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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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Conway Morris A, Sharrocks K, Bousfield R, Kermack L, Maes M, Higginson E, Forrest S, Pereira-Dias J, Cormie C, Old T, Brooks S, Hamed I, Koenig A, Turner A, White P, Floto RA, Dougan G, Gkrania-Klotsas E, Gouliouris T, Baker S, Navapurkar V. The Removal of Airborne Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Other Microbial Bioaerosols by Air Filtration on Coronavirus Disease 2019 (COVID-19) Surge Units. Clin Infect Dis 2022; 75:e97-e101. [PMID: 34718446 PMCID: PMC8689842 DOI: 10.1093/cid/ciab933] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [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: 09/23/2021] [Indexed: 11/29/2022] Open
Abstract
Airborne severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in a coronavirus disease 19 (COVID-19) ward before activation of HEPA-air filtration but not during filter operation; SARS-CoV-2 was again detected following filter deactivation. Airborne SARS-CoV-2 was infrequently detected in a COVID-19 intensive care unit. Bioaerosol was also effectively filtered.
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Affiliation(s)
- Andrew Conway Morris
- The John Farman ICU, Cambridge University Hospitals, National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
- University Division of Anaesthesia, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Katherine Sharrocks
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Rachel Bousfield
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Clinical Microbiology Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Leanne Kermack
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sally Forrest
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Claire Cormie
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Tim Old
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Sophie Brooks
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Islam Hamed
- The John Farman ICU, Cambridge University Hospitals, National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Alicia Koenig
- The John Farman ICU, Cambridge University Hospitals, National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Andrew Turner
- Department of Clinical Engineering, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Paul White
- Department of Clinical Engineering, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Medical Technology Research Centre and School of Medicine, Anglia Ruskin University, Chelmsford, United Kingdom
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Effrossyni Gkrania-Klotsas
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Theodore Gouliouris
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Clinical Microbiology Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Vilas Navapurkar
- The John Farman ICU, Cambridge University Hospitals, National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
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3
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Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Modis Y, Leigh KE, Briggs JAG, van Gils MJ, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. Author Correction: SARS-CoV-2 evolution during treatment of chronic infection. Nature 2022; 608:E23. [PMID: 35864233 PMCID: PMC9302216 DOI: 10.1038/s41586-022-05104-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Steven A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - Dami A Collier
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Salma Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Aminu Jahun
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Chloe Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | - Katherine Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Elizabeth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yorgo Modis
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kendra E Leigh
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - John A G Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Cambridge Bioresource, Cambridge, UK
| | - Chris Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
| | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- FES-Cuautitlán, UNAM, Cuautitlán Izcalli, Mexico
| | - David D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Anna Smielewska
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Jordan P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | - Theodore Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | | | | | - Christopher J R Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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4
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Ramsay I, Sharrocks K, Warne B, Sithole N, Ravji P, Bousfield R, Jones N, Leong CE, Suliman M, Tsui R, Toleman MS, Moody C, Smith R, Whitehorn J, Gouliouris T, Penciu F, Hofling C, Cunningham C, Enoch DA, Moore E. Investigation of healthcare-associated SARS-CoV-2 infection: Learning outcomes from an investigative process in the initial phase of the pandemic. J Infect Prev 2022; 23:197-205. [PMID: 36003131 PMCID: PMC9117956 DOI: 10.1177/17571774221092553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 02/21/2022] [Indexed: 11/17/2022] Open
Abstract
Background Healthcare-associated (HCA) SARS-CoV-2 infection is a significant contributor
to the spread of the 2020 pandemic. Timely review of HCA cases is essential
to identify learning to inform infection prevention and control (IPC)
policies and organisational response. Aim To identify key areas for improvement through rapid investigation of HCA
SARS-CoV-2 cases and to implement change. Methods Cases were identified based on date of first positive SARS-CoV-2 PCR sample
in relation to date of hospital admission. Cases were reviewed using a
structured gap analysis tool to identify key learning points. These were
discussed in weekly multidisciplinary meetings to gain consensus on learning
outcomes, level of harm incurred by the patient and required actions.
Learning was then promptly fed back to individual teams and the
organisation. Findings Of the 489 SARS-CoV-2 cases admitted between 10th March and
23rd June 2020, 114 suspected HCA cases (23.3%) were
reviewed; 58/489 (11.8%) were ultimately deemed to be HCA. Five themes were
identified: individual patient vulnerability, communication, IPC
implementation, policy issues and organisational response. Adaptations to
policies based on these reviews were completed within the course of the
initial phase of the pandemic. Conclusion This approach enabled timely learning and implementation of control measures
and policy development.
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Affiliation(s)
- Isobel Ramsay
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katherine Sharrocks
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ben Warne
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nyarie Sithole
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Pooja Ravji
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rachel Bousfield
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nick Jones
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clare E Leong
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mohamed Suliman
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rachel Tsui
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
| | | | - Christine Moody
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
| | - Richard Smith
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
| | - James Whitehorn
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Theodore Gouliouris
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Christian Hofling
- Infectious Diseases, Universidade Estadual de Campinas, Campinas, Brazil
| | - Chris Cunningham
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David A Enoch
- Clinical Microbiology & Public Health Laboratory, Cambridge, UK
| | - Elinor Moore
- Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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5
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Török ME, Underwood BR, Toshner M, Waddington C, Sidhom E, Sharrocks K, Bousfield R, Summers C, Saunders C, McIntyre Z, Morris H, Piper J, Calderon G, Dennis S, Assari T, de Rotrou AM, Shaw A, Bradley J, O’Brien J, Rintoul RC, Smith I, Bullmore E, Chatterjee K. Challenges and opportunities for conducting a vaccine trial during the COVID-19 pandemic in the United Kingdom. Clin Trials 2021; 18:615-621. [PMID: 34154428 PMCID: PMC8479147 DOI: 10.1177/17407745211024764] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The COVID-19 pandemic has resulted in unprecedented challenges for healthcare systems worldwide. It has also stimulated research in a wide range of areas including rapid diagnostics, novel therapeutics, use of technology to track patients and vaccine development. Here, we describe our experience of rapidly setting up and delivering a novel COVID-19 vaccine trial, using clinical and research staff and facilities in three National Health Service Trusts in Cambridgeshire, United Kingdom. We encountered and overcame a number of challenges including differences in organisational structures, research facilities available, staff experience and skills, information technology and communications infrastructure, and research training and assessment procedures. We overcame these by setting up a project team that included key members from all three organisations that met at least daily by teleconference. This group together worked to identify the best practices and procedures and to harmonise and cascade these to the wider trial team. This enabled us to set up the trial within 25 days and to recruit and vaccinate the participants within a further 23 days. The lessons learned from our experiences could be used to inform the conduct of clinical trials during a future infectious disease pandemic or public health emergency.
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Affiliation(s)
- M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK
- Departments of Infectious Diseases & Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Benjamin R Underwood
- Windsor Research Unit, Fulbourn Hospital, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
- Gnodde Goldman Sachs Translational Neuroscience Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mark Toshner
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Respiratory Medicine, Royal Papworth Hospital, Cambridge, UK
| | - Claire Waddington
- Department of Medicine, University of Cambridge, Cambridge, UK
- Departments of Infectious Diseases & Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Emad Sidhom
- Windsor Research Unit, Fulbourn Hospital, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
- Gnodde Goldman Sachs Translational Neuroscience Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Katherine Sharrocks
- Departments of Infectious Diseases & Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Rachel Bousfield
- Departments of Infectious Diseases & Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Charlotte Summers
- Department of Medicine, University of Cambridge, Cambridge, UK
- John V Farman Intensive Care Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Caroline Saunders
- NIHR Cambridge Clinical Research Facility, Cambridge Clinical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Zoe McIntyre
- Office for Translational Research, University of Cambridge, Cambridge, UK
| | - Helen Morris
- NIHR Cambridge Clinical Research Facility, Cambridge Clinical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jo Piper
- NIHR Cambridge Clinical Research Facility, Cambridge Clinical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gloria Calderon
- Windsor Research Unit, Fulbourn Hospital, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Sarah Dennis
- Department of Respiratory Medicine, Royal Papworth Hospital, Cambridge, UK
| | - Tracy Assari
