Analysis of SARS-CoV-2 genomes from across Africa reveals potentially clinically relevant mutations

  1. Modeline N. Longjohn
  2. Olivia S. Egbule
  3. Samuel O. Danso
  4. Eugene E. Akujuru
  5. Victor T. Ibubeleye
  6. Christabel I. Oweredaba
  7. Theodora Ogharanduku
  8. Alexander Manu
  9. Benson C. Iweriebor

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Abstract

SARS-CoV-2 is a betacoronavirus, the etiologic agent of the novel Coronavirus disease 2019 (COVID-19). The World Health Organization officially declared COVID-19 as a pandemic in March 2020 after the outbreak in Wuhan, China, in late 2019. Across the continents and specifically in Africa, all index cases were travel-related. Understanding how the virus’s transportation across continents and different climatic conditions affect the genetic composition and the consequent effects on transmissibility, infectivity, and virulence of the virus is critical. Thus, it is crucial to compare COVID-19 genome sequences from the African continent with sequences from selected COVID-19 hotspots/countries in Asia, Europe, North and South America and Oceania.

To identify possible distinguishing mutations in the African SARS-CoV-2 genomes compared to those from these selected countries, we conducted in silico analyses and comparisons. Complete African SARS-CoV-2 genomes deposited in GISAID and NCBI databases as of June 2020 were downloaded and aligned with genomes from Wuhan, China and other SARS-CoV-2 hotspots. Using phylogenetic analysis and amino acid sequence alignments of the spike and replicase (NSP12) proteins, we searched for possible vaccine coverage targets or potential therapeutic agents. Identity plots for the alignments were created with BioEdit software and the phylogenetic analyses with the MEGA X software.

Our results showed mutations in the spike and replicate proteins of the SARS-Cov-2 virus. Phylogenetic tree analyses demonstrated variability across the various regions/countries in Africa as there were different clades in the viral proteins. However, a substantial proportion of these mutations (90%) were similar to those described in all the other settings, including the Wuhan strain. There were, however, novel mutations in the genomes of the circulating strains of the virus in African. To the best of our knowledge, this is the first study reporting these findings from Africa. However, these findings’ implications on symptomatic or asymptomatic manifestations, progression to severe disease and case fatality for those affected, and the cross efficacy of vaccines developed from other settings when applied in Africa are unknown.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.08.287201: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Amino Acid alignment of the surface glycoprotein (spike protein): All African surface glycoproteins of the SARS-CoV-2 obtained from the NCBI GenBank were aligned using ClustalW and compared to a reference strain from Wuhan, China.
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    The consensus sequence of the African NSP12 was created and aligned with the Wuhan reference strain, and identity plot was created with BioEdit.
    BioEdit
    suggested: (BioEdit, RRID:SCR_007361)
    Phylogenetic tree construction by the neighbor joining method was performed using MEGA X software, with bootstrap values of 10005.
    MEGA X
    suggested: None
    Evolutionary analyses were conducted in MEGA X software while multiple alignment was performed using MUSCLE alignment as implemented in MEGA9,10.
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    MEGA9,10
    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: We detected the following sentences addressing limitations in the study:
    As with all studies, this study has strengths and weaknesses. This study’s main strength is widespread the target African countries, cutting across all African continent (East, west, north, south and central). Secondly, this study focusses on a previously unstudied part of the world, as other studies have excluded analyzing the SARS-CoV-2 genomes in Africa. Finally, this study draws on available real-time data that continues to evolve and is a reasonable representation of the landscape at this time. On the other hand, the limitations include the low number of complete genomes sequenced and deposited as at that time. Research labs within the African continent seemed to be slow in gathering sequencing data in the initial months of the outbreak in Africa, which resulted in a relatively small number of complete genomes. Additionally, we cannot control for errors, lab-specific bias, handling bias, and sample collection bias because we are working with existing data collected by multiple labs. These limitations reduce the power of our results and inference. Finally, the findings in this study need to be validated using wet lab-based experiments.

    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:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.09.08.287201v2 on bioRxiv
  3. Version published to 10.1101/2020.09.08.287201v1 on bioRxiv