IMR Press / FBL / Volume 27 / Issue 1 / DOI: 10.31083/j.fbl2701013
Open Access Original Research
Temporal evolution and adaptation of SARS-CoV-2 codon usage
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1 Physics Department, Sapienza University of Rome, 00185 Rome, Italy
2 Liceo Statale Maria Montessori, 00198 Rome, Italy
3 Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey
4 Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Balcova, Izmir, Turkey
5 DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), 15780 Athens, Greece
6 INFN Roma1 Unit, 00185 Rome, Italy

Academic Editor: Graham Pawelec

Front. Biosci. (Landmark Ed) 2022, 27(1), 13; https://doi.org/10.31083/j.fbl2701013
Submitted: 31 July 2021 | Revised: 20 September 2021 | Accepted: 12 November 2021 | Published: 11 January 2022
Copyright: © 2022 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.
Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first occurred in Wuhan (China) in December of 2019. Since the outbreak, it has accumulated mutations on its coding sequences to optimize its adaptation to the human host. The identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe. Methods: In this study, we compared 320,338 SARS-CoV-2 genomes isolated from all over the world to the first sequenced genome in Wuhan, China. To this end, we analysed over time the codon usage patterns of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), RNA-dependent RNA polymerase (RdRp) and ORF1ab. Results: We found that genes coding for the proteins N and S diverged more rapidly since the outbreak by accumulating mutations. Interestingly, all genes show a deoptimization of their codon usage with respect to the human host. Our findings suggest a general evolutionary trend of SARS-CoV-2, which evolves towards a sub-optimal codon usage bias to favour the host survival and its spread. Furthermore, we found that S protein and RdRp are more subject to an increasing purifying pressure over time, which implies that these proteins will reach a lower tendency to accept mutations. In contrast, proteins N and M tend to evolve more under the action of mutational bias, thus exploring a large region of their sequence space. Conclusions: Overall, our study shed more light on the evolution of SARS-CoV-2 genes and their adaptation to humans, helping to foresee their mutation patterns and the emergence of new variants.

Keywords
SARS-CoV-2
Codon usage bias
Viral adaptation
Forsdyke plot
Similarity index
ENC plot
Figures
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