Genetic variation and recombination analysis of the NSP11 gene of Porcine reproductive and respiratory syndrome-2 strains in China from 1996 to 2022.

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is caused by the PRRS virus (PRRSV). It leads to reproductive disorders and respiratory failure in sows and piglets. As an endoribonuclease, the PRRSV non-structural protein 11 (NSP11) is crucial in replication and assists immune system evasion. NSP11, which is relatively more conserved than NSP2, could potentially cause a new round of PRRSV epidemics, given a major mutation occurs. Here, we aimed to analyze the PRRSV-2 NSP11 genetic diversity in China between 1996-2022. The NSP11 nucleotide sequence was analyzed in 60 PRRSV-2 strains, revealing a similarity of 83.6% - 100%. Similarly, amino acid sequences exhibited homology ranges of 91.0% - 100.0%. Amino acid sequence alignment analysis revealed multiple substitutions in NSP11. NSP11 phylogenetic analysis of 489 PRRSV-2 strains revealed that Lineages 8 and 1 were the predominant strains of PRRSV circulating in China. These two lineages exhibit relatively close genetic relationships. Although unsupported by SimPlot analysis, recombination analysis suggested a potential recombination event in the 489 PRRSV-2 NSP11 sequences. Recombination analysis and amino acid sequence alignment confirmed the PRRSV NSP11 conservation. Our findings provide genetic diversity of PRRSV-2 NSP11 in China and contribute to effective strategy development to prevent and control PRRSV.