tetano
Editor, Senior Moderator
Virus Evol
. 2022 Mar 24;8(1):veac026.
doi: 10.1093/ve/veac026. eCollection 2022.
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution
Daniele Ramazzotti, Fabrizio Angaroni[SUP] 1 [/SUP], Davide Maspero[SUP] 1 [/SUP], Mario Mauri[SUP] 2 [/SUP], Deborah D'Aliberti[SUP] 2 [/SUP], Diletta Fontana[SUP] 2 [/SUP], Marco Antoniotti[SUP] 1 [/SUP], Elena Maria Elli[SUP] 2 [/SUP], Alex Graudenzi[SUP] 3 [/SUP], Rocco Piazza[SUP] 2 [/SUP]
Affiliations
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.
Keywords: SARS-CoV-2; codon usage; intra-host variants; viral adaptation; viral genomics.
. 2022 Mar 24;8(1):veac026.
doi: 10.1093/ve/veac026. eCollection 2022.
Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution
Daniele Ramazzotti, Fabrizio Angaroni[SUP] 1 [/SUP], Davide Maspero[SUP] 1 [/SUP], Mario Mauri[SUP] 2 [/SUP], Deborah D'Aliberti[SUP] 2 [/SUP], Diletta Fontana[SUP] 2 [/SUP], Marco Antoniotti[SUP] 1 [/SUP], Elena Maria Elli[SUP] 2 [/SUP], Alex Graudenzi[SUP] 3 [/SUP], Rocco Piazza[SUP] 2 [/SUP]
Affiliations
- PMID: 35371557
- PMCID: PMC8971538
- DOI: 10.1093/ve/veac026
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.
Keywords: SARS-CoV-2; codon usage; intra-host variants; viral adaptation; viral genomics.