Multivariate Analyses of Codon Usage of SARS-CoV-2 and other betacoronaviruses

  1. Haogao Gu
  2. Daniel Chu
  3. Malik Peiris
  4. Leo L.M. Poon

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Abstract

Coronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus Betacoronavirus which also includes severe acute respiratory syndrome related coronavirus (SARSr-CoV) and Middle East respiratory syndrome related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses can help identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, global correspondence analysis (CA), within-group correspondence analysis (WCA) and between-group correspondence analysis (BCA) were performed among different genes in coronavirus viral sequences. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.

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    SciScore for 10.1101/2020.02.15.950568: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Experimental Models: Organisms/Strains
    SentencesResources
    Six genomes in this study were used as special references (BetaCoV/bat/Yunnan/RaTG13/2013|EPI_ISL_402131; BetaCoV/pangolin/Guangxi/P1E/2017|EPI_ISL_410539; MG772934.1_Bat_SARS-like_coronavirus_isolate_bat-SL-CoVZXC21; MG772933.1_Bat_SARS-like_coronavirus_isolate_bat-SL-CoVZC45; KY352407.1_Severe_acute_respiratory_syndrome-related_coronavirus_strain_BtKY72 and GU190215.1_Bat_coronavirus_BM48-31/BGR/2008), as they have previously been reported to have close phylogenetic relationship with SARS-CoV-29–11.
    BetaCoV/bat/Yunnan/RaTG13/2013|EPI_ISL_402131; BetaCoV/pangolin/Guangxi/P1E/2017|EPI_ISL_410539; MG772934.1_Bat_SARS-like_coronavirus_isolate_bat-SL-CoVZXC21; MG772933.1_Bat_SARS-like_coronavirus_isolate_bat-SL-CoVZC45; KY352407.1_Severe_acute_respiratory_syndrome-related_coronavirus_strain_BtKY72
    suggested: None

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.02.15.950568v3 on bioRxiv
  3. Version published to 10.1101/2020.02.15.950568v1 on bioRxiv
  4. Version published to 10.1101/2020.02.15.950568v2 on bioRxiv
  5. Version published to 10.1093/ve/veaa032