Seasonal shedding of coronavirus by straw-colored fruit bats at urban roosts in Africa

Abstract

The straw-colored fruit bat ( Eidolon helvum ) is a pteropodid whose conservation is crucial for maintaining functional connectivity of plant populations in tropical Africa. Land conversion has pushed this species to adapt to roosting in urban centers across its range. These colonies often host millions of individuals, creating intensive human-bat contact interfaces that could facilitate the spillover of coronaviruses shed by these bats. A better understanding of coronavirus dynamics in these roosts is needed to identify peak times of exposure risk in order to propose evidence-based management that supports safe human-bat coexistence, as well as the conservation of this chiropteran. We studied the temporal patterns of coronavirus shedding in E . helvum , by testing thousands of longitudinally-collected fecal samples from two spatially distant urban roosts in Ghana and Tanzania. Shedding of coronaviruses peaked during the second part of pup weaning in both roosts. Assuming that coronavirus shedding is directly related to spillover risk, our results indicate that exposure mitigation should target reducing contact between people and E . helvum roosts during the pup “weaning” period. This recommendation can be applied across the many highly-populated urban sites occupied by E . helvum across Africa.

Coronaviruses Are Abundant and Genetically Diverse in West and Central African Bats, including Viruses Closely Related to Human Coronaviruses

“…We also confirmed that juvenile and subadult bats are infected at higher rates than adult bats, as previously reported [ 19 , 53 ]. This was observed in all species for which sufficient juvenile and/or subadults have been included.…”

A global-scale dataset of bat viral detection suggests that pregnancy reduces viral shedding

“…Further, careful attention to viral dynamics throughout the reproductive cycle in a wider variety of bat host species will help identify periods of increased zoonotic spillover risk to humans, since spillover is often associated with pulses of viral excretion in reservoir hosts [6,12,24,25]. Our work is congruent with recent, related studies that indicate the pup weaning period, not necessarily pregnancy or lactation periods, may be most strongly associated with viral shedding in bats [20,89]. Consideration of the interplay between reproductive biology and host defenses will improve our understanding of virus-host dynamics and ultimately bolster our ability to prevent spillover from bats and other important wildlife hosts of viral pathogens.…”

“…Seasonality of bat-associated viral outbreaks may be linked to features of bat life history and reproductive ecology, such as metapopulation structure, migration, or synchronous birthing [12,13,[18][19][20]. For example, some bat species form large maternity colonies which increase local population density and intraspecific contact rates, thus increasing the potential for pathogen transmission and providing an ideal context for researchers to conduct viral sampling [18,21,22].…”

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

“…Life-history parameters such as reproductive cycles influence virus infection dynamics, and gradual loss of maternal immunity among young bats increases the number of susceptible individuals [14,15]. Population estimates and identifying the proportion of naive individuals with longitudinal data are thus important to understand viral maintenance and infection dynamics; a recent paper published after our meta-analysis cut-off date that details longitudinal sampling for coronaviruses in Eidolon helvum illustrates the strength of this approach [46]. We encourage gathering more comprehensive data on target species and provide a data collection framework (figure 2; electronic supplementary material, figure S9) that will facilitate context-specific goals and priority establishment for bat-virus studies.…”