Molecular Evolution, Codon Usage Bias, and Population Differentiation of the E2 Gene in Classical Swine Fever Virus

Abstract

Codon usage bias reflects the interplay between mutational pressure and translational selection, influencing viral fitness and host adaptation. A comprehensive dataset of Classical swine fever virus (CSFV) sequences was retrieved from the NCBI GenBank database. Analysis of 568 global E2 gene sequences of Classical swine fever virus revealed moderate genetic diversity, comprising 75 polymorphic sites, 120 total mutations, and 207 distinct haplotypes. The gene exhibited high haplotype diversity (Hd = 0.9789) but moderate nucleotide diversity (π = 0.098), indicating the presence of numerous closely related variants. Negative neutrality indices (Tajima’s D = -1.39 and Fu’s Fs = -3.92) suggest the predominance of purifying selection acting to conserve protein structure. Codon usage analysis demonstrated a clear preference for A/T-ending codons, with moderate codon usage bias (ENC values ranging from 43 to 55). The narrow GC content range (44–52%) and balanced PR2 plot distribution indicate compositional stability, with codon usage patterns primarily driven by mutational pressure rather than translational selection. Population genetic analysis revealed low genetic differentiation among isolates from Asia, Europe, and the Americas, suggesting substantial gene flow or shared ancestry across these regions. In contrast, African isolates showed high genetic divergence (FST = 0.81–0.83; D² = 0.325–0.397), indicating limited gene flow and long-term evolutionary separation. Principal component analysis further supported these findings by distinctly separating African isolates, while Eurasian and American isolates clustered together, reflecting genetic cohesion among these populations.