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Mousa A, Cuomo-Dannenburg G, Thompson HA, Chico RM, Beshir KB, Sutherland CJ, Schellenberg D, Gosling R, Alifrangis M, Hocke EF, Hansson H, Chopo-Pizarro A, Mbacham WF, Ali IM, Chaponda M, Roper C, Okell LC. Measuring protective efficacy and quantifying the impact of drug resistance: A novel malaria chemoprevention trial design and methodology. PLoS Med 2024; 21:e1004376. [PMID: 38723040 PMCID: PMC11081503 DOI: 10.1371/journal.pmed.1004376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/14/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Recently revised WHO guidelines on malaria chemoprevention have opened the door to more tailored implementation. Countries face choices on whether to replace old drugs, target additional age groups, and adapt delivery schedules according to local drug resistance levels and malaria transmission patterns. Regular routine assessment of protective efficacy of chemoprevention is key. Here, we apply a novel modelling approach to aid the design and analysis of chemoprevention trials and generate measures of protection that can be applied across a range of transmission settings. METHODS AND FINDINGS We developed a model of genotype-specific drug protection, which accounts for underlying risk of infection and circulating genotypes. Using a Bayesian framework, we fitted the model to multiple simulated scenarios to explore variations in study design, setting, and participant characteristics. We find that a placebo or control group with no drug protection is valuable but not always feasible. An alternative approach is a single-arm trial with an extended follow-up (>42 days), which allows measurement of the underlying infection risk after drug protection wanes, as long as transmission is relatively constant. We show that the currently recommended 28-day follow-up in a single-arm trial results in low precision of estimated 30-day chemoprevention efficacy and low power in determining genotype differences of 12 days in the duration of protection (power = 1.4%). Extending follow-up to 42 days increased precision and power (71.5%) in settings with constant transmission over this time period. However, in settings of unstable transmission, protective efficacy in a single-arm trial was overestimated by 24.3% if recruitment occurred during increasing transmission and underestimated by 15.8% when recruitment occurred during declining transmission. Protective efficacy was estimated with greater precision in high transmission settings, and power to detect differences by resistance genotype was lower in scenarios where the resistant genotype was either rare or too common. CONCLUSIONS These findings have important implications for the current guidelines on chemoprevention efficacy studies and will be valuable for informing where these studies should be optimally placed. The results underscore the need for a comparator group in seasonal settings and provide evidence that the extension of follow-up in single-arm trials improves the accuracy of measures of protective efficacy in settings with more stable transmission. Extension of follow-up may pose logistical challenges to trial feasibility and associated costs. However, these studies may not need to be repeated multiple times, as the estimates of drug protection against different genotypes can be applied to different settings by adjusting for transmission intensity and frequency of resistance.
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Affiliation(s)
- Andria Mousa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Hayley A. Thompson
- Malaria and Neglected Tropical Diseases, PATH, Seattle, Washington, United States of America
| | - R. Matthew Chico
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Khalid B. Beshir
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Colin J. Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David Schellenberg
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Roly Gosling
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malaria Elimination Initiative, Institute of Global Health, University of California, San Francisco, California, United States of America
| | - Michael Alifrangis
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Emma Filtenborg Hocke
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Helle Hansson
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ana Chopo-Pizarro
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Wilfred F. Mbacham
- The Biotechnology Centre, University of Yaoundé, Yaoundé, Cameroon
- The Fobang Institutes for Innovation in Science and Technology, Yaoundé, Cameroon
- The Faculty of Northwest University, Faculty of Natural and Agricultural Sciences, Potchefstroom, South Africa
| | - Innocent M. Ali
- The Biotechnology Centre, University of Yaoundé, Yaoundé, Cameroon
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang, Cameroon
| | - Mike Chaponda
- Department of Clinical Sciences, Tropical Diseases Research Centre, Ndola, Zambia
| | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lucy C. Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
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Cuomo-Dannenburg G, McCain K, McCabe R, Unwin HJT, Doohan P, Nash RK, Hicks JT, Charniga K, Geismar C, Lambert B, Nikitin D, Skarp J, Wardle J, Kont M, Bhatia S, Imai N, van Elsland S, Cori A, Morgenstern C. Marburg virus disease outbreaks, mathematical models, and disease parameters: a systematic review. Lancet Infect Dis 2024; 24:e307-e317. [PMID: 38040006 PMCID: PMC7615873 DOI: 10.1016/s1473-3099(23)00515-7] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 12/03/2023]
Abstract
The 2023 Marburg virus disease outbreaks in Equatorial Guinea and Tanzania highlighted the importance of better understanding this lethal pathogen. We did a systematic review (PROSPERO CRD42023393345) of peer-reviewed articles reporting historical outbreaks, modelling studies, and epidemiological parameters focused on Marburg virus disease. We searched PubMed and Web of Science from database inception to March 31, 2023. Two reviewers evaluated all titles and abstracts with consensus-based decision making. To ensure agreement, 13 (31%) of 42 studies were double-extracted and a custom-designed quality assessment questionnaire was used for risk of bias assessment. We present detailed information on 478 reported cases and 385 deaths from Marburg virus disease. Analysis of historical outbreaks and seroprevalence estimates suggests the possibility of undetected Marburg virus disease outbreaks, asymptomatic transmission, or cross-reactivity with other pathogens, or a combination of these. Only one study presented a mathematical model of Marburg virus transmission. We estimate an unadjusted, pooled total random effect case fatality ratio of 61·9% (95% CI 38·8-80·6; I2=93%). We identify epidemiological parameters relating to transmission and natural history, for which there are few estimates. This systematic review and the accompanying database provide a comprehensive overview of Marburg virus disease epidemiology and identify key knowledge gaps, contributing crucial information for mathematical models to support future Marburg virus disease epidemic responses.
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Affiliation(s)
- Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Kelly McCain
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Ruth McCabe
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK; Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Patrick Doohan
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Rebecca K Nash
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Joseph T Hicks
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Kelly Charniga
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Cyril Geismar
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK
| | - Ben Lambert
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Dariya Nikitin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Janetta Skarp
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Jack Wardle
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Mara Kont
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK; Modelling and Economics Unit, UK Health Security Agency, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK; Health Protection Research Unit in Modelling and Health Economics, Imperial College London, London, UK
| | - Christian Morgenstern
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Jameel Institute, School of Public Health, Imperial College London, London, UK.
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3
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Bhatia S, Parag KV, Wardle J, Nash RK, Imai N, Elsland SLV, Lassmann B, Brownstein JS, Desai A, Herringer M, Sewalk K, Loeb SC, Ramatowski J, Cuomo-Dannenburg G, Jauneikaite E, Unwin HJT, Riley S, Ferguson N, Donnelly CA, Cori A, Nouvellet P. Retrospective evaluation of real-time estimates of global COVID-19 transmission trends and mortality forecasts. PLoS One 2023; 18:e0286199. [PMID: 37851661 PMCID: PMC10584190 DOI: 10.1371/journal.pone.0286199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/11/2023] [Indexed: 10/20/2023] Open
Abstract
Since 8th March 2020 up to the time of writing, we have been producing near real-time weekly estimates of SARS-CoV-2 transmissibility and forecasts of deaths due to COVID-19 for all countries with evidence of sustained transmission, shared online. We also developed a novel heuristic to combine weekly estimates of transmissibility to produce forecasts over a 4-week horizon. Here we present a retrospective evaluation of the forecasts produced between 8th March to 29th November 2020 for 81 countries. We evaluated the robustness of the forecasts produced in real-time using relative error, coverage probability, and comparisons with null models. During the 39-week period covered by this study, both the short- and medium-term forecasts captured well the epidemic trajectory across different waves of COVID-19 infections with small relative errors over the forecast horizon. The model was well calibrated with 56.3% and 45.6% of the observations lying in the 50% Credible Interval in 1-week and 4-week ahead forecasts respectively. The retrospective evaluation of our models shows that simple transmission models calibrated using routine disease surveillance data can reliably capture the epidemic trajectory in multiple countries. The medium-term forecasts can be used in conjunction with the short-term forecasts of COVID-19 mortality as a useful planning tool as countries continue to relax public health measures.
