Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony: considerations for spillover

Abstract

Novel coronavirus species of public health and veterinary importance have emerged in the first two decades of the twenty-first century, with bats identified as natural hosts for progenitors of many coronaviruses. Targeted wildlife surveillance is needed to identify the factors involved in viral perpetuation within natural host populations, and drivers of interspecies transmission. We monitored a natural colony of Egyptian rousette bats at monthly intervals across two years to identify circulating coronaviruses, and to investigate shedding dynamics and viral maintenance within the colony. Three distinct lineages were detected, with different seasonal temporal excretion dynamics. For two lineages, the highest periods of coronavirus shedding were at the start of the year, when large numbers of bats were found in the colony. Highest peaks for a third lineage were observed towards the middle of the year. Among individual bat-level factors (age, sex, reproductive status, and forearm mass index), only reproductive status showed significant effects on excretion probability, with reproductive adults having lower rates of detection, though factors were highly interdependent. Analysis of recaptured bats suggests that viral clearance may occur within one month. These findings may be implemented in the development of risk reduction strategies for potential zoonotic coronavirus transmission.

Figure 1

Bayesian phylogeny of the coronaviruses identified in the study. The phylogenetic tree was split into three parts for better visualization (with collapsed clades indicated). The Alphacoronavirus genus is shown in part A, the RouNobeCoV betacoronavirus identified in this study with related African sequences in part B, and the nobecoviruses related to the HKU9 species are shown in part C. Sequences in navy blue indicate reference species, specific subgenera or collapsed clades (to improve visualization). Sequences in light blue refer to the RouAlphaCoV, green to RouNobeCoV and red for the dominant HKU9-lineage sequences. Only posterior probabilities of greater than 0.5 are indicated. Three-letter country codes indicate sequence origins.

Figure 2

Reproductive cycle and coronavirus excretion dynamics in Rousettus aegyptiacus. (a) schematic representation of the timing of reproductive stages and general rainfall; (b) Total GAM-estimated coronavirus prevalence and environmental detection rate over time (individual rectal swabs—solid lines; pooling-corrected fecal samples—dotted lines), and raw positivity at specific sampling dates (rectal swabs—empty circles; pooling-corrected fecal samples—filled circles). Shaded areas and error bars areas depict 95% posterior intervals for model predictions and binomial intervals monthly samples, respectively. (c) Coronavirus detection dynamics for the HKU9-related lineage only, (d) detection of the RouAlphaCoV lineage and (e) detection of the RouNobeCoV lineage.

Figure 3

Estimates of peak seasonal dates of excretion for each coronavirus lineage. Plots show the GAMM posterior density for the date of highest rates of detection for fecal (dotted) and rectal (solid) samples. Rectal and fecal peak date distributions overlap within each lineage, while across lineages the peak date differs in > 95% of posterior samples for fecal samples of all lineages and overlaps only across rectal samples from the HKU9-related and RouAlphaCoV lineages.

Figure 4

Effect of demographic factors on prevalence for the HKU9-related BetaCoV lineage. Points and whiskers represent observed and 95% intervals for observed prevalence on sampling dates for all adults (red) and subadults (green). The thick line and shaded area show modelled estimates of prevalence for adults and subadults over time. The overlap indicates no significant effect. Thin lines show modelled estimates of prevalence for adults, as modified by the effects of different reproductive conditions: lactating (brown), pregnant (blue) or scrotal (purple). All estimates are conditional on a mean within-group FMI.

Figure 5

Details of the 11 bats excreting coronavirus RNA at their initial capture or second recapture, with subsequent recapture events. Bat tattoo numbers are provided as identity tags and the months captured indicated. Coronavirus RNA detected: purple/‘plus’ symbol; absence of coronavirus RNA: grey/‘minus’ symbols. The genus of detectable coronaviruses and months between recaptures are also indicated.