Ewan Colman, Rowland R. Kao

Background Testing samples of waste water for markers of infectious disease became a widespread method of surveillance during the COVID-19 pandemic. While these data generally correlate well with other indicators of national prevalence, samples that cover localised regions tend to be highly variable over short time scales.

Methods We introduce a procedure for estimating the realtime growth rate of pathogen prevalence using time series data from wastewater sampling. The number of copies of a target gene found in a sample is modelled as time-dependent random variable whose distribution is estimated using maximum likelihood. The output depends on a hyperparameter that controls the sensitivity to variability in the underlying data. We apply this procedure to data reporting the number of copies of the N1 gene of SARS-CoV-2 collected at water treatment works across Scotland between February 2021 and February 2023.

Results The real-time growth rate of…