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Nguyen LH, Anyane-Yeboa A, Klaser K, Merino J, Drew DA, Ma W, Mehta RS, Kim DY, Warner ET, Joshi AD, Graham MS, Sudre CH, Thompson EJ, May A, Hu C, Jørgensen S, Selvachandran S, Berry SE, David SP, Martinez ME, Figueiredo JC, Murray AM, Sanders AR, Koenen KC, Wolf J, Ourselin S, Spector TD, Steves CJ, Chan AT. The mental health burden of racial and ethnic minorities during the COVID-19 pandemic. PLoS One 2022; 17:e0271661. [PMID: 35947543 PMCID: PMC9365178 DOI: 10.1371/journal.pone.0271661] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Racial/ethnic minorities have been disproportionately impacted by COVID-19. The effects of COVID-19 on the long-term mental health of minorities remains unclear. To evaluate differences in odds of screening positive for depression and anxiety among various racial and ethnic groups during the latter phase of the COVID-19 pandemic, we performed a cross-sectional analysis of 691,473 participants nested within the prospective smartphone-based COVID Symptom Study in the United States (U.S.) and United Kingdom (U.K). from February 23, 2021 to June 9, 2021. In the U.S. (n=57,187), compared to White participants, the multivariable odds ratios (ORs) for screening positive for depression were 1·16 (95% CI: 1·02 to 1·31) for Black, 1·23 (1·11 to 1·36) for Hispanic, and 1·15 (1·02 to 1·30) for Asian participants, and 1·34 (1·13 to 1·59) for participants reporting more than one race/other even after accounting for personal factors such as prior history of a mental health disorder, COVID-19 infection status, and surrounding lockdown stringency. Rates of screening positive for anxiety were comparable. In the U.K. (n=643,286), racial/ethnic minorities had similarly elevated rates of positive screening for depression and anxiety. These disparities were not fully explained by changes in leisure time activities. Racial/ethnic minorities bore a disproportionate mental health burden during the COVID-19 pandemic. These differences will need to be considered as health care systems transition from prioritizing infection control to mitigating long-term consequences.
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Affiliation(s)
- Long H. Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Adjoa Anyane-Yeboa
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Jordi Merino
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - David A. Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Wenjie Ma
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Raaj S. Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Daniel Y. Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Erica T. Warner
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Amit D. Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Mark S. Graham
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Carole H. Sudre
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Ellen J. Thompson
- Harvard/MGH Center on Genomics, Vulnerable Populations, and Health Disparities, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | | | | | | | | | - Sarah E. Berry
- Department of Nutritional Sciences, King’s College London, London, United Kingdom
| | - Sean P. David
- Department of Family Medicine, University of Chicago, Evanston, IL, United States of America
| | - Maria Elena Martinez
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, United States of America
- Department of Family Medicine and Public Health, University of California at San Diego, La Jolla, CA, United States of America
| | - Jane C. Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Anne M. Murray
- Division of Geriatrics, Department of Medicine, Hennepin Healthcare, University of Minnesota, Minneapolis, MN, United States of America
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Minneapolis, MN, United States of America
| | - Alan R. Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL, United States of America
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, United States of America
| | - Karestan C. Koenen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | | | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health,
Boston, MA, United States of America
- Massachusetts Consortium on Pathogen Readiness, Cambridge, MA, United States of America
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Antonelli M, Penfold RS, Merino J, Sudre CH, Molteni E, Berry S, Canas LS, Graham MS, Klaser K, Modat M, Murray B, Kerfoot E, Chen L, Deng J, Österdahl MF, Cheetham NJ, Drew DA, Nguyen LH, Pujol JC, Hu C, Selvachandran S, Polidori L, May A, Wolf J, Chan AT, Hammers A, Duncan EL, Spector TD, Ourselin S, Steves CJ. Risk factors and disease profile of post-vaccination SARS-CoV-2 infection in UK users of the COVID Symptom Study app: a prospective, community-based, nested, case-control study. Lancet Infect Dis 2022; 22:43-55. [PMID: 34480857 PMCID: PMC8409907 DOI: 10.1016/s1473-3099(21)00460-6] [Citation(s) in RCA: 435] [Impact Index Per Article: 217.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND COVID-19 vaccines show excellent efficacy in clinical trials and effectiveness in real-world data, but some people still become infected with SARS-CoV-2 after vaccination. This study aimed to identify risk factors for post-vaccination SARS-CoV-2 infection and describe the characteristics of post-vaccination illness. METHODS This prospective, community-based, nested, case-control study used self-reported data (eg, on demographics, geographical location, health risk factors, and COVID-19 test results, symptoms, and vaccinations) from UK-based, adult (≥18 years) users of the COVID Symptom Study mobile phone app. For the risk factor analysis, cases had received a first or second dose of a COVID-19 vaccine between Dec 8, 2020, and July 4, 2021; had either a positive COVID-19 test at least 14 days after their first vaccination (but before their second; cases 1) or a positive test at least 7 days after their second vaccination (cases 2); and had no positive test before vaccination. Two control groups were selected (who also had not tested positive for SARS-CoV-2 before vaccination): users reporting a negative test at least 14 days after their first vaccination but before their second (controls 1) and users reporting a negative test at least 7 days after their second vaccination (controls 2). Controls 1 and controls 2 were matched (1:1) with cases 1 and cases 2, respectively, by the date of the post-vaccination test, health-care worker status, and sex. In the disease profile analysis, we sub-selected participants from cases 1 and cases 2 who had used the app for at least 14 consecutive days after testing positive for SARS-CoV-2 (cases 3 and cases 4, respectively). Controls 3 and controls 4 were unvaccinated participants reporting a positive SARS-CoV-2 test who had used the app for at least 14 consecutive days after the test, and were matched (1:1) with cases 3 and 4, respectively, by the date of the positive test, health-care worker status, sex, body-mass index (BMI), and age. We used univariate logistic regression models (adjusted for age, BMI, and sex) to analyse the associations between risk factors and post-vaccination infection, and the associations of individual symptoms, overall disease duration, and disease severity with vaccination status. FINDINGS Between Dec 8, 2020, and July 4, 2021, 1 240 009 COVID Symptom Study app users reported a first vaccine dose, of whom 6030 (0·5%) subsequently tested positive for SARS-CoV-2 (cases 1), and 971 504 reported a second dose, of whom 2370 (0·2%) subsequently tested positive for SARS-CoV-2 (cases 2). In the risk factor analysis, frailty was associated with post-vaccination infection in older adults (≥60 years) after their first vaccine dose (odds ratio [OR] 1·93, 95% CI 1·50-2·48; p<0·0001), and individuals living in highly deprived areas had increased odds of post-vaccination infection following their first vaccine dose (OR 1·11, 95% CI 1·01-1·23; p=0·039). Individuals without obesity (BMI <30 kg/m2) had lower odds of infection following their first vaccine dose (OR 0·84, 95% CI 0·75-0·94; p=0·0030). For the disease profile analysis, 3825 users from cases 1 were included in cases 3 and 906 users from cases 2 were included in cases 4. Vaccination (compared with no vaccination) was associated with reduced odds of hospitalisation or having more than five symptoms in the first week of illness following the first or second dose, and long-duration (≥28 days) symptoms following the second dose. Almost all symptoms were reported less frequently in infected vaccinated individuals than in infected unvaccinated individuals, and vaccinated participants were more likely to be completely asymptomatic, especially if they were 60 years or older. INTERPRETATION To minimise SARS-CoV-2 infection, at-risk populations must be targeted in efforts to boost vaccine effectiveness and infection control measures. Our findings might support caution around relaxing physical distancing and other personal protective measures in the post-vaccination era, particularly around frail older adults and individuals living in more deprived areas, even if these individuals are vaccinated, and might have implications for strategies such as booster vaccinations. FUNDING ZOE, the UK Government Department of Health and Social Care, the Wellcome Trust, the UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging and Artificial Intelligence Centre for Value Based Healthcare, the UK National Institute for Health Research, the UK Medical Research Council, the British Heart Foundation, and the Alzheimer's Society.
