Differential Impact of Quarantine Policies for Recovered COVID-19 Cases in England: A Case Cohort Study of Surveillance Data, June to December 2020 (preprint)

Background: From 12th March 2020, individuals in England were advised to quarantine in their home if a household member tested positive for SARS-CoV-2. A mandatory isolation period of 10 days was introduced on 28th September 2020 and applied to all individuals with COVID-19. We assessed the frequency, timing, and characteristics of recovered COVID-19 cases requiring subsequent quarantine episodes due to household re-exposure. Methods In this case cohort study, all laboratory-confirmed COVID-19 cases notified in England (29th June to 28th December 2020) were analysed to identify consecutive household case(s). Multivariable logistic regression was used to determine associations between case characteristics and need to quarantine following recent infection (within 28 days of diagnosis). Results Among 1,651,550 cases resident in private dwellings and Houses of Multiple Occupancy (HMOs), 56,179 (3.4%) were succeeded by further household cases diagnosed within 11–28 days of their diagnosis. Of 1,641,412 cases arising in private homes, the likelihood of further household cases was highest for Bangladeshi (aOR = 2.20, 95% CI = 2.10–2.31) and Pakistani (aOR = 2.15, 95% CI = 2.08–2.22) individuals compared to White British, as well as among young people (17-24y vs. 25-64y; aOR = 1.19, 95% CI = 1.16–1.22), men (vs. women; aOR = 1.06, 95% CI = 1.04–1.08), London residents (vs. Yorkshire and Humber; aOR = 1.57, 95% CI = 1.52–1.63) and areas of high deprivation (IMD 1 vs. 10; aOR = 1.13, 95% CI = 1.09–1.19). Conclusions Policies requiring quarantine on re-exposure of recently recovered cases differentially impact some of the most disadvantaged populations. Quarantine exemption for individuals recently (

Comparative transmission of SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants and the impact of vaccination: national cohort study, England (preprint)

Background The SARS-CoV-2 Omicron variant (B.1.1.529) has rapidly replaced the Delta variant (B.1.617.2) to become dominant in England. This epidemiological study assessed differences in transmissibility between the Omicron and Delta using two methods and data sources. Methods Omicron and Delta cases were identified through genomic sequencing, genotyping and S-gene target failure in England from 5-11 December 2021. Secondary attack rates for Omicron and Delta using named contacts and household clustering were calculated using national surveillance and contact tracing data. Logistic regression was used to control for factors associated with transmission. Findings Analysis of contact tracing data identified elevated secondary attack rates for Omicron vs Delta in household (15.0% vs 10.8%) and non-household (8.2% vs 3.7%) settings. The proportion of index cases resulting in residential clustering was twice as high for Omicron (16.1%) compared to Delta (7.3%). Transmission was significantly less likely from cases, or in named contacts, in receipt of three compared to two vaccine doses in household settings, but less pronounced for Omicron (aRR 0.78 and 0.88) compared to Delta (aRR 0.62 and 0.68). In non-household settings, a similar reduction was observed for Delta cases and contacts (aRR 0.84 and 0.51) but only for Omicron contacts (aRR 0.76, 95% CI: 0.58-0.93) and not cases in receipt of three vs two doses (aRR 0.95, 0.77-1.16). Interpretation Our study identified increased risk of onward transmission of Omicron, consistent with its successful global displacement of Delta. We identified a reduced effectiveness of vaccination in lowering risk of transmission, a likely contributor for the rapid propagation of Omicron.

The Impact of Returning University Students on COVID-19 Infections in England, 2020 (preprint)

Background: Universities in England returned to in–person teaching in September 2020, requiring a large migration of students across the country. To understand the impact this had on COVID–19 transmission, we identified and described student cases during the 2020 autumn term. Methods: Student COVID–19 cases were identified from two sources: contact tracing records identifying attendance at university prior to onset and residence in student accommodation identified from matching cases’ residential addresses against national property databases. Residential outbreaks were defined as ≥2 cases with specimen dates within 14 days residing in the same property. A matched analysis of COVID–19 rates and trends in towns/cities with and without a university campus was undertaken. Findings: We identified 53,430 student cases between 1 September and 31 December 2020, constituting 2·7% of all cases (n=1,999,180) in this time period; 39,032 reported attendance at a university during contact tracing; 19,901 resided in student accommodation premises. Cases increased rapidly following the start of term driven initially by cases in student accommodation. Over two thirds (72·2% n=14,375) of cases in student accommodation were part of a residential outbreak.Towns/cities with universities saw a threefold increase in rates amongst 18–23 year olds compared to non–university towns. Interpretation: This study suggests that the return to university teaching and associated movement of students in England was linked to large increases in SARS–CoV–2 transmission amongst this population and potentially contributing to subsequent large increases in the wider population surrounding a campus. Funding Information: No funding was received for this work. Declaration of Interests: None of the authors declare any conflicts of interest.Ethics Approval Statement: UKHSA has legal permission, provided by Regulation 3 of The Health Service (Control of Patient Information) Regulations 2002, to process patient confidential information for national surveillance of communicable diseases and as such, individual patient consent is not required.

