About: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

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About: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts
Creator	Kovařík, Aleš Matyášek, Roman
Source	Medline; PMC
abstract	The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide.
has issue date	2020-07-07(xsd:dateTime)
bibo:doi	10.3390/genes11070761
bibo:pmid	32646049
has license	cc-by
sha1sum (hex)	122a65c1048af4785f6db91589bd0086a16a091f
schema:url	https://doi.org/10.3390/genes11070761
resource representing a document's title	Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts
has PubMed Central identifier	PMC7397057
has PubMed identifier	32646049
schema:publication	Genes (Basel)
resource representing a document's body	covid:122a65c1048af4785f6db91589bd0086a16a091f#body_text
is schema:about of	named entity 'humans' named entity 'SARS-CoV-2' named entity 'adaptation' named entity 'transfer' named entity 'variations' named entity 'DECREASED' named entity 'DATA' named entity 'DEAMINATION' named entity 'CODONS' named entity 'AMINO ACIDS' named entity 'CONTENTS' named entity 'SUGGEST' named entity 'EVOLVING' named entity 'HIGH FREQUENCY' named entity 'amino acids' named entity 'period' named entity 'The' named entity 'mediated' named entity 'accumulation' named entity 'animal' named entity 'SARS-CoV-2' named entity 'Transitions' named entity 'genome' named entity 'SARS-CoV-2' named entity 'bat' named entity 'CpG' named entity 'closely related' named entity 'hydrophobic amino acids' named entity 'SARS-CoV-2' named entity 'human population' named entity 'Rapid Evolution' named entity 'phylogeny' named entity 'isoleucine' named entity 'SNV' named entity 'SARS-CoV-2' named entity 'reference genome' named entity 'protein' named entity 'amino acid residues' named entity 'spike protein' named entity 'negative strand' named entity 'genomes' named entity 'CpG' named entity 'GenBank' named entity 'betacoronaviruses' named entity 'nucleic acid' named entity 'virus' named entity 'amino acid residues' named entity 'Cytosine' named entity 'nucleotides' named entity 'Wuhan' named entity 'stop codons' named entity 'RBD' named entity 'deamination' named entity 'complete sequences' named entity 'nonsynonymous' named entity 'prokaryotic' named entity 'genomes' named entity 'CpG' named entity 'Wuhan' named entity 'Mutation' named entity 'double-stranded DNA' named entity 'protein' named entity 'genome' named entity 'SNVs' named entity 'RNA' named entity 'bat' named entity 'CpG' named entity 'highly conserved' named entity 'mutation' named entity 'eukaryotic' named entity 'HTLV1' named entity 'coronavirus' named entity 'Nucleotide' named entity 'Phylogenetically' named entity 'prokaryotic genomes' named entity 'SARS-CoV-2' named entity 'cytosine' named entity 'SARS-CoV-2' named entity 'box plot' named entity 'NL63'

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