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Affiliation(s)
- Michela Antonelli
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Rose S Penfold
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jordi Merino
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Programs in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Programs in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Carole H Sudre
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; MRC Unit for Lifelong Health and Ageing at UCL, University College London, London, UK; Centre for Medical Image Computing, University College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Sarah Berry
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Liane S Canas
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Kerstin Klaser
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Eric Kerfoot
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Liyuan Chen
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Jie Deng
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Marc F Österdahl
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Nathan J Cheetham
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alexander Hammers
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; King's College London and Guy's and St Thomas' PET Centre, London, UK
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Endocrinology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK.
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3
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Klaser K, Thompson EJ, Nguyen LH, Sudre CH, Antonelli M, Murray B, Canas LS, Molteni E, Graham MS, Kerfoot E, Chen L, Deng J, May A, Hu C, Guest A, Selvachandran S, Drew DA, Modat M, Chan AT, Wolf J, Spector TD, Hammers A, Duncan EL, Ourselin S, Steves CJ. Anxiety and depression symptoms after COVID-19 infection: results from the COVID Symptom Study app. J Neurol Neurosurg Psychiatry 2021; 92:1254-1258. [PMID: 34583944 PMCID: PMC8599635 DOI: 10.1136/jnnp-2021-327565] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/07/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Mental health issues have been reported after SARS-CoV-2 infection. However, comparison to prevalence in uninfected individuals and contribution from common risk factors (eg, obesity and comorbidities) have not been examined. We identified how COVID-19 relates to mental health in the large community-based COVID Symptom Study. METHODS We assessed anxiety and depression symptoms using two validated questionnaires in 413148 individuals between February and April 2021; 26998 had tested positive for SARS-CoV-2. We adjusted for physical and mental prepandemic comorbidities, body mass index (BMI), age and sex. FINDINGS Overall, 26.4% of participants met screening criteria for general anxiety and depression. Anxiety and depression were slightly more prevalent in previously SARS-CoV-2-positive (30.4%) vs SARS-CoV-2-negative (26.1%) individuals. This association was small compared with the effect of an unhealthy BMI and the presence of other comorbidities, and not evident in younger participants (≤40 years). Findings were robust to multiple sensitivity analyses. Association between SARS-CoV-2 infection and anxiety and depression was stronger in individuals with recent (<30 days) versus more distant (>120 days) infection, suggesting a short-term effect. INTERPRETATION A small association was identified between SARS-CoV-2 infection and anxiety and depression symptoms. The proportion meeting criteria for self-reported anxiety and depression disorders is only slightly higher than prepandemic.
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Affiliation(s)
- Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Ellen J Thompson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Long H Nguyen
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts, USA
| | - Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
- Department of Medical Physics and Bioengineering, UCL Centre for Medical Image Computing (CMIC), London, UK
- MRC Unit for Lifelong Health and Ageing, Department of Population Science and Experimental Medicine, University College London, London, UK
| | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Liane S Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Eric Kerfoot
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Liyuan Chen
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Jie Deng
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | | | | | | | - David A Drew
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts, USA
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Andrew T Chan
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Alexander Hammers
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
- PET Centre, Division of Imaging Sciences and Biomedical Engineering, King's College London, London, UK
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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4
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Canas LS, Österdahl MF, Deng J, Hu C, Selvachandran S, Polidori L, May A, Molteni E, Murray B, Chen L, Kerfoot E, Klaser K, Antonelli M, Hammers A, Spector T, Ourselin S, Steves C, Sudre CH, Modat M, Duncan EL. Disentangling post-vaccination symptoms from early COVID-19. EClinicalMedicine 2021; 42:101212. [PMID: 34873584 PMCID: PMC8635464 DOI: 10.1016/j.eclinm.2021.101212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Identifying and testing individuals likely to have SARS-CoV-2 is critical for infection control, including post-vaccination. Vaccination is a major public health strategy to reduce SARS-CoV-2 infection globally. Some individuals experience systemic symptoms post-vaccination, which overlap with COVID-19 symptoms. This study compared early post-vaccination symptoms in individuals who subsequently tested positive or negative for SARS-CoV-2, using data from the COVID Symptom Study (CSS) app. METHODS We conducted a prospective observational study in 1,072,313 UK CSS participants who were asymptomatic when vaccinated with Pfizer-BioNTech mRNA vaccine (BNT162b2) or Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19) between 8 December 2020 and 17 May 2021, who subsequently reported symptoms within seven days (N=362,770) (other than local symptoms at injection site) and were tested for SARS-CoV-2 (N=14,842), aiming to differentiate vaccination side-effects per se from superimposed SARS-CoV-2 infection. The post-vaccination symptoms and SARS-CoV-2 test results were contemporaneously logged by participants. Demographic and clinical information (including comorbidities) were recorded. Symptom profiles in individuals testing positive were compared with a 1:1 matched population testing negative, including using machine learning and multiple models considering UK testing criteria. FINDINGS Differentiating post-vaccination side-effects alone from early COVID-19 was challenging, with a sensitivity in identification of individuals testing positive of 0.6 at best. Most of these individuals did not have fever, persistent cough, or anosmia/dysosmia, requisite symptoms for accessing UK testing; and many only had systemic symptoms commonly seen post-vaccination in individuals negative for SARS-CoV-2 (headache, myalgia, and fatigue). INTERPRETATION Post-vaccination symptoms per se cannot be differentiated from COVID-19 with clinical robustness, either using symptom profiles or machine-derived models. Individuals presenting with systemic symptoms post-vaccination should be tested for SARS-CoV-2 or quarantining, to prevent community spread. FUNDING UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK National Institute for Health Research, UK Medical Research Council and British Heart Foundation, Chronic Disease Research Foundation, Zoe Limited.
