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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doaj-2f687f84331b4b9a9c3a8896a52fa82a2021-03-03T00:01:16ZengMDPI AGViruses1999-49152021-03-011339439410.3390/v13030394The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral DefenseCem Azgari0Zeynep Kilinc1Berk Turhan2Defne Circi3Ogun Adebali4Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, TurkeyFaculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, TurkeyFaculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, TurkeyFaculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, TurkeyFaculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, TurkeyUnderstanding 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.https://www.mdpi.com/1999-4915/13/3/394SARS-CoV-2COVID-19evolutionmutationphylogeneticsAPOBEC |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cem Azgari Zeynep Kilinc Berk Turhan Defne Circi Ogun Adebali |
spellingShingle |
Cem Azgari Zeynep Kilinc Berk Turhan Defne Circi Ogun Adebali The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense Viruses SARS-CoV-2 COVID-19 evolution mutation phylogenetics APOBEC |
author_facet |
Cem Azgari Zeynep Kilinc Berk Turhan Defne Circi Ogun Adebali |
author_sort |
Cem Azgari |
title |
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_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_sort |
mutation profile of sars-cov-2 is primarily shaped by the host antiviral defense |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2021-03-01 |
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. |
topic |
SARS-CoV-2 COVID-19 evolution mutation phylogenetics APOBEC |
url |
https://www.mdpi.com/1999-4915/13/3/394 |
work_keys_str_mv |
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