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Affiliation(s)
- Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- NIHR Health Protection Research Unit in Modelling and Health Economics, Modelling & Economics Unit, UK Health Security Agency, London, United Kingdom
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Jack Wardle
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Rebecca K. Nash
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Sabine L. Van Elsland
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Britta Lassmann
- ProMED-mail, International Society for Infectious Diseases, Brookline, MA, United States of America
| | - John S. Brownstein
- Boston Children’s Hospital, Computational Epidemiology Lab, Boston, MA, United States of America
| | - Angel Desai
- ProMED-mail, International Society for Infectious Diseases, Brookline, MA, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, University of California Davis, Sacramento, California, United States of America
| | - Mark Herringer
- Healthsites.io, The Global Healthsites Mapping Project, London, United Kingdom
| | - Kara Sewalk
- Boston Children’s Hospital, Computational Epidemiology Lab, Boston, MA, United States of America
| | - Sarah Claire Loeb
- ProMED-mail, International Society for Infectious Diseases, Brookline, MA, United States of America
| | - John Ramatowski
- ProMED-mail, International Society for Infectious Diseases, Brookline, MA, United States of America
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Elita Jauneikaite
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - H. Juliette T. Unwin
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Neil Ferguson
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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4
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Imai N, Gaythorpe KAM, Bhatia S, Mangal TD, Cuomo-Dannenburg G, Unwin HJT, Jauneikaite E, Ferguson NM. COVID-19 in Japan, January-March 2020: insights from the first three months of the epidemic. BMC Infect Dis 2022; 22:493. [PMID: 35614394 PMCID: PMC9130991 DOI: 10.1186/s12879-022-07469-1] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Understanding the characteristics and natural history of novel pathogens is crucial to inform successful control measures. Japan was one of the first affected countries in the COVID-19 pandemic reporting their first case on 14 January 2020. Interventions including airport screening, contact tracing, and cluster investigations were quickly implemented. Here we present insights from the first 3 months of the epidemic in Japan based on detailed case data. METHODS We conducted descriptive analyses based on information systematically extracted from individual case reports from 13 January to 31 March 2020 including patient demographics, date of report and symptom onset, symptom progression, travel history, and contact type. We analysed symptom progression and estimated the time-varying reproduction number, Rt, correcting for epidemic growth using an established Bayesian framework. Key delays and the age-specific probability of transmission were estimated using data on exposures and transmission pairs. RESULTS The corrected fitted mean onset-to-reporting delay after the peak was 4 days (standard deviation: ± 2 days). Early transmission was driven primarily by returning travellers with Rt peaking at 2.4 (95% CrI: 1.6, 3.3) nationally. In the final week of the trusted period (16-23 March 2020), Rt accounting for importations diverged from overall Rt at 1.1 (95% CrI: 1.0, 1.2) compared to 1.5 (95% CrI: 1.3, 1.6), respectively. Household (39.0%) and workplace (11.6%) exposures were the most frequently reported potential source of infection. The estimated probability of transmission was assortative by age with individuals more likely to infect, and be infected by, contacts in a similar age group to them. Across all age groups, cases most frequently onset with cough, fever, and fatigue. There were no reported cases of patients < 20 years old developing pneumonia or severe respiratory symptoms. CONCLUSIONS Information collected in the early phases of an outbreak are important in characterising any novel pathogen. The availability of timely and detailed data and appropriate analyses is critical to estimate and understand a pathogen's transmissibility, high-risk settings for transmission, and key symptoms. These insights can help to inform urgent response strategies.
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Affiliation(s)
- Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK.
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK
| | - Tara D Mangal
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK
| | - Elita Jauneikaite
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Jameel Institute, Imperial College London, London, UK
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5
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Gaythorpe KAM, Bhatia S, Mangal T, Unwin HJT, Imai N, Cuomo-Dannenburg G, Walters CE, Jauneikaite E, Bayley H, Kont MD, Mousa A, Whittles LK, Riley S, Ferguson NM. Publisher Correction: Children's role in the COVID-19 pandemic: a systematic review of early surveillance data on susceptibility, severity, and transmissibility. Sci Rep 2021; 11:18814. [PMID: 34531411 PMCID: PMC8444168 DOI: 10.1038/s41598-021-97183-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Tara Mangal
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Elita Jauneikaite
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Helena Bayley
- Department of Physics, University of Oxford, Oxford, UK
| | - Mara D Kont
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Andria Mousa
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
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6
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Gaythorpe KAM, Bhatia S, Mangal T, Unwin HJT, Imai N, Cuomo-Dannenburg G, Walters CE, Jauneikaite E, Bayley H, Kont MD, Mousa A, Whittles LK, Riley S, Ferguson NM. Children's role in the COVID-19 pandemic: a systematic review of early surveillance data on susceptibility, severity, and transmissibility. Sci Rep 2021; 11:13903. [PMID: 34230530 PMCID: PMC8260804 DOI: 10.1038/s41598-021-92500-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 12/08/2020] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 infections have been reported in all age groups including infants, children, and adolescents. However, the role of children in the COVID-19 pandemic is still uncertain. This systematic review of early studies synthesises evidence on the susceptibility of children to SARS-CoV-2 infection, the severity and clinical outcomes in children with SARS-CoV-2 infection, and the transmissibility of SARS-CoV-2 by children in the initial phases of the COVID-19 pandemic. A systematic literature review was conducted in PubMed. Reviewers extracted data from relevant, peer-reviewed studies published up to July 4th 2020 during the first wave of the SARS-CoV-2 outbreak using a standardised form and assessed quality using the NIH Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. For studies included in the meta-analysis, we used a random effects model to calculate pooled estimates of the proportion of children considered asymptomatic or in a severe or critical state. We identified 2775 potential studies of which 128 studies met our inclusion criteria; data were extracted from 99, which were then quality assessed. Finally, 29 studies were considered for the meta-analysis that included information of symptoms and/or severity, these were further assessed based on patient recruitment. Our pooled estimate of the proportion of test positive children who were asymptomatic was 21.1% (95% CI: 14.0-28.1%), based on 13 included studies, and the proportion of children with severe or critical symptoms was 3.8% (95% CI: 1.5-6.0%), based on 14 included studies. We did not identify any studies designed to assess transmissibility in children and found that susceptibility to infection in children was highly variable across studies. Children's susceptibility to infection and onward transmissibility relative to adults is still unclear and varied widely between studies. However, it is evident that most children experience clinically mild disease or remain asymptomatically infected. More comprehensive contact-tracing studies combined with serosurveys are needed to quantify children's transmissibility relative to adults. With children back in schools, testing regimes and study protocols that will allow us to better understand the role of children in this pandemic are critical.
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Affiliation(s)
- Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Tara Mangal
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Elita Jauneikaite
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Helena Bayley
- Department of Physics, University of Oxford, Oxford, UK
| | - Mara D Kont
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Andria Mousa
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis and WHO Collaborating Centre for Infectious Disease Modelling, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
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7
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Watson OJ, Alhaffar M, Mehchy Z, Whittaker C, Akil Z, Brazeau NF, Cuomo-Dannenburg G, Hamlet A, Thompson HA, Baguelin M, FitzJohn RG, Knock E, Lees JA, Whittles LK, Mellan T, Winskill P, Howard N, Clapham H, Checchi F, Ferguson N, Ghani A, Beals E, Walker P. Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria. Nat Commun 2021; 12:2394. [PMID: 33888698 PMCID: PMC8062464 DOI: 10.1038/s41467-021-22474-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/15/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic has resulted in substantial mortality worldwide. However, to date, countries in the Middle East and Africa have reported considerably lower mortality rates than in Europe and the Americas. Motivated by reports of an overwhelmed health system, we estimate the likely under-ascertainment of COVID-19 mortality in Damascus, Syria. Using all-cause mortality data, we fit a mathematical model of COVID-19 transmission to reported mortality, estimating that 1.25% of COVID-19 deaths (sensitivity range 1.00% - 3.00%) have been reported as of 2 September 2020. By 2 September, we estimate that 4,380 (95% CI: 3,250 - 5,550) COVID-19 deaths in Damascus may have been missed, with 39.0% (95% CI: 32.5% - 45.0%) of the population in Damascus estimated to have been infected. Accounting for under-ascertainment corroborates reports of exceeded hospital bed capacity and is validated by community-uploaded obituary notifications, which confirm extensive unreported mortality in Damascus.
