Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London

Chris Bailey¹, Theo Sanderson², Hermaleigh Townsley³, Jacki Goldman⁴, James R M Black⁵, George Young⁶, Robert Goldstone⁷, Ashley S Fowler⁸, Sophia Ward⁹, Deborah J Jackson⁸, Laura Cubitt⁸, Vicky Dearing⁸, Olga O'Neil⁸, Marg Crawford⁸, Daniel Snell⁸, Makis Finadis⁸, Amelia Edwards⁸, Jimena Perez-Lloret⁸, Joshua Gahir³, Edward J Carr¹⁰, Andy Riddell¹¹, Jim Aitken¹², Karen Ambrose⁴, Chelsea Sawyer⁴, Nicola O'Reilly¹³, Simon Caidan¹⁴, Mary Y Wu¹⁵, Philip A Walker¹⁶, Steve Hindmarsh⁴, Michael Howell¹⁷, Andrew Jordan¹², James Fleming¹², Catherine Houlihan¹⁸, Eleni Nastouli¹⁸, Rachel Moores¹⁹, Desmond Hsu¹⁹, Padmasayee Papineni²⁰, Tumena Corrah²⁰, Richard Gilson²¹, James MacRae²², Michael Hubank²³, Nicholas Van As²³, Samra Turajlic²⁴, Rupert Beale²⁵, Marcel Levi¹⁸; Crick COVID-19 Consortium; Sam Barrell¹⁴, Bryan Williams²⁶, Steve Gamblin¹⁴, Jerome Nicod²⁷, Sonia Gandhi²⁸, David L V Bauer²⁹, Emma C Wall³⁰, Charles Swanton¹

Affiliations

¹ Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK.
² Malaria Biochemistry Laboratory, London NW1 1AT, UK; COVID-19 Genomics UK Consortium, Wellcome Trust Sanger Institute, Cambridge, UK.
³ Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK.
⁴ Scientific Computing STP, London NW1 1AT, UK.
⁵ Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; University College London, London, UK.
⁶ Applied Biotechnology Laboratory, London NW1 1AT, UK.
⁷ Advanced Sequencing Facility, London NW1 1AT, UK; Bioinformatics and Biostatistics STP, London NW1 1AT, UK.
⁸ Advanced Sequencing Facility, London NW1 1AT, UK.
⁹ Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Advanced Sequencing Facility, London NW1 1AT, UK.
¹⁰ Cell Biology of Infection Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK.
¹¹ Flow Cytometry STP, London NW1 1AT, UK.
¹² Information Technology Office, London NW1 1AT, UK.
¹³ Protein Chemistry STP, London NW1 1AT, UK.
¹⁴ Francis Crick Institute, London NW1 1AT, UK.
¹⁵ COVID Surveillance Unit, London NW1 1AT, UK.
¹⁶ Structural Biology STP, London NW1 1AT, UK.
¹⁷ Highthroughput Screening Laboratory, London NW1 1AT, UK.
¹⁸ University College London Hospitals NHS Foundation Trust, London, UK.
¹⁹ Royal Free London NHS Foundation Trust, London, UK.
²⁰ London Northwest University Healthcare NHS Trust, London, UK.
²¹ Central and Northwest London NHS Foundation Trust, London, UK.
²² Metabolomics STP, London NW1 1AT, UK.
²³ Royal Marsden Hospitals NHS Foundation Trust, London, UK.
²⁴ Cancer Dynamics Laboratory, London NW1 1AT, UK.
²⁵ Cell Biology of Infection Laboratory, London NW1 1AT, UK; University College London, London, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK.
²⁶ University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK.
²⁷ Advanced Sequencing Facility, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK.
²⁸ Neurodegeneration Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK.
²⁹ RNA Virus Replication Laboratory, London NW1 1AT, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK.
³⁰ Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK. Electronic address: emma.wall@crick.ac.uk.

PMID: 37348521
PMCID: PMC10278995
DOI: 10.1016/S0140-6736(23)00917-0

Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London

Chris Bailey et al. Lancet. 2023.

