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.

Fig 1. Location of the studied Eidolon helvum roosts.

Panel A shows the locations of the roosts in Africa. Panel B shows some of the trees occupied at the 37 Military Hospital in Accra, Ghana and Panel C shows roosting bats at the Kikundi Market in Morogoro, Tanzania.

Fig 2. Eidolon helvum monthly abundance (blue line), precipitation (green line), and coronavirus shedding (red line) at the roost in Morogoro, Tanzania (left); and at the roost in Accra, Ghana (right).

Color bands indicate the “lactation” (orange), “weaning” (purple), and “rest of the year” (blue) reproductive periods.

Fig 3. The Posterior Probability Distributions (light blue) and the corresponding 95% Highest Posterior Density Interval (blue) of the odds ratio for coronavirus shedding by Eidolon helvum in the roost at Morogoro Tanzania during the “weaning” period versus the “rest of the year”, during the “weaning” period versus the “lactation” period, and during the “lactation” period versus the “rest of the year”.

The vertical black line indicates a neutral odds ratio with a value of one.