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Affiliation(s)
- Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
| | - Mervat Alhaffar
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Zaki Mehchy
- Syria Team, Conflict Research Programme, London Schools of Economics, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Zack Akil
- Google Cloud Developer Advocacy, Google, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Natasha Howard
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Hannah Clapham
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Francesco Checchi
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Neil Ferguson
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Azra Ghani
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Emma Beals
- European Institute of Peace, Brussels, Belgium
- Middle East Institute, Washington, DC, USA
| | - Patrick Walker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
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8
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Nouvellet P, Bhatia S, Cori A, Ainslie KEC, Baguelin M, Bhatt S, Boonyasiri A, Brazeau NF, Cattarino L, Cooper LV, Coupland H, Cucunuba ZM, Cuomo-Dannenburg G, Dighe A, Djaafara BA, Dorigatti I, Eales OD, van Elsland SL, Nascimento FF, FitzJohn RG, Gaythorpe KAM, Geidelberg L, Green WD, Hamlet A, Hauck K, Hinsley W, Imai N, Jeffrey B, Knock E, Laydon DJ, Lees JA, Mangal T, Mellan TA, Nedjati-Gilani G, Parag KV, Pons-Salort M, Ragonnet-Cronin M, Riley S, Unwin HJT, Verity R, Vollmer MAC, Volz E, Walker PGT, Walters CE, Wang H, Watson OJ, Whittaker C, Whittles LK, Xi X, Ferguson NM, Donnelly CA. Reduction in mobility and COVID-19 transmission. Nat Commun 2021; 12:1090. [PMID: 33597546 PMCID: PMC7889876 DOI: 10.1038/s41467-021-21358-2] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/13/2021] [Indexed: 01/02/2023] Open
Abstract
In response to the COVID-19 pandemic, countries have sought to control SARS-CoV-2 transmission by restricting population movement through social distancing interventions, thus reducing the number of contacts. Mobility data represent an important proxy measure of social distancing, and here, we characterise the relationship between transmission and mobility for 52 countries around the world. Transmission significantly decreased with the initial reduction in mobility in 73% of the countries analysed, but we found evidence of decoupling of transmission and mobility following the relaxation of strict control measures for 80% of countries. For the majority of countries, mobility explained a substantial proportion of the variation in transmissibility (median adjusted R-squared: 48%, interquartile range - IQR - across countries [27-77%]). Where a change in the relationship occurred, predictive ability decreased after the relaxation; from a median adjusted R-squared of 74% (IQR across countries [49-91%]) pre-relaxation, to a median adjusted R-squared of 30% (IQR across countries [12-48%]) post-relaxation. In countries with a clear relationship between mobility and transmission both before and after strict control measures were relaxed, mobility was associated with lower transmission rates after control measures were relaxed indicating that the beneficial effects of ongoing social distancing behaviours were substantial.
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Affiliation(s)
- Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK.
- School of Life Sciences, University of Sussex, Brighton, UK.
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Laura V Cooper
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Zulma M Cucunuba
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Bimandra A Djaafara
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Oliver D Eales
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Fabricia F Nascimento
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Lily Geidelberg
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - William D Green
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Katharina Hauck
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Benjamin Jeffrey
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Tara Mangal
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Thomas A Mellan
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Margarita Pons-Salort
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Michaela A C Vollmer
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, London, UK.
- Department of Statistics, University of Oxford, Oxford, UK.
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9
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Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Author Correction: Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2021; 590:E11. [PMID: 33452443 PMCID: PMC7810098 DOI: 10.1038/s41586-020-2956-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
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10
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Fu H, Wang H, Xi X, Boonyasiri A, Wang Y, Hinsley W, Fraser KJ, McCabe R, Olivera Mesa D, Skarp J, Ledda A, Dewé T, Dighe A, Winskill P, van Elsland SL, Ainslie KEC, Baguelin M, Bhatt S, Boyd O, Brazeau NF, Cattarino L, Charles G, Coupland H, Cucunuba ZM, Cuomo-Dannenburg G, Donnelly CA, Dorigatti I, Eales OD, FitzJohn RG, Flaxman S, Gaythorpe KAM, Ghani AC, Green WD, Hamlet A, Hauck K, Haw DJ, Jeffrey B, Laydon DJ, Lees JA, Mellan T, Mishra S, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Ragonnet-Cronin M, Riley S, Schmit N, Thompson HA, Unwin HJT, Verity R, Vollmer MAC, Volz E, Walker PGT, Walters CE, Watson OJ, Whittaker C, Whittles LK, Imai N, Bhatia S, Ferguson NM. Database of epidemic trends and control measures during the first wave of COVID-19 in mainland China. Int J Infect Dis 2021; 102:463-471. [PMID: 33130212 PMCID: PMC7603985 DOI: 10.1016/j.ijid.2020.10.075] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES In this data collation study, we aimed to provide a comprehensive database describing the epidemic trends and responses during the first wave of coronavirus disease 2019 (COVID-19) throughout the main provinces in China. METHODS From mid-January to March 2020, we extracted publicly available data regarding the spread and control of COVID-19 from 31 provincial health authorities and major media outlets in mainland China. Based on these data, we conducted descriptive analyses of the epidemic in the six most-affected provinces. RESULTS School closures, travel restrictions, community-level lockdown, and contact tracing were introduced concurrently around late January but subsequent epidemic trends differed among provinces. Compared with Hubei, the other five most-affected provinces reported a lower crude case fatality ratio and proportion of critical and severe hospitalised cases. From March 2020, as the local transmission of COVID-19 declined, switching the focus of measures to the testing and quarantine of inbound travellers may have helped to sustain the control of the epidemic. CONCLUSIONS Aggregated indicators of case notifications and severity distributions are essential for monitoring an epidemic. A publicly available database containing these indicators and information regarding control measures is a useful resource for further research and policy planning in response to the COVID-19 epidemic.
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Affiliation(s)
- Han Fu
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Keith J Fraser
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Ruth McCabe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Daniela Olivera Mesa
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Janetta Skarp
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Alice Ledda
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Tamsin Dewé
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Giovanni Charles
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Zulma M Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Oliver D Eales
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - William D Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Katharina Hauck
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - David J Haw
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Benjamin Jeffrey
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK; School of Life Sciences, University of Sussex, Brighton, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Nora Schmit
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Michaela A C Vollmer
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
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11
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Thompson HA, Imai N, Dighe A, Ainslie KEC, Baguelin M, Bhatia S, Bhatt S, Boonyasiri A, Boyd O, Brazeau NF, Cattarino L, Cooper LV, Coupland H, Cucunuba Z, Cuomo-Dannenburg G, Djaafara B, Dorigatti I, van Elsland S, FitzJohn R, Fu H, Gaythorpe KAM, Green W, Hallett T, Hamlet A, Haw D, Hayes S, Hinsley W, Jeffrey B, Knock E, Laydon DJ, Lees J, Mangal TD, Mellan T, Mishra S, Mousa A, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Ragonnet-Cronin M, Riley S, Unwin HJT, Verity R, Vollmer M, Volz E, Walker PGT, Walters C, Wang H, Wang Y, Watson OJ, Whittaker C, Whittles LK, Winskill P, Xi X, Donnelly CA, Ferguson NM. SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China. J Travel Med 2020; 27:5896041. [PMID: 32830853 PMCID: PMC7499665 DOI: 10.1093/jtm/taaa135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 11/14/2022]
Affiliation(s)
- Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Laura V Cooper
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Bimandra Djaafara
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Richard FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Timothy Hallett
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - David Haw
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Sarah Hayes
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Benjamin Jeffrey
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - John Lees
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Tara D Mangal
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Andria Mousa
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.,School of Life Sciences, University of Sussex, Sussex, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Caroline Walters
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.,Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
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12
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Unwin HJT, Mishra S, Bradley VC, Gandy A, Mellan TA, Coupland H, Ish-Horowicz J, Vollmer MAC, Whittaker C, Filippi SL, Xi X, Monod M, Ratmann O, Hutchinson M, Valka F, Zhu H, Hawryluk I, Milton P, Ainslie KEC, Baguelin M, Boonyasiri A, Brazeau NF, Cattarino L, Cucunuba Z, Cuomo-Dannenburg G, Dorigatti I, Eales OD, Eaton JW, van Elsland SL, FitzJohn RG, Gaythorpe KAM, Green W, Hinsley W, Jeffrey B, Knock E, Laydon DJ, Lees J, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Siveroni I, Thompson HA, Walker P, Walters CE, Watson OJ, Whittles LK, Ghani AC, Ferguson NM, Riley S, Donnelly CA, Bhatt S, Flaxman S. State-level tracking of COVID-19 in the United States. Nat Commun 2020. [PMID: 33273462 DOI: 10.25561/78677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. We estimate that Rt was only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%-4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals.