. 2023 Jul 1;402(10395):21-24.

doi: 10.1016/S0140-6736(23)00917-0. Epub 2023 Jun 19.

Authors

Affiliations

¹ Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK.
² Malaria Biochemistry Laboratory, London NW1 1AT, UK; COVID-19 Genomics UK Consortium, Wellcome Trust Sanger Institute, Cambridge, UK.
³ Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK.
⁴ Scientific Computing STP, London NW1 1AT, UK.
⁵ Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; University College London, London, UK.
⁶ Applied Biotechnology Laboratory, London NW1 1AT, UK.
⁷ Advanced Sequencing Facility, London NW1 1AT, UK; Bioinformatics and Biostatistics STP, London NW1 1AT, UK.
⁸ Advanced Sequencing Facility, London NW1 1AT, UK.
⁹ Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Advanced Sequencing Facility, London NW1 1AT, UK.
¹⁰ Cell Biology of Infection Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK.
¹¹ Flow Cytometry STP, London NW1 1AT, UK.
¹² Information Technology Office, London NW1 1AT, UK.
¹³ Protein Chemistry STP, London NW1 1AT, UK.
¹⁴ Francis Crick Institute, London NW1 1AT, UK.
¹⁵ COVID Surveillance Unit, London NW1 1AT, UK.
¹⁶ Structural Biology STP, London NW1 1AT, UK.
¹⁷ Highthroughput Screening Laboratory, London NW1 1AT, UK.
¹⁸ University College London Hospitals NHS Foundation Trust, London, UK.
¹⁹ Royal Free London NHS Foundation Trust, London, UK.
²⁰ London Northwest University Healthcare NHS Trust, London, UK.
²¹ Central and Northwest London NHS Foundation Trust, London, UK.
²² Metabolomics STP, London NW1 1AT, UK.
²³ Royal Marsden Hospitals NHS Foundation Trust, London, UK.
²⁴ Cancer Dynamics Laboratory, London NW1 1AT, UK.
²⁵ Cell Biology of Infection Laboratory, London NW1 1AT, UK; University College London, London, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK.
²⁶ University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK.
²⁷ Advanced Sequencing Facility, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK.
²⁸ Neurodegeneration Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK.
²⁹ RNA Virus Replication Laboratory, London NW1 1AT, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK.
³⁰ Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK. Electronic address: emma.wall@crick.ac.uk.

PMID: 37348521
PMCID: PMC10278995
DOI: 10.1016/S0140-6736(23)00917-0

No abstract available

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Conflict of interest statement

