Wastewater-Based Epidemiology (WBE) began to flourish in 2001 and was initially used for the detection of illegal drugs. Historically though, around the 1950's WBE was implemented for the detection of infectious diseases, when the first studies to detect poliovirus and enteroviruses in sewage samples were conducted. These studies were based on the fact that since viruses cannot grow outside of host cells, they lose the ability to evolve in wastewater, and thus the concentration values that were found in sewages are related to those that were initially egested by the population.
During the COVID-19 pandemic WBE became a community-wide monitoring tool which provided real-time data concerning both public health status, environmental monitoring as well as food safety. Moreover, in addition to the traditional wastewater surveillance metrics that rely on biochemical indicators, the pandemic led to the increased use of high-throughput sequencing data on wastewater samples. This led to a number of key challenges and questions in the field, ranging from the data capture efforts through biosensors, until the data management and data analysis efforts
The main goal of this project will be to define a framework for addressing specific health policy-related questions based on multi-modal wastewater surveillance, including a critical review on the applicable standards for (meta)data. The effort will build on the efforts of the relevant BH2022 project on wastewater surveillance, as well as on the collective expertise of the ELIXIR COVID19 Wastewater Surveillance Working Group. Ultimately, the proposed framework will be demonstrated using existing publicly available data.
- This is already an activity that the WG is working on. The BH project will help push this further and make quantifiable progress, while engaging with a wider community.
- Identify and short-list relevant standards
- Implement a proof-of-concept synthetic dataset process for Wastewater surveillance
- Researchers active in national wastewater surveillance efforts, experts in genomic data production and management - including metadata standards, bioinformaticians including people who are running wastewater surveillance pipelines
- workflow expertise (python, snakemake, nextflow), WES expertise, R/Python/HTML/CSS/Javascript developers
- pilot website, UI experience, Data Visualization
- Survey existing efforts and resources in order to collate information
- Rely on existing efforts under ELIXIR and the Synthetic data community, in order to defined specifications and requirements
Fotis Psomopoulos, Amy Fitzpatrick, Matthew Wade