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Key Words
- AUC, Area under the curve
- BMI, Body mass index
- CI, Confidence interval
- COVID-19 detection
- COVID-19, Coronavirus disease 2019
- CSS, COVID Symptoms Study
- DI, Data invalid
- Early detection
- IQR, inter quartile range
- KCL, King's College London
- LFAT, Lateral flow antigen test
- LR, Logistic Regression
- Mobile technology
- NHS UK, National Health Service of the United Kingdom
- O-AZ, Oxford-AstraZeneca adenovirus-vectored vaccine
- PB, Pfizer-BoiNTech mRNA vaccine
- RF, Random forest
- ROC, Receiver operating curve
- SARS-CoV-2, Severe acute respiratory syndrome-related coronavirus-2
- Self-reported symptoms
- Side-effects
- UK, United Kingdom of Great Britain and Nothern Ireland
- Vaccination
- bMEM, Bayesian mixed-effect model
- rtPCR, Reverse transcription polymerase chain reaction
- severe acute respiratory syndrome‐related coronavirus 2 (SARS-CoV-2)
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Affiliation(s)
- Liane S. Canas
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Marc F. Österdahl
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Jie Deng
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | | | | | | | | | - Erika Molteni
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Liyuan Chen
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Eric Kerfoot
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Kerstin Klaser
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Michela Antonelli
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Alexander Hammers
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- King's College London & Guy's and St Thomas’ PET Centre, London, UK
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Claire Steves
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Carole H. Sudre
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Medical Research Council Unit for Lifelong Health and Ageing, Department of Population Science and Experimental Medicine. UK
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Emma L. Duncan
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
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5
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Murray B, Kerfoot E, Chen L, Deng J, Graham MS, Sudre CH, Molteni E, Canas LS, Antonelli M, Klaser K, Visconti A, Hammers A, Chan AT, Franks PW, Davies R, Wolf J, Spector TD, Steves CJ, Modat M, Ourselin S. Accessible data curation and analytics for international-scale citizen science datasets. Sci Data 2021; 8:297. [PMID: 34811392 PMCID: PMC8608807 DOI: 10.1038/s41597-021-01071-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/03/2020] [Accepted: 09/29/2021] [Indexed: 11/21/2022] Open
Abstract
The Covid Symptom Study, a smartphone-based surveillance study on COVID-19 symptoms in the population, is an exemplar of big data citizen science. As of May 23rd, 2021, over 5 million participants have collectively logged over 360 million self-assessment reports since its introduction in March 2020. The success of the Covid Symptom Study creates significant technical challenges around effective data curation. The primary issue is scale. The size of the dataset means that it can no longer be readily processed using standard Python-based data analytics software such as Pandas on commodity hardware. Alternative technologies exist but carry a higher technical complexity and are less accessible to many researchers. We present ExeTera, a Python-based open source software package designed to provide Pandas-like data analytics on datasets that approach terabyte scales. We present its design and capabilities, and show how it is a critical component of a data curation pipeline that enables reproducible research across an international research group for the Covid Symptom Study.
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Affiliation(s)
- Benjamin Murray
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom.
| | - Eric Kerfoot
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Liyuan Chen
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Jie Deng
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Mark S Graham
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Carole H Sudre
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
- University College London, MRC Unit for Lifelong Health and Ageing, Department of Population Health Sciences, London, WC1E 7HB, United Kingdom
- University College London, Centre for Medical Image Computing, London, WC1E 6BT, United Kingdom
| | - Erika Molteni
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Liane S Canas
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Michela Antonelli
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Kerstin Klaser
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Alessia Visconti
- King's College London, Department of Twin Research and Genetic Epidemiology, Westminster Bridge Road, London, SE1 7EH, United Kingdom
| | - Alexander Hammers
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Andrew T Chan
- Massachusetts General Hospital, 55 Fruit Street, GRJ 825C, Boston, MA, 02116, United States
| | - Paul W Franks
- Lund University, Diabetes Centre, CRC, SUS Malmö, Jan Waldenströms gata 35, House 91:12, SE-214 28, Malmö, Sweden
| | - Richard Davies
- Zoe Limited, 164 Westminster Bridge Road, London, SE1 7RW, United Kingdom
| | - Jonathan Wolf
- Zoe Limited, 164 Westminster Bridge Road, London, SE1 7RW, United Kingdom
| | - Tim D Spector
- King's College London, Department of Twin Research and Genetic Epidemiology, Westminster Bridge Road, London, SE1 7EH, United Kingdom
| | - Claire J Steves
- King's College London, Department of Twin Research and Genetic Epidemiology, Westminster Bridge Road, London, SE1 7EH, United Kingdom
| | - Marc Modat
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
| | - Sebastien Ourselin
- King's College London, School of Biomedical Engineering & Imaging Sciences, London, SE1 7EU, United Kingdom
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6
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Sudre CH, Keshet A, Graham MS, Joshi AD, Shilo S, Rossman H, Murray B, Molteni E, Klaser K, Canas LD, Antonelli M, Nguyen LH, Drew DA, Modat M, Pujol JC, Ganesh S, Wolf J, Meir T, Chan AT, Steves CJ, Spector TD, Brownstein JS, Segal E, Ourselin S, Astley CM. Anosmia, ageusia, and other COVID-19-like symptoms in association with a positive SARS-CoV-2 test, across six national digital surveillance platforms: an observational study. Lancet Digit Health 2021; 3:e577-e586. [PMID: 34305035 PMCID: PMC8297994 DOI: 10.1016/s2589-7500(21)00115-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/05/2021] [Accepted: 06/04/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Multiple voluntary surveillance platforms were developed across the world in response to the COVID-19 pandemic, providing a real-time understanding of population-based COVID-19 epidemiology. During this time, testing criteria broadened and health-care policies matured. We aimed to test whether there were consistent associations of symptoms with SARS-CoV-2 test status across three surveillance platforms in three countries (two platforms per country), during periods of testing and policy changes. METHODS For this observational study, we used data of observations from three volunteer COVID-19 digital surveillance platforms (Carnegie Mellon