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Nunes MC, Thommes E, Fröhlich H, Flahault A, Arino J, Baguelin M, Biggerstaff M, Bizel-Bizellot G, Borchering R, Cacciapaglia G, Cauchemez S, Barbier--Chebbah A, Claussen C, Choirat C, Cojocaru M, Commaille-Chapus C, Hon C, Kong J, Lambert N, Lauer KB, Lehr T, Mahe C, Marechal V, Mebarki A, Moghadas S, Niehus R, Opatowski L, Parino F, Pruvost G, Schuppert A, Thiébaut R, Thomas-Bachli A, Viboud C, Wu J, Crépey P, Coudeville L. Redefining pandemic preparedness: Multidisciplinary insights from the CERP modelling workshop in infectious diseases, workshop report. Infect Dis Model 2024; 9:501-518. [PMID: 38445252 PMCID: PMC10912817 DOI: 10.1016/j.idm.2024.02.008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
In July 2023, the Center of Excellence in Respiratory Pathogens organized a two-day workshop on infectious diseases modelling and the lessons learnt from the Covid-19 pandemic. This report summarizes the rich discussions that occurred during the workshop. The workshop participants discussed multisource data integration and highlighted the benefits of combining traditional surveillance with more novel data sources like mobility data, social media, and wastewater monitoring. Significant advancements were noted in the development of predictive models, with examples from various countries showcasing the use of machine learning and artificial intelligence in detecting and monitoring disease trends. The role of open collaboration between various stakeholders in modelling was stressed, advocating for the continuation of such partnerships beyond the pandemic. A major gap identified was the absence of a common international framework for data sharing, which is crucial for global pandemic preparedness. Overall, the workshop underscored the need for robust, adaptable modelling frameworks and the integration of different data sources and collaboration across sectors, as key elements in enhancing future pandemic response and preparedness.
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Affiliation(s)
- Marta C. Nunes
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon (HCL) and Centre International de Recherche en Infectiologie (CIRI), Équipe Santé Publique, Épidémiologie et Écologie Évolutive des Maladies Infectieuses (PHE3ID), Inserm U1111, CNRS UMR5308, ENS de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Edward Thommes
- New Products and Innovation (NPI), Sanofi Vaccines (Global), Toronto, Ontario, Canada
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department of Bioinformatics, Schloss Birlinghoven, Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT (b-it), Bonn, Germany
| | - Antoine Flahault
- Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland and Swiss School of Public Health, Zürich, Switzerland
| | - Julien Arino
- Department of Mathematics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Matthew Biggerstaff
- National Center for Immunization and Respiratory Diseases (NCIRD), US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Gaston Bizel-Bizellot
- Departement of Computational Biology, Departement of Global Health, Institut Pasteur, Paris, France
| | - Rebecca Borchering
- National Center for Immunization and Respiratory Diseases (NCIRD), US Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Giacomo Cacciapaglia
- Institut de Physique des Deux Infinis de Lyon (IP2I), UMR5822, IN2P3/CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000 CNRS, Paris, France
| | - Alex Barbier--Chebbah
- Decision and Bayesian Computation, Institut Pasteur, Université Paris Cité, CNRS UMR 3571, France
| | - Carsten Claussen
- Fraunhofer-Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Christine Choirat
- Institute of Global Health, Faculty of Medicine, University of Geneva, Switzerland
| | - Monica Cojocaru
- Mathematics & Statistics Department, College of Engineering and Physical Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Chitin Hon
- Respiratory Disease AI Laboratory on Epidemic Intelligence and Medical Big Data Instrument Applications, Department of Engineering Science, Faculty of Innovation Engineering, Macau University of Science and Technology, Taipa, Macau, China
| | - Jude Kong
- Africa-Canada Artificial Intelligence and Data Innovation Consortium (ACADIC), Global South Artificial Intelligence for Pandemic and Epidemic Preparedness and Response Network (AI4PEP), Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada
| | | | | | - Thorsten Lehr
- Clinical Pharmacy, Saarland University, Saarbrücken, Germany
| | | | - Vincent Marechal
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, Paris, France
| | | | - Seyed Moghadas
- Agent-Based Modelling Laboratory, York University, Toronto, Ontario, Canada
| | - Rene Niehus
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Lulla Opatowski
- UMR 1018, Team “Anti-infective Evasion and Pharmacoepidemiology”, Université Paris-Saclay, UVSQ, INSERM, France
- Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur, Université Paris Cité, Paris, France
| | - Francesco Parino
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | | | - Andreas Schuppert
- Institute for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Rodolphe Thiébaut
- Bordeaux University, Department of Public Health, Inserm UMR 1219 Bordeaux Population Health Research Center, Inria SISTM, Bordeaux, France
| | | | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Jianhong Wu
- York Emergency Mitigation, Engagement, Response, and Governance Institute, Laboratory for Industrial and Applied Mathematics, York University, Toronto, Ontario, Canada
| | - Pascal Crépey
- EHESP, Université de Rennes, CNRS, IEP Rennes, Arènes - UMR 6051, RSMS – Inserm U 1309, Rennes, France
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2
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Cohen LE, Hansen CL, Andrew MK, McNeil SA, Vanhems P, Kyncl J, Domingo JD, Zhang T, Dbaibo G, Laguna-Torres VA, Draganescu A, Baumeister E, Gomez D, Raboni SM, Giamberardino HIG, Nunes MC, Burtseva E, Sominina A, Medić S, Coulibaly D, Salah AB, Otieno NA, Koul PA, Unal S, Tanriover MD, Mazur M, Bresee J, Viboud C, Chaves SS. Predictors of Severity of Influenza-Related Hospitalizations: Results From the Global Influenza Hospital Surveillance Network (GIHSN). J Infect Dis 2024; 229:999-1009. [PMID: 37527470 PMCID: PMC11011157 DOI: 10.1093/infdis/jiad303] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 07/13/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND The Global Influenza Hospital Surveillance Network (GIHSN) has since 2012 provided patient-level data on severe influenza-like-illnesses from >100 participating clinical sites worldwide based on a core protocol and consistent case definitions. METHODS We used multivariable logistic regression to assess the risk of intensive care unit admission, mechanical ventilation, and in-hospital death among hospitalized patients with influenza and explored the role of patient-level covariates and country income level. RESULTS The data set included 73 121 patients hospitalized with respiratory illness in 22 countries, including 15 660 with laboratory-confirmed influenza. After adjusting for patient-level covariates we found a 7-fold increase in the risk of influenza-related intensive care unit admission in lower middle-income countries (LMICs), compared with high-income countries (P = .01). The risk of mechanical ventilation and in-hospital death also increased by 4-fold in LMICs, though these differences were not statistically significant. We also find that influenza mortality increased significantly with older age and number of comorbid conditions. Across all severity outcomes studied and after controlling for patient characteristics, infection with influenza A/H1N1pdm09 was more severe than with A/H3N2. CONCLUSIONS Our study provides new information on influenza severity in underresourced populations, particularly those in LMICs.
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Affiliation(s)
- Lily E Cohen
- Ready2Respond p/o The Task Force for Global Health, Decatur, Georgia, USA
- Department of Medical Education, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chelsea L Hansen
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
- Brotman Baty Institute, University of Washington, Seattle, Washington, USA
- PandemiX Center, Department of Science & Environment, Roskilde University, Denmark
| | - Melissa K Andrew
- Canadian Center for Vaccinology, IWK Health Centre and Nova Scotia Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shelly A McNeil
- Canadian Center for Vaccinology, IWK Health Centre and Nova Scotia Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Jan Kyncl
- Department of Infectious Diseases Epidemiology, National Institute of Public Health, Prague, Czech Republic
- Department of Epidemiology and Biostatistics, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Javier Díez Domingo
- Fundación Para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO–Public Health), Valencia, Spain
| | - Tao Zhang
- School of Public Health, Fudan University, Shanghai, China
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | | | - Anca Draganescu
- National Institute for Infectious Diseases “Prof Dr Matei Bals”, Bucharest, Romania
| | - Elsa Baumeister
- Respiratory Virus Laboratory, Virology Department, INEI-ANLIS, Buenos Aires, Argentina
| | - Doris Gomez
- Grupo de Investigación UNIMOL, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias, Colombia
| | - Sonia M Raboni
- Virology Laboratory, Infectious Diseases Division, Universidade Federal do Paraná, Hospital Pequeno Principe, Curitiba, Paraná, Brazil
| | - Heloisa I G Giamberardino
- Virology Laboratory, Infectious Diseases Division, Universidade Federal do Paraná, Hospital Pequeno Principe, Curitiba, Paraná, Brazil
| | - Marta C Nunes
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Elena Burtseva
- Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Anna Sominina
- Smorodintsev Research Institute of Influenza, St Petersburg, Russia
| | - Snežana Medić
- Institute for Public Health of Vojvodina, Novi Sad, Serbia
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | | | - Afif Ben Salah
- Institut Pasteur de Tunis, Tunis, Tunisia
- Arabian Gulf University, Manama, Bahrain
| | - Nancy A Otieno
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Parvaiz A Koul
- Sheri Kashmir Institute of Medical Sciences, Srinagar, India
| | - Serhat Unal
- Department of Infectious Diseases and Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
- Turkish Society of Internal Medicine, Ankara, Turkey
| | - Mine Durusu Tanriover
- Turkish Society of Internal Medicine, Ankara, Turkey
- Department of Internal Medicine, Hacettepe University School of Medicine, Ankara, Turkey
| | - Marie Mazur
- Ready2Respond p/o The Task Force for Global Health, Decatur, Georgia, USA
| | - Joseph Bresee
- Ready2Respond p/o The Task Force for Global Health, Decatur, Georgia, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Sandra S Chaves
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
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Bay C, St-Onge G, Davis JT, Chinazzi M, Howerton E, Lessler J, Runge MC, Shea K, Truelove S, Viboud C, Vespignani A. Ensemble 2: Scenarios ensembling for communication and performance analysis. Epidemics 2024; 46:100748. [PMID: 38394928 DOI: 10.1016/j.epidem.2024.100748] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/19/2023] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Throughout the COVID-19 pandemic, scenario modeling played a crucial role in shaping the decision-making process of public health policies. Unlike forecasts, scenario projections rely on specific assumptions about the future that consider different plausible states-of-the-world that may or may not be realized and that depend on policy interventions, unpredictable changes in the epidemic outlook, etc. As a consequence, long-term scenario projections require different evaluation criteria than the ones used for traditional short-term epidemic forecasts. Here, we propose a novel ensemble procedure for assessing pandemic scenario projections using the results of the Scenario Modeling Hub (SMH) for COVID-19 in the United States (US). By defining a "scenario ensemble" for each model and the ensemble of models, termed "Ensemble2", we provide a synthesis of potential epidemic outcomes, which we use to assess projections' performance, bypassing the identification of the most plausible scenario. We find that overall the Ensemble2 models are well-calibrated and provide better performance than the scenario ensemble of individual models. The ensemble procedure accounts for the full range of plausible outcomes and highlights the importance of scenario design and effective communication. The scenario ensembling approach can be extended to any scenario design strategy, with potential refinements including weighting scenarios and allowing the ensembling process to evolve over time.
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Affiliation(s)
- Clara Bay
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Network Science Institute, Boston, MA, USA
| | - Guillaume St-Onge
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Network Science Institute, Boston, MA, USA
| | - Jessica T Davis
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Network Science Institute, Boston, MA, USA
| | - Matteo Chinazzi
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Network Science Institute, Boston, MA, USA; The Roux Institute, Northeastern University, Portland, ME, USA
| | - Emily Howerton
- Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
| | - Justin Lessler
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC, USA; Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA; Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Michael C Runge
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, USA
| | - Katriona Shea
- Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
| | - Shaun Truelove
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Network Science Institute, Boston, MA, USA; The Roux Institute, Northeastern University, Portland, ME, USA.
