{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T17:37:08Z","timestamp":1793381828458,"version":"4.5.0"},"update-to":[{"DOI":"10.12688\/openreseurope.20934.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000}},{"DOI":"10.12688\/openreseurope.20934.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000}}],"reference-count":24,"publisher":"CERN","license":[{"start":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T00:00:00Z","timestamp":1783296000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Commission","award":["101046203"],"award-info":[{"award-number":["101046203"]}],"id":[{"id":"https:\/\/ror.org\/00k4n6c32","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Canadian Institutes of Health Research","award":["FRN#175622"],"award-info":[{"award-number":["FRN#175622"]}],"id":[{"id":"https:\/\/ror.org\/01gavpb45","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Open Res Europe"],"abstract":"<jats:p>Genomic technologies such as PCR and next-generation sequencing (NGS) have greatly advanced public health surveillance, especially during COVID-19, by enabling detailed tracking of pathogen spread, origins, and variants. While PCR is vital for targeted detection, falling NGS costs have made large-scale, high-throughput sequencing more feasible, supporting broader pathogen monitoring\u2014including the detection of vaccine escape variants and new strains. Applying NGS to wastewater offers valuable population-level insights but faces challenges such as variable sample complexity, the need for skilled staff, suitable platforms, and robust IT infrastructure. Although there are currently a lot of efforts towards defining guidelines for sampling, analysis, and integrating wastewater data into public health policy, such as the recently published International Cookbook for Wastewater Practitioners, they often lack universal applicability, emphasizing the analytical approaches in favour of the NGS-based approaches. However, standardising protocols for sampling, sequencing, and analysis is crucial to ensure reliable, comparable data across surveillance systems worldwide. Pilot studies and continuous refinement are recommended to overcome implementation hurdles and fully realise the benefits of NGS in wastewater surveillance. This work attempts to outline these challenges and opportunities across the entire wastewater surveillance workflow, from data generation to reporting, and provide some concrete suggestions and considerations across the spectrum of activities. We further highlight that the infrastructure, funding and government-policy context in which surveillance operates acts as an enabling condition for these activities, and that technical standardisation alone is unlikely to deliver durable, comparable surveillance in its absence.<\/jats:p>","DOI":"10.12688\/openreseurope.20934.3","type":"journal-article","created":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T12:00:00Z","timestamp":1783339200000},"update-policy":"https:\/\/doi.org\/10.68336\/openreseurope.updatepolicy","source":"Crossref","is-referenced-by-count":1,"title":["Toward a unified approach: Considerations for bioinformatic and sequencing activities &amp; data in wastewater surveillance of biologic public health threats"],"prefix":"10.68336","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0222-4273","authenticated-orcid":true,"given":"Fotis","family":"Psomopoulos","sequence":"first","affiliation":[{"name":"Institute of Applied Biosciences, Centre for Research and 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Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4852-1318","authenticated-orcid":true,"given":"Marialuisa","family":"Lavitrano","sequence":"additional","affiliation":[{"name":"Department of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4899-5284","authenticated-orcid":true,"given":"Gabriele","family":"Leoni","sequence":"additional","affiliation":[{"name":"European Commission, Joint Research Centre (JRC), Ispra, 21027, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5366-7461","authenticated-orcid":true,"given":"Ju-Ling","family":"Liu","sequence":"additional","affiliation":[{"name":"McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Qu\u00e9bec, Canada"},{"name":"Department of Human Genetics, McGill University, 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This work was supported by ELIXIR, the research infrastructure for life science data. J.L. and J.R. were supported by the Coronavirus Variants Rapid Response Network (CoVaRR-Net). CoVaRR-Net is funded by an operating grant from the Canadian Institutes of Health Research (CIHR) \u2013 Instituts de recherche en sant\u00e9 du Canada (FRN#175622).\n\n                    The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","name":"funding_statement","label":"Funding Statement","group":{"name":"funding_information","label":"Funding Information"}}],"article-number":"267"}}