Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses

Abstract

The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae), represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardization for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a 387 nt region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with whole-genome analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses are sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, MyCoV, which provides a method for attributing subgenus and assessing the reliability of the attribution.

Best Molecular Tools to Investigate Coronavirus Diversity in Mammals: A Comparison

“…For all classified CoVs, this analysis allowed correct identification, confirming the specificity of the newly developed test. Besides, phylogenetic analysis of the sequences obtained was sufficiently informative to allow classification within known subgenera of all CoV strains that do not meet parameters for official classification (Figure 4) [49]. [50].…”

Clinical and molecular aspects of veterinary coronaviruses

“…nsp12 codifies for the RNA-dependent RNA polymerase (RdRp), a central component in the replication and transcription of the coronavirus family. Also, together with other seven nsp domains, nsp12 is used in the taxonomic classification of new virus isolates ( de Groot et al, 2013 ; Wilkinson et al, 2020 ). The activity of the exoribonuclease 3´-5´ of nsp14 increases the RdRp proofreading ability, with implications in the viral mutation rates and the host immune response ( Becares et al, 2016 ; Minskaia et al, 2006 ).…”

A Cross Sectional Sampling Reveals Novel Coronaviruses in Bat Populations of Georgia

“…CoVs are highly pathogenic for livestock, pets, wild animals, as well as birds where they were first described in chickens in the early 1930s [3,4]. During the period 2002-2003, coronaviruses were recognized as zoonotic agents with high pandemic potential after an outbreak of severe acute respiratory syndrome (SARS) that caused 8096 cases and 774 deaths [5,6]. In 2012, the Middle East respiratory syndrome (MERS) emerged as a new public health concern for it spread rapidly to several countries around the globe (mainly the Arabian Peninsula and the Republic of Korea) and for showing a considerably higher mortality rate (35%) than SARS.…”

“…In 2012, the Middle East respiratory syndrome (MERS) emerged as a new public health concern for it spread rapidly to several countries around the globe (mainly the Arabian Peninsula and the Republic of Korea) and for showing a considerably higher mortality rate (35%) than SARS. As of 31 July 2021, MERS has been implicated in 2578 confirmed cases and 888 deaths [6]. The most recent pandemic involving a CoV, SARS-CoV-2 resulted in coronavirus disease , began during 2019 and has caused more than 260 million cases and more than 5 million deaths, confirmed as of 10 December 2021 [7].…”

“…In 2018, the International Committee on Taxonomy of Viruses (ICTV) refined the classification of CoVs to re-organize a greater viral diversity based on newly discovered viruses [6]. Thus, CoVs are within the Riboviria realm that encompasses all viral families having an RNA-dependent RNA polymerase (RdRp), Orthornavirae kingdom, Pisuviricota phylum, Pisoniviricetes class, Nidovirales order, Cornidovirineae suborder, and Coronaviridae family.…”