Notable outbreaks of infectious viruses resulting from spillover events from bats have brought much attention to the ecological origins of bat-borne zoonoses, resulting in an increase in ecological and epidemiological studies on bat populations in Africa, Asia, and Australia. The aim of many of these studies is to identify new viral agents with field sampling methods that collect pooled urine samples from large plastic sheets placed under a bat roost. The efficiency of under-roost sampling also makes it an attractive method for gathering roost-level prevalence data. However, the method allows multiple individuals to contribute to a pooled sample, potentially introducing positive bias. To assess the ability of under-roost sampling to accurately estimate viral prevalence, we constructed a probabilistic model to explore the relationship between four sampling designs (quadrant, uniform, stratified, and random) and estimation bias. We modeled bat density and movement with a Poisson cluster process and spatial kernels and simulated the four under-roost sheet sampling designs by manipulating a spatial grid of hexagonal tiles. We performed global sensitivity analyses to identify major sources of estimation bias and provide recommendations for field studies that wish to estimate roost-level prevalence. We found that the quadrant-based design had a positive bias 5--7 times higher than other designs due to spatial autocorrelation among sampling sheets and clustering of bats in the roost. The sampling technique is therefore highly sensitive to viral presence; but lacks specificity, providing poor information regarding dynamics in viral prevalence. Given population sizes of 5000--14000, our simulation results indicate that using a stratified random design to collect 30--40 urine samples from 80--100 sheets, each with an area of 0.75--1m sq., would provide sufficient estimation of true prevalence with minimum sampling bias and false negatives. However, acknowledging the general problem of data aggregation, we emphasize that robust inference of true prevalence from field data require information of underpinning roost sizes. Our findings refine our understanding of the under-roost sampling technique with the aim of increasing its specificity and suggest that the method be further developed as an efficient non-invasive sampling technique that provides roost-level estimates of viral prevalence within a bat population.

Optimizing non-invasive sampling of an infectious bat virus