University and University of Maryland Facebook COVID-19 Symptom Survey, ZOE COVID Symptom Study app, and the Corona Israel study) targeting communities in three countries (Israel, the UK, and the USA; two platforms per country). The study population included adult respondents (age 18-100 years at baseline) who were not health-care workers. We did logistic regression of self-reported symptoms on self-reported SARS-CoV-2 test status (positive or negative), adjusted for age and sex, in each of the study cohorts. We compared odds ratios (ORs) across platforms and countries, and we did meta-analyses assuming a random effects model. We also evaluated testing policy changes, COVID-19 incidence, and time scales of duration of symptoms and symptom-to-test time. FINDINGS Between April 1 and July 31, 2020, 514 459 tests from over 10 million respondents were recorded in the six surveillance platform datasets. Anosmia-ageusia was the strongest, most consistent symptom associated with a positive COVID-19 test (robust aggregated rank one, meta-analysed random effects OR 16·96, 95% CI 13·13-21·92). Fever (rank two, 6·45, 4·25-9·81), shortness of breath (rank three, 4·69, 3·14-7·01), and cough (rank four, 4·29, 3·13-5·88) were also highly associated with test positivity. The association of symptoms with test status varied by duration of illness, timing of the test, and broader test criteria, as well as over time, by country, and by platform. INTERPRETATION The strong association of anosmia-ageusia with self-reported positive SARS-CoV-2 test was consistently observed, supporting its validity as a reliable COVID-19 signal, regardless of the participatory surveillance platform, country, phase of illness, or testing policy. These findings show that associations between COVID-19 symptoms and test positivity ranked similarly in a wide range of scenarios. Anosmia, fever, and respiratory symptoms consistently had the strongest effect estimates and were the most appropriate empirical signals for symptom-based public health surveillance in areas with insufficient testing or benchmarking capacity. Collaborative syndromic surveillance could enhance real-time epidemiological investigations and public health utility globally. FUNDING National Institutes of Health, National Institute for Health Research, Alzheimer's Society, Wellcome Trust, and Massachusetts Consortium on Pathogen Readiness.
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Affiliation(s)
- Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Medical Research Council Unit for Lifelong health and Ageing at UCL, Department of Population Science and Experimental Medicine, University College London, London, UK; Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK.
| | - Ayya Keshet
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mark S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Smadar Shilo
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Pediatric Diabetes Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, Haifa, Israel
| | - Hagai Rossman
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Liane D Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | | | | | - Tomer Meir
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; ZOE Global, London, UK
| | - John S Brownstein
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics and Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; AI Institute 3IA Côte d'Azur, Université Côte d'Azur, Nice, France
| | - Christina M Astley
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA; Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
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7
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Canas LS, Sudre CH, Capdevila Pujol J, Polidori L, Murray B, Molteni E, Graham MS, Klaser K, Antonelli M, Berry S, Davies R, Nguyen LH, Drew DA, Wolf J, Chan AT, Spector T, Steves CJ, Ourselin S, Modat M. Early detection of COVID-19 in the UK using self-reported symptoms: a large-scale, prospective, epidemiological surveillance study. Lancet Digit Health 2021; 3:e587-e598. [PMID: 34334333 PMCID: PMC8321433 DOI: 10.1016/s2589-7500(21)00131-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND Self-reported symptoms during the COVID-19 pandemic have been used to train artificial intelligence models to identify possible infection foci. To date, these models have only considered the culmination or peak of symptoms, which is not suitable for the early detection of infection. We aimed to estimate the probability of an individual being infected with SARS-CoV-2 on the basis of early self-reported symptoms to enable timely self-isolation and urgent testing. METHODS In this large-scale, prospective, epidemiological surveillance study, we used prospective, observational, longitudinal, self-reported data from participants in the UK on 19 symptoms over 3 days after symptoms onset and COVID-19 PCR test results extracted from the COVID-19 Symptom Study mobile phone app. We divided the study population into a training set (those who reported symptoms between April 29, 2020, and Oct 15, 2020) and a test set (those who reported symptoms between Oct 16, 2020, and Nov 30, 2020), and used three models to analyse the self-reported symptoms: the UK's National Health Service (NHS) algorithm, logistic regression, and the hierarchical Gaussian process model we designed to account for several important variables (eg, specific COVID-19 symptoms, comorbidities, and clinical information). Model performance to predict COVID-19 positivity was compared in terms of sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) in the test set. For the hierarchical Gaussian process model, we also evaluated the relevance of symptoms in the early detection of COVID-19 in population subgroups stratified according to occupation, sex, age, and body-mass index. FINDINGS The training set comprised 182 991 participants and the test set comprised 15 049 participants. When trained on 3 days of self-reported symptoms, the hierarchical Gaussian process model had a higher prediction AUC (0·80 [95% CI 0·80-0·81]) than did the logistic regression model (0·74 [0·74-0·75]) and the NHS algorithm (0·67 [0·67-0·67]). AUCs for all models increased with the number of days of self-reported symptoms, but were still high for the hierarchical Gaussian process model at day 1 (0·73 [95% CI 0·73-0·74]) and day 2 (0·79 [0·78-0·79]). At day 3, the hierarchical Gaussian process model also had a significantly higher sensitivity, but a non-statistically lower specificity, than did the two other models. The hierarchical Gaussian process model also identified different sets of relevant features to detect COVID-19 between younger and older subgroups, and between health-care workers and non-health-care workers. When used during different pandemic periods, the model was robust to changes in populations. INTERPRETATION Early detection of SARS-CoV-2 infection is feasible with our model. Such early detection is crucial to contain the spread of COVID-19 and efficiently allocate medical resources. FUNDING ZOE, the UK Government Department of Health and Social Care, the Wellcome Trust, the UK Engineering and Physical Sciences Research Council, the UK National Institute for Health Research, the UK Medical Research Council, the British Heart Foundation, the Alzheimer's Society, the Chronic Disease Research Foundation, and the Massachusetts Consortium on Pathogen Readiness.
