Journal
VIRUSES-BASEL
Volume 13, Issue 3, Pages -Publisher
MDPI
DOI: 10.3390/v13030394
Keywords
SARS-CoV-2; COVID-19; evolution; mutation; phylogenetics; APOBEC; ROS; ZAP; ADAR
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Funding
- EMBO Installation Grant [4163]
- Scientific and Technological Research Council of Turkey (TUBITAK)
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Understanding the evolution of SARS-CoV-2 is crucial in managing the COVID-19 pandemic, with mutagenesis and selection being key mechanisms. This study used a phylogenetic approach to reveal the contribution of mutagenesis and selection to the genetic diversity of SARS-CoV-2 genomes, showing that mutation patterns are influenced by host antiviral mechanisms and potential adaptive responses.
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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