RT Journal Article SR Electronic T1 Spike-based phylogenetically defined clades within the Alphacoronavirus 1 species JF bioRxiv FD Cold Spring Harbor Laboratory SP 101774 DO 10.1101/101774 A1 Gary R. Whittaker A1 Nicole M. André A1 Jean Kaoru Millet YR 2017 UL http://biorxiv.org/content/early/2017/01/19/101774.abstract AB 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.