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

Jacob Armstrong; Justine K. Rudkin; Naomi Allen; Derrick W. Crook; Daniel J. Wilson; David Wyllie; Anne Marie O'Connell

doi:10.1099/mgen.0.000397

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

Jacob Armstrong, Justine K. Rudkin, Naomi Allen, Derrick W. Crook, Daniel J. Wilson^*, David Wyllie, Anne Marie O'Connell

^*Corresponding author for this work

Cambridge Lab Public Health Activities

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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 500000 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.

Original language	English
Article number	000397
Number of pages	9
Journal	Microbial Genomics
Volume	6
Issue number	7
DOIs	https://doi.org/10.1099/mgen.0.000397
Publication status	Published - 18 Jun 2020

Bibliographical note

Funding Information: This work was funded by a Big Data Institute Robertson Fellowship (D.J.W.). D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (Grant 101237/Z/13/B).This research has been conducted using the UK Biobank Resource under Application Number 53 100. We acknowledge the support of the UK Biobank participants, the UK Biobank staff and members of the National Infection Service Information Management team. We thank Chris Spencer for helpful comments.

Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

Publisher Copyright: © 2020 Crown Copyright

Citation: Armstrong, Jacob, et al. "Dynamic linkage of covid-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank." Microbial genomics 6.7 (2020).

DOI: DOI 10.1099/mgen.0.000397

Keywords

Bugbank
COVID-19
Database linkage
Public Health England
SARS-CoV-2
UK Biobank

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Armstrong2020DynamicLinkageOfCOVID-19TestResultsMicrobGenomFinal published version, 2.45 MBLicence: CC BY

Cite this

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title = "Dynamic linkage of covid-19 test results between Public Health England{\textquoteright}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 500000 participants. Public Health England{\textquoteright}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.",

keywords = "Bugbank, COVID-19, Database linkage, Public Health England, SARS-CoV-2, UK Biobank",

author = "Jacob Armstrong and Rudkin, {Justine K.} and Naomi Allen and Crook, {Derrick W.} and Wilson, {Daniel J.} and David Wyllie and O'Connell, {Anne Marie}",

note = "Funding Information: This work was funded by a Big Data Institute Robertson Fellowship (D.J.W.). D.J.W. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (Grant 101237/Z/13/B).This research has been conducted using the UK Biobank Resource under Application Number 53 100. We acknowledge the support of the UK Biobank participants, the UK Biobank staff and members of the National Infection Service Information Management team. We thank Chris Spencer for helpful comments. Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author{\textquoteright}s institution. Publisher Copyright: {\textcopyright} 2020 Crown Copyright Citation: Armstrong, Jacob, et al. {"}Dynamic linkage of covid-19 test results between Public Health England{\textquoteright}s Second Generation Surveillance System and UK Biobank.{"} Microbial genomics 6.7 (2020). DOI: DOI 10.1099/mgen.0.000397",

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

Abstract

Bibliographical note

Keywords

UN SDGs

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