Hospitalisation risk for COVID-19 patients infected with SARS-CoV-2 variant B.1.1.7: cohort analysis (preprint)

Objective: To evaluate the relationship between coronavirus disease 2019 (COVID-19) diagnosis with SARS-CoV-2 variant B.1.1.7 (also known as Variant of Concern 202012/01) and the risk of hospitalisation compared to diagnosis with wildtype SARS-CoV-2 variants. Design: Retrospective cohort, analysed using stratified Cox regression. Setting: Community-based SARS-CoV-2 testing in England, individually linked with hospitalisation data. Participants: 839,278 laboratory-confirmed COVID-19 patients, of whom 36,233 had been hospitalised within 14 days, tested between 23rd November 2020 and 31st January 2021 and analysed at a laboratory with an available TaqPath assay that enables assessment of S-gene target failure (SGTF). SGTF is a proxy test for the B.1.1.7 variant. Patient data were stratified by age, sex, ethnicity, deprivation, region of residence, and date of positive test. Main outcome measures: Hospitalisation between 1 and 14 days after the first positive SARS-CoV-2 test. Results: 27,710 of 592,409 SGTF patients (4.7%) and 8,523 of 246,869 non-SGTF patients (3.5%) had been hospitalised within 1-14 days. The stratum-adjusted hazard ratio (HR) of hospitalisation was 1.52 (95% confidence interval [CI] 1.47 to 1.57) for COVID-19 patients infected with SGTF variants, compared to those infected with non-SGTF variants. The effect was modified by age (P<0.001), with HRs of 0.93-1.21 for SGTF compared to non-SGTF patients below age 20 years, 1.29 in those aged 20-29, and 1.45-1.65 in age groups 30 years or older. Conclusions: The results suggest that the risk of hospitalisation is higher for individuals infected with the B.1.1.7 variant compared to wildtype SARS-CoV-2, likely reflecting a more severe disease. The higher severity may be specific to adults above the age of 30.

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 (preprint)

Background: The emergence of VOC202012/01 in England, known as B.1.1.7 or informally as the ‘UK variant’, has coincided with rapid increases in the number of PCR-confirmed positive cases in areas where the variant has been concentrated. Methods: To assess whether infection with SARS-CoV-2 variant VOC202012/01 is associated with more severe clinical outcomes compared to wild-type infection, genomically sequenced and confirmed variant and wild-type cases were linked to routine healthcare and surveillance datasets. Two statistical analyses were conducted to compare the risk of hospital admission and death within 28 days of test between variant and wild-type cases: a case-control study and an adjusted Cox proportional hazards model. Differences in severity of disease were assessed by comparing hospital admission and mortality, including length of hospitalisation and time to death.Results: Of 63,609 genomically sequenced COVID-19 cases tested in England between October and December 2020 6,038 were variant cases. In the matched cohort analysis 2,821 variant cases were matched to 2,821 to wild-type cases. In the time to event analysis we observed a 34% increased risk in hospitalisation associated with the variant compared to wild-type cases, however, no significant difference in the risk of mortality was observed. Conclusion: We found evidence of increased risk of hospitalisation after adjusting for key confounders, suggesting increase infection severity associated with this variant. Follow-up studies are needed to assess potential longer-term differences in the clinical outcomes of people infected with the VOC-202012/01 variant.

Penetration and Impact of COVID-19 in Care Homes in England: Population Surveillance Study (preprint)

Background: Care homes worldwide have suffered high rates of COVID-19, reflecting their inherent vulnerability and the institutional nature of care delivered. This study describes the impact of the pandemic in care homes across England.Method: Laboratory confirmed SARS-CoV-2 cases in England notified to PHE from 01 Jan to 25 Dec 2020 were address-matched to identify residential property classifications. Data were analysed to characterise cases and identify clusters. Associated deaths were defined as death within 60 days of diagnosis or certified as cause of death.Findings: Of 1,936,315 COVID-19 cases, 81,275 (4·2%) and 10,050 (0·52%) were identified as resident or staff in a care home, respectively, with 20,544 associated deaths identified, accounting for 31·3% of all COVID-19 deaths. Cases were identified in 69·5% of all care homes in England, with 33.1% experiencing multiple outbreaks. Multivariable analysis showed a 67% increased odds of death in care home residents ( aOR: 1·67, 95% CI: 1·63-1·72) . A total of 10,321 outbreaks were identified at these facilities, of which 8·2% identified the first case as a staff member.Interpretation: Care homes have experienced large and widespread outbreaks of COVID-19, with almost 70% affected, and just under one-third of all COVID-19 deaths occurring in this setting in-spite of early policies. A key implication of our findings is upsurges in community incidences seemingly leading to increased care homes outbreaks, thus identifying and shielding residents from key sources of infection, particularly surrounding staff, is vital to reduce the number of future outbreaks.Funding Statement: Funded by Public Health EnglandDeclaration of Interests: We declare no conflicts of interest.Ethics Approval Statement: 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.