRRSV, QYYZ-like, VR2332-like and NADC34-like strains, and the recombination hotspots mainly concentrated in the 5 ´ -untranslated region (5′UTR)-Nsp2, Nsp3-Nsp9 and ORF2a-ORF5 regions. In summary, the prevalent strains of PRRSV in Zhejiang Province are dominated by NADC30-like strains, and the recombinant strains show complex recombination patterns and novel recombination hotspots. These findings provide a reference for further elucidating PRRSV recombination mechanisms and for developing scientific prevention and control strategies for the disease.(为了解浙江省猪繁殖与呼吸综合征病毒（porcine reproductive and respiratory syndrome virus, PRRSV）的分子流行病学特征及重组情况，于2023年采集浙江省8个地区40个猪场的749份猪临床血清样品，通过实时定量逆转录聚合酶链反应进行检测，并对部分阳性样品进行可读框5基因（open reading frame 5 gene, ORF5）、非结构蛋白2基因（non-structural protein 2 gene, Nsp2）和全基因组扩增与测序分析。结果显示：样品中PRRSV阳性率为7.61%（57/749），猪场阳性率为35.00%（14/40），冬季检出率较高（11.04%）。基于ORF5基因的系统发育分析表明，获得的30株PRRSV均属于基因2型，分别归属于谱系L1.8[类NADC30（NADC30-like）]、L3.5[类QYYZ（QYYZ-like）]、L8.7[高致病性PRRSV（highly pathogenic PRRSV, HP-PRRSV）]和L1.5[类NADC34（NADC34-like）]。对获得28株毒株的Nsp2氨基酸序列比对发现，25株呈现与类NADC30毒株一致的缺失模式，3株呈现与HP-PRRSV一致的缺失模式。对5株重组毒株的全基因组分析显示，它们均以类NADC30毒株为骨架，其重组片段来源于HP-PRRSV、类QYYZ、类VR2332（VR2332-like）和类NADC34毒株，重组热点主要集中在5 ´ 非翻译区～Nsp2、Nsp3～Nsp9和ORF2a～ORF5区域。综上所述，浙江省PRRSV流行株以类NADC30毒株为主，重组毒株表现出复杂的重组模式和新的重组热点。本研究结果可为PRRSV重组机制的深入解析及该病的科学防控提供参考。)