Nearly two years after the initial report of SARS-CoV-2 in Wuhan, China, the COVID-19 pandemic has affected over 485 million individuals. Wastewater surveillance has garnered substantial attention as a passive monitoring system to complement clinical genomic surveillance activities during the SARS-CoV-2 pandemic. Several effective methods are now in place for detecting and quantifying viral RNA in wastewater samples, and it is evident that RNA concentrations in wastewater correlate with reported case trends. Exploratory projects have demonstrated the potential of Wastewater Based Epidemiology (WBE), nevertheless it is imperative to coordinate efforts, establish standards, and create a catalog of available software tools and services. This coordination will streamline the deployment of end-to-end genomic wastewater surveillance pipelines and promote the adoption of these monitoring methods within the broader scientific community. The initial step involves identifying and cataloging the challenges of working with wastewater HTS and the pertinent methodologies and bioinformatics workflows essential for managing genomic data from wastewater samples, thus forming a coherent structure. The primary objective of this project was to systematically review, compile, and initiate the integration, standardization, and documentation of diverse approaches for genomic wastewater surveillance. Drawing on the expertise of the ELIXIR Wastewater Surveillance Working Group, our focus was to create a comprehensive framework of components, including modules and tools, to facilitate the practical implementation of end-to-end genomic wastewater surveillance pipelines.

PSOMOPOULOS Fotis;  KYRITSIS Konstantinos;  TOPOLSKY Ivan;  BATUT Bérénice;  FITZPATRICK Amy Heather;  LEONI Gabriele; 

2024-04-18

European Commission

JRC137604

https://publications.jrc.ec.europa.eu/repository/handle/JRC137604,