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.