Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank

Abstract

UK Biobank (UKB) is an international health resource enabling research into the genetic and lifestyle determinants of common diseases of middle and older age. It comprises 500 000 participants. Public Health England’s Second Generation Surveillance System is a centralized microbiology database covering English clinical diagnostics laboratories that provides national surveillance of legally notifiable infections, bacterial isolations and antimicrobial resistance. We previously developed secure, pseudonymized, individual-level linkage of these systems. In this study, we implemented rapid dynamic linkage, which allows us to provide a regular feed of new COVID-19 (SARS-CoV-2) test results to UKB to facilitate rapid and urgent research into the epidemiological and human genetic risk factors for severe infection in the cohort. Here, we have characterized the first 1352 cases of COVID-19 in UKB participants, of whom 895 met our working definition of severe COVID-19 as inpatients hospitalized on or after 16 March 2020. We found that the incidence of severe COVID-19 among UKB cases was 27.4 % lower than the general population in England, although this difference varied significantly by age and sex. The total number of UKB cases could be estimated as 0.6 % of the publicly announced number of cases in England. We considered how increasing case numbers will affect the power of genome-wide association studies. This new dynamic linkage system has further potential to facilitate the investigation of other infections and the prospective collection of microbiological cultures to create a microbiological biobank (bugbank) for studying the interaction of environment, human and microbial genetics on infection in the UKB cohort.

Collider bias undermines our understanding of COVID-19 disease risk and severity

“…In April 2020, General Practices across the UK released primary care data on COVID-19 testing for linkage to the participants in the UK Biobank project 101,102 and results from analyses are already appearing 103 . Of the 486,967 participants, 1410 currently have data on COVID-19 testing.…”

Will coronavirus disease (COVID-19) have an impact on antimicrobial resistance?

“…• Fewer transfers from long-term care facilities may lead to fewer cycles between long-term care facilities and hospitals [5] • Construction of new COVID-19 facilities without an established reservoir of MDROs [5] unlikely to be immediate, and that the necessary delays to observe these effects-as well as the thresholds above which changes in antibiotic prescribing and IPC result in an effect-will need to be taken into account when analysing data [28]. We should learn from the COVID-19 pandemic, with its rapid turnover and use of whole genome sequencing data, and dynamic linkage of various health databases [8,29]. Surveillance data based on clinical samples in particular, if focused only on bloodstream infections, may provide a distorted picture of the effect of COVID-19 on AMR since the effect may only manifest itself in other clinical sites or even only in the commensal flora.…”

COVID-19 and associations with frailty and multimorbidity: a prospective analysis of UK Biobank participants

“…COVID-19 diagnoses were sourced via available COVID-19 test results within the UK Biobank dataset at the time of manuscript preparation (from 16th March 2020 to 1st June 2020), sourced from Public Health England [21]. The vast majority of these COVID-19 tests were via a combined nasal and throat swab.…”