- Research & Development Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Ashley Shaw
- Medical Director’s Office, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - John Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- Research & Development Department, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - John O’Brien
- Gnodde Goldman Sachs Translational Neuroscience Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Robert C Rintoul
- Department of Respiratory Medicine, Royal Papworth Hospital, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Ian Smith
- Department of Respiratory Medicine, Royal Papworth Hospital, Cambridge, UK
| | - Ed Bullmore
- Gnodde Goldman Sachs Translational Neuroscience Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Krishna Chatterjee
- NIHR Cambridge Clinical Research Facility, Cambridge Clinical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Institute of Metabolic Science, University of Cambridge, Cambridge, UK
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6
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Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Modis Y, Leigh KE, Briggs JAG, van Gils MJ, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. SARS-CoV-2 evolution during treatment of chronic infection. Nature 2021. [PMID: 33545711 DOI: 10.1038/s41586-021-03291-y.33545711] [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] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
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Affiliation(s)
- Steven A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - Dami A Collier
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Salma Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Aminu Jahun
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Chloe Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | - Katherine Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Elizabeth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yorgo Modis
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kendra E Leigh
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - John A G Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Cambridge Bioresource, Cambridge, UK
| | - Chris Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
| | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- FES-Cuautitlán, UNAM, Cuautitlán Izcalli, Mexico
| | - David D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Anna Smielewska
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Jordan P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | - Theodore Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | | | | | - Christopher J R Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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7
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Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Modis Y, Leigh K, Briggs J, van Gils M, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. SARS-CoV-2 evolution during treatment of chronic infection. Nature 2021; 592:277-282. [PMID: 33545711 PMCID: PMC7610568 DOI: 10.1038/s41586-021-03291-y] [Citation(s) in RCA: 616] [Impact Index Per Article: 205.3] [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: 12/01/2020] [Accepted: 01/26/2021] [Indexed: 02/02/2023]
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
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Affiliation(s)
- Steven A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - Dami A Collier
- Division of Infection and Immunity, University College London, London, UK, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella ATM Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Salma Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Aminu Jahun
- Department of Pathology, University of Cambridge, Cambridge
| | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge
| | - Chloe Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK
| | - The CITIID-NIHR BioResource COVID-19 Collaboration BakerStephen23Principal InvestigatorsDouganGordon23Principal InvestigatorsHessChristoph232627Principal InvestigatorsKingstonNathalie2012Principal InvestigatorsLehnerPaul J.23Principal InvestigatorsLyonsPaul A.23Principal InvestigatorsMathesonNicholas J.23Principal InvestigatorsOwehandWillem H.20Principal InvestigatorsSaundersCaroline19Principal InvestigatorsSummersCharlotte3242528Principal InvestigatorsThaventhiranJames E.D.2322Principal InvestigatorsToshnerMark32425Principal InvestigatorsWeekesMichael P.2Principal InvestigatorsBuckeAshlea19CRF and Volunteer Research NursesCalderJo19CRF and Volunteer Research NursesCannaLaura19CRF and Volunteer Research NursesDomingoJason19CRF and Volunteer Research NursesElmerAnne19CRF and Volunteer Research NursesFullerStewart19CRF and Volunteer Research NursesHarrisJulie41CRF and Volunteer Research NursesHewittSarah19CRF and Volunteer Research NursesKennetJane19CRF and Volunteer Research NursesJoseSherly19CRF and Volunteer Research NursesKourampaJenny19CRF and Volunteer Research NursesMeadowsAnne19CRF and Volunteer Research NursesO’BrienCriona41CRF and Volunteer Research NursesPriceJane19CRF and Volunteer Research NursesPublicoCherry19CRF and Volunteer Research NursesRastallRebecca19CRF and Volunteer Research NursesRibeiroCarla19CRF and Volunteer Research NursesRowlandsJane19CRF and Volunteer Research