Sequencing data for all positive samples are publicly available through COG-UK resources. CB, TS, HT, JGo, RGi, JN, DLVB, and ECW accessed and verified the data. CB, ECW, DLVB, SGan, and CSw were responsible for the decision to submit the Correspondence for publication. CB and TS were responsible for formal analysis, investigation, methodology, visualisation, writing the original draft, and conceptualisation. HT was involved in the investigation, methodology, visualisation, manuscript review and editing, and conceptualisation. JGo was responsible for software, methodology, formal analysis, and data curation. JRMB performed formal analysis and validation. JGan was responsible for the methodology, resources, data curation, and project administration. GY performed formal analysis. RGo was responsible for software, resources, and data curation. ASF, SW, DJJ, LC, VD, OO'N, MC, DS, MF, AE, JP-L, AR, JA, NO'R, SC, MYW, PAW, and CSa were involved with the methodology, resources, data curation, and project administration. EJC was involved with software and project administration. SH, JF, and KA helped with supervision, software, and methodology. MHo performed project administration and supervision. AJ was responsible for methodology, resources, data curation, and project administration. CH, EN, MHu, RM, DH, PP, TC, RGi, JM, NVA, ST, RB, ML, and SB managed resources, data curation, and project administration. BW and SGam handled funding acquisition and project administration with SGam also providing supervision. JN was involved with project administration, supervision, and methodology. SGan performed supervision, funding acquisition, methodology, project administration, writing, review, and editing. DLVB was responsible for supervision, methodology, formal analysis, visualisation, conceptualisation, and writing the original draft. ECW performed supervision, investigation, data curation, conceptualisation, writing, review, and editing. CSw was responsible for supervision, funding acquisition, conceptualisation, project administration, writing, review, and editing. This research was funded in whole, or in part, by the Wellcome Trust (FC011104, FC011233, FC001030, FC001159, FC001827, FC001078, FC001099, and FC001169). TS is supported by a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust grant 210918/Z/18/Z. Unrelated to this Correspondence, CSw reports grants from BMS, Ono-Pharmaceuticals, Boehringer Ingelheim, Roche-Ventana, Pfizer, and Archer Dx; personal fees from Genentech, Sarah Canon Research Institute, Medicxi, Metabomed, Bicycle Therapeutics, GRAIL, Amgen, AstraZeneca, BMS, Illumina, GlaxoSmithKline, MSD, and Roche-Ventana; and stock options from Apogen Biotech, Epic Biosciences, GRAIL, Achilles Therapeutics, and Bicycle Therapeutics. We thank Sir Paul Nurse, Jules Marczack, Bobbi Clayton, Gita Mistry, and all the research staff who volunteered to work on the COVID-19 testing pipeline at the Francis Crick Institute. We also thank the staff of the National Institute for Health and Care Research Clinical Research Facility at University College London Hospitals NHS Foundation Trust including Dr Mike Brown, Martin Bruce, Kirsty Adams, Miguel Alvarez, Marivic Ricamara, and Dr Mike Gandy at the Health Services Laboratory.

Figures

**Figure**
The Crick COVID Testing Pipeline mirrors the dynamics of the first year of the COVID-19 pandemic in London (A) Prevalence of all SARS-CoV-2 infections in cases per 1000 residents, by London borough from April, 2020, to May, 2021. (B) Numbers of daily tests conducted by the CCTP from April, 2020, to April, 2022. (C) Rolling 7-day incidence of SARS-CoV-2 infections across all the CCTP sites from April, 2020, to May, 2021. Vertical lines indicate peak daily positive tests, smoothed lines indicate 7-day rolling mean. (D) SARS-CoV-2 lineage positive PCR tests as a monthly proportion of total positive tests from April, 2020, to March, 2022. (E) Phylogenetic tree showing variation in all SARS-CoV-2 lineages isolated by the CCTP between 2020 and 2022, and coloured according to variants of concern. (F) Detection lead time in days for three variants of concern related to WHO designation date. CCTP=Crick COVID Testing Pipeline. Crick=Francis Crick Institute. CNWL=Camden and Northwest London NHS Trust. NMUH=North Middlesex University Hospital. NWP=Northwick Park Hospital. RFH=Barnet and Royal Free Hospitals. UCLH=University College London Hospitals.

See this image and copyright information in PMC

References

1. Black JRM, Bailey C, Przewrocka J, Dijkstra KK, Swanton C. COVID-19: the case for health-care worker screening to prevent hospital transmission. Lancet. 2020;395:1418–1420. - PMC - PubMed
1. Aitken J, Ambrose K, Barrell S, et al. Scalable and robust SARS-CoV-2 testing in an academic center. Nat Biotechnol. 2020;38:927–931. - PubMed
1. Vöhringer HS, Sanderson T, Sinnott M, et al. Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature. 2021;600:506–511. - PMC - PubMed
1. Greater London Authority Coronavirus (COVID-19) weekly update. https://data.london.gov.uk/dataset/coronavirus--covid-19--cases
1. UK Health Security Agency Infection prevention and control for seasonal respiratory infections in health and care settings (including SARS-CoV-2) for winter 2021 to 2022. https://www.gov.uk/government/publications/wuhan-novel-coronavirus-infec...

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Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London

Affiliations

Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London

Authors

Affiliations

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous