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Hall VJ, Insalata F, Foulkes S, Kirwan P, Sparkes D, Atti A, Cole M, de Lacy E, Price L, Corrigan D, Brown CS, Islam J, Charlett A, Hopkins S. Effectiveness of BNT162b2 mRNA vaccine third doses and previous infection in protecting against SARS-CoV-2 infections during the Delta and Omicron variant waves; the UK SIREN cohort study September 2021 to February 2022. J Infect 2024; 88:30-40. [PMID: 37926119 DOI: 10.1016/j.jinf.2023.10.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 10/13/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Third doses of COVID-19 vaccines were widely deployed following the primary vaccine course waning and the emergence of the Omicron-variant. We investigated protection from third-dose vaccines and previous infection against SARS-CoV-2 infection during Delta-variant and Omicron-variant (BA.1 & BA.2) waves in our frequently PCR-tested cohort of healthcare-workers. Relative effectiveness of BNT162b2 third doses and infection-acquired immunity was assessed by comparing the time to PCR-confirmed infection in boosted participants with those with waned dose-2 protection (≥254 days after dose-2), by primary series vaccination type. Follow-up time was divided by dominant circulating variant: Delta 07 September 2021 to 30 November 2021, Omicron 13 December 2021t o 28 February 2022. We used a Cox regression model with adjustment/stratification for demographic characteristics and staff-type. We explored protection associated with vaccination, infection and both. We included 19,614 participants, 29% previously infected. There were 278 primary infections (4 per 10,000 person-days of follow-up) and 85 reinfections (0.8/10,000 person-days) during the Delta period and 2467 primary infections (43/10,000 person-days) and 881 reinfections (33/10,000) during the Omicron period. Relative Vaccine Effectiveness (VE) 0-2 months post-3rd dose (3rd dose) (3-doses BNT162b2) in the previously uninfected cohort against Delta infections was 63% (95% Confidence Interval (CI) 40%-77%) and was lower (35%) against Omicron infection (95% CI 21%-47%). The relative VE of 3rd dose (heterologous BNT162b2) was greater for primary course ChAdOX1 recipients, with VE 0-2 months post-3rd dose over ≥68% higher for both variants. Third-dose protection waned rapidly against Omicron, with no significant difference between two and three BNT162b2 doses observed after 4-months. Previous infection continued to provide additional protection against Omicron (67% (CI 56%-75%) 3-6 months post-infection), but this waned to about 25% after 9-months, approximately three times lower than against Delta. Infection rates surged with Omicron emergence. Third doses of BNT162b2 vaccine provided short-term protection, with rapid waning against Omicron infections. Protection associated with infections incurred before Omicron was markedly diminished against the Omicron wave. Our findings demonstrate the complexity of an evolving pandemic with the potential emergence of immune-escape variants and the importance of continued monitoring.
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Affiliation(s)
- Victoria J Hall
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom.
| | - Ferdinando Insalata
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom; Department of Mathematics, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Sarah Foulkes
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom.
| | - Peter Kirwan
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom; MRC Biostatistics Unit, University of Cambridge, Institute of Public Health, Forvie Site, Robinson Way, Cambridge CB2 0SR, United Kingdom.
| | - Dominic Sparkes
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom.
| | - Ana Atti
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom.
| | - Michelle Cole
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom.
| | - Elen de Lacy
- Public Health Wales, 2 Capital Quarter, Tyndall Street, Cardiff CF10 4BZ, United Kingdom.
| | - Lesley Price
- Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, United Kingdom; Public Health Scotland, Gyle Square 1 South Gyle Crescent, Edinburgh EH12 9EB, United Kingdom.
| | - Diane Corrigan
- Public Health Agency Northern Ireland, Unit 12-22 Linenhall Street, Belfast BT2 8BS, United Kingdom.
| | - Colin S Brown
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom.
| | - Jasmin Islam
- UK Health Security Agency, 10 South Colonnade, London E14 4PU, United Kingdom.
| | - Andre Charlett
- UK Health Security Agency, UK Health Security Agency, Nobel House, 17 Smith Square, London, SW1P 3JR.
| | - Susan Hopkins
- UK Health Security Agency, UK Health Security Agency, Nobel House, 17 Smith Square, London, SW1P 3JR.