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4
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Eales O, Plank MJ, Cowling BJ, Howden BP, Kucharski AJ, Sullivan SG, Vandemaele K, Viboud C, Riley S, McCaw JM, Shearer FM. Key Challenges for Respiratory Virus Surveillance while Transitioning out of Acute Phase of COVID-19 Pandemic. Emerg Infect Dis 2024; 30:e230768. [PMID: 38190760 PMCID: PMC10826770 DOI: 10.3201/eid3002.230768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
To support the ongoing management of viral respiratory diseases while transitioning out of the acute phase of the COVID-19 pandemic, many countries are moving toward an integrated model of surveillance for SARS-CoV-2, influenza virus, and other respiratory pathogens. Although many surveillance approaches catalyzed by the COVID-19 pandemic provide novel epidemiologic insight, continuing them as implemented during the pandemic is unlikely to be feasible for nonemergency surveillance, and many have already been scaled back. Furthermore, given anticipated cocirculation of SARS-CoV-2 and influenza virus, surveillance activities in place before the pandemic require review and adjustment to ensure their ongoing value for public health. In this report, we highlight key challenges for the development of integrated models of surveillance. We discuss the relative strengths and limitations of different surveillance practices and studies as well as their contribution to epidemiologic assessment, forecasting, and public health decision-making.
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5
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Pollett S, Johansson MA, Reich NG, Brett-Major D, Del Valle SY, Venkatramanan S, Lowe R, Porco T, Berry IM, Deshpande A, Kraemer MUG, Blazes DL, Pan-Ngum W, Vespigiani A, Mate SE, Silal SP, Kandula S, Sippy R, Quandelacy TM, Morgan JJ, Ball J, Morton LC, Althouse BM, Pavlin J, van Panhuis W, Riley S, Biggerstaff M, Viboud C, Brady O, Rivers C. Correction: Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines. PLoS Med 2023; 20:e1004316. [PMID: 37976465 PMCID: PMC10656116 DOI: 10.1371/journal.pmed.1004316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pmed.1003793.].
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6
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Bingham J, Tempia S, Moultrie H, Viboud C, Jassat W, Cohen C, Pulliam JR. Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves. PLoS One 2023; 18:e0287026. [PMID: 37738280 PMCID: PMC10516415 DOI: 10.1371/journal.pone.0287026] [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: 09/02/2022] [Accepted: 05/30/2023] [Indexed: 09/24/2023] Open
Abstract
OBJECTIVES The aim of this study was to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources, and using data from public and private sector service providers. METHODS R was estimated from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalisations, and hospital-associated deaths, using a method that models daily incidence as a weighted sum of past incidence, as implemented in the R package EpiEstim. R was also estimated separately using public and private sector data. RESULTS Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43-1.66), 1.56 (CI: 1.47-1.64), 1.46 (CI: 1.38-1.53) and 3.33 (CI: 2.84-3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves, respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves, but higher during the fourth wave for case-based estimates. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave. CONCLUSION Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. The high R estimates for Omicron relative to earlier waves are interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
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Affiliation(s)
- Jeremy Bingham
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Harry Moultrie
- Division of the National Health Laboratory Service, Centre for Tuberculosis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cecile Viboud
- Fogarty International Center, NIH, Bethesda, MD, United States of America
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliet R.C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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7
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Park SW, Sun K, Abbott S, Sender R, Bar-On YM, Weitz JS, Funk S, Grenfell BT, Backer JA, Wallinga J, Viboud C, Dushoff J. Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2221887120. [PMID: 37216529 DOI: 10.1073/pnas.2221887120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/20/2023] [Indexed: 05/24/2023] Open
Abstract
Estimating the differences in the incubation-period, serial-interval, and generation-interval distributions of SARS-CoV-2 variants is critical to understanding their transmission. However, the impact of epidemic dynamics is often neglected in estimating the timing of infection-for example, when an epidemic is growing exponentially, a cohort of infected individuals who developed symptoms at the same time are more likely to have been infected recently. Here, we reanalyze incubation-period and serial-interval data describing transmissions of the Delta and Omicron variants from the Netherlands at the end of December 2021. Previous analysis of the same dataset reported shorter mean observed incubation period (3.2 d vs. 4.4 d) and serial interval (3.5 d vs. 4.1 d) for the Omicron variant, but the number of infections caused by the Delta variant decreased during this period as the number of Omicron infections increased. When we account for growth-rate differences of two variants during the study period, we estimate similar mean incubation periods (3.8 to 4.5 d) for both variants but a shorter mean generation interval for the Omicron variant (3.0 d; 95% CI: 2.7 to 3.2 d) than for the Delta variant (3.8 d; 95% CI: 3.7 to 4.0 d). The differences in estimated generation intervals may be driven by the "network effect"-higher effective transmissibility of the Omicron variant can cause faster susceptible depletion among contact networks, which in turn prevents late transmission (therefore shortening realized generation intervals). Using up-to-date generation-interval distributions is critical to accurately estimating the reproduction advantage of the Omicron variant.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892
| | - Sam Abbott
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Ron Sender
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332
- Institut de Biologie, École Normale Supérieure, Paris 75005, France
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08542
| | - Jantien A Backer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 Bilthoven, The Netherlands
| | - Jacco Wallinga
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, 3720 Bilthoven, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 Leiden, The Netherlands
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, L8S 4L8 ON, Canada
- Department of Mathematics and Statistics, McMaster University, Hamilton, L8S 4L8 ON, Canada
- M. G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, L8S 4L8 ON, Canada
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8
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Shea K, Borchering RK, Probert WJM, Howerton E, Bogich TL, Li SL, van Panhuis WG, Viboud C, Aguás R, Belov AA, Bhargava SH, Cavany SM, Chang JC, Chen C, Chen J, Chen S, Chen Y, Childs LM, Chow CC, Crooker I, Del Valle SY, España G, Fairchild G, Gerkin RC, Germann TC, Gu Q, Guan X, Guo L, Hart GR, Hladish TJ, Hupert N, Janies D, Kerr CC, Klein DJ, Klein EY, Lin G, Manore C, Meyers LA, Mittler JE, Mu K, Núñez RC, Oidtman RJ, Pasco R, Pastore Y Piontti A, Paul R, Pearson CAB, Perdomo DR, Perkins TA, Pierce K, Pillai AN, Rael RC, Rosenfeld K, Ross CW, Spencer JA, Stoltzfus AB, Toh KB, Vattikuti S, Vespignani A, Wang L, White LJ, Xu P, Yang Y, Yogurtcu ON, Zhang W, Zhao Y, Zou D, Ferrari MJ, Pannell D, Tildesley MJ, Seifarth J, Johnson E, Biggerstaff M, Johansson MA, Slayton RB, Levander JD, Stazer J, Kerr J, Runge MC. Multiple models for outbreak decision support in the face of uncertainty. Proc Natl Acad Sci U S A 2023; 120:e2207537120. [PMID: 37098064 PMCID: PMC10160947 DOI: 10.1073/pnas.2207537120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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] [Indexed: 04/26/2023] Open
Abstract
Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020.
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Affiliation(s)
- Katriona Shea
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Rebecca K Borchering
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - William J M Probert
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Emily Howerton
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Tiffany L Bogich
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Shou-Li Li
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, and College of Pastoral, Agriculture Science and Technology, Lanzhou University, Lanzhou, 73000, People's Republic of China
| | - Willem G van Panhuis
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892
| | - Ricardo Aguás
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Artur A Belov
- Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993
| | | | - Sean M Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Joshua C Chang
- Epidemiology and Biostatistics Section, Rehabilitation Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892
- Mederrata Research Inc, Columbus, OH 43212
| | - Cynthia Chen
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195
| | - Jinghui Chen
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095
| | - Shi Chen
- Department of Public Health Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223
- School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223
| | - YangQuan Chen
- Mechatronics, Embedded Systems and Automation Laboratory, School of Engineering, University of California, Merced, CA 95343
| | - Lauren M Childs
- Department of Mathematics, Virginia Tech, Blacksburg, VA 24061
| | - Carson C Chow
- Mathematical Biology Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | | | | | - Guido España
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | | | - Richard C Gerkin
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | | | - Quanquan Gu
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095
| | - Xiangyang Guan
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195
| | - Lihong Guo
- School of Mathematics, Jilin University, Changchun, Jilin 130012, People's Republic of China
| | - Gregory R Hart
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA 98109
| | - Thomas J Hladish
- Department of Biology, University of Florida, Gainesville, FL 32611
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Nathaniel Hupert
- Department of Population Health Sciences, Division of Epidemiology, Weill Cornell Medicine, Cornell University, New York, NY 10065
| | - Daniel Janies
- Computational Intelligence to Predict Health and Environmental Risks, University of North Carolina at Charlotte, Charlotte, NC 28223
| | - Cliff C Kerr
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA 98109
| | - Daniel J Klein
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA 98109
| | - Eili Y Klein
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD 21209
- One Health Trust, Washington, DC 20015
| | - Gary Lin
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD 21209
- One Health Trust, Washington, DC 20015
| | - Carrie Manore
- Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - John E Mittler
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195
| | - Kunpeng Mu
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA 02115
| | - Rafael C Núñez
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA 98109
| | - Rachel J Oidtman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Remy Pasco
- Operations Research and Industrial Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Ana Pastore Y Piontti
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA 02115
| | - Rajib Paul
- Department of Public Health Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223
| | - Carl A B Pearson
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom
- South African Department of Science and Innovation - National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, 7600 South Africa
| | | | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Kelly Pierce
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX 78712
| | | | | | - Katherine Rosenfeld
- Institute for Disease Modeling, Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA 98109
| | | | | | - Arlin B Stoltzfus
- National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Kok Ben Toh
- School of Natural Resources and Environment, University of Florida, Gainesville, FL 32611
| | - Shashaank Vattikuti
- Mathematical Biology Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Network Science Institute, Northeastern University, Boston, MA 02115
| | - Lingxiao Wang
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095
| | - Lisa J White
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Pan Xu
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095
| | | | - Osman N Yogurtcu
- Office of Biostatistics and Pharmacovigilance, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993
| | - Weitong Zhang
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095
| | - Yanting Zhao
- The 28th Research Institute of China Technology Group Corporation, Nanjing, Jiangsu 210023, People's Republic of China
| | - Difan Zou
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095
| | - Matthew J Ferrari
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - David Pannell
- School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia
| | - Michael J Tildesley
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Jack Seifarth
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Elyse Johnson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Matthew Biggerstaff
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, GA 30329
| | - Michael A Johansson
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, GA 30329
| | - Rachel B Slayton
- Centers for Disease Control and Prevention COVID-19 Response, Atlanta, GA 30329
| | - John D Levander
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, PA 15260
| | - Jeff Stazer
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, PA 15260
| | - Jessica Kerr
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, PA 15260
| | - Michael C Runge
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD 20708
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Paget J, Staadegaard L, Wang X, Li Y, van Pomeren T, van Summeren J, Dückers M, Chaves SS, Johnson EK, Mahé C, Nair H, Viboud C, Spreeuwenberg P. Global and national influenza-associated hospitalisation rates: Estimates for 40 countries and administrative regions. J Glob Health 2023; 13:04003. [PMID: 36701368 PMCID: PMC9879557 DOI: 10.7189/jogh.13.04003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Background WHO estimates that seasonal influenza epidemics result in three to five million cases of severe illness (hospitalisations) every year. We aimed to improve the understanding of influenza-associated hospitalisation estimates at a national and global level. Methods We performed a systematic literature review of English- and Chinese-language studies published between 1995 and 2020 estimating influenza-associated hospitalisation. We included a total of 127 studies (seven in Chinese) in the meta-analysis and analyzed their data using a logit-logistic regression model to understand the influence of five study factors and produce national and global estimates by age groups. The five study factors assessed were: 1) the method used to calculate the influenza-associated hospitalisation estimates (rate- or time series regression-based), 2) the outcome measure (divided into three envelopes: narrow, medium, or wide), 3) whether every case was laboratory-confirmed or not, 4) whether the estimates were national or sub-national, 5) whether the rates were based on a single year or multiple years. Results The overall pooled influenza-associated hospitalisation rate was 40.5 (95% confidence interval (CI) = 24.3-67.4) per 100 000 persons, with rates varying substantially by age: 224.0 (95% CI = 118.8-420.0) in children aged 0-4 years and 96.8 (95% CI = 57.0-164.3) in the elderly aged >65 years. The overall pooled hospitalisation rates varied by calculation method; for all ages, the rates were significantly higher when they were based on rate-based methods or calculated on a single season and significantly lower when cases were laboratory-confirmed. The national hospitalisation rates (all ages) varied considerably, ranging from 11.7 (95% CI = 3.8-36.3) per 100 000 in New Zealand to 122.1 (95% CI = 41.5-358.4) per 100 000 in India (all age estimates). Conclusions Using the pooled global influenza-associated hospitalisation rate, we estimate that seasonal influenza epidemics result in 3.2 million cases of severe illness (hospitalisations) per annum. More extensive analyses are required to assess the influence of other factors on the estimates (e.g. vaccination and dominant virus (sub)types) and efforts to harmonize the methods should be encouraged. Our study highlights the high rates of influenza-associated hospitalisations in children aged 0-4 years and the elderly aged 65+ years.
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Affiliation(s)
- John Paget
- Netherlands Institute for Health Services Research (Nivel), Utrecht, the Netherlands
| | - Lisa Staadegaard
- Netherlands Institute for Health Services Research (Nivel), Utrecht, the Netherlands
| | - Xin Wang
- School of Public Health, Nanjing Medical University, Nanjing, China,Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - You Li
- School of Public Health, Nanjing Medical University, Nanjing, China,Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Tayma van Pomeren
- Netherlands Institute for Health Services Research (Nivel), Utrecht, the Netherlands
| | | | - Michel Dückers
- Netherlands Institute for Health Services Research (Nivel), Utrecht, the Netherlands
| | - Sandra S Chaves
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
| | - Emily K Johnson
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA
| | - Cédric Mahé
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
| | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Peter Spreeuwenberg
- Netherlands Institute for Health Services Research (Nivel), Utrecht, the Netherlands
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10
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Sun K, Loria V, Aparicio A, Porras C, Vanegas JC, Zúñiga M, Morera M, Avila C, Abdelnour A, Gail M, Pfeiffer R, Cohen J, Burbelo P, Abed M, Viboud C, Hildesheim A, Herrero R, Prevots DR. Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica. Res Sq 2022:rs.3.rs-2065331. [PMID: 36172128 PMCID: PMC9516868 DOI: 10.21203/rs.3.rs-2065331/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Variability in household secondary attack rates (SAR) and transmission risks factors of SARS-CoV-2 remain poorly understood. To characterize SARS-CoV-2 transmission in a household setting, we conducted a household serologic study of SARS-CoV-2 in Costa Rica, with SARS-CoV-2 index cases selected from a larger prospective cohort study and their household contacts were enrolled. A total of 719 household contacts of 304 household index cases were enrolled from November 21, 2020, through July 31, 2021. Demographic, clinical, and behavioral information was collected from the index cases and their household contacts. Blood specimens were collected from contacts within 30-60 days of index case diagnosis; and serum was tested for presence of spike and nucleocapsid SARS-CoV-2 IgG antibodies. Evidence of SARS-CoV-2 prior infections among household contacts was defined based on the presence of both spike and nucleocapsid antibodies. To avoid making strong assumptions that the index case was the sole source of infections among household contacts, we fitted a chain binomial model to the serologic data, which allowed us to account for exogenous community infection risk as well as potential multi-generational transmissions within the household. Overall seroprevalence was 53% (95% confidence interval (CI) 48% - 58%) among household contacts The estimated household secondary attack rate (SAR) was 32% (95% CI 5% - 74%) and the average community infection risk was 19% (95% CI 14% - 26%). Mask wearing by the index case was associated with the household transmission risk reduction by 67% (adjusted odds ratio = 0.33 with 95% CI: 0.09-0.75) and sleeping in a separate bedroom from the index case reduced the risk of household transmission by 78% (adjusted odds ratio = 0.22 with 95% CI 0.10-0.41). The estimated distribution of household secondary attack rates was highly heterogeneous across index cases, with 30% of index cases being the source for 80% of secondary cases. Modeling analysis suggests behavioral factors were important drivers of the observed SARS-CoV-2 transmission heterogeneity within the household.
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11
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Lee SS, Viboud C, Petersen E. Understanding the rebound of influenza in the post COVID-19 pandemic period holds important clues for epidemiology and control. Int J Infect Dis 2022; 122:1002-1004. [PMID: 35932966 PMCID: PMC9349026 DOI: 10.1016/j.ijid.2022.08.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Shui Shan Lee
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinse University of Hong Kong, Hong Kong, China,International Society for Infectious Diseases
| | - Cecile Viboud
- Fogarty International Center, National Institute of Health, Bethesda, USA
| | - Eskild Petersen
- International Society for Infectious Diseases,Institute for Clinical Medicine, Faculty of Health Sciences, University of Aarhus, Denmark,European Society for Clinical Microbiology and Infectious Diseases [ESCMID] Task Force for Emerging Infections, Basel, Switzerland
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12
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Bingham J, Tempia S, Moultrie H, Viboud C, Jassat W, Cohen C, Pulliam JRC. Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves. medRxiv 2022:2022.07.22.22277932. [PMID: 35982666 PMCID: PMC9387150 DOI: 10.1101/2022.07.22.22277932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Objectives We aimed to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources and using data from public and private sector service providers. Methods We estimated R from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalizations, and hospital-associated deaths, using a method which models daily incidence as a weighted sum of past incidence. We also estimated R separately using public and private sector data. Results Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43-1.66), 1.56 (CI: 1.47-1.64), 1.46 (CI: 1.38-1.53) and 3.33 (CI: 2.84-3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves but case-based estimates were higher during the fourth wave. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave. Discussion Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. High R estimates for Omicron relative to earlier waves is interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights the fact that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
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Affiliation(s)
- Jeremy Bingham
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cecile Viboud
- Fogarty International Center, NIH, Bethesda, MD, USA
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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13
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Truelove S, Smith CP, Qin M, Mullany LC, Borchering RK, Lessler J, Shea K, Howerton E, Contamin L, Levander J, Kerr J, Hochheiser H, Kinsey M, Tallaksen K, Wilson S, Shin L, Rainwater-Lovett K, Lemairtre JC, Dent J, Kaminsky J, Lee EC, Perez-Saez J, Hill A, Karlen D, Chinazzi M, Davis JT, Mu K, Xiong X, Pastore y Piontti A, Vespignani A, Srivastava A, Porebski P, Venkatramanan S, Adiga A, Lewis B, Klahn B, Outten J, Orr M, Harrison G, Hurt B, Chen J, Vullikanti A, Marathe M, Hoops S, Bhattacharya P, Machi D, Chen S, Paul R, Janies D, Thill JC, Galanti M, Yamana TK, Pei S, Shaman JL, Healy JM, Slayton RB, Biggerstaff M, Johansson MA, Runge MC, Viboud C. Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination. eLife 2022; 11:e73584. [PMID: 35726851 PMCID: PMC9232215 DOI: 10.7554/elife.73584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 06/03/2022] [Indexed: 01/01/2023] Open
Abstract
In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United States. At the time, with slowed vaccination uptake, this novel variant was expected to increase the risk of pandemic resurgence in the US in summer and fall 2021. As part of the COVID-19 Scenario Modeling Hub, an ensemble of nine mechanistic models produced 6-month scenario projections for July-December 2021 for the United States. These projections estimated substantial resurgences of COVID-19 across the US resulting from the more transmissible Delta variant, projected to occur across most of the US, coinciding with school and business reopening. The scenarios revealed that reaching higher vaccine coverage in July-December 2021 reduced the size and duration of the projected resurgence substantially, with the expected impacts was largely concentrated in a subset of states with lower vaccination coverage. Despite accurate projection of COVID-19 surges occurring and timing, the magnitude was substantially underestimated 2021 by the models compared with the of the reported cases, hospitalizations, and deaths occurring during July-December, highlighting the continued challenges to predict the evolving COVID-19 pandemic. Vaccination uptake remains critical to limiting transmission and disease, particularly in states with lower vaccination coverage. Higher vaccination goals at the onset of the surge of the new variant were estimated to avert over 1.5 million cases and 21,000 deaths, although may have had even greater impacts, considering the underestimated resurgence magnitude from the model.
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Affiliation(s)
- Shaun Truelove
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Claire P Smith
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Michelle Qin
- Harvard UniversityCambridge, MassachusettsUnited States
| | - Luke C Mullany
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | | | - Justin Lessler
- University of North Carolina at Chapel HillChapel HillUnited States
| | - Katriona Shea
- Pennsylvania State UniversityUniversity ParkUnited States
| | - Emily Howerton
- Pennsylvania State UniversityUniversity ParkUnited States
| | | | | | | | | | - Matt Kinsey
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | - Kate Tallaksen
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | - Shelby Wilson
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | - Lauren Shin
- Johns Hopkins University Applied Physics LaboratoryLaurelUnited States
| | | | | | - Juan Dent
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Joshua Kaminsky
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Elizabeth C Lee
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Javier Perez-Saez
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison Hill
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins UniversityBaltimoreUnited States
| | | | | | | | - Kunpeng Mu
- Northeastern UniversityBostonUnited States
| | | | | | | | | | | | | | | | - Bryan Lewis
- University of VirginiaCharlottesvilleUnited States
| | - Brian Klahn
- University of VirginiaCharlottesvilleUnited States
| | | | - Mark Orr
- University of VirginiaCharlottesvilleUnited States
| | | | | | | | | | | | - Stefan Hoops
- University of VirginiaCharlottesvilleUnited States
| | | | - Dustin Machi
- University of VirginiaCharlottesvilleUnited States
| | - Shi Chen
- University of North Carolina at CharlotteCharlotteUnited States
| | - Rajib Paul
- University of North Carolina at CharlotteCharlotteUnited States
| | - Daniel Janies
- University of North Carolina at CharlotteCharlotteUnited States
| | | | | | | | - Sen Pei
- Columbia UniversityNew YorkUnited States
| | | | | | | | | | | | | | - Cecile Viboud
- Fogarty International Center, National Institutes of HealthBethesdaUnited States
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Reich NG, Lessler J, Funk S, Viboud C, Vespignani A, Tibshirani RJ, Shea K, Schienle M, Runge MC, Rosenfeld R, Ray EL, Niehus R, Johnson HC, Johansson MA, Hochheiser H, Gardner L, Bracher J, Borchering RK, Biggerstaff M. Collaborative Hubs: Making the Most of Predictive Epidemic Modeling. Am J Public Health 2022; 112:839-842. [PMID: 35420897 PMCID: PMC9137029 DOI: 10.2105/ajph.2022.306831] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2022] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas G Reich
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Justin Lessler
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Sebastian Funk
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Cecile Viboud
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Alessandro Vespignani
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Ryan J Tibshirani
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Katriona Shea
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Melanie Schienle
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Michael C Runge
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Roni Rosenfeld
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Evan L Ray
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Rene Niehus
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Helen C Johnson
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Michael A Johansson
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Harry Hochheiser
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Lauren Gardner
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Johannes Bracher
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Rebecca K Borchering
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
| | - Matthew Biggerstaff
- Nicholas G. Reich and Evan L. Ray are with the Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst. Justin Lessler is with the Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill. Sebastian Funk is with the Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK. Cecile Viboud is with the Fogarty International Center, National Institutes of Health, Bethesda, MD. Alessandro Vespignani is with the Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA. Ryan J. Tibshirani is with the Department of Statistics & Data Science and the Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA. Katriona Shea and Rebecca K. Borchering are with the Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park. Melanie Schienle and Johannes Bracher are with the Chair of Statistics and Econometrics, Karlsruhe Institute of Technology, Karlsruhe, Germany. Michael C. Runge is with the Eastern Ecological Science Center, US Geological Survey, Laurel, MD. Roni Rosenfeld is with the Machine Learning Department, Carnegie Mellon University. Rene Niehus and Helen C. Johnson are with the European Centre for Disease Prevention and Control, Solna, Sweden. Michael A. Johansson and Matthew Biggerstaff are with the COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA. Harry Hochheiser is with the Department of Biomedical Informatics and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA. Lauren Gardner is with the Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD
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Abstract
In this review, we discuss the epidemiological dynamics of different viral infections to project how the transition from a pandemic to endemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) might take shape. Drawing from theories of disease invasion and transmission dynamics, waning immunity in the face of viral evolution and antigenic drift, and empirical data from influenza, dengue, and seasonal coronaviruses, we discuss the putative periodicity, severity, and age dynamics of SARS-CoV-2 as it becomes endemic. We review recent studies on SARS-CoV-2 epidemiology, immunology, and evolution that are particularly useful in projecting the transition to endemicity and highlight gaps that warrant further research.