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Affiliation(s)
- H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK.
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Axel Gandy
- Department of Mathematics, Imperial College, London, UK
| | - Thomas A Mellan
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Michaela A C Vollmer
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Xiaoyue Xi
- Department of Mathematics, Imperial College, London, UK
| | - Mélodie Monod
- Department of Mathematics, Imperial College, London, UK
| | | | | | | | - Harrison Zhu
- Department of Mathematics, Imperial College, London, UK
| | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Philip Milton
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Nick F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Oliver D Eales
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Jeffrey W Eaton
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - William Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Benjamin Jeffrey
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - John Lees
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Igor Siveroni
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Patrick Walker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, USA
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK.
| | - Seth Flaxman
- Department of Mathematics, Imperial College, London, UK.
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13
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Unwin HJT, Mishra S, Bradley VC, Gandy A, Mellan TA, Coupland H, Ish-Horowicz J, Vollmer MAC, Whittaker C, Filippi SL, Xi X, Monod M, Ratmann O, Hutchinson M, Valka F, Zhu H, Hawryluk I, Milton P, Ainslie KEC, Baguelin M, Boonyasiri A, Brazeau NF, Cattarino L, Cucunuba Z, Cuomo-Dannenburg G, Dorigatti I, Eales OD, Eaton JW, van Elsland SL, FitzJohn RG, Gaythorpe KAM, Green W, Hinsley W, Jeffrey B, Knock E, Laydon DJ, Lees J, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Siveroni I, Thompson HA, Walker P, Walters CE, Watson OJ, Whittles LK, Ghani AC, Ferguson NM, Riley S, Donnelly CA, Bhatt S, Flaxman S. State-level tracking of COVID-19 in the United States. Nat Commun 2020; 11:6189. [PMID: 33273462 PMCID: PMC7712910 DOI: 10.1038/s41467-020-19652-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [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: 07/15/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. We estimate that Rt was only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%-4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals.
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Affiliation(s)
- H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK.
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Axel Gandy
- Department of Mathematics, Imperial College, London, UK
| | - Thomas A Mellan
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Michaela A C Vollmer
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Xiaoyue Xi
- Department of Mathematics, Imperial College, London, UK
| | - Mélodie Monod
- Department of Mathematics, Imperial College, London, UK
| | | | | | | | - Harrison Zhu
- Department of Mathematics, Imperial College, London, UK
| | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Philip Milton
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Nick F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Oliver D Eales
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Jeffrey W Eaton
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - William Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Benjamin Jeffrey
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - John Lees
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Igor Siveroni
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Patrick Walker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, USA
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK.
| | - Seth Flaxman
- Department of Mathematics, Imperial College, London, UK.
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14
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Unwin HJT, Mishra S, Bradley VC, Gandy A, Mellan TA, Coupland H, Ish-Horowicz J, Vollmer MAC, Whittaker C, Filippi SL, Xi X, Monod M, Ratmann O, Hutchinson M, Valka F, Zhu H, Hawryluk I, Milton P, Ainslie KEC, Baguelin M, Boonyasiri A, Brazeau NF, Cattarino L, Cucunuba Z, Cuomo-Dannenburg G, Dorigatti I, Eales OD, Eaton JW, van Elsland SL, FitzJohn RG, Gaythorpe KAM, Green W, Hinsley W, Jeffrey B, Knock E, Laydon DJ, Lees J, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Siveroni I, Thompson HA, Walker P, Walters CE, Watson OJ, Whittles LK, Ghani AC, Ferguson NM, Riley S, Donnelly CA, Bhatt S, Flaxman S. State-level tracking of COVID-19 in the United States. Nat Commun 2020. [PMID: 33273462 DOI: 10.25561/79231] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly model the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We use changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. We estimate that Rt was only below one in 23 states on 1st June. We also estimate that 3.7% [3.4%-4.0%] of the total population of the US had been infected, with wide variation between states, and approximately 0.01% of the population was infectious. We demonstrate good 3 week model forecasts of deaths with low error and good coverage of our credible intervals.
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Affiliation(s)
- H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK.
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Axel Gandy
- Department of Mathematics, Imperial College, London, UK
| | - Thomas A Mellan
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Michaela A C Vollmer
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | | | - Xiaoyue Xi
- Department of Mathematics, Imperial College, London, UK
| | - Mélodie Monod
- Department of Mathematics, Imperial College, London, UK
| | | | | | | | - Harrison Zhu
- Department of Mathematics, Imperial College, London, UK
| | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Philip Milton
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Nick F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Oliver D Eales
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Jeffrey W Eaton
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - William Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Benjamin Jeffrey
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - John Lees
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Igor Siveroni
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Patrick Walker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, USA
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College, London, UK.
| | - Seth Flaxman
- Department of Mathematics, Imperial College, London, UK.
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15
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Dighe A, Cattarino L, Cuomo-Dannenburg G, Skarp J, Imai N, Bhatia S, Gaythorpe KAM, Ainslie KEC, Baguelin M, Bhatt S, Boonyasiri A, Brazeau NF, Cooper LV, Coupland H, Cucunuba Z, Dorigatti I, Eales OD, van Elsland SL, FitzJohn RG, Green WD, Haw DJ, Hinsley W, Knock E, Laydon DJ, Mellan T, Mishra S, Nedjati-Gilani G, Nouvellet P, Pons-Salort M, Thompson HA, Unwin HJT, Verity R, Vollmer MAC, Walters CE, Watson OJ, Whittaker C, Whittles LK, Ghani AC, Donnelly CA, Ferguson NM, Riley S. Response to COVID-19 in South Korea and implications for lifting stringent interventions. BMC Med 2020. [PMID: 33032601 DOI: 10.25561/79388] [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] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND After experiencing a sharp growth in COVID-19 cases early in the pandemic, South Korea rapidly controlled transmission while implementing less stringent national social distancing measures than countries in Europe and the USA. This has led to substantial interest in their "test, trace, isolate" strategy. However, it is important to understand the epidemiological peculiarities of South Korea's outbreak and characterise their response before attempting to emulate these measures elsewhere. METHODS We systematically extracted numbers of suspected cases tested, PCR-confirmed cases, deaths, isolated confirmed cases, and numbers of confirmed cases with an identified epidemiological link from publicly available data. We estimated the time-varying reproduction number, Rt, using an established Bayesian framework, and reviewed the package of interventions implemented by South Korea using our extracted data, plus published literature and government sources. RESULTS We estimated that after the initial rapid growth in cases, Rt dropped below one in early April before increasing to a maximum of 1.94 (95%CrI, 1.64-2.27) in May following outbreaks in Seoul Metropolitan Region. By mid-June, Rt was back below one where it remained until the end of our study (July 13th). Despite less stringent "lockdown" measures, strong social distancing measures were implemented in high-incidence areas and studies measured a considerable national decrease in movement in late February. Testing the capacity was swiftly increased, and protocols were in place to isolate suspected and confirmed cases quickly; however, we could not estimate the delay to isolation using our data. Accounting for just 10% of cases, individual case-based contact tracing picked up a relatively minor proportion of total cases, with cluster investigations accounting for 66%. CONCLUSIONS Whilst early adoption of testing and contact tracing is likely to be important for South Korea's successful outbreak control, other factors including regional implementation of strong social distancing measures likely also contributed. The high volume of testing and the low number of deaths suggest that South Korea experienced a small epidemic relative to other countries. Caution is needed in attempting to replicate the South Korean response in populations with larger more geographically widespread epidemics where finding, testing, and isolating cases that are linked to clusters may be more difficult.