NursesRuffoloValentina19CRF and Volunteer Research NursesTordesillasHugo19CRF and Volunteer Research NursesBullmanBen2Sample LogisticsDunmoreBenjamin J3Sample LogisticsFawkeStuart30Sample LogisticsGräfStefan31220Sample LogisticsHodgsonJosh3Sample LogisticsHuangChristopher3Sample LogisticsHunterKelvin23Sample LogisticsJonesEmma29Sample LogisticsLegchenkoEkaterina3Sample LogisticsMataraCecilia3Sample LogisticsMartinJennifer3Sample LogisticsMesciaFederica23Sample LogisticsO’DonnellCiara3Sample LogisticsPointonLinda3Sample LogisticsPondNicole23Sample LogisticsShihJoy3Sample LogisticsSutcliffeRachel3Sample LogisticsTillyTobias3Sample LogisticsTreacyCarmen3Sample LogisticsTongZhen3Sample LogisticsWoodJennifer3Sample LogisticsWylotMarta36Sample LogisticsBergamaschiLaura23Sample Processing and Data AcquisitionBetancourtAriana23Sample Processing and Data AcquisitionBowerGeorgie23Sample Processing and Data AcquisitionCossettiChiara23Sample Processing and Data AcquisitionDe SaAloka3Sample Processing and Data AcquisitionEppingMadeline23Sample Processing and Data AcquisitionFawkeStuart32Sample Processing and Data AcquisitionGleadallNick20Sample Processing and Data AcquisitionGrenfellRichard31Sample Processing and Data AcquisitionHinchAndrew23Sample Processing and Data AcquisitionHuhnOisin32Sample Processing and Data AcquisitionJacksonSarah3Sample Processing and Data AcquisitionJarvisIsobel3Sample Processing and Data AcquisitionLewisDaniel3Sample Processing and Data AcquisitionMarsdenJoe3Sample Processing and Data AcquisitionNiceFrancesca39Sample Processing and Data AcquisitionOkechaGeorgina3Sample Processing and Data AcquisitionOmarjeeOmmar3Sample Processing and Data AcquisitionPereraMarianne3Sample Processing and Data AcquisitionRichozNathan3Sample Processing and Data AcquisitionRomashovaVeronika23Sample Processing and Data AcquisitionYarkoniNatalia Savinykh3Sample Processing and Data AcquisitionSharmaRahul3Sample Processing and Data AcquisitionStefanucciLuca20Sample Processing and Data AcquisitionStephensJonathan20Sample Processing and Data AcquisitionStrezleckiMateusz31Sample Processing and Data AcquisitionTurnerLori23Sample Processing and Data AcquisitionDe BieEckart M.D.D.3Clinical Data CollectionBunclarkKatherine3Clinical Data CollectionJosipovicMasa40Clinical Data CollectionMackayMichael3Clinical Data CollectionMesciaFederica23Clinical Data CollectionMichaelAlice25Clinical Data CollectionRossiSabrina35Clinical Data CollectionSelvanMayurun3Clinical Data CollectionSpencerSarah15Clinical Data CollectionYongCissy35Clinical Data CollectionAnsaripourAli25Royal Papworth Hospital ICUMichaelAlice25Royal Papworth Hospital ICUMwauraLucy25Royal Papworth Hospital ICUPattersonCaroline25Royal Papworth Hospital ICUPolwarthGary25Royal Papworth Hospital ICUPolgarovaPetra28Addenbrooke’s Hospital ICUdi StefanoGiovanni28Addenbrooke’s Hospital ICUFaheyCodie34Cambridge and Peterborough Foundation TrustMichelRachel34Cambridge and Peterborough Foundation TrustBongSze-How21ANPC and Centre for Molecular Medicine and Innovative TherapeuticsCoudertJerome D.33ANPC and Centre for Molecular Medicine and Innovative TherapeuticsHolmesElaine37ANPC and Centre for Molecular Medicine and Innovative TherapeuticsAllisonJohn2012NIHR BioResourceButcherHelen1238NIHR BioResourceCaputoDaniela1238NIHR BioResourceClapham-RileyDebbie1238NIHR BioResourceDewhurstEleanor1238NIHR BioResourceFurlongAnita1238NIHR BioResourceGravesBarbara1238NIHR BioResourceGrayJennifer1238NIHR BioResourceIversTasmin1238NIHR BioResourceKasanickiMary1228NIHR BioResourceLe GresleyEmma1238NIHR BioResourceLingerRachel1238NIHR BioResourceMeloySarah1238NIHR BioResourceMuldoonFrancesca1238NIHR BioResourceOvingtonNigel1220NIHR BioResourcePapadiaSofia1238NIHR BioResourcePhelanIsabel1238NIHR BioResourceStarkHannah1238NIHR BioResourceStirrupsKathleen E1220NIHR BioResourceTownsendPaul1220NIHR BioResourceWalkerNeil1220NIHR BioResourceWebsterJennifer1238NIHR BioResourceCambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UKDepartment of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UKAustralian National Phenome Centre, Murdoch University, Murdoch, Western Australia WA 6150, AustraliaMRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UKR&D Department, Hycult Biotech, 5405 PD Uden, The NetherlandsHeart and Lung Research Institute, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UKRoyal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UKDepartment of Biomedicine, University and University Hospital Basel, 4031Basel, SwitzerlandBotnar Research Centre for Child Health (BRCCH) University Basel & ETH Zurich, 4058 Basel, SwitzerlandAddenbrooke’s Hospital, Cambridge CB2 0QQ, UKDepartment of Veterinary Medicine, Madingley Road, Cambridge, CB3 0ES, UKCambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UKCancer Research UK, Cambridge Institute, University of Cambridge CB2 0RE, UKDepartment of Obstetrics & Gynaecology, The Rosie Maternity Hospital, Robinson Way, Cambridge CB2 0SW, UKCentre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, AustraliaCambridge and Peterborough Foundation Trust, Fulbourn Hospital, Fulbourn, Cambridge CB21 5EF, UKDepartment of Surgery, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UKDepartment of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UKCentre of Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, AustraliaDepartment of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UKCancer Molecular Diagnostics Laboratory, Department of Oncology, University of Cambridge, Cambridge CB2 0AH, UKMetabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UKDepartment of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | | | - Katherine Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Elizabeth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yorgo Modis
