Analysis of Genetic Variations in NSP4 of Type 1 Porcine Reproductive and Respiratory Syndrome Virus in China

Abstract

Abstract Background Porcine reproductive and respiratory syndrome virus (PRRSV) is constantly evolving, and the detection rate of PRRSV-1 in China has been increasing annually. To investigate the prevalence and genetic variation of NSP4 in PRRSV-1 in China, 40 PRRSV whole-genomes sequences were collected and the NSP4 sequences were selected for nucleotide and amino acid homology analysis. In addition, amino acid site variation analysis was performed on the NSP4 sequences of the 40 PRRSV strains, and phylogenetic trees were constructed based on the whole-genomes and NSP4 sequences of 86 PRRSV strains. Results The nucleotide homology of NSP4 between 32 PRRSV-1 and 8 PRRSV-2 strains ranged from 57.3–62.4%, and the amino acid homology ranged from 58.6–64.5%. The nucleotide homology of NSP4 among the 32 PRRSV-1 strains ranged from 75.4–100.0%, and the amino acid homology ranged from 81.3–100.0%. Comparison of the NSP4 amino acid sequences of 32 PRRSV-1 and 8 PRRSV-2 strains revealed that the biggest difference was a deletion at the 83rd amino acid residue in PRRSV-1, and other differences manifested as varying degrees of mutations at multiple amino acid sites. Phylogenetic analysis showed that the PRRSV-1 strains isolated in China clustered into four subgroups of Subtype 1 Global: Amervac-like, BJEU06-1-like, HKEU16-like, and NMEU09-1-like strains. Conclusion PRRSV-1 NSP4 exhibits similarities to Subtype 1 Global strains and clusters into four subgroups. Although it differs from PRRSV-2 with a deletion in the 83rd amino acid residue, the catalytic triad amino acid residues are conserved. These findings have important implications for the development of secure and reliable detection methods and guide further research on PRRSV-1, providing a theoretical foundation for the development of new drugs and vaccines.