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Affiliation(s)
- Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Janetta Skarp
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Laura V Cooper
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Oliver D Eales
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - William D Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - David J Haw
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Margarita Pons-Salort
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Michaela A C Vollmer
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, USA
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
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16
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Dighe A, Cattarino L, Cuomo-Dannenburg G, Skarp J, Imai N, Bhatia S, Gaythorpe KAM, Ainslie KEC, Baguelin M, Bhatt S, Boonyasiri A, Brazeau NF, Cooper LV, Coupland H, Cucunuba Z, Dorigatti I, Eales OD, van Elsland SL, FitzJohn RG, Green WD, Haw DJ, Hinsley W, Knock E, Laydon DJ, Mellan T, Mishra S, Nedjati-Gilani G, Nouvellet P, Pons-Salort M, Thompson HA, Unwin HJT, Verity R, Vollmer MAC, Walters CE, Watson OJ, Whittaker C, Whittles LK, Ghani AC, Donnelly CA, Ferguson NM, Riley S. Response to COVID-19 in South Korea and implications for lifting stringent interventions. BMC Med 2020; 18:321. [PMID: 33032601 PMCID: PMC7544529 DOI: 10.1186/s12916-020-01791-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [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: 06/05/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND After experiencing a sharp growth in COVID-19 cases early in the pandemic, South Korea rapidly controlled transmission while implementing less stringent national social distancing measures than countries in Europe and the USA. This has led to substantial interest in their "test, trace, isolate" strategy. However, it is important to understand the epidemiological peculiarities of South Korea's outbreak and characterise their response before attempting to emulate these measures elsewhere. METHODS We systematically extracted numbers of suspected cases tested, PCR-confirmed cases, deaths, isolated confirmed cases, and numbers of confirmed cases with an identified epidemiological link from publicly available data. We estimated the time-varying reproduction number, Rt, using an established Bayesian framework, and reviewed the package of interventions implemented by South Korea using our extracted data, plus published literature and government sources. RESULTS We estimated that after the initial rapid growth in cases, Rt dropped below one in early April before increasing to a maximum of 1.94 (95%CrI, 1.64-2.27) in May following outbreaks in Seoul Metropolitan Region. By mid-June, Rt was back below one where it remained until the end of our study (July 13th). Despite less stringent "lockdown" measures, strong social distancing measures were implemented in high-incidence areas and studies measured a considerable national decrease in movement in late February. Testing the capacity was swiftly increased, and protocols were in place to isolate suspected and confirmed cases quickly; however, we could not estimate the delay to isolation using our data. Accounting for just 10% of cases, individual case-based contact tracing picked up a relatively minor proportion of total cases, with cluster investigations accounting for 66%. CONCLUSIONS Whilst early adoption of testing and contact tracing is likely to be important for South Korea's successful outbreak control, other factors including regional implementation of strong social distancing measures likely also contributed. The high volume of testing and the low number of deaths suggest that South Korea experienced a small epidemic relative to other countries. Caution is needed in attempting to replicate the South Korean response in populations with larger more geographically widespread epidemics where finding, testing, and isolating cases that are linked to clusters may be more difficult.
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Affiliation(s)
- Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Janetta Skarp
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Laura V Cooper
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Helen Coupland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Oliver D Eales
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Richard G FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - William D Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - David J Haw
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Daniel J Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Margarita Pons-Salort
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Michaela A C Vollmer
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, USA
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.
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17
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Ainslie KEC, Walters CE, Fu H, Bhatia S, Wang H, Xi X, Baguelin M, Bhatt S, Boonyasiri A, Boyd O, Cattarino L, Ciavarella C, Cucunuba Z, Cuomo-Dannenburg G, Dighe A, Dorigatti I, van Elsland SL, FitzJohn R, Gaythorpe K, Ghani AC, Green W, Hamlet A, Hinsley W, Imai N, Jorgensen D, Knock E, Laydon D, Nedjati-Gilani G, Okell LC, Siveroni I, Thompson HA, Unwin HJT, Verity R, Vollmer M, Walker PGT, Wang Y, Watson OJ, Whittaker C, Winskill P, Donnelly CA, Ferguson NM, Riley S. Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment. Wellcome Open Res 2020; 5:81. [PMID: 32500100 PMCID: PMC7236587 DOI: 10.12688/wellcomeopenres.15843.2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [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] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 11/20/2022] Open
Abstract
Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies.
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Affiliation(s)
- Kylie E. C. Ainslie
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Caroline E. Walters
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, SW7 2AZ, UK
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Igor Siveroni
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - H. Juliette T. Unwin
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, 02912, USA
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
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18
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Hogan AB, Jewell BL, Sherrard-Smith E, Vesga JF, Watson OJ, Whittaker C, Hamlet A, Smith JA, Winskill P, Verity R, Baguelin M, Lees JA, Whittles LK, Ainslie KEC, Bhatt S, Boonyasiri A, Brazeau NF, Cattarino L, Cooper LV, Coupland H, Cuomo-Dannenburg G, Dighe A, Djaafara BA, Donnelly CA, Eaton JW, van Elsland SL, FitzJohn RG, Fu H, Gaythorpe KAM, Green W, Haw DJ, Hayes S, Hinsley W, Imai N, Laydon DJ, Mangal TD, Mellan TA, Mishra S, Nedjati-Gilani G, Parag KV, Thompson HA, Unwin HJT, Vollmer MAC, Walters CE, Wang H, Wang Y, Xi X, Ferguson NM, Okell LC, Churcher TS, Arinaminpathy N, Ghani AC, Walker PGT, Hallett TB. Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study. Lancet Glob Health 2020; 8:e1132-e1141. [PMID: 32673577 PMCID: PMC7357988 DOI: 10.1016/s2214-109x(20)30288-6] [Citation(s) in RCA: 453] [Impact Index Per Article: 113.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND COVID-19 has the potential to cause substantial disruptions to health services, due to cases overburdening the health system or response measures limiting usual programmatic activities. We aimed to quantify the extent to which disruptions to services for HIV, tuberculosis, and malaria in low-income and middle-income countries with high burdens of these diseases could lead to additional loss of life over the next 5 years. METHODS Assuming a basic reproduction number of 3·0, we constructed four scenarios for possible responses to the COVID-19 pandemic: no action, mitigation for 6 months, suppression for 2 months, or suppression for 1 year. We used established transmission models of HIV, tuberculosis, and malaria to estimate the additional impact on health that could be caused in selected settings, either due to COVID-19 interventions limiting activities, or due to the high demand on the health system due to the COVID-19 pandemic. FINDINGS In high-burden settings, deaths due to HIV, tuberculosis, and malaria over 5 years could increase by up to 10%, 20%, and 36%, respectively, compared with if there was no COVID-19 pandemic. The greatest impact on HIV was estimated to be from interruption to antiretroviral therapy, which could occur during a period of high health system demand. For tuberculosis, the greatest impact would be from reductions in timely diagnosis and treatment of new cases, which could result from any prolonged period of COVID-19 suppression interventions. The greatest impact on malaria burden could be as a result of interruption of planned net campaigns. These disruptions could lead to a loss of life-years over 5 years that is of the same order of magnitude as the direct impact from COVID-19 in places with a high burden of malaria and large HIV and tuberculosis epidemics. INTERPRETATION Maintaining the most critical prevention activities and health-care services for HIV, tuberculosis, and malaria could substantially reduce the overall impact of the COVID-19 pandemic. FUNDING Bill & Melinda Gates Foundation, Wellcome Trust, UK Department for International Development, and Medical Research Council.
