PT - JOURNAL ARTICLE AU - Gary R. Whittaker AU - Nicole M. André AU - Jean Kaoru Millet TI - Spike-based phylogenetically defined clades within the <em>Alphacoronavirus 1</em> species AID - 10.1101/101774 DP - 2017 Jan 01 TA - bioRxiv PG - 101774 4099 - http://biorxiv.org/content/early/2017/01/19/101774.short 4100 - http://biorxiv.org/content/early/2017/01/19/101774.full 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.