Comprehensive E2 gene-based phylogeny uncovers emerging lineages and refines global genotype framework of classical swine fever virus.

Abstract

This study presents a comprehensive phylogenetic reclassification of classical swine fever virus (CSFV) genotypes based on E2 gene analysis of 558 isolates collected worldwide between 1951 and 2024. The E2 gene, a major antigenic determinant, was used to reconstruct evolutionary relationships and refine the global genotype framework. Phylogenetic analysis confirmed the validity of the major genotypes (1-5) while providing enhanced resolution among their subgenotypes. Several previously unclassified or misassigned isolates were confidently reassigned, leading to the identification of newly recognized and epidemiologically important lineages such as 2.1d, 2.5, 2.6, and 2.7. Genotype 2 emerged as the most genetically diverse and globally distributed group, with 2.2 dominating in South Asia and 2.6-2.7 showing broad transcontinental spread. In contrast, genotypes 3, 4, and 5 displayed regional confinement and long-term persistence-genotype 3 in East Asia, genotype 4 in Cuba, and genotype 5 in South Korea-indicating historical maintenance and limited genetic drift. Pairwise nucleotide distance analysis revealed low intra-subgenotypic variation (0.04-0.09) and higher inter-genotypic divergence (0.15-0.19), reflecting hierarchical evolutionary separation. The persistence of distinct regional lineages, despite extensive vaccination, underscores genotype-vaccine mismatches and the need for region-specific control strategies. Overall, this E2 gene-based reclassification provides an updated, standardized framework for CSFV genotyping, offering improved resolution for molecular epidemiology, vaccine design, and global disease surveillance.