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Affiliation(s)
- Lily E. Cohen
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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16
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Burstein R, Althouse BM, Adler A, Akullian A, Brandstetter E, Cho S, Emanuels A, Fay K, Gamboa L, Han P, Huden K, Ilcisin M, Izzo M, Jackson ML, Kim AE, Kimball L, Lacombe K, Lee J, Logue JK, Rogers J, Chung E, Sibley TR, Van Raay K, Wenger E, Wolf CR, Boeckh M, Chu H, Duchin J, Rieder M, Shendure J, Starita LM, Viboud C, Bedford T, Englund JA, Famulare M. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data. medRxiv 2022:2022.02.04.22270474. [PMID: 35169816 PMCID: PMC8845514 DOI: 10.1101/2022.02.04.22270474] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae (SPn, 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load. Conclusions Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.
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Affiliation(s)
- Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Benjamin M. Althouse
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Department of Biology, New Mexico State University, Las Cruces, NM
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle WA USA
| | - Adam Akullian
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Shari Cho
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle WA USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Peter Han
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Kristen Huden
- Department of Medicine, University of Washington, Seattle WA USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Mandy Izzo
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Ashley E. Kim
- Department of Medicine, University of Washington, Seattle WA USA
| | - Louise Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Julia Rogers
- Department of Medicine, University of Washington, Seattle WA USA
| | - Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Edward Wenger
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle WA USA
| | - Michael Boeckh
- Department of Medicine, University of Washington, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Jeff Duchin
- Department of Medicine, University of Washington, Seattle WA USA
- Public Health Seattle & King County, Seattle WA USA
| | - Mark Rieder
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
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17
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Liu QH, Zhang J, Peng C, Litvinova M, Huang S, Poletti P, Trentini F, Guzzetta G, Marziano V, Zhou T, Viboud C, Bento AI, Lv J, Vespignani A, Merler S, Yu H, Ajelli M. Model-based evaluation of alternative reactive class closure strategies against COVID-19. Nat Commun 2022; 13:322. [PMID: 35031600 PMCID: PMC8760266 DOI: 10.1038/s41467-021-27939-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3% (95%CI: 8.0-26.8%), due to the low probability of timely identification of infections in the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Depending on the contribution of schools to transmission, this strategy can greatly reduce COVID-19 burden even when school contribution to transmission and immunity in the population is low. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to be rolled out.
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Affiliation(s)
- Quan-Hui Liu
- College of Computer Science, Sichuan University, Chengdu, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Cheng Peng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Shudong Huang
- College of Computer Science, Sichuan University, Chengdu, China
| | - Piero Poletti
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Filippo Trentini
- Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy
| | - Giorgio Guzzetta
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | | | - Tao Zhou
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Jiancheng Lv
- College of Computer Science, Sichuan University, Chengdu, China
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Stefano Merler
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
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18
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Pollett S, Johansson MA, Reich NG, Brett-Major D, Del Valle SY, Venkatramanan S, Lowe R, Porco T, Berry IM, Deshpande A, Kraemer MUG, Blazes DL, Pan-ngum W, Vespigiani A, Mate SE, Silal SP, Kandula S, Sippy R, Quandelacy TM, Morgan JJ, Ball J, Morton LC, Althouse BM, Pavlin J, van Panhuis W, Riley S, Biggerstaff M, Viboud C, Brady O, Rivers C. Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines. PLoS Med 2021; 18:e1003793. [PMID: 34665805 PMCID: PMC8525759 DOI: 10.1371/journal.pmed.1003793] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. METHODS AND FINDINGS We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. CONCLUSIONS These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.
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Affiliation(s)
- Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Michael A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, San Juan, Puerto Rico, United States of America
| | - Nicholas G. Reich
- University of Massachusetts–Amherst, School of Public Health and Health Sciences, Amherst, Massachusetts, United States of America
| | - David Brett-Major
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sara Y. Del Valle
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Srinivasan Venkatramanan
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, Virginia, United States of America
| | - Rachel Lowe
- Centre for Mathematical Modelling of Infectious Diseases and Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Barcelona Institute for Global Health, Barcelona, Spain
| | - Travis Porco
- University of California at San Francisco, San Francisco, California, United States of America
| | - Irina Maljkovic Berry
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Alina Deshpande
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | - David L. Blazes
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Wirichada Pan-ngum
- Mahidol-Oxford Tropical Medicine Research Unit and Department of Tropical Hygiene, Mahidol University, Thailand
| | - Alessandro Vespigiani
- Network Science Institute, Northeastern University, Boston, Massachusetts, United States of America
| | - Suzanne E. Mate
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sheetal P. Silal
- Modelling and Simulation Hub, Africa, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sasikiran Kandula
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, New York, United States of America
| | - Rachel Sippy
- Institute for Global Health and Translational Science, State University of New York Upstate Medical University, Syracuse, New York, United States of America
| | - Talia M. Quandelacy
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, San Juan, Puerto Rico, United States of America
| | - Jeffrey J. Morgan
- Catholic University of America, Washington, DC, United States of America
| | - Jacob Ball
- U.S. Army Public Health Center, Edgewood, Maryland, United States of America
| | - Lindsay C. Morton
- Armed Forces Health Surveillance Division, Global Emerging Infections Surveillance, Silver Spring, Maryland, United States of America
- George Washington University, Milken Institute School of Public Health, Washington, DC, United States of America
| | - Benjamin M. Althouse
- University of Washington, Seattle, Washington, United States of America
- Institute for Disease Modeling, Bellevue, Washington, United States of America
- New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Julie Pavlin
- National Academies of Sciences, Engineering, and Medicine, Washington, DC, United States of America
| | - Wilbert van Panhuis
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College, London, United Kingdom
| | - Matthew Biggerstaff
- Influenza Division, Centers for Disease Control & Prevention, Atlanta, Georgia, United States of America
| | - Cecile Viboud
- Fogarty International Center, National Institutes for Health, Bethesda, Maryland, United States of America
| | - Oliver Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Caitlin Rivers
- Johns Hopkins Center for Health Security, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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19
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Abstract
COVID-19 ‘excess mortality’ has been estimated for more than 100 countries and shows a dramatic death toll in many countries.
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Affiliation(s)
- Lone Simonsen
- PandemiX Center, Institute of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, United States
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20
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Deng X, Yang J, Wang W, Wang X, Zhou J, Chen Z, Li J, Chen Y, Yan H, Zhang J, Zhang Y, Wang Y, Qiu Q, Gong H, Wei X, Wang L, Sun K, Wu P, Ajelli M, Cowling BJ, Viboud C, Yu H. Case Fatality Risk of the First Pandemic Wave of Coronavirus Disease 2019 (COVID-19) in China. Clin Infect Dis 2021; 73:e79-e85. [PMID: 32409826 PMCID: PMC7239217 DOI: 10.1093/cid/ciaa578] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023] Open
Abstract
Objective To assess the case fatality risk (CFR) of COVID-19 in mainland China, stratified by region and clinical category, and estimate key time-to-event intervals. Methods We collected individual information and aggregated data on COVID-19 cases from publicly available official sources from December 29, 2019 to April 17, 2020. We accounted for right-censoring to estimate the CFR and explored the risk factors for mortality. We fitted Weibull, gamma, and lognormal distributions to time-to-event data using maximum-likelihood estimation. Results We analyzed 82,719 laboratory-confirmed cases reported in mainland China, including 4,632 deaths, and 77,029 discharges. The estimated CFR was 5.65% (95%CI: 5.50%-5.81%) nationally, with highest estimate in Wuhan (7.71%), and lowest in provinces outside Hubei (0.86%). The fatality risk among critical patients was 3.6 times that of all patients, and 0.8-10.3 fold higher than that of mild-to-severe patients. Older age (OR 1.14 per year; 95%CI: 1.11-1.16), and being male (OR 1.83; 95%CI: 1.10-3.04) were risk factors for mortality. The time from symptom onset to first healthcare consultation, time from symptom onset to laboratory confirmation, and time from symptom onset to hospitalization were consistently longer for deceased patients than for those who recovered. Conclusions Our CFR estimates based on laboratory-confirmed cases ascertained in mainland China suggest that COVID-19 is more severe than the 2009 H1N1 influenza pandemic in hospitalized patients, particularly in Wuhan. Our study provides a comprehensive picture of the severity of the first wave of the pandemic in China. Our estimates can help inform models and the global response to COVID-19.
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Affiliation(s)
- Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wei Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiling Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiaxin Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jing Li
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yinzi Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Han Yan
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yongli Zhang
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hui Gong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xianglin Wei
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lili Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Marco Ajelli
- Bruno Kessler Foundation, Trento, Italy.,Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, Indiana, USA
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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21
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Johnson EK, Sylte D, Chaves SS, Li Y, Mahe C, Nair H, Paget J, van Pomeren T, Shi T, Viboud C, James SL. Hospital utilization rates for influenza and RSV: a novel approach and critical assessment. Popul Health Metr 2021; 19:31. [PMID: 34126993 PMCID: PMC8204427 DOI: 10.1186/s12963-021-00252-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/26/2020] [Accepted: 03/31/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Influenza and respiratory syncytial virus (RSV) contribute significantly to the burden of acute lower respiratory infection (ALRI) inpatient care, but heterogeneous coding practices and availability of inpatient data make it difficult to estimate global hospital utilization for either disease based on coded diagnoses alone. METHODS This study estimates rates of influenza and RSV hospitalization by calculating the proportion of ALRI due to influenza and RSV and applying this proportion to inpatient admissions with ALRI coded as primary diagnosis. Proportions of ALRI attributed to influenza and RSV were extracted from a meta-analysis of 360 total sources describing inpatient hospital admissions which were input to a Bayesian mixed effects model over age with random effects over location. Results of this model were applied to inpatient admission datasets for 44 countries to produce rates of hospital utilization for influenza and RSV respectively, and rates were compared to raw coded admissions for each disease. RESULTS For most age groups, these methods estimated a higher national admission rate than the rate of directly coded influenza or RSV admissions in the same inpatient sources. In many inpatient sources, International Classification of Disease (ICD) coding detail was insufficient to estimate RSV burden directly. The influenza inpatient burden estimates in older adults appear to be substantially underestimated using this method on primary diagnoses alone. Application of the mixed effects model reduced heterogeneity between countries in influenza and RSV which was biased by coding practices and between-country variation. CONCLUSIONS This new method presents the opportunity of estimating hospital utilization rates for influenza and RSV using a wide range of clinical databases. Estimates generally seem promising for influenza and RSV associated hospitalization, but influenza estimates from primary diagnosis seem highly underestimated among older adults. Considerable heterogeneity remains between countries in ALRI coding (i.e., primary vs non-primary cause), and in the age profile of proportion positive for influenza and RSV across studies. While this analysis is interesting because of its wide data utilization and applicability in locations without laboratory-confirmed admission data, understanding the sources of variability and data quality will be essential in future applications of these methods.