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Kirwan PD, Hall VJ, Foulkes S, Otter AD, Munro K, Sparkes D, Howells A, Platt N, Broad J, Crossman D, Norman C, Corrigan D, Jackson CH, Cole M, Brown CS, Atti A, Islam J, Presanis AM, Charlett A, De Angelis D, Hopkins S. Effect of second booster vaccinations and prior infection against SARS-CoV-2 in the UK SIREN healthcare worker cohort. Lancet Reg Health Eur 2024; 36:100809. [PMID: 38111727 PMCID: PMC10727938 DOI: 10.1016/j.lanepe.2023.100809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Background The protection of fourth dose mRNA vaccination against SARS-CoV-2 is relevant to current global policy decisions regarding ongoing booster roll-out. We aimed to estimate the effect of fourth dose vaccination, prior infection, and duration of PCR positivity in a highly-vaccinated and largely prior-COVID-19 infected cohort of UK healthcare workers. Methods Participants underwent fortnightly PCR and regular antibody testing for SARS-CoV-2 and completed symptoms questionnaires. A multi-state model was used to estimate vaccine effectiveness (VE) against infection from a fourth dose compared to a waned third dose, with protection from prior infection and duration of PCR positivity jointly estimated. Findings 1298 infections were detected among 9560 individuals under active follow-up between September 2022 and March 2023. Compared to a waned third dose, fourth dose VE was 13.1% (95% CI 0.9 to 23.8) overall; 24.0% (95% CI 8.5 to 36.8) in the first 2 months post-vaccination, reducing to 10.3% (95% CI -11.4 to 27.8) and 1.7% (95% CI -17.0 to 17.4) at 2-4 and 4-6 months, respectively. Relative to an infection >2 years ago and controlling for vaccination, 63.6% (95% CI 46.9 to 75.0) and 29.1% (95% CI 3.8 to 43.1) greater protection against infection was estimated for an infection within the past 0-6, and 6-12 months, respectively. A fourth dose was associated with greater protection against asymptomatic infection than symptomatic infection, whilst prior infection independently provided more protection against symptomatic infection, particularly if the infection had occurred within the previous 6 months. Duration of PCR positivity was significantly lower for asymptomatic compared to symptomatic infection. Interpretation Despite rapid waning of protection, vaccine boosters remain an important tool in responding to the dynamic COVID-19 landscape; boosting population immunity in advance of periods of anticipated pressure, such as surging infection rates or emerging variants of concern. Funding UK Health Security Agency, Medical Research Council, NIHR HPRU Oxford, Bristol, and others.
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Affiliation(s)
- Peter D. Kirwan
- MRC Biostatistics Unit, University of Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | - David Crossman
- School of Medicine, University of St Andrews, United Kingdom
| | | | | | | | | | | | - Ana Atti
- UK Health Security Agency, United Kingdom
| | | | | | | | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, United Kingdom
- UK Health Security Agency, United Kingdom
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Foulkes S, Monk EJM, Sparkes D, Hettiarachchi N, Milligan ID, Munro K, Taylor-Kerr A, Platt N, Howells A, Kyaw JYA, Adaji E, Gallagher E, Khawam J, Wellington E, Price L, Crossman D, Norman C, de Lacy E, Cromey L, Corrigan D, Lackenby A, Barbero P, Elegunde B, Zambon M, Chand MA, Brown CS, Islam J, Atti A, Hopkins S, Hall VJ, Cole MJ. Early Warning Surveillance for SARS-CoV-2 Omicron Variants, United Kingdom, November 2021-September 2022. Emerg Infect Dis 2023; 29:184-188. [PMID: 36454718 PMCID: PMC9796219 DOI: 10.3201/eid2901.221293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Since June 2020, the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study has conducted routine PCR testing in UK healthcare workers and sequenced PCR-positive samples. SIREN detected increases in infections and reinfections and delected Omicron subvariant waves emergence contemporaneous with national surveillance. SIREN's sentinel surveillance methods can be used for variant surveillance.
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4
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Cooper DJ, Lear S, Watson L, Shaw A, Ferris M, Doffinger R, Bousfield R, Sharrocks K, Weekes MP, Warne B, Sparkes D, Jones NK, Rivett L, Routledge M, Chaudhry A, Dempsey K, Matson M, Lakha A, Gathercole G, O'Connor O, Wilson E, Shahzad O, Toms K, Thompson R, Halsall I, Halsall D, Houghton S, Papadia S, Kingston N, Stirrups KE, Graves B, Townsend P, Walker N, Stark H, De Angelis D, Seaman S, Dougan G, Bradley JR, Török ME, Goodfellow I, Baker S. A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital. J Infect 2022; 85:557-564. [PMID: 36058413 PMCID: PMC9436870 DOI: 10.1016/j.jinf.2022.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To describe the risk factors for SARS-CoV-2 infection in UK healthcare workers (HCWs). METHODS We conducted a prospective sero-epidemiological study of HCWs at a major UK teaching hospital using a SARS-CoV-2 immunoassay. Risk factors for seropositivity were analysed using multivariate logistic regression. RESULTS 410/5,698 (7·2%) staff tested positive for SARS-CoV-2 antibodies. Seroprevalence was higher in those working in designated COVID-19 areas compared with other areas (9·47% versus 6·16%) Healthcare assistants (aOR 2·06 [95%CI 1·14-3·71]; p=0·016) and domestic and portering staff (aOR 3·45 [95% CI 1·07-11·42]; p=0·039) had significantly higher seroprevalence than other staff groups after adjusting for age, sex, ethnicity and COVID-19 working location. Staff working in acute medicine and medical sub-specialities were also at higher risk (aOR 2·07 [95% CI 1·31-3·25]; p<0·002). Staff from Black, Asian and minority ethnic (BAME) backgrounds had an aOR of 1·65 (95% CI 1·32 - 2·07; p<0·001) compared to white staff; this increased risk was independent of COVID-19 area working. The only symptoms significantly associated with seropositivity in a multivariable model were loss of sense of taste or smell, fever, and myalgia; 31% of staff testing positive reported no prior symptoms. CONCLUSIONS Risk of SARS-CoV-2 infection amongst HCWs is highly heterogeneous and influenced by COVID-19 working location, role, age and ethnicity. Increased risk amongst BAME staff cannot be accounted for solely by occupational factors.
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Affiliation(s)
- Daniel J Cooper
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Global and Tropical Health Division, Menzies School of Heath Research and Charles Darwin University, Darwin, Northern Territory, Australia; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
| | - Sara Lear
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Ashley Shaw
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mark Ferris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rainer Doffinger
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Michael P Weekes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ben Warne
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, United Kingdom
| | - Nick K Jones
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, United Kingdom
| | - Lucy Rivett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, United Kingdom
| | - Matthew Routledge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, United Kingdom
| | - Afzal Chaudhry
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Adil Lakha
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | | | - Olivia O'Connor
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Emily Wilson
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Orthi Shahzad
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Kieran Toms
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Rachel Thompson
- University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Ian Halsall
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David Halsall
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sally Houghton
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sofia Papadia
- NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Haematology, School of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kathleen E Stirrups
- NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Haematology, School of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Barbara Graves
- NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Paul Townsend
- NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Neil Walker
- NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Haematology, School of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Hannah Stark
- NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK; Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Shaun Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - John R Bradley
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; NIHR BioResource, NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - M Estée Török
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Ian Goodfellow
- Department of pathology, Division of virology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
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5
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Illingworth CJR, Hamilton WL, Jackson C, Warne B, Popay A, Meredith L, Hosmillo M, Jahun A, Fieldman T, Routledge M, Houldcroft CJ, Caller L, Caddy S, Yakovleva A, Hall G, Khokhar FA, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Curran M, Parmar S, Sparkes D, Rivett L, Jones NK, Sridhar S, Forrest S, Dymond T, Grainger K, Workman C, Gkrania-Klotsas E, Brown NM, Weekes MP, Baker S, Peacock SJ, Gouliouris T, Goodfellow I, Angelis DD, Török ME. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol Biol Evol 2022; 39:6519868. [PMID: 35106603 PMCID: PMC8892943 DOI: 10.1093/molbev/msac025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.
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Affiliation(s)
- Christopher J R Illingworth
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom,MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom,Institut für Biologische Physik, Universität zu Köln, Köln, Germany,Corresponding author: E-mail:
| | - William L Hamilton
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | - Ben Warne
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ashley Popay
- Public Health England Field Epidemiology Unit, Cambridge Institute of Public Health, Cambridge, United Kingdom
| | - Luke Meredith
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Myra Hosmillo
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Aminu Jahun
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Tom Fieldman
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Matthew Routledge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | | | - Sarah Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Anna Yakovleva
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Grant Hall
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad A Khokhar
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Theresa Feltwell
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malte L Pinckert
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Iliana Georgana
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Martin Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Lucy Rivett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Nick K Jones
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Sushmita Sridhar
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom,Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Tom Dymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Kayleigh Grainger
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Chris Workman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Effrossyni Gkrania-Klotsas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,MRC Epidemiology Unit, University of Cambridge, Level 3 Institute of Metabolic Science, Cambridge, United Kingdom,School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Michael P Weekes
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ian Goodfellow
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom,Public Health England, National Infection Service, London, United Kingdom
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
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6
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Illingworth CJR, Hamilton WL, Warne B, Routledge M, Popay A, Jackson C, Fieldman T, Meredith LW, Houldcroft CJ, Hosmillo M, Jahun AS, Caller LG, Caddy SL, Yakovleva A, Hall G, Khokhar FA, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Curran MD, Parmar S, Sparkes D, Rivett L, Jones NK, Sridhar S, Forrest S, Dymond T, Grainger K, Workman C, Ferris M, Gkrania-Klotsas E, Brown NM, Weekes MP, Baker S, Peacock SJ, Goodfellow IG, Gouliouris T, de Angelis D, Török ME. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections. eLife 2021; 10:e67308. [PMID: 34425938 PMCID: PMC8384420 DOI: 10.7554/elife.67308] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.
