Faecal shedding models for SARS-CoV-2 RNA among hospitalised patients and implications for wastewater-based epidemiology

SummaryThe concentration of SARS-CoV-2 RNA in faeces is not well established, posing challenges for wastewater-based surveillance of COVID-19 and risk assessments of environmental transmission. We develop versatile hierarchical models for faecal RNA shedding and apply them to data collected in six studies. We find that the mean number of gene copies per mL of faeces is 1.9 × 106 (2.3 × 105–2.0 × 108 95% credible interval) among unvaccinated hospitalised patients. Using Bayesian model comparison, we find no evidence for a subpopulation of patients who do not shed RNA: limits of quantification can account for negative stool samples. Our models indicate that hospitalised patients represent the tail of the shedding profile with a half-life of 34 hours (28–43 95% credible interval), suggesting that wastewater-based surveillance signals are more indicative of incidence than prevalence and can be a leading indicator of clinical presentation. Shedding among inpatients cannot explain high RNA concentrations observed in wastewater, consistent with more abundant shedding during the early infection course. We show that the models generalise and can predict summary statistics of held-out clinical datasets. However, shedding prior to hospitalisation cannot be constrained due to lack of samples, and information on viral variants was not available.