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Affiliation(s)
- Liane S Canas
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK.
| | - Carole H Sudre
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Medical Research Council Unit for Lifelong Health and Ageing, Department of Population Science and Experimental Medicine, University College London, London, UK; Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | | | | | - Benjamin Murray
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Kerstin Klaser
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Michela Antonelli
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Sarah Berry
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
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8
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Klaser K, Thompson EJ, Nguyen LH, Sudre CH, Antonelli M, Murray B, Canas LS, Molteni E, Graham MS, Kerfoot E, Chen L, Deng J, May A, Hu C, Guest A, Selvachandran S, Drew DA, Modat M, Chan AT, Wolf J, Spector TD, Hammers A, Duncan EL, Ourselin S, Steves CJ. Anxiety and depression symptoms after COVID-19 infection: results from the COVID Symptom Study app. medRxiv 2021:2021.07.07.21260137. [PMID: 34268526 PMCID: PMC8282115 DOI: 10.1101/2021.07.07.21260137] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Mental health issues have been reported after SARS-CoV-2 infection. However, comparison to prevalence in uninfected individuals and contribution from common risk factors (e.g., obesity, comorbidities) have not been examined. We identified how COVID-19 relates to mental health in the large community-based COVID Symptom Study. METHODS We assessed anxiety and depression symptoms using two validated questionnaires in 413,148 individuals between February and April 2021; 26,998 had tested positive for SARS-CoV-2. We adjusted for physical and mental pre-pandemic comorbidities, BMI, age, and sex. FINDINGS Overall, 26.4% of participants met screening criteria for general anxiety and depression. Anxiety and depression were slightly more prevalent in previously SARS-CoV-2 positive (30.4%) vs. negative (26.1%) individuals. This association was small compared to the effect of an unhealthy BMI and the presence of other comorbidities, and not evident in younger participants (≤40 years). Findings were robust to multiple sensitivity analyses. Association between SARS-CoV-2 infection and anxiety and depression was stronger in individuals with recent (<30 days) vs. more distant (>120 days) infection, suggesting a short-term effect. INTERPRETATION A small association was identified between SARS-CoV-2 infection and anxiety and depression symptoms. The proportion meeting criteria for self-reported anxiety and depression disorders is only slightly higher than pre-pandemic. FUNDING Zoe Limited, National Institute for Health Research, Chronic Disease Research Foundation, National Institutes of Health, Medical Research Council UK.
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Affiliation(s)
- Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Ellen J Thompson
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Long H Nguyen
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, 100 Cambridge Street, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, 100 Cambridge Street, Boston, MA, USA
| | - Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
- MRC Unit for Lifelong Health and Ageing, Department of Population Science and Experimental Medicine, University College London, UK
- Centre for Medical Image Computing, Department of Computer Science, University College London, UK
| | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Liane S Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Mark S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Eric Kerfoot
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Liyuan Chen
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Jie Deng
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | | | | | | | | | - David A Drew
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, 100 Cambridge Street, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, 100 Cambridge Street, Boston, MA, USA
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Andrew T Chan
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, 100 Cambridge Street, Boston, MA, USA
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, 100 Cambridge Street, Boston, MA, USA
| | | | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Alexander Hammers
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
- King's College London & Guy's and St Thomas' PET Centre, London, UK
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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9
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Menni C, Klaser K, May A, Polidori L, Capdevila J, Louca P, Sudre CH, Nguyen LH, Drew DA, Merino J, Hu C, Selvachandran S, Antonelli M, Murray B, Canas LS, Molteni E, Graham MS, Modat M, Joshi AD, Mangino M, Hammers A, Goodman AL, Chan AT, Wolf J, Steves CJ, Valdes AM, Ourselin S, Spector TD. Vaccine side-effects and SARS-CoV-2 infection after vaccination in users of the COVID Symptom Study app in the UK: a prospective observational study. Lancet Infect Dis 2021; 21:939-949. [PMID: 33930320 PMCID: PMC8078878 DOI: 10.1016/s1473-3099(21)00224-3] [Citation(s) in RCA: 576] [Impact Index Per Article: 192.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND The Pfizer-BioNTech (BNT162b2) and the Oxford-AstraZeneca (ChAdOx1 nCoV-19) COVID-19 vaccines have shown excellent safety and efficacy in phase 3 trials. We aimed to investigate the safety and effectiveness of these vaccines in a UK community setting. METHODS In this prospective observational study, we examined the proportion and probability of self-reported systemic and local side-effects within 8 days of vaccination in individuals using the COVID Symptom Study app who received one or two doses of the BNT162b2 vaccine or one dose of the ChAdOx1 nCoV-19 vaccine. We also compared infection rates in a subset of vaccinated individuals subsequently tested for SARS-CoV-2 with PCR or lateral flow tests with infection rates in unvaccinated controls. All analyses were adjusted by age (≤55 years vs >55 years), sex, health-care worker status (binary variable), obesity (BMI <30 kg/m2vs ≥30 kg/m2), and comorbidities (binary variable, with or without comorbidities). FINDINGS Between Dec 8, and March 10, 2021, 627 383 individuals reported being vaccinated with 655 590 doses: 282 103 received one dose of BNT162b2, of whom 28 207 received a second dose, and 345 280 received one dose of ChAdOx1 nCoV-19. Systemic side-effects were reported by 13·5% (38 155 of 282 103) of individuals after the first dose of BNT162b2, by 22·0% (6216 of 28 207) after the second dose of BNT162b2, and by 33·7% (116 473 of 345 280) after the first dose of ChAdOx1 nCoV-19. Local side-effects were reported by 71·9% (150 023 of 208 767) of individuals after the first dose of BNT162b2, by 68·5% (9025 of 13 179) after the second dose of BNT162b2, and by 58·7% (104 282 of 177 655) after the first dose of ChAdOx1 nCoV-19. Systemic side-effects were more common (1·6 times after the first dose of ChAdOx1 nCoV-19 and 2·9 times after the first dose of BNT162b2) among individuals with previous SARS-CoV-2 infection than among those without known past infection. Local effects were similarly higher in individuals previously infected than in those without known past infection (1·4 times after the first dose of ChAdOx1 nCoV-19 and 1·2 times after the first dose of BNT162b2). 3106 of 103 622 vaccinated individuals and 50 340 of 464 356 unvaccinated controls tested positive for SARS-CoV-2 infection. Significant reductions in infection risk were seen starting at 12 days after the first dose, reaching 60% (95% CI 49-68) for ChAdOx1 nCoV-19 and 69% (66-72) for BNT162b2 at 21-44 days and 72% (63-79) for BNT162b2 after 45-59 days. INTERPRETATION Systemic and local side-effects after BNT162b2 and ChAdOx1 nCoV-19 vaccination occur at frequencies lower than reported in phase 3 trials. Both vaccines decrease the risk of SARS-CoV-2 infection after 12 days. FUNDING ZOE Global, National Institute for Health Research, Chronic Disease Research Foundation, National Institutes of Health, UK Medical Research Council, Wellcome Trust, UK Research and Innovation, American Gastroenterological Association.
