Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution. Issue 1 (24th March 2022)

• Record Type: Journal Article
• Authors: Ramazzotti, Daniele; Angaroni, Fabrizio; Maspero, Davide; Mauri, Mario; D'Aliberti, Deborah; Fontana, Diletta; Antoniotti, Marco; Elli, Elena Maria; Graudenzi, Alex; Piazza, Rocco
• Is Part Of: Virus evolution. Volume 8:Issue 1(2022)
• Publication Date: 2022-03-24
• Subjects: viral adaptation -- intra-host variants -- codon usage -- SARS-CoV-2 -- viral genomics; Viruses -- Evolution -- Periodicals; 579.2138
• DOI: 10.1093/ve/veac026
• Languages: English
• ISSNs: 2057-1577

Abstract

Abstract: Many large national and transnational studies have been dedicated to the analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome, most of which focused on missense and nonsense mutations. However, approximately 30 per cent 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 overtime. 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 Summary. Synonymous SARS-CoV-2 mutations related to the activity of different mutational processes may positively impact viral evolution by increasing its adaptation to the human codon usage.