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Affiliation(s)
- Christopher JR Illingworth
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson WayCambridgeUnited Kingdom
- Institut für Biologische Physik, Universität zu KölnKölnGermany
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical SciencesCambridgeUnited States
| | - William L Hamilton
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Ben Warne
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Matthew Routledge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Ashley Popay
- Public Health England Field Epidemiology Unit, Cambridge Institute of Public Health, Forvie Site, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Chris Jackson
- MRC Biostatistics Unit, University of Cambridge, East Forvie Building, Forvie Site, Robinson WayCambridgeUnited Kingdom
| | - Tom Fieldman
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Luke W Meredith
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Charlotte J Houldcroft
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Myra Hosmillo
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Aminu S Jahun
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Laura G Caller
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Sarah L Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Anna Yakovleva
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Grant Hall
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Fahad A Khokhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Theresa Feltwell
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Malte L Pinckert
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Iliana Georgana
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Martin D Curran
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Surendra Parmar
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Lucy Rivett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Nick K Jones
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Sushmita Sridhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
| | - Sally Forrest
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Tom Dymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Kayleigh Grainger
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Chris Workman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Mark Ferris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Effrossyni Gkrania-Klotsas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- MRC Epidemiology Unit, University of Cambridge, Level 3 Institute of Metabolic ScienceCambridgeUnited Kingdom
- University of Cambridge, School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Michael P Weekes
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Stephen Baker
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical CentreCambridgeUnited Kingdom
| | - Sharon J Peacock
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Trust Genome CampusHinxtonUnited Kingdom
- Public Health England, National Infection ServiceLondonUnited Kingdom
| | - Ian G Goodfellow
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Theodore Gouliouris
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Daniela de Angelis
- Institut für Biologische Physik, Universität zu KölnKölnGermany
- Public Health England, National Infection ServiceLondonUnited Kingdom
| | - M Estée Török
- University of Cambridge, Department of Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical CampusCambridgeUnited Kingdom
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7
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DONALD M, Beanlands H, Straus S, Smekal S, Herrington G, Waldvogel B, Sparkes D, Delgado M, Hemmelgarn B. POS-479 ACCEPTABILITY AND FEASIBILITY OF A WEB-BASED SELF-MANAGEMENT SUPPORT INTERVENTION FOR ADULTS WITH CHRONIC KIDNEY DISEASE: A MIXED-METHODS STUDY. Kidney Int Rep 2021. [DOI: 10.1016/j.ekir.2021.03.506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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8
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SMEKAL M, Donald M, Beanlands H, Straus S, Herrington G, Waldvogel B, Delgado M, Sparkes D, Bello A, Brenda H. POS-346 DEVELOPMENT AND TESTING OF THE EARLY-STAGE CHRONIC KIDNEY DISEASE SELF-MANAGEMENT (esCKD-SM) QUESTIONNAIRE. Kidney Int Rep 2021. [DOI: 10.1016/j.ekir.2021.03.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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9
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Murdoch A, Madore F, Sparkes D, Tennankore K, Vorster H, Suri R. POS-491 A NEW VISION FOR NEPHROLOGY TRIALS IN CANADA. Kidney Int Rep 2021. [DOI: 10.1016/j.ekir.2021.03.518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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10
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Wilson MJ, Sparkes D, Myers C, Smielewska AA, Husain MM, Smith C, Rolfe KJ, Zhang H, Jalal H. Streamlining SARS-CoV-2 confirmatory testing to reduce false positive results. J Clin Virol 2021; 136:104762. [PMID: 33607351 PMCID: PMC7877812 DOI: 10.1016/j.jcv.2021.104762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/09/2021] [Indexed: 10/26/2022]
Abstract
BACKGROUND Confirmatory testing of SARS-CoV-2 results is essential to reduce false positives, but comes at a cost of significant extra workload for laboratories and increased turnaround time. A balance must be sought. We analysed our confirmatory testing pathway to produce a more refined approach in preparation for rising case numbers. METHODS Over a 10-week low prevalence period we performed confirmatory testing on all newly positive results. Turnaround time was measured and results were analysed to identify a threshold that could be applied as a cut-off for future confirmatory testing and reduce overall workload for the laboratory. RESULTS Between 22/06/20 and 31/08/20 confirmatory testing was performed on 108 newly positive samples, identifying 32 false positive results (30 %). Turnaround time doubled, increasing by an extra 17 h. There was a highly statistically significant difference between initial Relative Light Unit (RLU) of results that confirmed compared to those that did not, 1176 vs 721 (P < 0.00001). RLU = 1000 was identified as a suitable threshold for confirmatory testing in our laboratory: with RLU ≥ 1000, 55/56 (98 %) confirmed as positive, whereas with RLU < 1000 only 12/38 (32 %) confirmed. CONCLUSIONS False positive SARS-CoV-2 tests can be identified by confirmatory testing, yet this may significantly delay results. Establishing a threshold for confirmatory testing streamlines this process to focus only on samples where it is most required. We advise all laboratories to follow a similar process to identify thresholds that trigger confirmatory testing for their own assays, increasing accuracy while maintaining efficiency for when case numbers are high.