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Affiliation(s)
- Alexandra B Hogan
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Britta L Jewell
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Ellie Sherrard-Smith
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Juan F Vesga
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Oliver J Watson
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Arran Hamlet
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Jennifer A Smith
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Peter Winskill
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Robert Verity
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Marc Baguelin
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - John A Lees
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Lilith K Whittles
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Kylie E C Ainslie
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Nicholas F Brazeau
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Lorenzo Cattarino
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Laura V Cooper
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Helen Coupland
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Amy Dighe
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Bimandra A Djaafara
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christl A Donnelly
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK
| | - Jeff W Eaton
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Sabine L van Elsland
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Richard G FitzJohn
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Han Fu
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Katy A M Gaythorpe
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - William Green
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - David J Haw
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Sarah Hayes
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Wes Hinsley
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Natsuko Imai
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Daniel J Laydon
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Tara D Mangal
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Thomas A Mellan
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Swapnil Mishra
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Kris V Parag
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Hayley A Thompson
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - H Juliette T Unwin
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Michaela A C Vollmer
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Caroline E Walters
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Haowei Wang
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Yuanrong Wang
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Xiaoyue Xi
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Neil M Ferguson
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Lucy C Okell
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Thomas S Churcher
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Nimalan Arinaminpathy
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Azra C Ghani
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Patrick G T Walker
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Timothy B Hallett
- Medical Research Council Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
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19
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Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2020; 584:425-429. [PMID: 32604404 DOI: 10.1038/s41586-020-2488-1] [Citation(s) in RCA: 623] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/23/2020] [Indexed: 01/12/2023]
Abstract
On 21 February 2020, a resident of the municipality of Vo', a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1-3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8-1.8%). Notably, 42.5% (95% CI: 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon-Mann-Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.
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Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
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20
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Lavezzo E, Franchin E, Ciavarella C, Cuomo-Dannenburg G, Barzon L, Del Vecchio C, Rossi L, Manganelli R, Loregian A, Navarin N, Abate D, Sciro M, Merigliano S, De Canale E, Vanuzzo MC, Besutti V, Saluzzo F, Onelia F, Pacenti M, Parisi SG, Carretta G, Donato D, Flor L, Cocchio S, Masi G, Sperduti A, Cattarino L, Salvador R, Nicoletti M, Caldart F, Castelli G, Nieddu E, Labella B, Fava L, Drigo M, Gaythorpe KAM, Brazzale AR, Toppo S, Trevisan M, Baldo V, Donnelly CA, Ferguson NM, Dorigatti I, Crisanti A. Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'. Nature 2020. [PMID: 32604404 DOI: 10.1101/2020.04.17.20053157] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
On 21 February 2020, a resident of the municipality of Vo', a small town near Padua (Italy), died of pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection1. This was the first coronavirus disease 19 (COVID-19)-related death detected in Italy since the detection of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. Here we collected information on the demography, clinical presentation, hospitalization, contact network and the presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. From the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI): 2.1-3.3%). From the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% CI: 0.8-1.8%). Notably, 42.5% (95% CI: 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (that is, did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI: 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (P = 0.62 and 0.74 for E and RdRp genes, respectively, exact Wilcoxon-Mann-Whitney test). This study sheds light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides insights into its transmission dynamics and the efficacy of the implemented control measures.
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Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Nicolò Navarin
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Davide Abate
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Francesco Onelia
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Saverio G Parisi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | - Silvia Cocchio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Giulia Masi
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Alessandro Sperduti
- Department of Mathematics "Tullio Levi-Civita", University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Renato Salvador
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | | | | | | | | | - Ludovico Fava
- School of Medicine, University of Padova, Padua, Italy
| | - Matteo Drigo
- School of Medicine, University of Padova, Padua, Italy
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marta Trevisan
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Vincenzo Baldo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padua, Italy
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
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21
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Walker PGT, Whittaker C, Watson OJ, Baguelin M, Winskill P, Hamlet A, Djafaara BA, Cucunubá Z, Olivera Mesa D, Green W, Thompson H, Nayagam S, Ainslie KEC, Bhatia S, Bhatt S, Boonyasiri A, Boyd O, Brazeau NF, Cattarino L, Cuomo-Dannenburg G, Dighe A, Donnelly CA, Dorigatti I, van Elsland SL, FitzJohn R, Fu H, Gaythorpe KAM, Geidelberg L, Grassly N, Haw D, Hayes S, Hinsley W, Imai N, Jorgensen D, Knock E, Laydon D, Mishra S, Nedjati-Gilani G, Okell LC, Unwin HJ, Verity R, Vollmer M, Walters CE, Wang H, Wang Y, Xi X, Lalloo DG, Ferguson NM, Ghani AC. The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries. Science 2020; 369:413-422. [PMID: 32532802 PMCID: PMC7292504 DOI: 10.1126/science.abc0035] [Citation(s) in RCA: 483] [Impact Index Per Article: 120.8] [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: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 12/28/2022]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic poses a severe threat to public health worldwide. We combine data on demography, contact patterns, disease severity, and health care capacity and quality to understand its impact and inform strategies for its control. Younger populations in lower-income countries may reduce overall risk, but limited health system capacity coupled with closer intergenerational contact largely negates this benefit. Mitigation strategies that slow but do not interrupt transmission will still lead to COVID-19 epidemics rapidly overwhelming health systems, with substantial excess deaths in lower-income countries resulting from the poorer health care available. Of countries that have undertaken suppression to date, lower-income countries have acted earlier. However, this will need to be maintained or triggered more frequently in these settings to keep below available health capacity, with associated detrimental consequences for the wider health, well-being, and economies of these countries.
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Affiliation(s)
- Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Bimandra A Djafaara
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniela Olivera Mesa
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Shevanthi Nayagam
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lily Geidelberg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Nicholas Grassly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - David Haw
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sarah Hayes
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - H Juliette Unwin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
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22
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Walker PGT, Whittaker C, Watson OJ, Baguelin M, Winskill P, Hamlet A, Djafaara BA, Cucunubá Z, Olivera Mesa D, Green W, Thompson H, Nayagam S, Ainslie KEC, Bhatia S, Bhatt S, Boonyasiri A, Boyd O, Brazeau NF, Cattarino L, Cuomo-Dannenburg G, Dighe A, Donnelly CA, Dorigatti I, van Elsland SL, FitzJohn R, Fu H, Gaythorpe KAM, Geidelberg L, Grassly N, Haw D, Hayes S, Hinsley W, Imai N, Jorgensen D, Knock E, Laydon D, Mishra S, Nedjati-Gilani G, Okell LC, Unwin HJ, Verity R, Vollmer M, Walters CE, Wang H, Wang Y, Xi X, Lalloo DG, Ferguson NM, Ghani AC. The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries. Science 2020; 369:413-422. [PMID: 32532802 DOI: 10.25561/77735] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 05/26/2023]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic poses a severe threat to public health worldwide. We combine data on demography, contact patterns, disease severity, and health care capacity and quality to understand its impact and inform strategies for its control. Younger populations in lower-income countries may reduce overall risk, but limited health system capacity coupled with closer intergenerational contact largely negates this benefit. Mitigation strategies that slow but do not interrupt transmission will still lead to COVID-19 epidemics rapidly overwhelming health systems, with substantial excess deaths in lower-income countries resulting from the poorer health care available. Of countries that have undertaken suppression to date, lower-income countries have acted earlier. However, this will need to be maintained or triggered more frequently in these settings to keep below available health capacity, with associated detrimental consequences for the wider health, well-being, and economies of these countries.