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Affiliation(s)
- Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.
| | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | | | | | - Panayiotis Louca
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Medical Research Council Unit for Lifelong Health and Ageing, Department of Population Science and Experimental Medicine, and Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | - Long H Nguyen
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David A Drew
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jordi Merino
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | | | | | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Liane S Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Amit D Joshi
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK; National Institute for Health Research (NIHR) Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Alexander Hammers
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Anna L Goodman
- Department of Infection, Guy's and St Thomas' Foundation Trust, St Thomas Hospital, London, UK
| | - Andrew T Chan
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Ana M Valdes
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK; Nottingham NIHR Biomedical Research Centre at the School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
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10
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Sudre CH, Murray B, Varsavsky T, Graham MS, Penfold RS, Bowyer RC, Pujol JC, Klaser K, Antonelli M, Canas LS, Molteni E, Modat M, Jorge Cardoso M, May A, Ganesh S, Davies R, Nguyen LH, Drew DA, Astley CM, Joshi AD, Merino J, Tsereteli N, Fall T, Gomez MF, Duncan EL, Menni C, Williams FMK, Franks PW, Chan AT, Wolf J, Ourselin S, Spector T, Steves CJ. Author Correction: Attributes and predictors of long COVID. Nat Med 2021; 27:1116. [PMID: 34045738 DOI: 10.1038/s41591-021-01361-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK.,MRC Unit for Lifelong Health and Ageing, Department of Population Health Sciences, University College London, London, UK.,Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Thomas Varsavsky
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Rose S Penfold
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | | | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Liane S Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - M Jorge Cardoso
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | | | | | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Christina M Astley
- Division of Endocrinology & Computational Epidemiology, Boston Children's Hospital, Boston, MA, USA
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jordi Merino
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Neli Tsereteli
- Lund University Diabetes Centre, Department of Clinical Sciences, Malmö, Sweden
| | - Tove Fall
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Maria F Gomez
- Lund University Diabetes Centre, Department of Clinical Sciences, Malmö, Sweden
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Paul W Franks
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.,Lund University Diabetes Centre, Department of Clinical Sciences, Malmö, Sweden
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK.,AI Institute '3IA Côte d'Azur', Université Côte d'Azur, Nice, France
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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11
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Louca P, Murray B, Klaser K, Graham MS, Mazidi M, Leeming ER, Thompson E, Bowyer R, Drew DA, Nguyen LH, Merino J, Gomez M, Mompeo O, Costeira R, Sudre CH, Gibson R, Steves CJ, Wolf J, Franks PW, Ourselin S, Chan AT, Berry SE, Valdes AM, Calder PC, Spector TD, Menni C. Modest effects of dietary supplements during the COVID-19 pandemic: insights from 445 850 users of the COVID-19 Symptom Study app. BMJ Nutr Prev Health 2021; 4:149-157. [PMID: 34308122 PMCID: PMC8061565 DOI: 10.1136/bmjnph-2021-000250] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [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] [Received: 02/01/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Dietary supplements may ameliorate SARS-CoV-2 infection, although scientific evidence to support such a role is lacking. We investigated whether users of the COVID-19 Symptom Study app who regularly took dietary supplements were less likely to test positive for SARS-CoV-2 infection. DESIGN App-based community survey. SETTING 445 850 subscribers of an app that was launched to enable self-reported information related to SARS-CoV-2 infection for use in the general population in the UK (n=372 720), the USA (n=45 757) and Sweden (n=27 373). MAIN EXPOSURE Self-reported regular dietary supplement usage (constant use during previous 3 months) in the first waves of the pandemic up to 31 July 2020. MAIN OUTCOME MEASURES SARS-CoV-2 infection confirmed by viral RNA reverse transcriptase PCR test or serology test before 31 July 2020. RESULTS In 372 720 UK participants (175 652 supplement users and 197 068 non-users), those taking probiotics, omega-3 fatty acids, multivitamins or vitamin D had a lower risk of SARS-CoV-2 infection by 14% (95% CI (8% to 19%)), 12% (95% CI (8% to 16%)), 13% (95% CI (10% to 16%)) and 9% (95% CI (6% to 12%)), respectively, after adjusting for potential confounders. No effect was observed for those taking vitamin C, zinc or garlic supplements. On stratification by sex, age and body mass index (BMI), the protective associations in individuals taking probiotics, omega-3 fatty acids, multivitamins and vitamin D were observed in females across all ages and BMI groups, but were not seen in men. The same overall pattern of association was observed in both the US and Swedish cohorts. CONCLUSION In women, we observed a modest but significant association between use of probiotics, omega-3 fatty acid, multivitamin or vitamin D supplements and lower risk of testing positive for SARS-CoV-2. We found no clear benefits for men nor any effect of vitamin C, garlic or zinc. Randomised controlled trials are required to confirm these observational findings before any therapeutic recommendations can be made.