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Affiliation(s)
- Michael J Wilson
- Department of Virology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK.
| | - Dominic Sparkes
- Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Chloe Myers
- Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK
| | - Anna A Smielewska
- Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Mir Mubariz Husain
- Department of Virology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christopher Smith
- Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK
| | - Kathryn J Rolfe
- Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hongyi Zhang
- Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK
| | - Hamid Jalal
- Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK.
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11
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Sridhar S, Forrest S, Kean I, Young J, Bartholdson Scott J, Maes M, Pereira-Dias J, Parmar S, Routledge M, Sparkes D, Rivett L, Dougan G, Weekes M, Curran M, Goodfellow I, Baker S. A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities. Wellcome Open Res 2020; 5:110. [PMID: 33134554 PMCID: PMC7590889 DOI: 10.12688/wellcomeopenres.15937.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the method for a quantitative real-time reverse transcriptase PCR detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame.
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Affiliation(s)
- Sushmita Sridhar
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Iain Kean
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jamie Young
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Surendra Parmar
- Public Health England Diagnostic Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | | | | | - Lucy Rivett
- Infectious Diseases, Addenbrooke's Hospital, Cambridge, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Michael Weekes
- Infectious Diseases, Addenbrooke's Hospital, Cambridge, UK
| | - Martin Curran
- Public Health England Diagnostic Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridghe, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
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12
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Sparkes D, Leong C, Sharrocks K, Wilson M, Moore E, Matheson NJ. Rebooting medical education with virtual grand rounds during the COVID-19 pandemic. Future Healthc J 2020; 8:e11-e14. [PMID: 33791467 DOI: 10.7861/fhj.2020-0180] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Social distancing during the coronavirus disease 2019 (COVID-19) pandemic has necessitated drastic changes in the practice of hospital medicine, including the cancellation of many educational activities. At the same time, the emergence of a new disease with a rapidly evolving knowledge base has mandated timely educational updates. To resolve this conflict in our hospital, we substituted 'traditional' grand rounds with 'virtual' grand rounds delivered over Zoom, consisting of a local situation report and operational update, followed by a specialty-specific clinical presentation on management of COVID-19. Attendance was greatly increased (mean 384 attendees) compared to traditional grand rounds (mean 44 attendees) and included a diverse audience of medical professionals. Feedback was overwhelmingly positive, with >80% of responders stating that the sessions would or might inform their clinical practice. COVID-19 has therefore provided an opportunity to modernise grand rounds, and develop a new model matching the needs of medical education beyond the pandemic.
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Affiliation(s)
- Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,These authors contributed equally
| | - Clare Leong
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, Uk.,These authors contributed equally
| | | | - Michael Wilson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Elinor Moore
- Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge, UK, honorary consultant in infectious diseases at Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK and honorary consultant in virology at NHS Blood and Transplant, Cambridge, UK
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13
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Skittrall JP, Wilson M, Smielewska AA, Parmar S, Fortune MD, Sparkes D, Curran MD, Zhang H, Jalal H. Specificity and positive predictive value of SARS-CoV-2 nucleic acid amplification testing in a low-prevalence setting. Clin Microbiol Infect 2020; 27:469.e9-469.e15. [PMID: 33068757 PMCID: PMC7554481 DOI: 10.1016/j.cmi.2020.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 02/01/2023]
Abstract
Objectives When the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is low, many positive test results are false positives. Confirmatory testing reduces overdiagnosis and nosocomial infection and enables real-world estimates of test specificity and positive predictive value. This study estimates these parameters to evaluate the impact of confirmatory testing and to improve clinical diagnosis, epidemiological estimation and interpretation of vaccine trials. Methods Over 1 month we took all respiratory samples from our laboratory with a patient's first detection of SARS-CoV-2 RNA (Hologic Aptima SARS-CoV-2 assay or in-house RT-PCR platform), and repeated testing using two platforms. Samples were categorized by source, and by whether clinical details suggested COVID-19 or corroborative testing from another laboratory. We estimated specificity and positive predictive value using approaches based on maximum likelihood. Results Of 19 597 samples, SARS-CoV-2 RNA was detected in 107; 52 corresponded to first-time detection (0.27% of tests on samples without previous detection). Further testing detected SARS-CoV-2 RNA once or more (‘confirmed’) in 29 samples (56%), and failed to detect SARS-CoV-2 RNA (‘not confirmed’) in 23 (44%). Depending upon assumed parameters, point estimates for specificity and positive predictive value were 99.91–99.98% and 61.8–89.8% respectively using the Hologic Aptima SARS-CoV-2 assay, and 97.4–99.1% and 20.1–73.8% respectively using an in-house assay. Conclusions Nucleic acid amplification testing for SARS-CoV-2 is highly specific. Nevertheless, when prevalence is low a significant proportion of initially positive results fail to confirm, and confirmatory testing substantially reduces the detection of false positives. Omitting additional testing in samples with higher prior detection probabilities focuses testing where it is clinically impactful and minimizes delay.
