Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

David A Wilkinson; Lea Joffrin; Camille Lebarbenchon; Patrick Mavingui

The Pedacoviruses, for which multiple genome holotypes were supplied for the description of 185 subgenus, were split into multiple clades by the imposition of a common height threshold for cluster 186 definition using the presented methodology. The two holotype-containing clades corresponded to a 187 single group of Porcine epidemic diarrhoea virus (PEDV) -related viruses distributed globally but 188 entirely from pigs (Pedacovirus I in Figure 2) An alternative strategy for coronavirus classification from partial sequence data may be using the 247 spike protein-encoding S-gene, which is another commonly sequenced region of coronavirus 248 genomes. However, the use of this region is more common in epidemic outbreak scenarios and thus 249 there are many S gene sequences in public databases that are either identical or extremely closely 250 related. Performing comparative sequence searches by querying the NCBI nucleotide database with 251 the two search terms "((coronavir* spike) OR (coronavir* S gene)) AND 252 "viruses"[porgn:__txid10239]" and "((coronavir* RdRp) OR (coronavir* polymerase)) AND 253 "viruses"[porgn:__txid10239]" shows that there are approximately three times more sequences 254 from the S gene, but that these sequences originate from approximately three times fewer viral 255 author/funder. All rights reserved. No reuse allowed without permission.