Recent studies have demonstrated that porcine reproductive and respiratory syndrome virus 1 (PRRSV-1) strains isolated from different farms in China have significant genomic heterogeneity, whereas strains from the same farm present a high degree of genomic similarity. In this study, primary alveolar macrophages (PAMs) and high-throughput sequencing technology were used to successfully isolate and characterize two different PRRSV-1 strains (designated TZJ3556-1 and TZJ3556-2) in a single pig from a farm in Shandong Province with a PRRSV-1 outbreak. Phylogenetic analysis based on ORF5 and complete genome sequences revealed that both TZJ3556-1 and TZJ3556-2 belong to the BJEU06-1-like subgroup. Nucleotide (nt) sequence alignment revealed that the pairwise genomic similarity between TZJ3556-1 and TZJ3556-2 was only 86.03%. Additionally, both strains exhibited the characteristic 5 (4+1) discontinuous amino acid (aa) deletion in the Nsp2 region. Recombination analysis revealed that TZJ3556-1 is one of the parental strains for the recombinant strain TZJ3556-2, contributing Nsp1β, partial Nsp2, partial ORF4, and ORF5-3'UTR genes. This study reports, for the first time, coinfection with multiple PRRSV-1 strains in a single pig and the emergence of an intrasubgroup recombinant strain within the BJEU06-1-like subgroup. The genetic diversity of PRRSV-1 strains in China is likely to become increasingly complex, and these strains may have overcome physical barriers between farms. The emergence of complex and diverse PRRSV-1 strains poses a serious challenge for the prevention and control of PRRS in China.

Keywords: PRRSV-1; coinfection; high-throughput sequencing; recombination and evolution; whole-genome characteristics.