Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats

  1. Babatunde O. Motayo
  2. Olukunle Oluwapamilerin Oluwasemowo
  3. Paul A. Akinduti

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Abstract

Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus (βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an evolutionary rate of 1.301 × 10 −3 , HPD (1.064 × 10 −3 –1.434 × 10 −3 ) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus , Hibecovirus and Merbecovirus . The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats; we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.

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  5. Version published to 10.7717/peerj.10434
  6. Version published to 10.1101/2020.05.14.056085v2 on bioRxiv
  7. ScreenIT

    SciScore for 10.1101/2020.05.14.056085: (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

    Software and Algorithms
    SentencesResources
    Phylogenetic trees were constructed in MEGA 7.0 software www.megasoftwre.net using the maximum likelihood method with a general time reversible GTR with a gama distributed rate variation (T4) and a p-distance model with 1000 bootstrap resampling.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Discrete Phylogeographic analysis: Aligned sequences were analyzed for evidence of sufficient temporal clock signal using TempEst version 1.5 [16].
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    Bayesian skyride analysis was carried out to visualize the epidemic evolutionary history using Tracer v 1.8.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    To reconstruct the ancestral-state phylogeographic transmission across countries and hosts, we used the discrete-trait model implemented in BEAST version 1.10.4 [17].
    BEAST
    suggested: (BEAST, RRID:SCR_010228)

    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:
    • 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.

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  8. Version published to 10.1101/2020.05.14.056085v1 on bioRxiv