Version 1
: Received: 27 May 2020 / Approved: 28 May 2020 / Online: 28 May 2020 (16:21:05 CEST)
Version 2
: Received: 28 July 2020 / Approved: 30 July 2020 / Online: 30 July 2020 (06:22:00 CEST)
Version 3
: Received: 3 October 2020 / Approved: 5 October 2020 / Online: 5 October 2020 (10:56:36 CEST)
How to cite:
Roy, C.; Mandal, S.M.; Mondol, S.K.; Mukherjee, S.; Ghosh, W.; Chakraborty, R. Trends of Mutation Accumulation Across Global SARS-CoV-2 Genomes: Implications for the Evolution of the Novel Coronavirus. Preprints2020, 2020050463 (doi: 10.20944/preprints202005.0463.v3).
Roy, C.; Mandal, S.M.; Mondol, S.K.; Mukherjee, S.; Ghosh, W.; Chakraborty, R. Trends of Mutation Accumulation Across Global SARS-CoV-2 Genomes: Implications for the Evolution of the Novel Coronavirus. Preprints 2020, 2020050463 (doi: 10.20944/preprints202005.0463.v3).
Cite as:
Roy, C.; Mandal, S.M.; Mondol, S.K.; Mukherjee, S.; Ghosh, W.; Chakraborty, R. Trends of Mutation Accumulation Across Global SARS-CoV-2 Genomes: Implications for the Evolution of the Novel Coronavirus. Preprints2020, 2020050463 (doi: 10.20944/preprints202005.0463.v3).
Roy, C.; Mandal, S.M.; Mondol, S.K.; Mukherjee, S.; Ghosh, W.; Chakraborty, R. Trends of Mutation Accumulation Across Global SARS-CoV-2 Genomes: Implications for the Evolution of the Novel Coronavirus. Preprints 2020, 2020050463 (doi: 10.20944/preprints202005.0463.v3).
Abstract
To understand SARS-CoV-2 microevolution, this study explored the genome-wide frequency, gene-wise distribution, and molecular nature of all point-mutations detected across its 71,703 RNA-genomes deposited in the GISAID repository, till 21 August 2020. Globally, nsp1/nsp2/nsp3/ nsp11 and orf7a/orf3a/S were the most mutation-ridden non-structural and structural genes respectively. Phylogeny based on 4,618 spatiotemporally-representative genomes revealed that entities belonging to the early lineages are mostly spread over Asian countries (including India, the biggest hotspot of the pandemic) whereas the recently-derived lineages are more globally distributed. Of the total 16,602 polymorphism-bearing sites in the pan-genome, 11,037 and 4,965 involved transitions and transversions, which in turn were predominated by cytidine-to-uridine and guanosine-to-uridine conversions, respectively. Positive selection of nonsynonymous mutations (dN/dS >1) in most of the structural, but not non-structural, genes indicated that SARS-CoV-2 has already harmonized its replication/transcription machineries with the host’s metabolic system, while it is still redefining virulence/transmissibility strategies at the molecular level.
Keywords
SARS-CoV-2; genome-wide mutations; transition; transversion; nonsynonymous and synonymous mutations; microevolution
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Received:
5 October 2020
Commenter:
Ranadhir Chakraborty
Commenter's Conflict of Interests:
Author
Comment:
SARS-CoV-2 microevolution was studied alongside the global trends of point-mutation in a universal dataset of 71,703 genomes. Globally, nsp1/nsp2/nsp3/ nsp11 and orf7a/orf3a/S were the most mutation-ridden non-structural and structural genes respectively. Whole-genome phylogeny revealed that entities belonging to the early lineages are mostly spread over Asian countries (including India) whereas the recently-derived lineages are more globally distributed. A transition:transversion ratio of 2.22 characterized the nucleotide substitution bias of SARS-CoV-2, with cytidine-to-uridine and guanosine-to-uridine conversions being the predominant transition and transversion types respectively. Nonsynonymous mutations are under positive selection in most of the structural, but not non-structural, genes.
Chayan Roy
,
Commenter: Ranadhir Chakraborty
Commenter's Conflict of Interests: Author