Spike-based phylogenetically defined clades within the Alphacoronavirus 1 species
Taxonomic classification for the Coronaviridae can be challenging, due to the wide host tropism and highly variable genome of the viruses in this Family. Within the Alphacoronavirus genus, there is a single species Alphacoronavirus 1 that encompasses several biologically distinct viruses of distinct animal species. Here, we carried out phylogenetic analysis of members of the Alphacoronavirus genus, focusing on the viral spike gene, which is a primary driver of viral tropism and pathogenesis. We identify two distinct clades (A and B) within the Alphacoronavirus 1 species. Alphacoronavirus 1 clade A encompasses serotype I FCoV and CCoV, and Alphacoronavirus 1 clade B, encompasses serotype II FCoV and CCoV and TGEV-like viruses. We propose this clade designation, along with the newly proposed Alphacoronavirus 2 species, as an improved way to classify the diverse Alphacoronavirus genus.