To date, the genetic characteristics of feline caliciviruses (FCVs) in Hokkaido (Japan) have not been investigated. Here, 28 FCVs obtained in 2022-2023 from the Hidaka and Tokachi Districts were phylogenetically analyzed. Recombination breakpoints within open reading frame 2 (ORF2) were detected using the Genetic Algorithm for Recombination Detection (GARD) and the Recombination Detection Program v5.5 (RDP5). In addition, recombination was independently verified using permutation-based statistics in SimPlot++. Codon-level selection analysis using Hypothesis Testing using the Phylogenies framework were performed. Amino acid (aa) diversity at epitope-focused sites was quantified using entropy profiles. The ORF2 phylogeny grouped Hokkaido FCV strains into genogroups I and II. Their terminal branch lengths were comparable to other time-matched Japanese FCV strains, supporting a shared evolutionary background. Within region E of the capsid precursor protein encoded by ORF2, GARD delimited a recombination window at nucleotides 1284-1388 (aa 428-463), and RDP5 identified two events overlapping this region. SimPlot++ analyses also supported recombination signals. Among Hokkaido strains, aa diversity was detected at multiple epitope-focused sites. Codon-level analysis identified episodic positive selection at codon 447 within the linear neutralizing epitope (aa 445-451), supported across MEME, FEL, SLAC, and FUBAR. Two Hokkaido FCV strains carried an aa variation (T → D/S) at aa 447. Although entropy profiles indicated diversity across epitope-focused sites, aa 447 exhibited low entropy. The results support epitope-focused diversification in region E superimposed on a shared ORF2 backbone among Hokkaido FCV strains and highlight codon 447 as a candidate site warranting further structural and immunological validation.
Nguyen et al. (Fri,) studied this question.