Figure and table legends
Table 1. Detection and typing results of FCoV
Table 2. Correlation of the FCoV prevalence with clinical symptoms and living environments
Figure 1. Heatmap based on the nucleotide sequence homology between 23 FCoV strains and reference strains (window size, 100 nucleotides). 1a, based on the nucleotide sequence homology between the 18 type I FCoV strains in this study and the classical strain Black. 1b, based on the nucleotide sequence homology between the five type II FCoV strains in this study and the classical strain 79-1146. The colors represent sequence identity (blue for lower identities and red for higher identities) among different strains. The bar on the right represents the hierarchical similarity among the 43 or 44 meta-clusters.
Figure 2. Phylogenetic tree based on the nucleotide sequences of the entire S genes of 23 FCoV strains and other 82 FCoV strains, 14 CCoV strains, and one TGEV strain. The tree was constructed using the neighbor-joining method. The red font indicates the S gene sequences of type I FCoV, and the blue font indicates the S gene sequences of type II FCoV in this study. The reference sequences from GenBank are indicated by strain abbreviations, including GenBank accession number, genotype, country, and collection year.
Figure 3. Recombination analysis of the FCoV S gene. (a). SimPlot analysis of the complete genome represented by M/SMU-CD9/2017/FCoV1 strain; window size, 200 bases; step, 20 bases. The vertical axis indicates nucleotide sequence similarity (%) between the query strain and reference strains. (b) Phylogenetic trees for region A (nucleotides 1–135), region B (nucleotides 136–625), and region C (nucleotides 626–4410) of the FCoV strains were constructed using the neighbor-joining method. Red circles indicate the S gene in this study. Black squares indicate major and minor parental strains.