Genetic variation in NSP4 of type 1 porcine reproductive and respiratory syndrome virus in China

Abstract

Abstract Background Porcine reproductive and respiratory syndrome virus (PRRSV) is characterized by a high mutation rate. Although research has largely focused on PRRSV-2, the detection rate of PRRSV-1 in China is increasing. To investigate the prevalence and genetic variation of NSP4, a key gene in the regulation of host immunity, in PRRSV-1 in China, publicly available whole-genome sequence data and NSP4 sequences were obtained for analyses of nucleotide and amino acid homology, substitutions, and phylogenetic relationships. Results The nucleotide homology of NSP4 between 32 PRRSV-1 and 8 PRRSV-2 strains ranged from 57.3 to 62.4%, and the amino acid homology ranged from 58.6 to 64.5%. Among the 32 PRRSV-1 strains, the nucleotide homology of NSP4 ranged from 75.4 to 100.0% and the amino acid homology ranged from 81.3 to 100.0%. Comparisons of NSP4 amino acid sequences of 32 PRRSV-1 and 8 PRRSV-2 strains revealed a deletion at the 83rd amino acid residue in PRRSV-1 and mutations at various amino acid residues. A phylogenetic analysis showed that the PRRSV-1 strains isolated in China clustered into four subgroups of Subtype I Global: Amervac-like, BJEU06-1-like, HKEU16-like, and NMEU09-1-like strains. Conclusion PRRSV-1 NSP4 exhibits similarities to Subtype I Global strains and clusters into four subgroups. Although it differs from PRRSV-2 NSP4 with a deletion in the 83rd amino acid residue, the amino acid residues of the catalytic triad are conserved. These findings have important implications for the development of secure and reliable detection methods as well as new drugs and vaccines and are expected to guide further research on PRRSV-1.