Genomic Analysis of Classical Swine Fever Virus: Single Nucleotide Polymorphism Profiling, Phylogenetic Insights and Implications for Disease Control

Control efforts are complicated by the genetic variety among genotypes 1, 2 and 3 of the Classical Swine Fever Virus (CSFV), which continues to pose a serious threat to the global swine economy. 225 full or nearly complete CSFV genomes from the NCBI GenBank database, representing genotypes 1, 2 and 3, as well as subgenotypes 1.1, 2.1 and 2.3, were analyzed genomically in this study. To clarify genetic diversity and evolutionary factors, we used phylogenetic reconstruction, comparative analysis and Single Nucleotide Polymorphism (SNP) profiling with Biopython (v1.81) and MUSCLE (v3.8.31). Subgenotypes 2.1 and 2.3 had greater diversity (151-183 SNPs) than genotype 1.1 (2-19 SNPs), especially in the 5’UTR, E2 gene and 3′ UTR, indicating vaccine-driven selection and geographic adaptation, according to SNP analysis, which found 0-188 SNPs per genome. Different genotype grouping was confirmed by phylogenetic analysis, with Asian strains showing more diversity. The statistical analysis (ANOVA, p