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Affiliation(s)
- Jordan P Skittrall
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom; Department of Infection, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom.
| | - Michael Wilson
- Department of Infection, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Anna A Smielewska
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom; Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Surendra Parmar
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Mary D Fortune
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Dominic Sparkes
- Department of Infection, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Martin D Curran
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Hongyi Zhang
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Hamid Jalal
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
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14
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Mlcochova P, Collier D, Ritchie A, Assennato SM, Hosmillo M, Goel N, Meng B, Chatterjee K, Mendoza V, Temperton N, Kiss L, James LC, Ciazynska KA, Xiong X, Briggs JA, Nathan JA, Mescia F, Bergamaschi L, Zhang H, Barmpounakis P, Demeris N, Skells R, Lyons PA, Bradley J, Baker S, Allain JP, Smith KG, Bousfield R, Wilson M, Sparkes D, Amoroso G, Gkrania-Klotsas E, Hardwick S, Boyle A, Goodfellow I, Gupta RK. Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Cell Rep Med 2020; 1:100099. [PMID: 32905045 PMCID: PMC7462534 DOI: 10.1016/j.xcrm.2020.100099] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/05/2020] [Accepted: 08/27/2020] [Indexed: 12/20/2022]
Abstract
Rapid COVID-19 diagnosis in the hospital is essential, although this is complicated by 30%-50% of nose/throat swabs being negative by SARS-CoV-2 nucleic acid amplification testing (NAAT). Furthermore, the D614G spike mutant dominates the pandemic and it is unclear how serological tests designed to detect anti-spike antibodies perform against this variant. We assess the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease due to either wild-type or the D614G spike mutant SARS-CoV-2. The overall detection rate for COVID-19 is 79.2% (95% CI 57.8-92.9) by rapid NAAT alone. The combined point of care antibody test and rapid NAAT is not affected by D614G and results in very high sensitivity for COVID-19 diagnosis with very high specificity.
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Affiliation(s)
- Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Allyson Ritchie
- Diagnostics for the Real World EU, Chesterford Research Park, UK
| | | | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Neha Goel
- Diagnostics for the Real World EU, Chesterford Research Park, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Vivien Mendoza
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Kent, UK
| | - Leo Kiss
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Leo C. James
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Xiaoli Xiong
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - John A.G. Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - James A. Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hongyi Zhang
- Clinical Microbiology & Public Health Laboratory, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Petros Barmpounakis
- Department of Statistics, Athens University of Economics and Business, Athens, Greece
| | - Nikos Demeris
- Department of Statistics, Athens University of Economics and Business, Athens, Greece
- Cambridge Clinical Trials Unit-Cancer Theme, University of Cambridge, Cambridge, UK
| | - Richard Skells
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
- Cambridge Clinical Trials Unit-Cancer Theme, University of Cambridge, Cambridge, UK
| | - Paul A. Lyons
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John Bradley
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- National Institutes for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
| | - Steven Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Kenneth G.C. Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rachel Bousfield
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Michael Wilson
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Dominic Sparkes
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Glenn Amoroso
- Department of Emergency Medicine, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Effrosyni Gkrania-Klotsas
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Susie Hardwick
- Department of Emergency Medicine, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Adrian Boyle
- Department of Emergency Medicine, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
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15
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Jones NK, Rivett L, Sparkes D, Forrest S, Sridhar S, Young J, Pereira-Dias J, Cormie C, Gill H, Reynolds N, Wantoch M, Routledge M, Warne B, Levy J, Córdova Jiménez WD, Samad FNB, McNicholas C, Ferris M, Gray J, Gill M, Curran MD, Fuller S, Chaudhry A, Shaw A, Bradley JR, Hannon GJ, Goodfellow IG, Dougan G, Smith KGC, Lehner PJ, Wright G, Matheson NJ, Baker S, Weekes MP. Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19. eLife 2020; 9:e59391. [PMID: 32558644 PMCID: PMC7326489 DOI: 10.7554/elife.59391] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/19/2020] [Indexed: 12/21/2022] Open
Abstract
Previously, we showed that 3% (31/1032)of asymptomatic healthcare workers (HCWs) from a large teaching hospital in Cambridge, UK, tested positive for SARS-CoV-2 in April 2020. About 15% (26/169) HCWs with symptoms of coronavirus disease 2019 (COVID-19) also tested positive for SARS-CoV-2 (Rivett et al., 2020). Here, we show that the proportion of both asymptomatic and symptomatic HCWs testing positive for SARS-CoV-2 rapidly declined to near-zero between 25th April and 24th May 2020, corresponding to a decline in patient admissions with COVID-19 during the ongoing UK 'lockdown'. These data demonstrate how infection prevention and control measures including staff testing may help prevent hospitals from becoming independent 'hubs' of SARS-CoV-2 transmission, and illustrate how, with appropriate precautions, organizations in other sectors may be able to resume on-site work safely.
