3.3 Phylogenetic analysis of FCoV S Gene
To track the evolution of FCoV strains identified in southwest China, all FCoV strains in the GenBank database were downloaded, the S genes of 82 FCoV strains, 14 CCoV strains, and one transmissible gastroenteritis virus (TGEV) strain in the GenBank database. The 23 FCoV strains S genes identified in this study were used to construct a phylogenetic tree. The 82 type I FCoV strains were formed five clusters in the S gene-based on the phylogenetic tree (Figure 2), which were tentatively named type Ia, Ib, Ic, Id, and Ie in this study. Type Ia, Ib, and Ic clusters were composed of strains from Europe and North America. The Id cluster consists of strains from Europe and America. All 18 type I FCoV strains belonged to the type Ie cluster, including strains from countries such as Japan, the Netherlands, and Belgium. These results indicate that the type Ie is a mixed cluster consisting of strains from Asia and Europe and is more complex than the other clusters’ genetic diversity.
All type II FCoV in the GenBank database form two distinct clusters in the phylogenetic tree (Figure 2), tentatively named type IIa FCoV and type IIb FCoV, respectively. Type IIa FCoV consists of strains from China and the USA. The five type II FCoV in this study clustered with four other type II FCoV strains and five CCoV strains as type IIb FCoV and were most closely related to the isolated CCoV strains in China in 2019. In the present study, 18 type I FCoV belonged to type Ie FCoV, and five type II FCoV belonged to type IIb FCoV.