4.7 Article

Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS-CoV-2 mitigation strategies

Journal

JOURNAL OF MEDICAL VIROLOGY
Volume 93, Issue 9, Pages 5630-5634

Publisher

WILEY
DOI: 10.1002/jmv.27056

Keywords

codon deoptimization; codon usage; coronaviruses; COVID-19; SARS-CoV-2

Categories

Funding

  1. CNPq [421598/2018-2]
  2. Fundacao de Amparo a Pesquisa do Estado do Rio de Janeiro FAPERJ
  3. CAPES [88882.349290/201901]
  4. South African Medical Research Council [MRC-RFA-UFSP-01-2013/UKZN HIVEPI]

Ask authors/readers for more resources

The COVID-19 pandemic caused by SARS-CoV-2 has become a major global health issue, with vaccine rollouts bringing hope of herd immunity. However, concerns arise with the emergence of virus variants that may possess enhanced virulence. Codon usage analysis helps elucidate viral evolution and potential variants, highlighting the importance of genomic monitoring to prevent and mitigate the pandemic.
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly widespread worldwide becoming one of the major global public health issues of the last centuries. Currently, COVID-19 vaccine rollouts are finally upon us carrying the hope of herd immunity once a sufficient proportion of the population has been vaccinated or infected, as a new horizon. However, the emergence of SARS-CoV-2 variants brought concerns since, as the virus is exposed to environmental selection pressures, it can mutate and evolve, generating variants that may possess enhanced virulence. Codon usage analysis is a strategy to elucidate the evolutionary pressure of the viral genome suffered by different hosts, as possible cause of the emergence of new variants. Therefore, to get a better picture of the SARS-CoV-2 codon bias, we first identified the relative codon usage rate of all Betacoronaviruses lineages. Subsequently, we correlated putative cognate transfer ribonucleic acid (tRNAs) to reveal how those viruses adapt to hosts in relation to their preferred codon usage. Our analysis revealed seven preferred codons located in three different open reading frame which appear preferentially used by SARS-CoV-2. In addition, the tRNA adaptation analysis indicates a wide strategy of competition between the virus and mammalian as principal hosts highlighting the importance to reinforce the genomic monitoring to prompt identify any potential adaptation of the virus into new potential hosts which appear to be crucial to prevent and mitigate the pandemic.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available