key: cord-0991126-wticl922 authors: Vusirikala, A.; Flannagan, J.; Czachorowski, M.; Zaidi, A.; Twohig, K. A.; Plugge, E.; Ellaby, N.; Rice, W.; Dabrera, G.; Chudasama, D. Y.; Lamagni, T. title: Impact of SARS-CoV-2 Alpha Variant (B.1.1.7) on Prisons, England date: 2021-12-28 journal: Public Health DOI: 10.1016/j.puhe.2021.12.018 sha: c55d0b53699d192e3bfd03a0545335011e6ff213 doc_id: 991126 cord_uid: wticl922 Background Prisons are high-risk settings for infectious disease outbreaks due to their highly dynamic and crowded nature. During late 2020, prisons in England observed a surge in COVID-19 infection. This study describes the emergence of the Alpha variant in prisons during this period. Methods Alpha and non-Alpha variant COVID-19 cases were identified in prisoners in England using address-matched laboratory notifications and genomic information from COG-UK. Results Of 14,094 COVID-19 positive prisoner cases between 1st October 2020 – 28th March 2021, 11.5% (n=1,621) had sequencing results. Of these, 1,082 (66.7%) were identified as the Alpha variant. 29 (2.7%) Alpha cases required hospitalisation compared to only 5 (1.0%; p=0.02) non-Alpha cases. A total of 14 outbreaks were identified with the median attack rate higher for Alpha (17.9%, IQR 3.2% - 32.2%; p=0.11) than non-Alpha outbreaks (3.5%, IQR 2.0% - 10.2%). Conclusion Higher attack rates and increased likelihood of hospitalisations were observed for Alpha cases compared to non-Alpha. This suggests a key contribution to the rise in cases, hospitalisations and outbreaks in prisons in the second wave. With prisons prone to COVID-19 outbreaks, and the potential to act as reservoirs for variants of concern, sequencing of prison-associated cases alongside whole-institution vaccination should be prioritised. In November 2020, a rise in SARS-CoV-2 infections was observed in the UK despite lockdown measures, coinciding with the emergence of a new a SARS-CoV-2 variant, Alpha (B.1.1.7), first identified in Southeast England. Surveillance and modelling data indicated that this variant had greater transmissibility compared to non-Alpha cases 1, 2 leading to widespread concern and immediate foreign travel restrictions. During late 2020, prisons in England observed a rise in COVID-19 outbreaks as well as increased case and age-standardised mortality rates compared with community settings 3 . To protect residents and staff, the Ministry of Justice implemented measures across the prison estate which included restricting regimes to implement social distancing, stopping all visits, limiting movement of prisoners between facilities, and compartmentalising prisons to isolate symptomatic prisoners, shield the vulnerable, and quarantine new entrants 4 . Reception testing of prisoners and mass testing of prison residents during outbreaks were also introduced during the second wave of the pandemic in England. Given the increased risk of SARS-CoV-2 transmission and illness due to both the prison environment and the susceptibility of the population, understanding the introduction of variants into such institutional settings is a public health priority. The aim of this study was to describe the impact of the emergence of the Alpha variant on prisonassociated cases and outbreaks of COVID-19. As a statutory requirement, positive SARS-CoV-2 tests are notified to the national Second Generation Surveillance System (SGSS), capturing both laboratory and point-of-care tests. Records for cases among prisoners were identified between 1 October 2020 -28 March 2021 using an addressmatching process described elsewhere 5 . Alpha and non-Alpha variant cases were identified from the national COG-UK consortium database. As no other variants of concern (VOC) or variant under investigation (VUI) were identified within this cohort, non-Alpha refers to non-VOC/VUI samples identified in this study. Hospitalisation data were obtained by linkage to national hospital admission and accident and emergency data 6 . Outbreaks in prisons were defined as >2 cases within a 14-day rolling window (by specimen date) residing at the same prison. Outbreaks were classified as Alpha or non-Alpha according to sequencing results available. Outbreaks still ongoing at the end of the study period were excluded, as were outbreaks containing mixed sequencing results. Outbreaks with at least one sequenced case were included regardless of the order of sequenced and non-sequenced cases. Analyses were conducted on all cases within the outbreaks regardless of whether sequenced. Attack rates were defined as the number of cases among prisoners in the outbreak (numerator) divided by the population of prisoners in that specific facility (denominator) derived from the February 2021 Prison Population Bulletin 7 . Attack rates were only calculated on the first outbreak in prisons where multiple outbreaks were identified. Hospitalisation was defined as an admission to hospital within 14 days following a positive COVID-19 test. Associated deaths were defined as deaths in cases occurring up to 60 days following the earliest positive specimen date or where COVID-19 was stated on their death certificate. Alpha and non-Alpha cases were compared using the Mann-Whitney U and Chi-square tests as appropriate. The distribution of attack rates were compared using Kruskal-Wallis tests. We identified 14,094 SARS-CoV-2 cases among those residing in prisons during the study period, with every prison in England (n=112) identified as having ≥1 confirmed case. Of these cases, 11.5% (n=1,621) were sequenced with 79.5% of all prisons (n=89) having at least one sequenced case. The median size of Alpha outbreaks (24; IQR 6-63) was