Analysis of Genetic Diversity Based on Sequences of Feline Calicivirus Strains Isolated in China

In recent years, feline calicivirus (FCV) has caused increasingly severe harm in China, posing a significant threat to feline health. However, our understanding of the complex epidemiology and genetic diversity of FCV in China remains limited. In this study, we integrated various bioinformatics methods and used isolates from China as the primary research subjects. The approach ranged from basic prevalence statistics to genome sequence analysis, systematic exploration of spatiotemporal evolution, recombination studies, comparisons of specific sites, structural biology predictions, protein adaptation analysis, and molecular dynamics simulations. This comprehensive approach aimed to obtain a thorough understanding of the characteristics of FCV in China. An in-depth analysis of the results indicates that FCV exhibits a nationwide epidemic trend in China mainly consisting of two genotypes: GI and GII. The prevalence rate of genotype GI exceeds 70%, making it the predominant epidemic genotype. Spatiotemporal evolution predicts that the ancestor of genotype GI emerged in 1821 while the ancestor of genotype GII emerged in 1879. After the 1950s, there was rapid expansion in the spread of FCV which extended from eastern parts to regions in southwest, southeast, and northeast after 1990. The analysis on recombinant evolution suggests that FCV can undergo recombination within same genotypes or across different genotypes enhancing its cross-species transmission and infectivity capabilities. Amino acid sequence analysis reveals mutations at key amino acid site position 481 involved in receptor binding where K mutated into E or N in domestic prevalent strains recently. All seven amino acid sites related virulence have undergone mutations. The results of protein adaptability analysis indicate that the amino acid residue at position 281 (N) in the VP1 protein is a site of adaptive selection. In some strains, the amino acid at this position has mutated from N to G, S, or R. Further molecular dynamics simulations reveal that these mutations affect the structural stability of the VP1 protein. The results of this study are essential for gaining a thorough understanding of the FCV profile in China and can be used to create better prevention and control strategies.