Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats

Abstract

Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.

Keywords: African Chiroptera; One Health; framing; virological metadata; virus–host relationship.

Figure 1.

Summaries of review findings (162 papers; 1978–2020). (a) Bat diversity, proportion of five most frequently sampled species relative to standing species richness (first bar) and total sampling effort (out of 742 species–study combinations) (second bar), and the proportion of the two most frequently sampled species being euthanized (third bar). (b) Bat identification, proportion of samples where bats were identified to the genus or species level, or not at all (first bar), and whether morphology and/or molecular methods were used (second bar). (c) Bat sampling, proportion of studies that did or did not provide capture data (first bar), and how captured bats were sampled: lethal, non-lethal (i.e. blood, skin, urine, oral or rectal swab), faeces (roost collected) or unknown (sample type not given) (second bar). (d) Virus sampling, proportion of studies by detection type (first bar), and by type of evidence (second bar). (e) Number of bat virological studies recorded from each African country. (f) Number of bats recorded to have been studied by country (number of bats in Algeria and Namibia not available, numbers are nearest estimates as some studies included more than one country and did not delineate provenance). (g) Viral sampling efforts normalized by species-level bat biodiversity (no. studies/no. species × 100).

Figure 2.

(a) Schematic approach to assess available knowledge on specific virus–host relationships (adapted from [47,48]). How well a system has been described is a function of: green: virological data (longitudinal/repeated versus one-off studies; virus isolated/full genomes obtained versus short sequences/inconclusive serology; choice of methods; experimental studies), blue: bat species data (accuracy of species identification; quantity and quality of collected data; sampling strategy), and purple: ecological/environmental metadata (description of habitat, roost site, colony size, life history data); examples shown are for filoviruses, indicating inadequate data on the putative host status of a given bat for EBOV (e.g. for virological data, no EBOV has yet been isolated from any bat, bat species data—confirmation of any bat species as a host is lacking) and high confidence for MARV. See electronic supplementary material, figure S9 for a more schematic illustration allowing qualitative scoring. (b) Recommended best practices for bat sampling and identification. Figure created using BioRender.com; Epomops franqueti image modified from photo 303584, (c) Jakob Fahr, some rights reserved (CC BY-NC), iNaturalist. Rousettus aegyptiacus modified from iStock photo.