Comparison of gene targets and sampling regimes for SARS-CoV-2 quantification for wastewater epidemiology in UK prisons.

Prisons are high-risk settings for infectious disease transmission, due to their enclosed and semi-enclosed environments. 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 < 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.

The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model.

BACKGROUND: High incidence of cases and deaths due to coronavirus disease 2019 (COVID-19) have been reported in prisons worldwide. This study aimed to evaluate the impact of different COVID-19 vaccination strategies in epidemiologically semi-enclosed settings such as prisons, where staff interact regularly with those incarcerated and the wider community. METHODS: We used a metapopulation transmission-dynamic model of a local prison in England and Wales. Two-dose vaccination strategies included no vaccination, vaccination of all individuals who are incarcerated and/or staff, and an age-based approach. Outcomes were quantified in terms of COVID-19-related symptomatic cases, losses in quality-adjusted life-years (QALYs), and deaths. RESULTS: Compared to no vaccination, vaccinating all people living and working in prison reduced cases, QALY loss and deaths over a one-year period by 41%, 32% and 36% respectively. However, if vaccine introduction was delayed until the start of an outbreak, the impact was negligible. Vaccinating individuals who are incarcerated and staff over 50 years old averted one death for every 104 vaccination courses administered. All-staff-only strategies reduced cases by up to 5%. Increasing coverage from 30 to 90% among those who are incarcerated reduced cases by around 30 percentage points. CONCLUSIONS: The impact of vaccination in prison settings was highly dependent on early and rapid vaccine delivery. If administered to both those living and working in prison prior to an outbreak occurring, vaccines could substantially reduce COVID-19-related morbidity and mortality in prison settings.

Determining the Prevalence and Incidence of SARS-CoV-2 Infection in Prisons in England: Protocol for a Repeated Panel Survey and Enhanced Outbreak Study.

BACKGROUND: There are over 80,000 people imprisoned in England and Wales in 117 prisons. The management of the COVID-19 pandemic presents particular challenges in this setting where confined, crowded, and poorly ventilated conditions facilitate the rapid spread of infectious diseases. OBJECTIVE: The COVID-19 in Prison Study aims to examine the epidemiology of SARS-CoV-2 in prisons in England in order to inform public health policy and practice during the pandemic and recovery. The primary objective is to estimate the proportion of positive tests of SARS-CoV-2 infection among residents and staff within selected prisons. The secondary objectives include estimating the incidence rate of SARS-CoV-2 infection and examining how the proportion of positive tests and the incidence rate vary among individual, institutional, and system level factors. METHODS: Phase 1 comprises a repeated panel survey of prison residents and staff in a representative sample of 28 prisons across England. All residents and staff in the study prisons are eligible for inclusion. Participants will be tested for SARS-CoV-2 using a nasopharyngeal swab twice (6 weeks apart). Staff will also be tested for antibodies to SARS-CoV-2. Phase 2 focuses on SARS-CoV-2 infection in prisons with recognized COVID-19 outbreaks. Any prison in England will be eligible to participate if an outbreak is declared. In 3 outbreak prisons, all participating staff and residents will be tested for SARS-CoV-2 antigens at the following 3 timepoints: as soon as possible after the outbreak is declared (day 0), 7 days later (day 7), and at day 28. They will be swabbed twice (a nasal swab for lateral flow device testing and a nasopharyngeal swab for polymerase chain reaction testing). Testing will be done by external contractors. Data will also be collected on individual, prison level, and community factors. Data will be stored and handled at the University of Southampton and Public Health England. Summary statistics will summarize the prison and participant characteristics. For the primary objective, simple proportions of individuals testing positive for SARS-CoV-2 and incidence rates will be calculated. Linear regression will examine the individual, institutional, system, and community factors associated with SARS-CoV-2 infection within prisons. RESULTS: The UK Government's Department for Health and Social Care funds the study. Data collection started on July 20, 2020, and will end on May 31, 2021. As of May 2021, we had enrolled 4192 staff members and 6496 imprisoned people in the study. Data analysis has started, and we expect to publish the initial findings in summer/autumn 2021. The main ethical consideration is the inclusion of prisoners, who are vulnerable participants. CONCLUSIONS: This study will provide unique data to inform the public health management of SARS-CoV-2 in prisons. Its findings will be of relevance to health policy makers and practitioners working in prisons. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/30749.

Insights gained from early modelling of COVID-19 to inform the management of outbreaks in UK prisons.

PURPOSE: In this work, the authors present some of the key results found during early efforts to model the COVID-19 outbreak inside a UK prison. In particular, this study describes outputs from an idealised disease model that simulates the dynamics of a COVID-19 outbreak in a prison setting when varying levels of social interventions are in place, and a Monte Carlo-based model that assesses the reduction in risk of case importation, resulting from a process that requires incoming prisoners to undergo a period of self-isolation prior to admission into the general prison population. DESIGN/METHODOLOGY/APPROACH: Prisons, typically containing large populations confined in a small space with high degrees of mixing, have long been known to be especially susceptible to disease outbreaks. In an attempt to meet rising pressures from the emerging COVID-19 situation in early 2020, modellers for Public Health England's Joint Modelling Cell were asked to produce some rapid response work that sought to inform the approaches that Her Majesty's Prison and Probation Service (HMPPS) might take to reduce the risk of case importation and sustained transmission in prison environments. FINDINGS: Key results show that deploying social interventions has the potential to considerably reduce the total number of infections, while such actions could also reduce the probability that an initial infection will propagate into a prison-wide outbreak. For example, modelling showed that a 50% reduction in the risk of transmission (compared to an unmitigated outbreak) could deliver a 98% decrease in total number of cases, while this reduction could also result in 86.8% of outbreaks subsiding before more than five persons have become infected. Furthermore, this study also found that requiring new arrivals to self-isolate for 10 and 14 days prior to admission could detect up to 98% and 99% of incoming infections, respectively. RESEARCH LIMITATIONS/IMPLICATIONS: In this paper we have presented models which allow for the studying of COVID-19 in a prison scenario, while also allowing for the assessment of proposed social interventions. By publishing these works, the authors hope these methods might aid in the management of prisoners across additional scenarios and even during subsequent disease outbreaks. Such methods as described may also be readily applied use in other closed community settings. ORIGINALITY/VALUE: These works went towards informing HMPPS on the impacts that the described strategies might have during COVID-19 outbreaks inside UK prisons. The works described herein are readily amendable to the study of a range of addition outbreak scenarios. There is also room for these methods to be further developed and built upon which the timeliness of the original project did not permit.