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Affiliation(s)
- Panayiotis Louca
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Mohsen Mazidi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Emily R Leeming
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ellen Thompson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ruth Bowyer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - David A Drew
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Long H Nguyen
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jordi Merino
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maria Gomez
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Olatz Mompeo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Carole H Sudre
- MRC Unit for Lifelong Health and Ageing at UCL, University College London, London, UK
| | - Rachel Gibson
- Department of Nutritional Sciences, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Paul W Franks
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Andrew T Chan
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Ana M Valdes
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Division of Rheumatology, Orthopaedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, Nottinghamshire, UK
| | - Philip C Calder
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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12
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Sudre CH, Murray B, Varsavsky T, Graham MS, Penfold RS, Bowyer RC, Pujol JC, Klaser K, Antonelli M, Canas LS, Molteni E, Modat M, Jorge Cardoso M, May A, Ganesh S, Davies R, Nguyen LH, Drew DA, Astley CM, Joshi AD, Merino J, Tsereteli N, Fall T, Gomez MF, Duncan EL, Menni C, Williams FMK, Franks PW, Chan AT, Wolf J, Ourselin S, Spector T, Steves CJ. Attributes and predictors of long COVID. Nat Med 2021; 27:626-631. [PMID: 33692530 DOI: 10.1038/s41591-021-01292-y] [Citation(s) in RCA: 1235] [Impact Index Per Article: 411.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/19/2021] [Indexed: 02/07/2023]
Abstract
Reports of long-lasting coronavirus disease 2019 (COVID-19) symptoms, the so-called 'long COVID', are rising but little is known about prevalence, risk factors or whether it is possible to predict a protracted course early in the disease. We analyzed data from 4,182 incident cases of COVID-19 in which individuals self-reported their symptoms prospectively in the COVID Symptom Study app1. A total of 558 (13.3%) participants reported symptoms lasting ≥28 days, 189 (4.5%) for ≥8 weeks and 95 (2.3%) for ≥12 weeks. Long COVID was characterized by symptoms of fatigue, headache, dyspnea and anosmia and was more likely with increasing age and body mass index and female sex. Experiencing more than five symptoms during the first week of illness was associated with long COVID (odds ratio = 3.53 (2.76-4.50)). A simple model to distinguish between short COVID and long COVID at 7 days (total sample size, n = 2,149) showed an area under the curve of the receiver operating characteristic curve of 76%, with replication in an independent sample of 2,472 individuals who were positive for severe acute respiratory syndrome coronavirus 2. This model could be used to identify individuals at risk of long COVID for trials of prevention or treatment and to plan education and rehabilitation services.
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Affiliation(s)
- Carole H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK.,MRC Unit for Lifelong Health and Ageing, Department of Population Health Sciences, University College London, London, UK.,Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Thomas Varsavsky
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Mark S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Rose S Penfold
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | | | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Liane S Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - M Jorge Cardoso
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | | | | | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Christina M Astley
- Division of Endocrinology & Computational Epidemiology, Boston Children's Hospital, Boston, MA, USA
| | - Amit D Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jordi Merino
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Neli Tsereteli
- Lund University Diabetes Centre, Department of Clinical Sciences, Malmö, Sweden
| | - Tove Fall
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Maria F Gomez
- Lund University Diabetes Centre, Department of Clinical Sciences, Malmö, Sweden
| | - Emma L Duncan
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Paul W Franks
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.,Lund University Diabetes Centre, Department of Clinical Sciences, Malmö, Sweden
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK.,AI Institute '3IA Côte d'Azur', Université Côte d'Azur, Nice, France
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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13
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Antonelli M, Capdevila J, Chaudhari A, Granerod J, Canas LS, Graham MS, Klaser K, Modat M, Molteni E, Murray B, Sudre CH, Davies R, May A, Nguyen LH, Drew DA, Joshi A, Chan AT, Cramer JP, Spector T, Wolf J, Ourselin S, Steves CJ, Loeliger AE. Optimal symptom combinations to aid COVID-19 case identification: Analysis from a community-based, prospective, observational cohort. J Infect 2021; 82:384-390. [PMID: 33592254 PMCID: PMC7881291 DOI: 10.1016/j.jinf.2021.02.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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] [Received: 12/17/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 01/10/2023]
Abstract
Objectives Diagnostic work-up following any COVID-19 associated symptom will lead to extensive testing, potentially overwhelming laboratory capacity whilst primarily yielding negative results. We aimed to identify optimal symptom combinations to capture most cases using fewer tests with implications for COVID-19 vaccine developers across different resource settings and public health. Methods UK and US users of the COVID-19 Symptom Study app who reported new-onset symptoms and an RT-PCR test within seven days of symptom onset were included. Sensitivity, specificity, and number of RT-PCR tests needed to identify one case (test per case [TPC]) were calculated for different symptom combinations. A multi-objective evolutionary algorithm was applied to generate combinations with optimal trade-offs between sensitivity and specificity. Findings UK and US cohorts included 122,305 (1,202 positives) and 3,162 (79 positive) individuals. Within three days of symptom onset, the COVID-19 specific symptom combination (cough, dyspnoea, fever, anosmia/ageusia) identified 69% of cases requiring 47 TPC. The combination with highest sensitivity (fatigue, anosmia/ageusia, cough, diarrhoea, headache, sore throat) identified 96% cases requiring 96 TPC. Interpretation We confirmed the significance of COVID-19 specific symptoms for triggering RT-PCR and identified additional symptom combinations with optimal trade-offs between sensitivity and specificity that maximize case capture given different resource settings.
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Affiliation(s)
- M Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | | | - A Chaudhari
- Coalition for Epidemic Preparedness Innovations, London, United Kingdom
| | - J Granerod
- Coalition for Epidemic Preparedness Innovations, London, United Kingdom
| | - L S Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | - M S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | - K Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | - M Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | - E Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | - B Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | - C H Sudre
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom; MRC Unit for Lifelong Health and Ageing at UCL/Centre for Medical Image Computing, Department of Computer Science, UCL, London, United Kingdom
| | - R Davies
- Zoe Global, London, United Kingdom
| | - A May
- Zoe Global, London, United Kingdom
| | - L H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - D A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - A Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - A T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - J P Cramer
- Coalition for Epidemic Preparedness Innovations, London, United Kingdom
| | - T Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - J Wolf
- Zoe Global, London, United Kingdom
| | - S Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom
| | - C J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom.