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Affiliation(s)
- Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Bimandra A Djafaara
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniela Olivera Mesa
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Shevanthi Nayagam
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Kylie E C Ainslie
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy A M Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lily Geidelberg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Nicholas Grassly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - David Haw
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sarah Hayes
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - H Juliette Unwin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Caroline E Walters
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
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23
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Jeffrey B, Walters CE, Ainslie KEC, Eales O, Ciavarella C, Bhatia S, Hayes S, Baguelin M, Boonyasiri A, Brazeau NF, Cuomo-Dannenburg G, FitzJohn RG, Gaythorpe K, Green W, Imai N, Mellan TA, Mishra S, Nouvellet P, Unwin HJT, Verity R, Vollmer M, Whittaker C, Ferguson NM, Donnelly CA, Riley S. Anonymised and aggregated crowd level mobility data from mobile phones suggests that initial compliance with COVID-19 social distancing interventions was high and geographically consistent across the UK. Wellcome Open Res 2020; 5:170. [PMID: 32954015 PMCID: PMC7479499 DOI: 10.12688/wellcomeopenres.15997.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
Background: Since early March 2020, the COVID-19 epidemic across the United Kingdom has led to a range of social distancing policies, which have resulted in reduced mobility across different regions. Crowd level data on mobile phone usage can be used as a proxy for actual population mobility patterns and provide a way of quantifying the impact of social distancing measures on changes in mobility. Methods: Here, we use two mobile phone-based datasets (anonymised and aggregated crowd level data from O2 and from the Facebook app on mobile phones) to assess changes in average mobility, both overall and broken down into high and low population density areas, and changes in the distribution of journey lengths. Results: We show that there was a substantial overall reduction in mobility, with the most rapid decline on the 24th March 2020, the day after the Prime Minister's announcement of an enforced lockdown. The reduction in mobility was highly synchronized across the UK. Although mobility has remained low since 26th March 2020, we detect a gradual increase since that time. We also show that the two different datasets produce similar trends, albeit with some location-specific differences. We see slightly larger reductions in average mobility in high-density areas than in low-density areas, with greater variation in mobility in the high-density areas: some high-density areas eliminated almost all mobility. Conclusions: These analyses form a baseline from which to observe changes in behaviour in the UK as social distancing is eased and inform policy towards the future control of SARS-CoV-2 in the UK.
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Affiliation(s)
- Benjamin Jeffrey
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Caroline E. Walters
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Kylie E. C. Ainslie
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Oliver Eales
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Sarah Hayes
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Nicholas F. Brazeau
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Richard G. FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - William Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Thomas A. Mellan
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
- School of Life Sciences, University of Sussex, Brighton, UK
| | - H. Juliette T. Unwin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Neil M. Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA),, Imperial College London, London, UK
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24
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Verity R, Okell LC, Dorigatti I, Winskill P, Whittaker C, Imai N, Cuomo-Dannenburg G, Thompson H, Walker PGT, Fu H, Dighe A, Griffin JT, Baguelin M, Bhatia S, Boonyasiri A, Cori A, Cucunubá Z, FitzJohn R, Gaythorpe K, Green W, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Riley S, van Elsland S, Volz E, Wang H, Wang Y, Xi X, Donnelly CA, Ghani AC, Ferguson NM. Estimates of the severity of coronavirus disease 2019: a model-based analysis. Lancet Infect Dis 2020; 20:669-677. [PMID: 32240634 PMCID: PMC7158570 DOI: 10.1016/s1473-3099(20)30243-7] [Citation(s) in RCA: 2105] [Impact Index Per Article: 526.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND In the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting for censoring and ascertainment biases. METHODS We collected individual-case data for patients who died from COVID-19 in Hubei, mainland China (reported by national and provincial health commissions to Feb 8, 2020), and for cases outside of mainland China (from government or ministry of health websites and media reports for 37 countries, as well as Hong Kong and Macau, until Feb 25, 2020). These individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. We also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland China. Using data on the prevalence of PCR-confirmed cases in international residents repatriated from China, we obtained age-stratified estimates of the infection fatality ratio. Furthermore, data on age-stratified severity in a subset of 3665 cases from China were used to estimate the proportion of infected individuals who are likely to require hospitalisation. FINDINGS Using data on 24 deaths that occurred in mainland China and 165 recoveries outside of China, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval [CrI] 16·9-19·2) and to hospital discharge to be 24·7 days (22·9-28·1). In all laboratory confirmed and clinically diagnosed cases from mainland China (n=70 117), we estimated a crude case fatality ratio (adjusted for censoring) of 3·67% (95% CrI 3·56-3·80). However, after further adjusting for demography and under-ascertainment, we obtained a best estimate of the case fatality ratio in China of 1·38% (1·23-1·53), with substantially higher ratios in older age groups (0·32% [0·27-0·38] in those aged <60 years vs 6·4% [5·7-7·2] in those aged ≥60 years), up to 13·4% (11·2-15·9) in those aged 80 years or older. Estimates of case fatality ratio from international cases stratified by age were consistent with those from China (parametric estimate 1·4% [0·4-3·5] in those aged <60 years [n=360] and 4·5% [1·8-11·1] in those aged ≥60 years [n=151]). Our estimated overall infection fatality ratio for China was 0·66% (0·39-1·33), with an increasing profile with age. Similarly, estimates of the proportion of infected individuals likely to be hospitalised increased with age up to a maximum of 18·4% (11·0-37·6) in those aged 80 years or older. INTERPRETATION These early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and show a strong age gradient in risk of death. FUNDING UK Medical Research Council.
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Affiliation(s)
- Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jamie T Griffin
- School of Mathematical Sciences, Queen Mary University of London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
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25
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Verity R, Okell LC, Dorigatti I, Winskill P, Whittaker C, Imai N, Cuomo-Dannenburg G, Thompson H, Walker PGT, Fu H, Dighe A, Griffin JT, Baguelin M, Bhatia S, Boonyasiri A, Cori A, Cucunubá Z, FitzJohn R, Gaythorpe K, Green W, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Riley S, van Elsland S, Volz E, Wang H, Wang Y, Xi X, Donnelly CA, Ghani AC, Ferguson NM. Estimates of the severity of coronavirus disease 2019: a model-based analysis. Lancet Infect Dis 2020; 20:669-677. [PMID: 32240634 DOI: 10.1101/2020.03.09.20033357] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND In the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting for censoring and ascertainment biases. METHODS We collected individual-case data for patients who died from COVID-19 in Hubei, mainland China (reported by national and provincial health commissions to Feb 8, 2020), and for cases outside of mainland China (from government or ministry of health websites and media reports for 37 countries, as well as Hong Kong and Macau, until Feb 25, 2020). These individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. We also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland China. Using data on the prevalence of PCR-confirmed cases in international residents repatriated from China, we obtained age-stratified estimates of the infection fatality ratio. Furthermore, data on age-stratified severity in a subset of 3665 cases from China were used to estimate the proportion of infected individuals who are likely to require hospitalisation. FINDINGS Using data on 24 deaths that occurred in mainland China and 165 recoveries outside of China, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval [CrI] 16·9-19·2) and to hospital discharge to be 24·7 days (22·9-28·1). In all laboratory confirmed and clinically diagnosed cases from mainland China (n=70 117), we estimated a crude case fatality ratio (adjusted for censoring) of 3·67% (95% CrI 3·56-3·80). However, after further adjusting for demography and under-ascertainment, we obtained a best estimate of the case fatality ratio in China of 1·38% (1·23-1·53), with substantially higher ratios in older age groups (0·32% [0·27-0·38] in those aged <60 years vs 6·4% [5·7-7·2] in those aged ≥60 years), up to 13·4% (11·2-15·9) in those aged 80 years or older. Estimates of case fatality ratio from international cases stratified by age were consistent with those from China (parametric estimate 1·4% [0·4-3·5] in those aged <60 years [n=360] and 4·5% [1·8-11·1] in those aged ≥60 years [n=151]). Our estimated overall infection fatality ratio for China was 0·66% (0·39-1·33), with an increasing profile with age. Similarly, estimates of the proportion of infected individuals likely to be hospitalised increased with age up to a maximum of 18·4% (11·0-37·6) in those aged 80 years or older. INTERPRETATION These early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and show a strong age gradient in risk of death. FUNDING UK Medical Research Council.
