Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

Abstract

9The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic 10 categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, 11subfamily Orthocoronavirinae) represents a major shift in how official classifications are used to 12 designate specific viral lineages. While the newly defined subgenera provide much-needed 13 standardisation for commonly cited viruses of public health importance, no method has been 14 proposed for the assignment of subgenus based on partial sequence data, or for sequences that are 15 divergent from the designated holotype reference genomes. Here, we describe the genetic variation 16 of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the 17 most used partial sequence loci for both detection and classification of coronaviruses in molecular 18 epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus 19 sequences and examine clade groupings relative to all subgenus holotype sequences. Our 20 phylogenetic analyses are largely coherent with genome-scale analyses based on designated 21 holotype members for each subgenus. Distance measures between sequences form discrete clusters 22 between taxa, offering logical threshold boundaries that can attribute subgenus or indicate 23 sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus 24propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of 25 subgenus-level taxonomic classifications and we supply the R package, "MyCoV", which provides a 26 method for attributing subgenus and assessing the reliability of the attribution. 27 author/funder. All rights reserved. No reuse allowed without permission.