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Affiliation(s)
- Emily K Johnson
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA.
| | - Dillon Sylte
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA
| | - Sandra S Chaves
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
- Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | - You Li
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cedric Mahe
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
- Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - John Paget
- Netherlands Institute for Health Services Research (Nivel), Utrecht, Netherlands
| | - Tayma van Pomeren
- Netherlands Institute for Health Services Research (Nivel), Utrecht, Netherlands
| | - Ting Shi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Spencer L James
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA
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22
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Aiken EL, Nguyen AT, Viboud C, Santillana M. Toward the use of neural networks for influenza prediction at multiple spatial resolutions. Sci Adv 2021; 7:7/25/eabb1237. [PMID: 34134985 PMCID: PMC8208709 DOI: 10.1126/sciadv.abb1237] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/29/2021] [Indexed: 05/24/2023]
Abstract
Mitigating the effects of disease outbreaks with timely and effective interventions requires accurate real-time surveillance and forecasting of disease activity, but traditional health care-based surveillance systems are limited by inherent reporting delays. Machine learning methods have the potential to fill this temporal "data gap," but work to date in this area has focused on relatively simple methods and coarse geographic resolutions (state level and above). We evaluate the predictive performance of a gated recurrent unit neural network approach in comparison with baseline machine learning methods for estimating influenza activity in the United States at the state and city levels and experiment with the inclusion of real-time Internet search data. We find that the neural network approach improves upon baseline models for long time horizons of prediction but is not improved by real-time internet search data. We conduct a thorough analysis of feature importances in all considered models for interpretability purposes.
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Affiliation(s)
- Emily L Aiken
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
| | - Andre T Nguyen
- Booz Allen Hamilton, Columbia, MD 21044, USA
- University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mauricio Santillana
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02215, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
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23
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Cozza V, Campbell H, Chang HH, Iuliano AD, Paget J, Patel NN, Reiner RC, Troeger C, Viboud C, Bresee JS, Fitzner J. Global Seasonal Influenza Mortality Estimates: A Comparison of 3 Different Approaches. Am J Epidemiol 2021; 190:718-727. [PMID: 32914184 DOI: 10.1093/aje/kwaa196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 09/03/2020] [Indexed: 01/30/2023] Open
Abstract
Prior to updating global influenza-associated mortality estimates, the World Health Organization convened a consultation in July 2017 to understand differences in methodology and implications for results of 3 influenza mortality projects from the US Centers for Disease Control and Prevention (CDC), the Netherlands Institute for Health Service Research's Global Pandemic Mortality Project II (GLaMOR), and the Institute for Health Metrics and Evaluation (IHME). The expert panel reviewed estimates and discussed differences in data sources, analysis, and modeling assumptions. We performed a comparison analysis of the estimates. Influenza-associated respiratory death counts were comparable between CDC and GLaMOR; the IHME estimate was considerably lower. The greatest country-specific influenza-associated fold differences in mortality rate between CDC and IHME estimates and between GLaMOR and IHME estimates were among countries in Southeast Asia and the Eastern Mediterranean region. The data envelope used for the calculation was one of the major differences (CDC and GLaMOR: all respiratory deaths; IHME: lower-respiratory infection deaths). With the assumption that there is only one cause of death for each death, IHME estimates a fraction of the full influenza-associated respiratory mortality that is measured by the other 2 groups. Wide variability of parameters was observed. Continued coordination between groups could assist with better understanding of methodological differences and new approaches to estimating influenza deaths globally.
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Chen X, Chen Z, Azman AS, Deng X, Sun R, Zhao Z, Zheng N, Chen X, Lu W, Zhuang T, Yang J, Viboud C, Ajelli M, Leung DT, Yu H. Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis. Lancet Glob Health 2021; 9:e598-e609. [PMID: 33705690 PMCID: PMC8049592 DOI: 10.1016/s2214-109x(21)00026-7] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND A rapidly increasing number of serological surveys for antibodies to SARS-CoV-2 have been reported worldwide. We aimed to synthesise, combine, and assess this large corpus of data. METHODS In this systematic review and meta-analysis, we searched PubMed, Embase, Web of Science, and five preprint servers for articles published in English between Dec 1, 2019, and Dec 22, 2020. Studies evaluating SARS-CoV-2 seroprevalence in humans after the first identified case in the area were included. Studies that only reported serological responses among patients with COVID-19, those using known infection status samples, or any animal experiments were all excluded. All data used for analysis were extracted from included papers. Study quality was assessed using a standardised scale. We estimated age-specific, sex-specific, and race-specific seroprevalence by WHO regions and subpopulations with different levels of exposures, and the ratio of serology-identified infections to virologically confirmed cases. This study is registered with PROSPERO, CRD42020198253. FINDINGS 16 506 studies were identified in the initial search, 2523 were assessed for eligibility after removal of duplicates and inappropriate titles and abstracts, and 404 serological studies (representing tests in 5 168 360 individuals) were included in the meta-analysis. In the 82 studies of higher quality, close contacts (18·0%, 95% CI 15·7-20·3) and high-risk health-care workers (17·1%, 9·9-24·4) had higher seroprevalence than did low-risk health-care workers (4·2%, 1·5-6·9) and the general population (8·0%, 6·8-9·2). The heterogeneity between included studies was high, with an overall I2 of 99·9% (p<0·0001). Seroprevalence varied greatly across WHO regions, with the lowest seroprevalence of general populations in the Western Pacific region (1·7%, 95% CI 0·0-5·0). The pooled infection-to-case ratio was similar between the region of the Americas (6·9, 95% CI 2·7-17·3) and the European region (8·4, 6·5-10·7), but higher in India (56·5, 28·5-112·0), the only country in the South-East Asia region with data. INTERPRETATION Antibody-mediated herd immunity is far from being reached in most settings. Estimates of the ratio of serologically detected infections per virologically confirmed cases across WHO regions can help provide insights into the true proportion of the population infected from routine confirmation data. FUNDING National Science Fund for Distinguished Young Scholars, Key Emergency Project of Shanghai Science and Technology Committee, Program of Shanghai Academic/Technology Research Leader, National Science and Technology Major project of China, the US National Institutes of Health. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland; Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Ruijia Sun
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zeyao Zhao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Nan Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinghui Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wanying Lu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Tingyu Zhuang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Daniel T Leung
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China; Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
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Zhang J, Litvinova M, Liang Y, Zheng W, Shi H, Vespignani A, Viboud C, Ajelli M, Yu H. The impact of relaxing interventions on human contact patterns and SARS-CoV-2 transmission in China. Sci Adv 2021; 7:eabe2584. [PMID: 33962957 PMCID: PMC8104862 DOI: 10.1126/sciadv.abe2584] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/19/2021] [Indexed: 05/22/2023]
Abstract
Nonpharmaceutical interventions to control SARS-CoV-2 spread have been implemented with different intensity, timing, and impact on transmission. As a result, post-lockdown COVID-19 dynamics are heterogeneous and difficult to interpret. We describe a set of contact surveys performed in four Chinese cities (Wuhan, Shanghai, Shenzhen, and Changsha) during the pre-pandemic, lockdown and post-lockdown periods to quantify changes in contact patterns. In the post-lockdown period, the mean number of contacts increased by 5 to 17% as compared to the lockdown period. However, it remains three to seven times lower than its pre-pandemic level sufficient to control SARS-CoV-2 transmission. We find that the impact of school interventions depends nonlinearly on the intensity of other activities. When most community activities are halted, school closure leads to a 77% decrease in the reproduction number; in contrast, when social mixing outside of schools is at pre-pandemic level, school closure leads to a 5% reduction in transmission.
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Affiliation(s)
- Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
- ISI Foundation, Turin, Italy
| | - Yuxia Liang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wen Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Huilin Shi
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
- ISI Foundation, Turin, Italy
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Department of infectious diseases, Huashan Hospital, Fudan University
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University
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26
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Liu QH, Zhang J, Peng C, Litvinova M, Huang S, Poletti P, Trentini F, Guzzetta G, Marziano V, Zhou T, Viboud C, Bento AI, Lv J, Vespignani A, Merler S, Yu H, Ajelli M. Model-based evaluation of alternative reactive class closure strategies against COVID-19. medRxiv 2021:2021.04.18.21255683. [PMID: 33907769 PMCID: PMC8077629 DOI: 10.1101/2021.04.18.21255683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, here we develop a data-driven computational model of SARS-CoV-2 transmission to investigate mechanistically the effect on COVID-19 outbreaks of school closure strategies based on syndromic surveillance and antigen screening of students. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 13.1% (95%CI: 8.6%-20.2 %), due to the low probability of timely symptomatic case identification among the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Should population-level social distancing measures unrelated to schools enable maintaining the reproduction number ( R ) at 1.3 or lower, an antigen-based screening strategy is estimated to fully prevent COVID-19 outbreaks in the general population. Depending on the contribution of schools to transmission, this strategy can either prevent COVID-19 outbreaks for R up to 1.9 or to at least greatly reduce outbreak size in very conservative scenarios about school contribution to transmission. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to roll out through 2021, especially in light of possible continued emergence of SARS-CoV-2 variants.
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Affiliation(s)
- Quan-Hui Liu
- College of Computer Science, Sichuan University, Chengdu, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Cheng Peng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Maria Litvinova
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Shudong Huang
- College of Computer Science, Sichuan University, Chengdu, China
| | - Piero Poletti
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Filippo Trentini
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Giorgio Guzzetta
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | | | - Tao Zhou
- Big Data Research Center, University of Electronic Science and Technology of China, Chengdu, China
- Tianfu Complexity Science Research Center, Chengdu, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ana I. Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Jiancheng Lv
- College of Computer Science, Sichuan University, Chengdu, China
| | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
- ISI Foundation, Turin, Italy
| | - Stefano Merler
- Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
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27
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Nachega JB, Atteh R, Ihekweazu C, Sam-Agudu NA, Adejumo P, Nsanzimana S, Rwagasore E, Condo J, Paleker M, Mahomed H, Suleman F, Ario AR, Kiguli-Malwadde E, Omaswa FG, Sewankambo NK, Viboud C, Reid MJA, Zumla A, Kilmarx PH. Contact Tracing and the COVID-19 Response in Africa: Best Practices, Key Challenges, and Lessons Learned from Nigeria, Rwanda, South Africa, and Uganda. Am J Trop Med Hyg 2021; 104:1179-1187. [PMID: 33571138 PMCID: PMC8045625 DOI: 10.4269/ajtmh.21-0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 01/05/2023] Open
Abstract
Most African countries have recorded relatively lower COVID-19 burdens than Western countries. This has been attributed to early and strong political commitment and robust implementation of public health measures, such as nationwide lockdowns, travel restrictions, face mask wearing, testing, contact tracing, and isolation, along with community education and engagement. Other factors include the younger population age strata and hypothesized but yet-to-be confirmed partially protective cross-immunity from parasitic diseases and/or other circulating coronaviruses. However, the true burden may also be underestimated due to operational and resource issues for COVID-19 case identification and reporting. In this perspective article, we discuss selected best practices and challenges with COVID-19 contact tracing in Nigeria, Rwanda, South Africa, and Uganda. Best practices from these country case studies include sustained, multi-platform public communications; leveraging of technology innovations; applied public health expertise; deployment of community health workers; and robust community engagement. Challenges include an overwhelming workload of contact tracing and case detection for healthcare workers, misinformation and stigma, and poorly sustained adherence to isolation and quarantine. Important lessons learned include the need for decentralization of contact tracing to the lowest geographic levels of surveillance, rigorous use of data and technology to improve decision-making, and sustainment of both community sensitization and political commitment. Further research is needed to understand the role and importance of contact tracing in controlling community transmission dynamics in African countries, including among children. Also, implementation science will be critically needed to evaluate innovative, accessible, and cost-effective digital solutions to accommodate the contact tracing workload.