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kendra Leigh
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - John Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marit van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Kenneth GC Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK, NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Chris Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, FES-Cuautitlán, UNAM, Mexico
| | - David D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Anna Smielewska
- Department of Pathology, University of Cambridge, Cambridge,Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - Jordan P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK,Clinical Microbiology and Public Health Laboratory, Addenbrookes’ Hospital, Cambridge, UK
| | - Theodore Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | | | | | - Christopher JR Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK, MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK,Africa Health Research Institute, Durban, South Africa
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8
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Kemp SA, Collier DA, Datir R, Ferreira I, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Briggs J, van GM, Smith K, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth C, McCoy LE, Gupta RK. Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. medRxiv 2020:2020.12.05.20241927. [PMID: 33398302 PMCID: PMC7781345 DOI: 10.1101/2020.12.05.20241927] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against ΔH69/ΔV70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.
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Affiliation(s)
- S A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - D A Collier
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - R Datir
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Iatm Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - S Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - A Jahun
- Department of Pathology, University of Cambridge, Cambridge
| | - M Hosmillo
- Department of Pathology, University of Cambridge, Cambridge
| | - C Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - P Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - N Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK
| | - K Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - E Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jag Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gils Mj van
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Kgc Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - J R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - C Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - R Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - L Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - G Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - D D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - R A Goldstein
- Division of Infection and Immunity, University College London, London, UK
| | - A Smielewska
- Department of Pathology, University of Cambridge, Cambridge
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - J P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Addenbrookes' Hospital, Cambridge, UK
| | - T Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - I G Goodfellow
- Department of Pathology, University of Cambridge, Cambridge
| | - E Gkrania-Klotsas
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Cjr Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - L E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - R K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
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9
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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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Sharrocks K, Spicer J, Camidge DR, Papa S. The impact of socioeconomic status on access to cancer clinical trials. Br J Cancer 2014; 111:1684-7. [PMID: 25093493 PMCID: PMC4453719 DOI: 10.1038/bjc.2014.108] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/02/2014] [Accepted: 02/03/2014] [Indexed: 11/22/2022] Open
Abstract
Cancer clinical trials enable the development of novel agents for the potential benefit of cancer patients. Enrolment in a trial offers patients the chance of superior efficacy coupled to the risk of unanticipated toxicity. For trial results to be generalisable, the data need to be collected in patients' representative of the general cancer population. Socioeconomic deprivation is associated with poor cancer outcomes. In the developed world, the gap between the most and least deprived is widening. This mini-review explores the evidence regarding socioeconomics and access to cancer trials, highlighting the underrepresentation of deprived patients, and exploring reasons for this disparity.