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MESH Headings
- Adult
- Asymptomatic Diseases
- Betacoronavirus/genetics
- Betacoronavirus/isolation & purification
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques/statistics & numerical data
- Community-Acquired Infections/transmission
- Contact Tracing
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/transmission
- Disease Transmission, Infectious/prevention & control
- England/epidemiology
- Family Characteristics
- Female
- Health Personnel
- Hospital Units
- Hospitals, Teaching/organization & administration
- Hospitals, Teaching/statistics & numerical data
- Hospitals, University/organization & administration
- Hospitals, University/statistics & numerical data
- Humans
- Infection Control
- Infectious Disease Transmission, Patient-to-Professional/statistics & numerical data
- Male
- Mass Screening/organization & administration
- Mass Screening/statistics & numerical data
- Middle Aged
- Nasopharynx/virology
- Occupational Diseases/epidemiology
- Occupational Diseases/prevention & control
- Pandemics/prevention & control
- Patient Admission/statistics & numerical data
- Pneumonia, Viral/diagnosis
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/transmission
- Prevalence
- Program Evaluation
- Real-Time Polymerase Chain Reaction
- SARS-CoV-2
- Symptom Assessment
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Affiliation(s)
- Nick K Jones
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology & Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Lucy Rivett
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology & Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Dominic Sparkes
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology & Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Sally Forrest
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Sushmita Sridhar
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Jamie Young
- Academic Department of Medical Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Joana Pereira-Dias
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Claire Cormie
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Harmeet Gill
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Nicola Reynolds
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Michelle Wantoch
- Wellcome - MRC Cambridge Stem Cell Institute, University of CambridgeCambridgeUnited Kingdom
- Department of Haematology, School of Clinical Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Matthew Routledge
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology & Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Ben Warne
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Jack Levy
- Institute for Manufacturing, Department of Engineering, University of CambridgeCambridgeUnited Kingdom
| | | | - Fathima Nisha Begum Samad
- Institute for Manufacturing, Department of Engineering, University of CambridgeCambridgeUnited Kingdom
| | - Chris McNicholas
- Improvement and Transformation Team, Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - Mark Ferris
- Occupational Health and Wellbeing, Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - Jane Gray
- Cancer Research United Kingdom Cambridge Institute, University of CambridgeCambridgeUnited Kingdom
| | - Michael Gill
- Cancer Research United Kingdom Cambridge Institute, University of CambridgeCambridgeUnited Kingdom
| | - Martin D Curran
- Clinical Microbiology & Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Stewart Fuller
- National Institutes for Health Research Cambridge Biomedical Research CentreCambridgeUnited Kingdom
| | - Afzal Chaudhry
- Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - Ashley Shaw
- Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - John R Bradley
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- National Institutes for Health Research Cambridge, Clinical Research FacilityCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research United Kingdom Cambridge Institute, University of CambridgeCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Gordon Dougan
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Kenneth GC Smith
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Paul J Lehner
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Giles Wright
- Occupational Health and Wellbeing, Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - Nicholas J Matheson
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
- NHS Blood and TransplantCambridgeUnited Kingdom
| | - Stephen Baker
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Michael P Weekes
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
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16
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Sridhar S, Forrest S, Kean I, Young J, Bartholdson Scott J, Maes M, Pereira-Dias J, Parmar S, Routledge M, Sparkes D, Rivett L, Dougan G, Weekes M, Curran M, Goodfellow I, Baker S. A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities. Wellcome Open Res 2020; 5:110. [PMID: 33134554 PMCID: PMC7590889 DOI: 10.12688/wellcomeopenres.15937.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2020] [Indexed: 11/20/2022] Open
Abstract
The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the method for a quantitative real-time reverse transcriptase PCR detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame.
