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The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense

Understanding SARS-CoV-2 evolution is a fundamental effort in coping with the COVID-19 pandemic. The virus genomes have been broadly evolving due to the high number of infected hosts world-wide. Mutagenesis and selection are two inter-dependent mechanisms of virus diversification. However, which mec...

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Autores principales: Azgari, Cem, Kilinc, Zeynep, Turhan, Berk, Circi, Defne, Adebali, Ogun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7999997/
https://www.ncbi.nlm.nih.gov/pubmed/33801257
http://dx.doi.org/10.3390/v13030394
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author Azgari, Cem
Kilinc, Zeynep
Turhan, Berk
Circi, Defne
Adebali, Ogun
author_facet Azgari, Cem
Kilinc, Zeynep
Turhan, Berk
Circi, Defne
Adebali, Ogun
author_sort Azgari, Cem
collection PubMed
description Understanding SARS-CoV-2 evolution is a fundamental effort in coping with the COVID-19 pandemic. The virus genomes have been broadly evolving due to the high number of infected hosts world-wide. Mutagenesis and selection are two inter-dependent mechanisms of virus diversification. However, which mechanisms contribute to the mutation profiles of SARS-CoV-2 remain under-explored. Here, we delineate the contribution of mutagenesis and selection to the genome diversity of SARS-CoV-2 isolates. We generated a comprehensive phylogenetic tree with representative genomes. Instead of counting mutations relative to the reference genome, we identified each mutation event at the nodes of the phylogenetic tree. With this approach, we obtained the mutation events that are independent of each other and generated the mutation profile of SARS-CoV-2 genomes. The results suggest that the heterogeneous mutation patterns are mainly reflections of host (i) antiviral mechanisms that are achieved through APOBEC, ADAR, and ZAP proteins, and (ii) probable adaptation against reactive oxygen species.
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spelling pubmed-79999972021-03-28 The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense Azgari, Cem Kilinc, Zeynep Turhan, Berk Circi, Defne Adebali, Ogun Viruses Article Understanding SARS-CoV-2 evolution is a fundamental effort in coping with the COVID-19 pandemic. The virus genomes have been broadly evolving due to the high number of infected hosts world-wide. Mutagenesis and selection are two inter-dependent mechanisms of virus diversification. However, which mechanisms contribute to the mutation profiles of SARS-CoV-2 remain under-explored. Here, we delineate the contribution of mutagenesis and selection to the genome diversity of SARS-CoV-2 isolates. We generated a comprehensive phylogenetic tree with representative genomes. Instead of counting mutations relative to the reference genome, we identified each mutation event at the nodes of the phylogenetic tree. With this approach, we obtained the mutation events that are independent of each other and generated the mutation profile of SARS-CoV-2 genomes. The results suggest that the heterogeneous mutation patterns are mainly reflections of host (i) antiviral mechanisms that are achieved through APOBEC, ADAR, and ZAP proteins, and (ii) probable adaptation against reactive oxygen species. MDPI 2021-03-02 /pmc/articles/PMC7999997/ /pubmed/33801257 http://dx.doi.org/10.3390/v13030394 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Azgari, Cem
Kilinc, Zeynep
Turhan, Berk
Circi, Defne
Adebali, Ogun
The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense
title The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense
title_full The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense
title_fullStr The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense
title_full_unstemmed The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense
title_short The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense
title_sort mutation profile of sars-cov-2 is primarily shaped by the host antiviral defense
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7999997/
https://www.ncbi.nlm.nih.gov/pubmed/33801257
http://dx.doi.org/10.3390/v13030394
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