Spatiotemporal distribution and genetic characteristics of porcine reproductive and respiratory syndrome virus-2 lineage 1 in Japan from 2020 to 2023.

Abstract

Porcine reproductive and respiratory syndrome (PRRS), caused by the PRRS virus (PRRSV), is a major swine disease globally. This study analyzed 1207 PRRSV sequences (2020-2023) detected through routine diagnostic submissions in Japan using the standardized open reading frame 5-based lineage classification system. Phylogenetic analysis identified six lineages in Japan: L1, L4, L5, L8, L9, and L11. Notably, the prevalence of L1 showed a marked increase during the study period. L1 strains were predominantly detected in the Kanto and Kyushu regions. In Kanto, L1B was predominant (80 %), whereas Kyushu exhibited greater sublineage diversity (L1A, L1B, L1E, and L1I). Pairwise nucleotide identity analysis revealed high genetic heterogeneity within the L1 population (mean identity 90.1 %), while L5 and L8 populations were highly homogenous (97.9 % and 98.3 %, respectively) and showed high sequence identity (>95 %) to commercial vaccine strains. This study presents the first nationwide molecular epidemiological analysis of PRRSV in Japan based on the global lineage system. The findings highlight Japan's distinct L1 sublineage dynamics (e.g., L1B dominance) compared to global trends (e.g., L1C.5 in the US and NADC30/34-like strains in China and Korea), offering critical insights for informing effective PRRSV control strategies.