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Affiliation(s)
- Jean B Nachega
- 1Department of Medicine and Center for Infectious Diseases, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa.,2Department of Epidemiology, Infectious Diseases and Microbiology, Center for Global Health, University of Pittsburgh, Pittsburgh, Pennsylvania.,3Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,4Department of International Health, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Rhoda Atteh
- 5Surveillance and Epidemiology, Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Chikwe Ihekweazu
- 6Office of the Director-General, Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Nadia A Sam-Agudu
- 7International Research Center of Excellence, Institute of Human Virology Nigeria, Abuja, Nigeria.,8Department of Pediatrics, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland.,9Department of Pediatrics and Child Health, School of Medical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Prisca Adejumo
- 10Department of Nursing, University of Ibadan, Ibadan, Nigeria
| | | | - Edson Rwagasore
- 11Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Jeanine Condo
- 12University of Rwanda, School of Public Health, Kigali, Rwanda.,13School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - Masudah Paleker
- 14South African Department of Health, Western Cape Province, Cape Town, South Africa.,15Division of Health Systems and Public Health, Department of Global Health, Stellenbosch Faculty of Medicine and Health Sciences and Western Cape Department of Health, Cape Town, South Africa
| | - Hassan Mahomed
- 14South African Department of Health, Western Cape Province, Cape Town, South Africa.,15Division of Health Systems and Public Health, Department of Global Health, Stellenbosch Faculty of Medicine and Health Sciences and Western Cape Department of Health, Cape Town, South Africa
| | - Fatima Suleman
- 16Discipline of Pharmaceutical Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Alex Riolexus Ario
- 17Uganda National Institute of Public Health, Ministry of Health, Kampala, Uganda
| | | | - Francis G Omaswa
- 18African Centre for Global Health and Social Transformation, Kampala, Uganda
| | - Nelson K Sewankambo
- 19Department of Internal Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Cecile Viboud
- 20Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Michael J A Reid
- 21University of California San Francisco, San Francisco, California
| | - Alimuddin Zumla
- 22Division of Infection and Immunity, University College London, London, United Kingdom.,23NIHR Biomedical Research Centre, University College London Hospitals, London, United Kingdom
| | - Peter H Kilmarx
- 20Fogarty International Center, National Institutes of Health, Bethesda, Maryland
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28
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Yang J, Zheng W, Shi H, Yan X, Dong K, You Q, Zhong G, Gong H, Chen Z, Jit M, Viboud C, Ajelli M, Yu H. Who should be prioritized for COVID-19 vaccination in China? A descriptive study. BMC Med 2021; 19:45. [PMID: 33563270 PMCID: PMC7872877 DOI: 10.1186/s12916-021-01923-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/20/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND All countries are facing decisions about which population groups to prioritize for access to COVID-19 vaccination after the first vaccine products have been licensed, at which time supply shortages are inevitable. Our objective is to define the key target populations, their size, and priority for a COVID-19 vaccination program in the context of China. METHODS On the basis of utilitarian and egalitarian principles, we define and estimate the size of tiered target population groups for a phased introduction of COVID-19 vaccination, considering evolving goals as vaccine supplies increase, detailed information on the risk of illness and transmission, and past experience with vaccination during the 2009 influenza pandemic. Using publicly available data, we estimated the size of target population groups, and the number of days needed to vaccinate 70% of the target population. Sensitivity analyses considered higher vaccine coverages and scaled up vaccine delivery relative to the 2009 pandemic. RESULTS Essential workers, including staff in the healthcare, law enforcement, security, nursing homes, social welfare institutes, community services, energy, food and transportation sectors, and overseas workers/students (49.7 million) could be prioritized for vaccination to maintain essential services in the early phase of a vaccination program. Subsequently, older adults, individuals with underlying health conditions and pregnant women (563.6 million) could be targeted for vaccination to reduce the number of individuals with severe COVID-19 outcomes, including hospitalizations, critical care admissions, and deaths. In later stages, the vaccination program could be further extended to target adults without underlying health conditions and children (784.8 million), in order to reduce symptomatic infections and/or to stop virus transmission. Given 10 million doses administered per day, and a two-dose vaccination schedule, it would take 1 week to vaccinate essential workers but likely up to 7 months to vaccinate 70% of the overall population. CONCLUSIONS The proposed framework is general but could assist Chinese policy-makers in the design of a vaccination program. Additionally, this exercise could be generalized to inform other national and regional strategies for use of COVID-19 vaccines, especially in low- and middle-income countries.
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Affiliation(s)
- Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wen Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Huilin Shi
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xuemei Yan
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Kaige Dong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qian You
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Guangjie Zhong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hui Gong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Mark Jit
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Special Administrative Region, Hong Kong, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
- Department of infectious diseases, Huashan Hospital, Fudan University, Shanghai, China.
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29
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Shea K, Borchering RK, Probert WJM, Howerton E, Bogich TL, Li S, van Panhuis WG, Viboud C, Aguás R, Belov A, Bhargava SH, Cavany S, Chang JC, Chen C, Chen J, Chen S, Chen Y, Childs LM, Chow CC, Crooker I, Del Valle SY, España G, Fairchild G, Gerkin RC, Germann TC, Gu Q, Guan X, Guo L, Hart GR, Hladish TJ, Hupert N, Janies D, Kerr CC, Klein DJ, Klein E, Lin G, Manore C, Meyers LA, Mittler J, Mu K, Núñez RC, Oidtman R, Pasco R, Piontti APY, Paul R, Pearson CAB, Perdomo DR, Perkins TA, Pierce K, Pillai AN, Rael RC, Rosenfeld K, Ross CW, Spencer JA, Stoltzfus AB, Toh KB, Vattikuti S, Vespignani A, Wang L, White L, Xu P, Yang Y, Yogurtcu ON, Zhang W, Zhao Y, Zou D, Ferrari M, Pannell D, Tildesley M, Seifarth J, Johnson E, Biggerstaff M, Johansson M, Slayton RB, Levander J, Stazer J, Salerno J, Runge MC. COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support. medRxiv 2020. [PMID: 33173914 PMCID: PMC7654910 DOI: 10.1101/2020.11.03.20225409] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Policymakers make decisions about COVID-19 management in the face of considerable uncertainty. We convened multiple modeling teams to evaluate reopening strategies for a mid-sized county in the United States, in a novel process designed to fully express scientific uncertainty while reducing linguistic uncertainty and cognitive biases. For the scenarios considered, the consensus from 17 distinct models was that a second outbreak will occur within 6 months of reopening, unless schools and non-essential workplaces remain closed. Up to half the population could be infected with full workplace reopening; non-essential business closures reduced median cumulative infections by 82%. Intermediate reopening interventions identified no win-win situations; there was a trade-off between public health outcomes and duration of workplace closures. Aggregate results captured twice the uncertainty of individual models, providing a more complete expression of risk for decision-making purposes.
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Chen X, Chen Z, Azman AS, Deng X, Chen X, Lu W, Zhao Z, Yang J, Viboud C, Ajelli M, Leung DT, Yu H. Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis. medRxiv 2020. [PMID: 32935122 DOI: 10.1101/2020.09.11.20192773] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background A rapidly increasing number of serological surveys for anti-SARS-CoV-2 antibodies have been reported worldwide. A synthesis of this large corpus of data is needed. Purpose To evaluate the quality of serological studies and provide a global picture of seroprevalence across demographic and occupational groups, and to provide guidance for conducting better serosurveys. Data sources We searched PubMed, Embase, Web of Science, and 4 pre-print servers for English-language papers published from December 1, 2019 to September 25, 2020. Study selection Serological studies evaluating SARS-CoV-2 seroprevalence in humans. Data extraction Two investigators independently extracted data from studies. Data Synthesis Most of 230 serological studies, representing tests in >1,400,000 individuals, identified were of low quality based on a standardized study quality scale. In the 51 studies of higher quality, high-risk healthcare workers had higher seroprevalence of 17.1% (95% CI: 9.9-24.4%), compared to low-risk healthcare workers and general population of 5.4% (0.7-10.1%) and 5.3% (4.2-6.4%). Seroprevalence varied hugely across WHO regions, with lowest seroprevalence of general population in Western Pacific region (1.7%, 0.0-5.0%). Generally, the young (<20 years) and the old (≥65 years) were less likely to be seropositive compared to middle-aged (20-64 years) populations.Seroprevalence correlated with clinical COVID-19 reports, with pooled average of 7.7 (range: 2.0 to 23.1) serologically-detected-infections per confirmed COVID-19 case. Limitations Some heterogeneity cannot be well explained quantitatively. Conclusions The overall quality of seroprevalence studies examined was low. The relatively low seroprevalence among general populations suggest that in most settings, antibody-mediated herd immunity is far from being reached. Given the relatively narrow range of estimates of the ratio of serologically-detected infections to confirmed cases across different locales, reported case counts may help provide insights into the true proportion of the population infected. Primary Funding source National Science Fund for Distinguished Young Scholars (PROSPERO: CRD42020198253).
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Yang J, Chen X, Deng X, Chen Z, Gong H, Yan H, Wu Q, Shi H, Lai S, Ajelli M, Viboud C, Yu PH. Disease burden and clinical severity of the first pandemic wave of COVID-19 in Wuhan, China. Nat Commun 2020; 11:5411. [PMID: 33110070 PMCID: PMC7591855 DOI: 10.1038/s41467-020-19238-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) was first reported in Wuhan, China, where the initial wave of intense community transmissions was cut short by interventions. Using multiple data sources, here we estimate the disease burden and clinical severity by age of COVID-19 in Wuhan from December 1, 2019 to March 31, 2020. Our estimates account for the sensitivity of the laboratory assays, prospective community screenings, and healthcare seeking behaviors. Rates of symptomatic cases, medical consultations, hospitalizations and deaths were estimated at 796 (95% CI: 703-977), 489 (472-509), 370 (358-384), and 36.2 (35.0-37.3) per 100,000 persons, respectively. The COVID-19 outbreak in Wuhan had a higher burden than the 2009 influenza pandemic or seasonal influenza in terms of hospitalization and mortality rates, and clinical severity was similar to that of the 1918 influenza pandemic. Our comparison puts the COVID-19 pandemic into context and could be helpful to guide intervention strategies and preparedness for the potential resurgence of COVID-19.
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Affiliation(s)
- Juan Yang
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Xinhua Chen
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Xiaowei Deng
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Hui Gong
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Han Yan
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Qianhui Wu
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Huilin Shi
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
| | - Shengjie Lai
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China
- WorldPop, Department of Geography and Environment, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, 47405, USA
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, 02115, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Prof Hongjie Yu
- School of Public Health, Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, 200030, Shanghai, China.
