2019—2023年我国PRRSV系统发育、基因重组和多样性分析

Phylogenetic,Genomic Recombination and Diversity Analysis of Porcine Reproductive and Respiratory Syndrome Virus in China from 2019 to 2023

为了解我国猪繁殖与呼吸综合征病毒(PRRSV)的流行、核苷酸多样性和病毒重组情况,本试验对2019—2023年我国分离获得的154条PRRSV全基因组序列进行遗传进化、核苷酸多样性和基因重组分析。遗传进化分析结果显示,2019—2023年我国PRRSV流行毒株主要是基因Ⅱ型的4个谱系,分别是谱系1(Lineage 1)、谱系3(Lineage 3)、谱系5.1(Lineage 5.1)和谱系(Lineage 8.7),也有基因I型流行毒株出现。PRRSV全基因组核苷酸多样性分析结果显示,相对其他基因,ORF1a基因存在较高遗传多样性。基因重组分析结果显示,PRRSV基因Ⅱ型的4个谱系均发生重组;我国PRRSV流行毒株重组热点基因为ORF1a和ORF1b基因,其中重组主要和次要亲本都以Lineage 1和Lineage 8.7为主。进一步分析基因Ⅱ型的不同谱系之间的重组情况,结果显示,谱系间重组频率高于谱系内重组频率,谱系内重组模式以Lineage 1为主。本试验结果提示,2019—2023年我国流行PRRSV毒株具有多样性,且基因Ⅱ型不同谱系间频发重组,表明临床上PRRSV流行情况越来越复杂,应加以重视。

To understand the prevalence,nucleotide diversity,and recombination of porcine reproductive and respiratory syndrome virus(PRRSV)in China,this study conducted genetic evolution,nucleotide diversity analysis,and gene recombination analysis on 154 PRRSV whole-genome sequences isolated in China from 2019 to 2023.Phylogenetic analysis results showed that from 2019 to 2023,the prevalent strains of PRRSV in China were mainly from four lineages within genotype Ⅱ:Lineage 1,Lineage 3,Lineage 5.1,and Lineage 8.7,with genotype Ⅰ strains also present.Whole-genome nucleotide diversity analysis indicated that the ORF 1 a gene had higher genetic diversity compared to other genes.Recombination analysis showed that all four lineages of genotype Ⅱ underwent recombination,with the main recombination hotspots being the ORF 1 a and ORF 1 b genes.The primary and secondary parental strains in recombination were predominantly from Lineage 1 and Lineage 8.7.Further analysis of recombination among different lineages within genotype Ⅱ revealed that inter-lineage recombination frequency was higher than intra-lineage recombination frequency,with intra-lineage recombination mainly occurring within Lineage 1.These results suggest that PRRSV strains prevalent in China from 2019 to 2023 have high diversity,with frequent recombination between different lineages within genotype Ⅱ,indicating an increasingly complex epidemiological situation for PRRSV in clinical settings that warrants attention.