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Affiliation(s)
- K Sharrocks
- Department of Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, Great Maze Pond, London SE1 9RT, UK
| | - J Spicer
- Department of Medicine, King's College London, Guy's Hospital, 3rd Floor Bermondsey Wing, Great Maze Pond, London SE1 9RT, UK
| | - D R Camidge
- Developmental Therapeutics Program, University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - S Papa
- Department of Medicine, King's College London, Guy's Hospital, 3rd Floor Bermondsey Wing, Great Maze Pond, London SE1 9RT, UK
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11
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Sharrocks K, Jones CB, Naftalin C, Darling D, Fisher M, Fidler S, Fox J. Missed opportunities for identifying primary HIV within genitourinary medical/HIV services. Int J STD AIDS 2012; 23:540-3. [PMID: 22930288 DOI: 10.1258/ijsa.2012.011450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To assess the ability of three genitourinary medical centres to clinically identify primary HIV infection (PHI). Cases of recently acquired HIV infection, identified using the Health Protection Agency (HPA) avidity assay on all HIV diagnoses from January to August 2009, were investigated by case-note review. Sixty-four individuals were identified as PHI using the HPA avidity assay. Of 64 individuals, 31 (48%) were identified clinically. Imperial College identified 8/26 (31%), Guys and St Thomas' 15/27 (56%) and Brighton 8/11 (73%). Clinical suspicion of PHI was associated with reported unprotected anal intercourse (P = 0.017), seroconversion symptoms (P = 0.0004), a negative HIV test within six months (P = 0.024) and avidity assay result availability (P = 0.0169). Seventy percent of PHI cases missed had a documented risk factor. Thirty-five percent of those clinically identified with PHI were documented as informed of the associated enhanced infectivity. Suspicion of PHI was low despite documented risk factors and recent HIV-negative antibody tests. Counselling to prevent onward transmission was suboptimal.
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Affiliation(s)
- K Sharrocks
- Harrison Wing, Guys and St Thomas' Hospital, Lambeth Palace Road, London SE1 7EH
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Hodges A, Sharrocks K, Edelmann M, Baban D, Moris A, Schwartz O, Drakesmith H, Davies K, Kessler B, McMichael A, Simmons A. Activation of the lectin DC-SIGN induces an immature dendritic cell phenotype triggering Rho-GTPase activity required for HIV-1 replication. Nat Immunol 2007; 8:569-77. [PMID: 17496896 DOI: 10.1038/ni1470] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 04/18/2007] [Indexed: 12/26/2022]
Abstract
DC-SIGN, a C-type lectin expressed on dendritic cells (DCs), can sequester human immunodeficiency virus (HIV) virions in multivesicular bodies. Here, using large-scale gene expression profiling and tyrosine-phosphorylated proteome analyses, we characterized signaling mediated by DC-SIGN after activation by either HIV or a DC-SIGN-specific antibody. Activation of DC-SIGN resulted in downregulation of genes encoding major histocompatibility complex class II, Jagged 1 and interferon-response molecules and upregulation of the gene encoding transcription factor ATF3. Phosphorylated proteome analysis showed that HIV- or antibody-stimulated DC-SIGN signaling was mediated by the Rho guanine nucleotide-exchange factor LARG and led to increased Rho-GTPase activity. Activation of LARG in DCs exposed to HIV was required for the formation of virus-T cell synapses. Thus, HIV sequestration by and stimulation of DC-SIGN helps HIV evade immune responses and spread to cells.
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Affiliation(s)
- Ashleigh Hodges
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
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Simmons A, Gangadharan B, Hodges A, Sharrocks K, Prabhakar S, García A, Dwek R, Zitzmann N, McMichael A. Nef-mediated lipid raft exclusion of UbcH7 inhibits Cbl activity in T cells to positively regulate signaling. Immunity 2006; 23:621-34. [PMID: 16356860 DOI: 10.1016/j.immuni.2005.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 09/09/2005] [Accepted: 11/09/2005] [Indexed: 12/23/2022]
Abstract
Lentiviral Nef increases T cell signaling activity, but the molecular nature of the stimulus involved is incompletely described. We explored CD4 T cell lipid raft composition in the presence and absence of Nef. Here, the E2 ubiquitin-conjugating enzyme UbcH7, which acts in conjunction with c-Cbl, is absent from lipid rafts. This Nef-mediated exclusion is associated with failure of ubiquitination of activated Vav. In the presence of Nef, lipid raft Cdc42 is activated and forms a ternary complex between the c-Cbl-interacting protein p85Cool-1/betaPix and c-Cbl, displacing UbcH7 from rafts. Suppression of p85Cool-1/betaPix expression restores UbcH7 raft localization and Vav ubiquitination and diminishes Cdc42 activity. Moreover, p85Cool-1/betaPix knockdown attenuates HIV replication. Thresholds for activation of signaling involve the intricate balance of positive and negative regulators. Here we provide evidence for Nef disruption of a negative regulator of T cell signaling in promoting HIV replication.
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Affiliation(s)
- Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom.
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