Refining Lineage Classification and Updated RFLP Patterns of PRRSV-2 Revealed Viral Spatiotemporal Distribution Characteristics in China in 1991–2023

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) is a significant infectious disease impacting the global swine industry. Due to high frequency of viral mutation and recombination, PRRSV exhibits complex genetic diversity; however, its lineage classification, restriction fragment length polymorphism (RFLP) patterns, and spatiotemporal distribution have not been systematically analyzed in China. In this study, we sequenced PRRSV-2 open reading frame (ORF)5 sequences from clinical samples (n = 364) and retrieved all the available PRRSV-2 ORF5 sequences in China in 1991–2023 from GenBank (n = 5773). Systematically analysis revealed that PRRSV-2 strains in China were classified into five lineages (L1, L3, L5, L8, and L9) and eight sublineages (L1A-L1C, L5A, L5B, L8C, L8E, and L9B), the L8E and L1C PRRSV-2 were widely distributed across almost all provinces in China, the L1C and L1A strains were increasing and gradually replacing L8 as dominant epidemic strains, and L1B PRRSV-2 in China was analyzed for the first time. The L3 PRRSV-2 has a trend of spreading gradually from the southern to the northern provinces, which needs to be paid attention to the monitoring and prevention of PRRSV-2. Meanwhile, PRRSV-2 strains in China were classified into 112 different RFLP patterns. RFLP 1-4-4 PRRSVs were detectable in China, which accounted for 12.71% of all Chinese PRRSV-2 strains. Although they are different from the RFLP 1-4-4 L1C variant in the United States, it is necessary to enhance surveillance of the RFLP 1-4-4 L1C PRRSVs. These results contributed the understanding of genetic diversity and spatiotemporal distribution of PRRSV-2 in China and provide important references for future PRRSV-2 monitoring and control in China.