Longitudinal Survey of Coronavirus Circulation and Diversity in Insectivorous Bat Colonies in Zimbabwe

Abstract

Background: Studies have linked bats to outbreaks of viral diseases in human populations such as SARS-CoV-1 and MERS-CoV and the ongoing SARS-CoV-2 pandemic.

Methods: We carried out a longitudinal survey from August 2020 to July 2021 at two sites in Zimbabwe with bat-human interactions: Magweto cave and Chirundu farm. A total of 1732 and 1866 individual bat fecal samples were collected, respectively. Coronaviruses and bat species were amplified using PCR systems.

Results: Analysis of the coronavirus sequences revealed a high genetic diversity, and we identified different sub-viral groups in the Alphacoronavirus and Betacoronavirus genus. The established sub-viral groups fell within the described Alphacoronavirus sub-genera: Decacovirus, Duvinacovirus, Rhinacovirus, Setracovirus and Minunacovirus and for Betacoronavirus sub-genera: Sarbecoviruses, Merbecovirus and Hibecovirus. Our results showed an overall proportion for CoV positive PCR tests of 23.7% at Chirundu site and 16.5% and 38.9% at Magweto site for insectivorous bats and Macronycteris gigas, respectively.

Conclusions: The higher risk of bat coronavirus exposure for humans was found in December to March in relation to higher viral shedding peaks of coronaviruses in the parturition, lactation and weaning months of the bat populations at both sites. We also highlight the need to further document viral infectious risk in human/domestic animal populations surrounding bat habitats in Zimbabwe.

Keywords: Zimbabwe; bat coronavirus (Bt CoVs); genetic diversity; human–bat interaction; reproductive phenology.

Figure 1

The study sites highlighted on the map show the sampling areas for insectivorous bat colonies in Hurungwe district.

Figure 2

Results of the longitudinal sampling at two sites for coronaviruses. (A) Estimation of the coronavirus prevalence (with 95% CI) at Chirundu site, (B,C) the same for bats and Macronycteris gigas (respectively) at Magweto cave site. The areas colored green, cyan, navy blue, magenta, red and pink show periods of gestation, parturition, lactation, weaning, 4–6 months old juvenile and non-gestation periods, respectively, observed in the dominant bat species at both sites.

Figure 2

Results of the longitudinal sampling at two sites for coronaviruses. (A) Estimation of the coronavirus prevalence (with 95% CI) at Chirundu site, (B,C) the same for bats and Macronycteris gigas (respectively) at Magweto cave site. The areas colored green, cyan, navy blue, magenta, red and pink show periods of gestation, parturition, lactation, weaning, 4–6 months old juvenile and non-gestation periods, respectively, observed in the dominant bat species at both sites.

Figure 3

Phylogenetic tree of AlphaCoV partial RdRp gene. The sequences detected at Chirundu site are in red color and from Magweto site in blue color. Pink = more sequences detected at Chirundu than Magweto within the same subclade and purple = more sequences detected at Magweto site than Chirundu site within the subclade. The tree was built using the maximum likelihood method based on the GTR + G4 + I model. The robustness of nodes was assessed with 1000 bootstrap replicates. Bootstrap values >70 are denoted with asterisks, and those <70 are not shown.

Figure 4

Phylogenetic tree of BetaCoV partial RdRp gene. The sequences detected at Chirundu site are in red color and at Magweto site in blue color. Pink = more sequences detected at Chirundu than Magweto site within the same subclade. The tree was built using the maximum likelihood method based on the GTR + G4 + I model. The robustness of nodes was assessed with 1000 bootstrap replicates. Bootstrap values >70 are denoted with asterisks, and those <70 are not shown.