Emergence of a novel subgenotype 2.4 of classical swine fever virus in India.

Abstract

Classical Swine Fever Virus (CSFV) remains a major constraint to pig production worldwide, despite vaccination and control efforts. This study investigated the genetic diversity, phylogeography, and population structure of CSFV using E2 gene sequences from 53 Indian isolates spanning 18 states and union territories and 85 global isolates from 28 countries. Phylogenetic analysis revealed that Indian CSFV strains predominantly belong to genotype 2, with subgenotype 2.2 as the dominant and widely distributed lineage across India, reflecting long-term endemic circulation. Subgenotype 2.4, restricted mainly to Northeast India, clustered closely with Southeast Asian strains, suggesting regional evolution and transboundary transmission, while subgenotype 1.1 persisted as an older lineage alongside genotype 2 viruses. Global analysis demonstrated extensive genetic structuring, with genotype 2 exhibiting the highest diversity and broader geographic spread compared to other genotypes. Haplotype analysis identified high haplotype diversity in both Indian (Hd = 0.9853) and global (Hd = 0.9871) datasets, characterized by numerous region-specific haplotypes and limited shared haplotypes indicative of localized evolution punctuated by occasional long-distance dissemination. Shared haplotypes among Indian states and between countries highlight the role of animal movement and trade in CSFV spread. Overall, the combined phylogenetic and population genetic analyses underscore the complex evolutionary dynamics of CSFV in India and globally, emphasizing the need for continuous molecular surveillance and region-specific control.