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Weinberger DM, Chen J, Cohen T, Crawford FW, Mostashari F, Olson D, Pitzer VE, Reich NG, Russi M, Simonsen L, Watkins A, Viboud C. Estimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020. JAMA Intern Med 2020; 180:1336-1344. [PMID: 32609310 PMCID: PMC7330834 DOI: 10.1001/jamainternmed.2020.3391] [Citation(s) in RCA: 281] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
IMPORTANCE Efforts to track the severity and public health impact of coronavirus disease 2019 (COVID-19) in the United States have been hampered by state-level differences in diagnostic test availability, differing strategies for prioritization of individuals for testing, and delays between testing and reporting. Evaluating unexplained increases in deaths due to all causes or attributed to nonspecific outcomes, such as pneumonia and influenza, can provide a more complete picture of the burden of COVID-19. OBJECTIVE To estimate the burden of all deaths related to COVID-19 in the United States from March to May 2020. DESIGN, SETTING, AND POPULATION This observational study evaluated the numbers of US deaths from any cause and deaths from pneumonia, influenza, and/or COVID-19 from March 1 through May 30, 2020, using public data of the entire US population from the National Center for Health Statistics (NCHS). These numbers were compared with those from the same period of previous years. All data analyzed were accessed on June 12, 2020. MAIN OUTCOMES AND MEASURES Increases in weekly deaths due to any cause or deaths due to pneumonia/influenza/COVID-19 above a baseline, which was adjusted for time of year, influenza activity, and reporting delays. These estimates were compared with reported deaths attributed to COVID-19 and with testing data. RESULTS There were approximately 781 000 total deaths in the United States from March 1 to May 30, 2020, representing 122 300 (95% prediction interval, 116 800-127 000) more deaths than would typically be expected at that time of year. There were 95 235 reported deaths officially attributed to COVID-19 from March 1 to May 30, 2020. The number of excess all-cause deaths was 28% higher than the official tally of COVID-19-reported deaths during that period. In several states, these deaths occurred before increases in the availability of COVID-19 diagnostic tests and were not counted in official COVID-19 death records. There was substantial variability between states in the difference between official COVID-19 deaths and the estimated burden of excess deaths. CONCLUSIONS AND RELEVANCE Excess deaths provide an estimate of the full COVID-19 burden and indicate that official tallies likely undercount deaths due to the virus. The mortality burden and the completeness of the tallies vary markedly between states.
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Affiliation(s)
- Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut
| | - Jenny Chen
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut
| | - Forrest W Crawford
- Department of Biostatistics and the Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut.,Departments of Ecology and Evolutionary Biology, Statistics and Data Science, Yale School of Management, New Haven, Connecticut
| | | | - Don Olson
- Department of Health and Mental Hygiene, New York, New York
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut
| | - Nicholas G Reich
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst
| | - Marcus Russi
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut
| | - Lone Simonsen
- Department of Science and Environment, Roskilde University, Fredeiksberg, Denmark
| | - Anne Watkins
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland
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Yang J, Gong H, Chen X, Chen Z, Deng X, Qian M, Hou Z, Ajelli M, Viboud C, Yu H. Health-seeking behaviors of patients with acute respiratory infections during the outbreak of novel coronavirus disease 2019 in Wuhan, China. Influenza Other Respir Viruses 2020; 15:188-194. [PMID: 32909400 PMCID: PMC7902258 DOI: 10.1111/irv.12804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/12/2022] Open
Abstract
We conducted two surveys to evaluate the health‐seeking behaviors of individuals with acute respiratory infections (ARI) during the COVID‐19 outbreak in Wuhan, China. Among 351 participants reporting ARI (10.3%, 351/3,411), 36.5% sought medical assistance. Children were more likely to seek medical assistance than other age‐groups (66.1% vs. 28.0%‐35.1%). This population‐based study demonstrates that the majority of patients with ARI symptoms did not seek medical assistance during the COVID‐19 outbreak in Wuhan. These findings may be used to refine the estimates of disease burden and clinical severity of COVID‐19 and to plan for health resources allocation.
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Affiliation(s)
- Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hui Gong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Mengcen Qian
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Hou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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Yang J, Chen X, Deng X, Chen Z, Gong H, Yan H, Wu Q, Shi H, Lai S, Ajelli M, Viboud C, Yu H. Disease burden and clinical severity of the first pandemic wave of COVID-19 in Wuhan, China. medRxiv 2020:2020.08.27.20183228. [PMID: 32909016 PMCID: PMC7480068 DOI: 10.1101/2020.08.27.20183228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The pandemic of novel coronavirus disease 2019 (COVID-19) began in Wuhan, China, where a first wave of intense community transmission was cut short by interventions. Using multiple data source, we estimated the disease burden and clinical severity of COVID-19 by age in Wuhan from December 1, 2019 to March 31, 2020. We adjusted estimates for sensitivity of laboratory assays and accounted for prospective community screenings and healthcare seeking behaviors. Rates of symptomatic cases, medical consultations, hospitalizations and deaths were estimated at 796 (95%CI: 703-977), 489 (472-509), 370 (358-384), and 36.2 (35.0-37.3) per 100,000 persons, respectively. The COVID-19 outbreak in Wuhan had higher burden than the 2009 influenza pandemic or seasonal influenza, and that clinical severity was similar to that of the 1918 influenza pandemic. Our comparison puts the COVID-19 pandemic into context and could be helpful to guide intervention strategies and preparedness for the potential resurgence of COVID-19.
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Affiliation(s)
- Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hui Gong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Han Yan
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qianhui Wu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Huilin Shi
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Shengjie Lai
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- WorldPop, Department of Geography and Environment, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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35
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Zhang J, Litvinova M, Liang Y, Zheng W, Shi H, Vespignani A, Viboud C, Ajelli M, Yu H. The impact of relaxing interventions on human contact patterns and SARS-CoV-2 transmission in China. medRxiv 2020. [PMID: 32793917 DOI: 10.1101/2020.08.03.20167056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Non-pharmaceutical interventions to control COVID-19 spread have been implemented in several countries with different intensity, timing, and impact on transmission. As a result, post-lockdown COVID-19 dynamics are heterogenous and difficult to interpret. Here we describe a set of contact surveys performed in four Chinese cities (Wuhan, Shanghai, Shenzhen, and Changsha) during the pre-pandemic, lockdown, and post-lockdown period to quantify the transmission impact of relaxing interventions via changes in age-specific contact patterns. We estimate that the mean number of contacts increased 5%-17% since the end of the lockdown but are still 3-7 times lower than their pre-pandemic levels. We find that post-lockdown contact patterns in China are still sufficiently low to keep SARS-CoV-2 transmission under control. We also find that the impact of school interventions depends non-linearly on the share of other activities being resumed. When most community activities are halted, school closure leads to a 77% decrease in the reproductive number; in contrast, when social mixing outside of schools is at pre-pandemic level, school closure leads to a 5% reduction in transmission. Moving forward, to control COVID-19 spread without resorting to a lockdown, it will be key to dose relaxation in social mixing in the community and strengthen targeted interventions.
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36
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Aiken EL, McGough SF, Majumder MS, Wachtel G, Nguyen AT, Viboud C, Santillana M. Real-time estimation of disease activity in emerging outbreaks using internet search information. PLoS Comput Biol 2020; 16:e1008117. [PMID: 32804932 PMCID: PMC7451983 DOI: 10.1371/journal.pcbi.1008117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/27/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding the behavior of emerging disease outbreaks in, or ahead of, real-time could help healthcare officials better design interventions to mitigate impacts on affected populations. Most healthcare-based disease surveillance systems, however, have significant inherent reporting delays due to data collection, aggregation, and distribution processes. Recent work has shown that machine learning methods leveraging a combination of traditionally collected epidemiological information and novel Internet-based data sources, such as disease-related Internet search activity, can produce meaningful "nowcasts" of disease incidence ahead of healthcare-based estimates, with most successful case studies focusing on endemic and seasonal diseases such as influenza and dengue. Here, we apply similar computational methods to emerging outbreaks in geographic regions where no historical presence of the disease of interest has been observed. By combining limited available historical epidemiological data available with disease-related Internet search activity, we retrospectively estimate disease activity in five recent outbreaks weeks ahead of traditional surveillance methods. We find that the proposed computational methods frequently provide useful real-time incidence estimates that can help fill temporal data gaps resulting from surveillance reporting delays. However, the proposed methods are limited by issues of sample bias and skew in search query volumes, perhaps as a result of media coverage.
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Affiliation(s)
- Emily L. Aiken
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Sarah F. McGough
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Maimuna S. Majumder
- Department of Healthcare Policy, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gal Wachtel
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Andre T. Nguyen
- Booz Allen Hamilton, Columbia, Maryland, United States of America
- University of Maryland, Baltimore County, Baltimore, Maryland, United States of America
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mauricio Santillana
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
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37
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Muniz-Rodriguez K, Chowell G, Cheung CH, Jia D, Lai PY, Lee Y, Liu M, Ofori SK, Roosa KM, Simonsen L, Viboud C, Fung ICH. Doubling Time of the COVID-19 Epidemic by Province, China. Emerg Infect Dis 2020; 26:1912-1914. [PMID: 32330410 PMCID: PMC7392464 DOI: 10.3201/eid2608.200219] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In China, the doubling time of the coronavirus disease epidemic by province increased during January 20-February 9, 2020. Doubling time estimates ranged from 1.4 (95% CI 1.2-2.0) days for Hunan Province to 3.1 (95% CI 2.1-4.8) days for Xinjiang Province. The estimate for Hubei Province was 2.5 (95% CI 2.4-2.6) days.
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38
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Pollett S, Johansson M, Biggerstaff M, Morton LC, Bazaco SL, Brett Major DM, Stewart-Ibarra AM, Pavlin JA, Mate S, Sippy R, Hartman LJ, Reich NG, Maljkovic Berry I, Chretien JP, Althouse BM, Myer D, Viboud C, Rivers C. Identification and evaluation of epidemic prediction and forecasting reporting guidelines: A systematic review and a call for action. Epidemics 2020; 33:100400. [PMID: 33130412 PMCID: PMC8667087 DOI: 10.1016/j.epidem.2020.100400] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/24/2020] [Accepted: 06/25/2020] [Indexed: 01/26/2023] Open
Abstract
Introduction: High quality epidemic forecasting and prediction are critical to support response to local, regional and global infectious disease threats. Other fields of biomedical research use consensus reporting guidelines to ensure standardization and quality of research practice among researchers, and to provide a framework for end-users to interpret the validity of study results. The purpose of this study was to determine whether guidelines exist specifically for epidemic forecast and prediction publications. Methods: We undertook a formal systematic review to identify and evaluate any published infectious disease epidemic forecasting and prediction reporting guidelines. This review leveraged a team of 18 investigators from US Government and academic sectors. Results: A literature database search through May 26, 2019, identified 1467 publications (MEDLINE n = 584, EMBASE n = 883), and a grey-literature review identified a further 407 publications, yielding a total 1777 unique publications. A paired-reviewer system screened in 25 potentially eligible publications, of which two were ultimately deemed eligible. A qualitative review of these two published reporting guidelines indicated that neither were specific for epidemic forecasting and prediction, although they described reporting items which may be relevant to epidemic forecasting and prediction studies. Conclusions: This systematic review confirms that no specific guidelines have been published to standardize the reporting of epidemic forecasting and prediction studies. These findings underscore the need to develop such reporting guidelines in order to improve the transparency, quality and implementation of epidemic forecasting and prediction research in operational public health.
