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J Med Virol . Betacoronaviruses genome analysis reveals evolution toward specific codons usage: implications for SARS-CoV-2 mitigation strategies

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  • J Med Virol . Betacoronaviruses genome analysis reveals evolution toward specific codons usage: implications for SARS-CoV-2 mitigation strategies


    J Med Virol


    . 2021 May 2.
    doi: 10.1002/jmv.27056. Online ahead of print.
    Betacoronaviruses genome analysis reveals evolution toward specific codons usage: implications for SARS-CoV-2 mitigation strategies


    Elisson Nogueira Lopes 1 , Vagner Fonseca 2 3 , Diego Frias 4 , Stephane Tosta 1 , Álvaro Salgado 1 , Ricardo Assunção Vialle 5 , Toscano Soares Paulo Eduardo 6 , Fernanda Khouri Barreto 7 , Vasco Ariston de Azevedo 1 , Michele Guarino 8 , Silvia Angeletti 9 , Massimo Ciccozzi 10 , Luiz Carlos Junior Alcantara 1 11 , Marta Giovanetti 1 11



    Affiliations

    Abstract

    Since the start of the COVID-19 pandemic, the 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 tRNAs to reveal how those viruses adapt to hosts in relation to their preferred codon usage. Our analysis revealed 7 preferred codons located in 3 different ORFs 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 in order to prompt identify any potential adaptation of the virus into new potential hosts which appear to be crucial to prevent and mitigate the pandemic. This article is protected by copyright. All rights reserved.

    Keywords: COVID-19; Coronaviruses; SARS-CoV-2; codon deoptimization; codon usage.

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