slightly greater than non-Alpha outbreaks (18; IQR 9-63) but the median outbreak duration was greater in non-Alpha outbreaks (31 days; IQR 17-46) compared to Alpha variant outbreaks (22 days; IQR 14-51) however these differences were not statistically significant (p>0.05). Attack rates were just over five times higher in Alpha only outbreaks compared to non-Alpha only, 17.9% (IQR 3.2% -32.2%) and 3.5% (IQR 2.0% -10.2%) respectively, however there was only weak evidence for a difference (p=0.11). This study is the first nationwide assessment of the impact of the Alpha variant in prisons, benefiting from a robust enrichment process of residential property assignment and genomic sequencing results. We identified Alpha as the predominant variant in prisons during England's second pandemic wave, reflecting the COVID-19 trend nationally. Prisons are not isolated from society and ingress of infection from staff, visitors and new receptions remains an ongoing threat 8 . In its assessment of emerging threats during the pandemic, the Scientific Advisory Group for Emergencies (SAGE) in England has cited prisons as a particular infection hazard to the community given the risk that these establishments can become "reservoirs and amplifiers of infection, including variants of concern" 9 . This risk is not limited to SARS-CoV-2, and a recent systematic review has identified examples of the public health risk of prison outbreaks including, the release of prisoners exposed to TB into the community 10 . Among sequenced cases, there was some evidence for greater hospitalisations in Alpha cases when compared to non-alpha cases, consistent with findings in the wider population 6 . Attack rates were 5 times higher in Alpha variant outbreaks compared to non-Alpha only outbreaks which suggest increased transmissibility of the Alpha variant, in line with other published findings 1 and its contribution to the rise in cases in prisons in the second wave. However, with the majority of Alpha outbreaks in December and January, this finding may also be reflective of greater indoor mixing during the winter months, higher community incidence and change in testing regimes 4 . Limitations of this study include low sequencing coverage over the study period hence the need to assume that non-sequenced cases within an outbreak were of the same variant as the sequenced cases and secondly, the crude assessment of hospitalisations, potentially limiting generalizability. Furthermore, we were unable to discern whether there were multiple introductions of Alpha into the prison rather than a continuous outbreak using our dataset. Prisons are prone to infectious disease outbreaks due to their highly dynamic and crowded nature and the vulnerability of residents. These factors can lead to prisons acting as potential reservoirs for variants of concern, therefore, alongside early whole-institution vaccination, prioritisation of prisonassociated cases for sequencing is important. This would allow for early identification of variants of concern, improve understanding of transmission dynamics and changing epidemiology, thus informing disease-control measures to prevent further spread of COVID-19 in prisons and the wider community. The authors have no relevant financial or non-financial conflicts of interest to disclose. Data are incorporated into the article and material contained within. Individual level data cannot be shared due to ethical/privacy reasons. AV, TL, DC were the principal investigators and AV led the writing of this report. TL, DC and AV made significant contributions to conception of the study design. All authors contributed to the interpretation of results and critical review. All data were collected within statutory approvals granted to Public Health England for infectious disease surveillance and control. Information was held securely and in accordance with the Data Protection Act 2018 and Caldicott guidelines. All data were collected within statutory approvals granted to Public Health England for infectious disease surveillance and control. Information was held securely and in accordance with the Data Protection Act 2018 and Caldicott guidelines. All data were collected within statutory approvals granted to Public Health England for infectious disease surveillance and control. Information was held securely and in accordance with the Data Protection Act 2018 and Caldicott guidelines. Estimated transmissibility and impact of SARS-CoV-2 lineage B. 1.1. 7 in England Investigation of novel SARS-CoV-2 variant Variant of Concern Investigation of SARS-CoV-2 variants of concern: technical briefings -GOV.UK (www.gov.uk) High COVID-19 death rates in prisons in England and Wales, and the need for early vaccination COVID-19 Transmission in Prison Settings pdf (publishing.service.gov.uk) [accessed 10 Household clustering of SARS-CoV-2 variant of concern B. 1.1. 7 (VOC-202012-01) in England Assessment of mortality and hospital admissions associated with confirmed infection with SARS-CoV-2 variant of concern VOC-202012/01 (B. 1.1. 7) a matched cohort and time-to-event analysis Official Statistics: Prison population figures: 2021. Population Bulletin: monthly Prisons and custodial settings are part of a comprehensive response to COVID-19 Scientific Advisory Group for Emergencies (SAGE) Managing outbreaks of highly contagious diseases in prisons: a systematic review We would like to thank all the staff of the Public Health England COVID-19 National Epidemiology year epiweekPrisoner none Non-Alpha variant cases Alpha variant cases Cases (sequenced & non-sequenced) 2020-40 27-09-2020 78 0 3 0 78 2020-41 04-10-2020 147 0 25 0 147