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The proximity between prisoners and staff, and the diversity of prisons reduces the effectiveness of non-pharmaceutical interventions, such as social distancing. Therefore, alternative health monitoring methods, such as wastewater-based epidemiology (WBE), are needed to track pathogens, including SARS-CoV-2. This pilot study assessed WBE to quantify SARS-CoV-2 prevalence in prison wastewater to determine its utility within a health protection system for residents. The study analysed 266 samples from six prisons in England over a 12-week period for nucleoprotein 1 (N1 gene) and envelope protein (E gene) using quantitative reverse transcriptase-polymerase chain reaction. Both gene assays successfully detected SARS-CoV-2 fragments in wastewater samples, with both genes significantly correlating with COVID-19 case numbers across the prisons (p &amp;lt; 0.01). However, in 25% of the SARS-positive samples, only one gene target was detected, suggesting that both genes be used to reduce false-negative results. No significant differences were observed between 14- and 2-h composite samples, although 2-h samples showed greater signal variance. Population normalisation did not improve correlations between the N1 and E genes and COVID-19 case data. Overall, WBE shows considerable promise for health protection in prison settings.<\/jats:p>","DOI":"10.2166\/wh.2023.093","type":"journal-article","created":{"date-parts":[[2023,12,2]],"date-time":"2023-12-02T13:12:12Z","timestamp":1701522732000},"page":"64-76","update-policy":"https:\/\/doi.org\/10.2166\/iwapcrossmarkpolicypage","source":"Crossref","is-referenced-by-count":5,"title":["Comparison of gene targets and sampling regimes for SARS-CoV-2 quantification for wastewater epidemiology in UK prisons"],"prefix":"10.2166","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3586-8083","authenticated-orcid":false,"given":"Kelly","family":"Jobling","sequence":"first","affiliation":[{"name":"a School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcos","family":"Quintela-Baluja","sequence":"additional","affiliation":[{"name":"a School of Engineering, Newcastle University, Newcastle upon 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