Whole‐Genomic Characterization of Two Different PRRSV‐1 Strains Isolated From a Single Pig

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.