Global genetic patterns reveal host tropism versus cross-taxon transmission of bat Betacoronaviruses

  1. Michael G. Bacus
  2. Stephen Adrian H. Dayap
  3. Nikki Vanesa T. Tampon
  4. Marielle M. Udarbe
  5. Roberto P. Puentespina
  6. Sharon Yvette Angelina M. Villanueva
  7. Aleyla E. de Cadiz
  8. Marion John Michael M. Achondo
  9. Lyre Anni E. Murao

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. The diversity, distribution, and host associations of bat CoVs were investigated to assess their potential for zoonotic transmission. Phylogenetic, network, and principal coordinate analysis confirmed the classification of betacoronaviruses (BetaCoVs) into five groups (2A to 2E) and a potentially novel group, with further division of 2D into five subgroups. The genetic co-clustering of BetaCoVs among closely related bats reflects host taxon-specificity with each bat family as the host for a specific BetaCoV group, potentially a natural barrier against random transmission. The divergent pathway of BetaCoV and host evolution suggests that the viruses were introduced just prior to bat dispersal and speciation. As such, deviant patterns were observed such as for 2D-IV, wherein cross-taxon transmission due to overlap in bat habitats and geographic range among genetically divergent African bat hosts could have played a strong role on their shared CoV lineages. In fact, a few bat taxa especially the subfamily Pteropodinae were shown to host diverse groups of BetaCoVs. Therefore, ecological imbalances that disturb bat distribution may lead to loss of host specificity through cross-taxon transmission and multi-CoV infection. Hence, initiatives that minimize the destruction of wildlife habitats and limit wildlife-livestock-human interfaces are encouraged to help maintain the natural state of bat BetaCoVs in the wild.

Importance

Bat Betacoronaviruses (BetaCoVs) pose a significant threat to global public health and have been implicated in several epidemics such as the recent pandemic by severe acute respiratory syndrome coronavirus 2. Here, we show that bat BetaCoVs are predominantly host-specific, which could be a natural barrier against infection of other host types. However, a strong overlap in bat habitat and geographic range may facilitate viral transmission to unrelated hosts, and a few bat families have already been shown to host multi-CoV variants. We predict that continued disturbances on the ecological balance may eventually lead to loss of host specificity. When combined with enhanced wildlife-livestock-human interfaces, spillover to humans may be further facilitated. We should therefore start to define the ecological mechanisms surrounding zoonotic events. Global surveillance should be expanded and strengthened to assess the complete picture of bat coronavirus diversity and distribution and their potential to cause spillover infections.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.05.04.076281: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIACUC: Prior to the conduct of the study, Wildlife Gratuitous Permit (WGP No. XI-2018-07) and IACUC approval (protocol no.: 2018-019) were secured from the Department of Environment and Natural Resources XI and the Institutional Animal Care and Use Committee of the University of the Philippines Manila, respectively.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequences were cleaned using the FinchTV software (Geospiza, USA) and distance analysis was performed using the Basic Local Alignment Search Tool (BLAST) of the National Center for Biotechnology Information (NCBI) (
    FinchTV
    suggested: (FinchTV, RRID:SCR_005584)
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    (http://www.ncbi.nlm.nih.gov/).
    http://www.ncbi.nlm.nih.gov/
    suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)
    Multiple sequence alignment was performed with the MAFFT software using the default algorithm and the leave gappy regions function.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The final alignment was trimmed and cleaned in MEGA 7 software in order to come up with a 325 bp alignment of the CoV partial RdRp gene.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    The best phylogenetic model was calculated using jModelTest v.
    jModelTest
    suggested: (jModelTest, RRID:SCR_015244)
    Phylogenetic inference was performed using BEAST v.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    A Maximum Clade Credibility (MCC) tree was generated using TreeAnnotator v.1.10.4. and the resulting MCC tree was visualized with FigTree v.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Phylogenetic analysis of bats: Cytochrome B (Cyt B) gene of 43 different bat species representing the bat hosts of the betacoronavirus lineage were obtained from the NCBI database.
    NCBI
    suggested: (NCBI, RRID:SCR_006472)

    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.
    • 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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.05.04.076281v1 on bioRxiv