Challenges in realising the potential of wastewater-based epidemiology to quantitatively monitor and predict the spread of disease

This repository provides code and links to data supporting the published article https://doi.org/10.2166/wh.2022.020

Abstract

Researchers around the world have demonstrated correlations between measurements of SARS-CoV-2 RNA in wastewater and case rates derived from direct testing of individuals. This has raised hopes that WBE methods might be used to quantify the spread of disease, perhaps faster than direct testing, and with less expense and intrusion. We illustrate, using data from Scotland and the USA, the issues regarding the construction of effective predictive models for disease case rates. We discuss the effects of variation in, and the problem of aligning, public health reporting and wastewater measurements. We investigate time-varying effects in public health-reported case rates and their relationship to wastewater measurements. We show the lack of proportionality of wastewater measurements to case rates with associated spatial heterogeneity. We illustrate how the level of aggregation chosen affects the precision of predictions. We determine whether public health or wastewater measurements are the leading indicator of disease and how they may be used in conjunction to produce predictive models. The prospects of using wastewater based predictive models with or without ongoing public health data are discussed.

Data

• Scottish RNA data can be found at <https://informatics.sepa.org.uk/RNAmonitoring
• Case data can be downloaded from https://www.opendata.nhs.scot/dataset/covid-19-in-scotland and pick Daily Case Trends by Health Board
• ONS Scottish infection survey data from https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/covid19infectionsurveyscotland/2021
• Scottish population data is from https://www.opendata.nhs.scot/dataset/population-estimates and pick Health Board (2019) Population Estimates
• USA data from https://github.com/biobotanalytics/covid19-wastewater-data and displayed at https://biobot.io/data/.

CSVs derived from these are in the data directory (note that more recently collected data has not been used)

Code

• Process Scottish cases and RNA counts: R script
• Modelling Scottish data: Rscript and output
• Process the USA data R script
• Model the USA data R script and output