Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.
Genome Biol Evol
; 13(5)2021 05 07.
Article
in English
| MEDLINE | ID: covidwho-1199488
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
ABSTRACT
The COVID-19 pandemic has seen an unprecedented response from the sequencing community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we study mutation rates and selective pressures affecting the virus. Understanding the processes and effects of mutation and selection has profound implications for the study of viral evolution, for vaccine design, and for the tracking of viral spread. We highlight and address some common genome sequence analysis pitfalls that can lead to inaccurate inference of mutation rates and selection, such as ignoring skews in the genetic code, not accounting for recurrent mutations, and assuming evolutionary equilibrium. We find that two particular mutation rates, G âU and C âU, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. Although previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Selection, Genetic
/
Mutation Rate
/
Silent Mutation
/
SARS-CoV-2
Type of study:
Randomized controlled trials
Topics:
Vaccines
Language:
English
Journal subject:
Biology
/
Molecular Biology
Year:
2021
Document Type:
Article
Affiliation country:
Gbe
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