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Affiliation(s)
- Sushmita Sridhar
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Iain Kean
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jamie Young
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Surendra Parmar
- Public Health England Diagnostic Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | | | | | - Lucy Rivett
- Infectious Diseases, Addenbrooke's Hospital, Cambridge, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Michael Weekes
- Infectious Diseases, Addenbrooke's Hospital, Cambridge, UK
| | - Martin Curran
- Public Health England Diagnostic Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Cambridghe, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
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17
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Rivett L, Sridhar S, Sparkes D, Routledge M, Jones NK, Forrest S, Young J, Pereira-Dias J, Hamilton WL, Ferris M, Torok ME, Meredith L, Curran MD, Fuller S, Chaudhry A, Shaw A, Samworth RJ, Bradley JR, Dougan G, Smith KGC, Lehner PJ, Matheson NJ, Wright G, Goodfellow IG, Baker S, Weekes MP. Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission. eLife 2020; 9:e58728. [PMID: 32392129 PMCID: PMC7314537 DOI: 10.7554/elife.58728] [Citation(s) in RCA: 346] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 12/30/2022] Open
Abstract
Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff.
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Affiliation(s)
- Lucy Rivett
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology and Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Sushmita Sridhar
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Dominic Sparkes
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology and Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Matthew Routledge
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology and Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Nick K Jones
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology and Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Sally Forrest
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Jamie Young
- Academic Department of Medical Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Joana Pereira-Dias
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - William L Hamilton
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Clinical Microbiology and Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Mark Ferris
- Occupational Health and Wellbeing, Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - M Estee Torok
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
- Department of Microbiology, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
| | - Luke Meredith
- Division of Virology, Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Public Health EnglandCambridgeUnited Kingdom
| | - Stewart Fuller
- National Institutes for Health Research Cambridge, Clinical Research FacilityCambridgeUnited Kingdom
| | - Afzal Chaudhry
- Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - Ashley Shaw
- National Institutes for Health Research Cambridge, Clinical Research FacilityCambridgeUnited Kingdom
| | - Richard J Samworth
- Statistical Laboratory, Centre for Mathematical SciencesCambridgeUnited Kingdom
| | - John R Bradley
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- National Institutes for Health Research Cambridge Biomedical Research CentreCambridgeUnited Kingdom
| | - Gordon Dougan
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Kenneth GC Smith
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Paul J Lehner
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Nicholas J Matheson
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
- NHS Blood and TransplantCambridgeUnited Kingdom
| | - Giles Wright
- Occupational Health and Wellbeing, Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Stephen Baker
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Michael P Weekes
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation TrustCambridgeUnited Kingdom
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
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18
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Affiliation(s)
- Lucy Hedley
- Senior Clinical Pharmacist in HIV and Infectious Diseases in the Department of Pharmacy, University College London Hospitals NHS Foundation Trust, London NW1 2BU
| | - Douglas Fink
- Registrar in Infectious Diseases and General Internal Medicine in the Department of Infectious Diseases, University College London Hospitals NHS Foundation Trust, London
| | - Dominic Sparkes
- Foundation Doctor in Infectious Diseases in the Department of Infectious Diseases, University College London Hospitals NHS Foundation Trust, London
| | - Peter L Chiodini
- Consultant Parasitologist in the Department of Infectious Diseases and Parasitology, Hospital for Tropical Diseases, London
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19
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Tagle K, Yoon S, Malhi R, Silva ASD, Depala A, Doherty R, Greenfield S, James A, Sparkes D, Uthayakumar A, Watson L, Jones H, Wu L, Pathiraja F. Quality improvement programmes: a model for clinical leadership training for foundation doctors. Future Hosp J 2016. [DOI: 10.7861/futurehosp.3-2-s34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Tagle K, Yoon S, Malhi R, Silva ASD, Depala A, Doherty R, Greenfield S, James A, Sparkes D, Uthayakumar A, Watson L, Jones H, Wu L, Pathiraja F. Quality improvement programmes: a model for clinical leadership training for foundation doctors. Future Hosp J 2016; 3:s34. [PMID: 31098263 PMCID: PMC6465920 DOI: 10.7861/futurehosp.3-2s-s34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
| | - Soo Yoon
- University College London Hospital, London, UK
| | - Ranu Malhi
- University College London Hospital, London, UK
| | | | | | | | | | | | | | | | - Liam Watson
- University College London Hospital, London, UK
| | | | - Li Wu
- University College London Hospital, London, UK
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21
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Mann T, Hammarstrom O, Burca D, O'Hagan L, Sparkes D, Mikkelsen S. P1649 Determination of antibiotic breakpoints using a novel electrochemical respiratory activity assay. Int J Antimicrob Agents 2007. [DOI: 10.1016/s0924-8579(07)71488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Sparkes D, Baylis R. Randomized clinical trial of local bupivacaine perfusion versus parenteral morphine infusion for pain relief after laparotomy (Br J Surg 2001; 88: 357-9). Letter 2. Br J Surg 2001; 88:1267. [PMID: 11531886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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