| | - A E Loeliger
- Coalition for Epidemic Preparedness Innovations, London, United Kingdom
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14
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Antonelli M, Capdevila J, Chaudhari A, Granerod J, Canas LS, Graham MS, Klaser K, Modat M, Molteni E, Murray B, Sudre CH, Davies R, May A, Nguyen LH, Drew DA, Joshi A, Chan AT, Cramer JP, Spector T, Wolf J, Ourselin S, Steves CJ, Loeliger AE. Optimal symptom combinations to aid COVID-19 case identification: analysis from a community-based, prospective, observational cohort. medRxiv 2021:2020.11.23.20237313. [PMID: 33269364 PMCID: PMC7709185 DOI: 10.1101/2020.11.23.20237313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Diagnostic work-up following any COVID-19 associated symptom will lead to extensive testing, potentially overwhelming laboratory capacity whilst primarily yielding negative results. We aimed to identify optimal symptom combinations to capture most cases using fewer tests with implications for COVID-19 vaccine developers across different resource settings and public health. METHODS UK and US users of the COVID-19 Symptom Study app who reported new-onset symptoms and an RT-PCR test within seven days of symptom onset were included. Sensitivity, specificity, and number of RT-PCR tests needed to identify one case (test per case [TPC]) were calculated for different symptom combinations. A multi-objective evolutionary algorithm was applied to generate combinations with optimal trade-offs between sensitivity and specificity. FINDINGS UK and US cohorts included 122,305 (1,202 positives) and 3,162 (79 positive) individuals. Within three days of symptom onset, the COVID-19 specific symptom combination (cough, dyspnoea, fever, anosmia/ageusia) identified 69% of cases requiring 47 TPC. The combination with highest sensitivity (fatigue, anosmia/ageusia, cough, diarrhoea, headache, sore throat) identified 96% cases requiring 96 TPC. INTERPRETATION We confirmed the significance of COVID-19 specific symptoms for triggering RT-PCR and identified additional symptom combinations with optimal trade-offs between sensitivity and specificity that maximize case capture given different resource settings.
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Affiliation(s)
- M Antonelli
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | - A Chaudhari
- Coalition for Epidemic Preparedness Innovations, London, UK
| | - J Granerod
- Coalition for Epidemic Preparedness Innovations, London, UK
| | - L S Canas
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - M S Graham
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - K Klaser
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - M Modat
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - E Molteni
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - B Murray
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - C H Sudre
- MRC Unit for Lifelong Health and Ageing at UCL/Centre for Medical Image Computing, Department of Computer Science, UCL, London, UK
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | | | | | - L H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - D A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - A Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - A T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - J P Cramer
- Coalition for Epidemic Preparedness Innovations, London, UK
| | - T Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - S Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - C J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - A E Loeliger
- Coalition for Epidemic Preparedness Innovations, London, UK
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15
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Sudre CH, Keshet A, Graham MS, Joshi AD, Shilo S, Rossman H, Murray B, Molteni E, Klaser K, Canas LD, Antonelli M, Modat M, Capdevila Pujol J, Ganesh S, Wolf J, Meir T, Chan AT, Steves CJ, Spector TD, Brownstein JS, Segal E, Ourselin S, Astley CM. Anosmia and other SARS-CoV-2 positive test-associated symptoms, across three national, digital surveillance platforms as the COVID-19 pandemic and response unfolded: an observation study. medRxiv 2020:2020.12.15.20248096. [PMID: 33354683 PMCID: PMC7755145 DOI: 10.1101/2020.12.15.20248096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Multiple participatory surveillance platforms were developed across the world in response to the COVID-19 pandemic, providing a real-time understanding of community-wide COVID-19 epidemiology. During this time, testing criteria broadened and healthcare policies matured. We sought to test whether there were consistent associations of symptoms with SARS-CoV-2 test status across three national surveillance platforms, during periods of testing and policy changes, and whether inconsistencies could better inform our understanding and future studies as the COVID-19 pandemic progresses. Methods Four months (1st April 2020 to 31st July 2020) of observation through three volunteer COVID-19 digital surveillance platforms targeting communities in three countries (Israel, United Kingdom, and United States). Logistic regression of self-reported symptom on self-reported SARS-CoV-2 test status (or test access), adjusted for age and sex, in each of the study cohorts. Odds ratios over time were compared to known changes in testing policies and fluctuations in COVID-19 incidence. Findings Anosmia/ageusia was the strongest, most consistent symptom associated with a positive COVID-19 test, based on 658,325 tests (5% positive) from over 10 million respondents in three digital surveillance platforms using longitudinal and cross-sectional survey methodologies. During higher-incidence periods with broader testing criteria, core COVID-19 symptoms were more strongly associated with test status. Lower incidence periods had, overall, larger confidence intervals. Interpretation The strong association of anosmia/ageusia with self-reported SARS-CoV-2 test positivity is omnipresent, supporting its validity as a reliable COVID-19 signal, regardless of the participatory surveillance platform or testing policy. This analysis highlights that precise effect estimates, as well as an understanding of test access patterns to interpret differences, are best done only when incidence is high. These findings strongly support the need for testing access to be as open as possible both for real-time epidemiologic investigation and public health utility. Funding NIH, NIHR, Alzheimer's Society, Wellcome Trust.
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Affiliation(s)
- Carole H. Sudre
- MRC Unit for Lifelong health and Ageing at UCL, Department of Population Science and Experimental Medicine, University College London, London, UK
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Ayya Keshet
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Mark S. Graham
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Amit D. Joshi
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, USA
| | - Smadar Shilo
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Pediatric Diabetes Unit, Ruth Rappaport Children’s Hospital, Rambam Healthcare Campus, Haifa, Israel
| | - Hagai Rossman
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Murray
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Erika Molteni
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Kerstin Klaser
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Liane D Canas
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Michela Antonelli
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Marc Modat
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | | | - Sajaysurya Ganesh
- Department of Twin Research and Genetic Epidemiology, King’s College London, UK
| | - Jonathan Wolf
- Department of Twin Research and Genetic Epidemiology, King’s College London, UK
| | - Tomer Meir
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, USA
| | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, UK
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, UK
- Zoe Global Limited
| | - John S. Brownstein
- Computational Epidemiology Lab, Boston Children’s Hospital, Boston, MA, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King’s College London, London, UK
| | - Christina M. Astley
- Computational Epidemiology Lab, Boston Children’s Hospital, Boston, MA, USA
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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