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Affiliation(s)
- Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jamie T Griffin
- School of Mathematical Sciences, Queen Mary University of London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
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26
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Verity R, Okell LC, Dorigatti I, Winskill P, Whittaker C, Imai N, Cuomo-Dannenburg G, Thompson H, Walker PGT, Fu H, Dighe A, Griffin JT, Baguelin M, Bhatia S, Boonyasiri A, Cori A, Cucunubá Z, FitzJohn R, Gaythorpe K, Green W, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Riley S, van Elsland S, Volz E, Wang H, Wang Y, Xi X, Donnelly CA, Ghani AC, Ferguson NM. Estimates of the severity of coronavirus disease 2019: a model-based analysis. Lancet Infect Dis 2020; 20:669-677. [PMID: 32240634 DOI: 10.1101/2020.03.09.20033357v1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND In the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting for censoring and ascertainment biases. METHODS We collected individual-case data for patients who died from COVID-19 in Hubei, mainland China (reported by national and provincial health commissions to Feb 8, 2020), and for cases outside of mainland China (from government or ministry of health websites and media reports for 37 countries, as well as Hong Kong and Macau, until Feb 25, 2020). These individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. We also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland China. Using data on the prevalence of PCR-confirmed cases in international residents repatriated from China, we obtained age-stratified estimates of the infection fatality ratio. Furthermore, data on age-stratified severity in a subset of 3665 cases from China were used to estimate the proportion of infected individuals who are likely to require hospitalisation. FINDINGS Using data on 24 deaths that occurred in mainland China and 165 recoveries outside of China, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval [CrI] 16·9-19·2) and to hospital discharge to be 24·7 days (22·9-28·1). In all laboratory confirmed and clinically diagnosed cases from mainland China (n=70 117), we estimated a crude case fatality ratio (adjusted for censoring) of 3·67% (95% CrI 3·56-3·80). However, after further adjusting for demography and under-ascertainment, we obtained a best estimate of the case fatality ratio in China of 1·38% (1·23-1·53), with substantially higher ratios in older age groups (0·32% [0·27-0·38] in those aged <60 years vs 6·4% [5·7-7·2] in those aged ≥60 years), up to 13·4% (11·2-15·9) in those aged 80 years or older. Estimates of case fatality ratio from international cases stratified by age were consistent with those from China (parametric estimate 1·4% [0·4-3·5] in those aged <60 years [n=360] and 4·5% [1·8-11·1] in those aged ≥60 years [n=151]). Our estimated overall infection fatality ratio for China was 0·66% (0·39-1·33), with an increasing profile with age. Similarly, estimates of the proportion of infected individuals likely to be hospitalised increased with age up to a maximum of 18·4% (11·0-37·6) in those aged 80 years or older. INTERPRETATION These early estimates give an indication of the fatality ratio across the spectrum of COVID-19 disease and show a strong age gradient in risk of death. FUNDING UK Medical Research Council.
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Affiliation(s)
- Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Jamie T Griffin
- School of Mathematical Sciences, Queen Mary University of London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Department of Statistics, University of Oxford, Oxford, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics, and Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
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Ainslie KEC, Walters CE, Fu H, Bhatia S, Wang H, Xi X, Baguelin M, Bhatt S, Boonyasiri A, Boyd O, Cattarino L, Ciavarella C, Cucunuba Z, Cuomo-Dannenburg G, Dighe A, Dorigatti I, van Elsland SL, FitzJohn R, Gaythorpe K, Ghani AC, Green W, Hamlet A, Hinsley W, Imai N, Jorgensen D, Knock E, Laydon D, Nedjati-Gilani G, Okell LC, Siveroni I, Thompson HA, Unwin HJT, Verity R, Vollmer M, Walker PGT, Wang Y, Watson OJ, Whittaker C, Winskill P, Donnelly CA, Ferguson NM, Riley S. Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment. Wellcome Open Res 2020; 5:81. [PMID: 32500100 PMCID: PMC7236587 DOI: 10.12688/wellcomeopenres.15843.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2020] [Indexed: 11/20/2022] Open
Abstract
Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies.
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Affiliation(s)
- Kylie E. C. Ainslie
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Caroline E. Walters
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, SW7 2AZ, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, SW7 2AZ, UK
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Lorenzo Cattarino
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Zulma Cucunuba
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Amy Dighe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Sabine L van Elsland
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Will Green
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Edward Knock
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Igor Siveroni
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Hayley A Thompson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - H. Juliette T. Unwin
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Michaela Vollmer
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
- Department of Laboratory Medicine and Pathology, Brown University, Providence, RI, 02912, USA
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Peter Winskill
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, W2 1PG, UK
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28
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Bhatia S, Imai N, Cuomo-Dannenburg G, Baguelin M, Boonyasiri A, Cori A, Cucunubá Z, Dorigatti I, FitzJohn R, Fu H, Gaythorpe K, Ghani A, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Okell L, Riley S, Thompson H, van Elsland S, Volz E, Wang H, Wang Y, Whittaker C, Xi X, Donnelly CA, Ferguson NM. Estimating the number of undetected COVID-19 cases among travellers from mainland China. Wellcome Open Res 2020; 5:143. [PMID: 34632083 PMCID: PMC8477353.3 DOI: 10.12688/wellcomeopenres.15805.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background: As of August 2021, every region of the world has been affected by the COVID-19 pandemic, with more than 196,000,000 cases worldwide. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries. Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that up to 70% (95% CI: 54% - 80%) of imported cases could remain undetected relative to the sensitivity of surveillance in Singapore. The percentage of undetected imported cases rises to 75% (95% CI 66% - 82%) when comparing to the surveillance sensitivity in multiple countries. Conclusions: Our analysis shows that a large number of COVID-19 cases remain undetected across the world. These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China.
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Affiliation(s)
- Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Azra Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M. Ferguson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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29
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Bhatia S, Imai N, Cuomo-Dannenburg G, Baguelin M, Boonyasiri A, Cori A, Cucunubá Z, Dorigatti I, FitzJohn R, Fu H, Gaythorpe K, Ghani A, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Okell L, Riley S, Thompson H, van Elsland S, Volz E, Wang H, Wang Y, Whittaker C, Xi X, Donnelly CA, Ferguson NM. Estimating the number of undetected COVID-19 cases among travellers from mainland China. Wellcome Open Res 2020; 5:143. [PMID: 34632083 PMCID: PMC8477353.2 DOI: 10.12688/wellcomeopenres.15805.2] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background: As of August 2021, every region of the world has been affected by the COVID-19 pandemic, with more than 196,000,000 cases worldwide. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries. Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that up to 70% (95% CI: 54% - 80%) of imported cases could remain undetected relative to the sensitivity of surveillance in Singapore. The percentage of undetected imported cases rises to 75% (95% CI 66% - 82%) when comparing to the surveillance sensitivity in multiple countries. Conclusions: Our analysis shows that a large number of COVID-19 cases remain undetected across the world. These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China.
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Affiliation(s)
- Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Azra Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M. Ferguson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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30
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Bhatia S, Imai N, Cuomo-Dannenburg G, Baguelin M, Boonyasiri A, Cori A, Cucunubá Z, Dorigatti I, FitzJohn R, Fu H, Gaythorpe K, Ghani A, Hamlet A, Hinsley W, Laydon D, Nedjati-Gilani G, Okell L, Riley S, Thompson H, van Elsland S, Volz E, Wang H, Wang Y, Whittaker C, Xi X, Donnelly CA, Ferguson NM. Estimating the number of undetected COVID-19 cases among travellers from mainland China. Wellcome Open Res 2020; 5:143. [PMID: 34632083 PMCID: PMC8477353 DOI: 10.12688/wellcomeopenres.15805.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Since the start of the COVID-19 epidemic in late 2019, there have been more than 152 affected regions and countries with over 110,000 confirmed cases outside mainland China. Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries. Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that more than two thirds (70%, 95% CI: 54% - 80%, compared to Singapore; 75%, 95% CI: 66% - 82%, compared to multiple countries) of cases exported from mainland China have remained undetected. Conclusions: These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China.
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Affiliation(s)
- Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gina Cuomo-Dannenburg
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Adhiratha Boonyasiri
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma Cucunubá
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Rich FitzJohn
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Han Fu
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Azra Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Arran Hamlet
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Wes Hinsley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Daniel Laydon
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Gemma Nedjati-Gilani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lucy Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Hayley Thompson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sabine van Elsland
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Haowei Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Yuanrong Wang
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Xiaoyue Xi
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A. Donnelly
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Neil M. Ferguson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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