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bioRxiv · 10.1101/2021.04.23.441151

Large-scale analysis of synonymous viral variants reveals global adaptation of the SARS-CoV-2 to the human codon usage

Ramazzotti, D.·Angaroni, F.·Maspero, D.·Mauri, M.·D'Aliberti, D.·Antoniotti, M.·Graudenzi, A.·Piazza, R.
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Abstract

Many large national and transnational studies have been dedicated to the analysis of SARS-CoV-2 genome, most of which focused on missense and nonsense mutations. However, approximately 30% of the SARS-CoV-2 variants are synonymous, therefore changing the target codon without affecting the corresponding protein sequence. By performing a large-scale analysis of sequencing data generated from almost 400,000 SARS-CoV-2 samples, we show that silent mutations increasing the similarity of viral codons to the human ones tend to fixate in the viral genome over-time. This indicates that SARS-CoV-2 codon usage is adapting to the human host, likely improving its effectiveness in using the human aminoacyl-tRNA set through the accumulation of deceitfully neutral silent mutations. One-Sentence SummarySynonymous SARS-CoV-2 mutations related to the activity of different mutational processes may positively impact viral evolution by increasing its adaptation to human codon usage.

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Ramazzotti, D., Angaroni, F., Maspero, D., Mauri, M., D'Aliberti, D., Antoniotti, M., Graudenzi, A., Piazza, R.. 2021-04-23. Large-scale analysis of synonymous viral variants reveals global adaptation of the SARS-CoV-2 to the human codon usage. https://doi.org/10.1101/2021.04.23.441151

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