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Affiliation(s)
- Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, MD, USA.
| | - Michael Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, San Juan, Puerto Rico, USA
| | | | - Lindsay C Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Division, Silver Spring, MD, USA; Cherokee Nation Strategic Programs, Tulsa, OK, USA; Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Sara L Bazaco
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Division, Silver Spring, MD, USA; General Dynamics Information Technology, Falls Church, VA, USA
| | | | - Anna M Stewart-Ibarra
- Institute for Global Health and Translational Science, State University of New York Upstate Medical University, Syracuse, NY, USA; InterAmerican Institute for Global Change Research (IAI), Montevideo, Department of Montevideo, Uruguay
| | - Julie A Pavlin
- National Academies of Sciences, Engineering, and Medicine, DC, USA
| | - Suzanne Mate
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, MD, USA
| | - Rachel Sippy
- Institute for Global Health and Translational Science, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Laurie J Hartman
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Division, Silver Spring, MD, USA; Cherokee Nation Strategic Programs, Tulsa, OK, USA
| | | | | | | | - Benjamin M Althouse
- University of Washington, WA, USA; Institute for Disease Modeling, Bellevue, WA, USA; New Mexico State University, Las Cruces, NM, USA
| | - Diane Myer
- Johns Hopkins Center for Health Security, MD, USA
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, MD, USA
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Affiliation(s)
- Caitlin Rivers
- Johns Hopkins Center for Health Security, Maryland, United States of America
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Marlyand, United States of America
- Uniformed Services University of the Health Sciences, Maryland, United States of America
- Marie Bashir Institute, University of Sydney, New South Wales, Australia
| | - Cecile Viboud
- National Institutes of Health, Maryland, United States of America
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40
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Zhang J, Litvinova M, Wang W, Wang Y, Deng X, Chen X, Li M, Zheng W, Yi L, Chen X, Wu Q, Liang Y, Wang X, Yang J, Sun K, Longini IM, Halloran ME, Wu P, Cowling BJ, Merler S, Viboud C, Vespignani A, Ajelli M, Yu H. Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modelling study. Lancet Infect Dis 2020; 20:793-802. [PMID: 32247326 PMCID: PMC7269887 DOI: 10.1016/s1473-3099(20)30230-9] [Citation(s) in RCA: 370] [Impact Index Per Article: 92.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) epidemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), began in Wuhan city, Hubei province, in December, 2019, and has spread throughout China. Understanding the evolving epidemiology and transmission dynamics of the outbreak beyond Hubei would provide timely information to guide intervention policy. METHODS We collected individual information from official public sources on laboratory-confirmed cases reported outside Hubei in mainland China for the period of Jan 19 to Feb 17, 2020. We used the date of the fourth revision of the case definition (Jan 27) to divide the epidemic into two time periods (Dec 24 to Jan 27, and Jan 28 to Feb 17) as the date of symptom onset. We estimated trends in the demographic characteristics of cases and key time-to-event intervals. We used a Bayesian approach to estimate the dynamics of the net reproduction number (Rt) at the provincial level. FINDINGS We collected data on 8579 cases from 30 provinces. The median age of cases was 44 years (33-56), with an increasing proportion of cases in younger age groups and in elderly people (ie, aged >64 years) as the epidemic progressed. The mean time from symptom onset to hospital admission decreased from 4·4 days (95% CI 0·0-14·0) for the period of Dec 24 to Jan 27, to 2·6 days (0·0-9·0) for the period of Jan 28 to Feb 17. The mean incubation period for the entire period was estimated at 5·2 days (1·8-12·4) and the mean serial interval at 5·1 days (1·3-11·6). The epidemic dynamics in provinces outside Hubei were highly variable but consistently included a mixture of case importations and local transmission. We estimated that the epidemic was self-sustained for less than 3 weeks, with mean Rt reaching peaks between 1·08 (95% CI 0·74-1·54) in Shenzhen city of Guangdong province and 1·71 (1·32-2·17) in Shandong province. In all the locations for which we had sufficient data coverage of Rt, Rt was estimated to be below the epidemic threshold (ie, <1) after Jan 30. INTERPRETATION Our estimates of the incubation period and serial interval were similar, suggesting an early peak of infectiousness, with possible transmission before the onset of symptoms. Our results also indicate that, as the epidemic progressed, infectious individuals were isolated more quickly, thus shortening the window of transmission in the community. Overall, our findings indicate that strict containment measures, movement restrictions, and increased awareness of the population might have contributed to interrupt local transmission of SARS-CoV-2 outside Hubei province. FUNDING National Science Fund for Distinguished Young Scholars, National Institute of General Medical Sciences, and European Commission Horizon 2020.
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Affiliation(s)
- Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | | | - Wei Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinghui Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Mei Li
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wen Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lan Yi
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qianhui Wu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yuxia Liang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiling Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Ira M Longini
- Department of Biostatistics, College of Public Health, Health Professions, and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - M Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Vespignani
- ISI Foundation, Turin, Italy; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | | | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
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41
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Metcalf CJE, Viboud C, Spiro DJ, Grenfell BT. Using Serology with Models to Clarify the Trajectory of the SARS-CoV-2 Emerging Outbreak. Trends Immunol 2020; 41:849-851. [PMID: 32680648 PMCID: PMC7323642 DOI: 10.1016/j.it.2020.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 11/28/2022]
Affiliation(s)
- C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - David J Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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42
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Kupfer LE, Beecroft B, Viboud C, Wang X, Brouwers P. A call to action: strengthening the capacity for data capture and computational modelling of HIV integrated care in low- and middle-income countries. J Int AIDS Soc 2020; 23 Suppl 1:e25475. [PMID: 32562312 PMCID: PMC7305411 DOI: 10.1002/jia2.25475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Linda E Kupfer
- Fogarty International CenterUS National Institutes of HealthBethesdaMDUSA
| | - Blythe Beecroft
- Fogarty International CenterUS National Institutes of HealthBethesdaMDUSA
| | - Cecile Viboud
- Fogarty International CenterUS National Institutes of HealthBethesdaMDUSA
| | - Xujing Wang
- National Institute of Diabetes and Digestive and Kidney DiseasesUS National Institutes of HealthBethesdaMDUSA
| | - Pim Brouwers
- National Institute of Mental HealthUS National Institutes of HealthBethesdaMDUSA
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43
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Hansen CL, McCormick BJJ, Azam SI, Ahmed K, Baker JM, Hussain E, Jahan A, Jamison AF, Knobler SL, Samji N, Shah WH, Spiro DJ, Thomas ED, Viboud C, Rasmussen ZA. Substantial and sustained reduction in under-5 mortality, diarrhea, and pneumonia in Oshikhandass, Pakistan: evidence from two longitudinal cohort studies 15 years apart. BMC Public Health 2020; 20:759. [PMID: 32448276 PMCID: PMC7245818 DOI: 10.1186/s12889-020-08847-7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 05/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oshikhandass is a rural village in northern Pakistan where a 1989-1991 verbal autopsy study showed that diarrhea and pneumonia were the top causes of under-5 mortality. Intensive surveillance, active community health education and child health interventions were delivered in 1989-1996; here we assess improvements in under-5 mortality, diarrhea, and pneumonia over this period and 15 years later. METHODS Two prospective open-cohort studies in Oshikhandass from 1989 to 1996 (Study 1) and 2011-2014 (Study 2) enrolled all children under age 60 months. Study staff trained using WHO guidelines, conducted weekly household surveillance and promoted knowledge on causes and management of diarrhea and pneumonia. Information about household characteristics and socioeconomic status was collected. Hurdle models were constructed to examine putative risk factors for diarrhea and pneumonia. RESULTS Against a backdrop of considerable change in the socioeconomic status of the community, under-5 mortality, which declined over the course of Study 1 (from 114.3 to 79.5 deaths/1000 live births (LB) between 1989 and 1996), exceeded Sustainable Development Goal 3 by Study 2 (19.8 deaths/ 1000 LB). Reductions in diarrhea prevalence (20.3 to 2.2 days/ Child Year [CY]), incidence (2.1 to 0.5 episodes/ CY), and number of bloody diarrhea episodes (18.6 to 5.2%) seen during Study 1, were sustained in Study 2. Pneumonia incidence was 0.5 episodes /CY in Study 1 and 0.2/CY in Study 2; only 5% of episodes were categorized as severe or very severe in both studies. While no individual factors predicted a statistically significant difference in diarrhea or pneumonia episodes, the combined effect of water, toilet and housing materials was associated with a significant decrease in diarrhea; higher household income was the most protective factor for pneumonia in Study 1. CONCLUSIONS We report a 4-fold decrease in overall childhood mortality, and a 2-fold decrease in childhood morbidity from diarrhea and pneumonia in a remote rural village in Pakistan between 1989 and 2014. We conclude that significant, sustainable improvements in child health may be achieved through improved socioeconomic status and promoting interactions between locally engaged health workers and the community, but that continued efforts are needed to improve health worker training, supervision, and the rational use of medications. TRIAL REGISTRATION Not Applicable.
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Affiliation(s)
- C L Hansen
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - B J J McCormick
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - S I Azam
- Department of Community Health Sciences, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - K Ahmed
- Karakoram International University, University Road, Gilgit, Pakistan
| | - J M Baker
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - E Hussain
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Jahan
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A F Jamison
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - S L Knobler
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - N Samji
- Department of Community Health Sciences, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - W H Shah
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - D J Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - E D Thomas
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - C Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Z A Rasmussen
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA.
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44
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Heraud JM, Razanajatovo NH, Viboud C. Global circulation of respiratory viruses: from local observations to global predictions. Lancet Glob Health 2020; 7:e982-e983. [PMID: 31303303 DOI: 10.1016/s2214-109x(19)30277-3] [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] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 05/30/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Jean-Michel Heraud
- National Influenza Centre, Virology Unit, Institut Pasteur de Madagascar, Antananarivo 101, Madagascar.
| | | | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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45
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Yang J, Gong H, Chen X, Chen Z, Deng X, Qian M, Hou Z, Ajelli M, Viboud C, Yu H. Health seeking behaviors of patients with acute respiratory infections during the outbreak of novel coronavirus disease 2019 in Wuhan, China. medRxiv 2020. [PMID: 32511468 DOI: 10.1101/2020.05.05.20091553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We conducted two surveys to evaluate the health-seeking behaviors of individuals with acute respiratory infections (ARI) during the COVID-19 outbreak in Wuhan, China. Among 351 participants reporting ARI (10.3%, 351/3,411), 36.5% sought medical assistance. Children were more likely to seek medical assistance than other age groups (66.1% vs. 28.0%-35.1%).
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Affiliation(s)
- Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hui Gong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Mengcen Qian
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Hou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Marco Ajelli
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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46
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Weinberger DM, Cohen T, Crawford FW, Mostashari F, Olson D, Pitzer VE, Reich NG, Russi M, Simonsen L, Watkins A, Viboud C. Estimating the early death toll of COVID-19 in the United States. medRxiv 2020. [PMID: 32511293 PMCID: PMC7217085 DOI: 10.1101/2020.04.15.20066431] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Efforts to track the severity and public health impact of the novel coronavirus, COVID-19, in the US have been hampered by testing issues, reporting lags, and inconsistency between states. Evaluating unexplained increases in deaths attributed to broad outcomes, such as pneumonia and influenza (P&I) or all causes, can provide a more complete and consistent picture of the burden caused by COVID-19. Methods We evaluated increases in the occurrence of deaths due to P&I above a seasonal baseline (adjusted for influenza activity) or due to any cause across the United States in February and March 2020. These estimates are compared with reported deaths due to COVID-19 and with testing data. Results There were notable increases in the rate of death due to P&I in February and March 2020. In a number of states, these deaths pre-dated increases in COVID-19 testing rates and were not counted in official records as related to COVID-19. There was substantial variability between states in the discrepancy between reported rates of death due to COVID-19 and the estimated burden of excess deaths due to P&I. The increase in all-cause deaths in New York and New Jersey is 1.5-3 times higher than the official tally of COVID-19 confirmed deaths or the estimated excess death due to P&I. Conclusions Excess P&I deaths provide a conservative estimate of COVID-19 burden and indicate that COVID-19-related deaths are missed in locations with inadequate testing or intense pandemic activity.
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Affiliation(s)
- Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT
| | - Forrest W Crawford
- Department of Biostatistics and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT; Yale Departments of Ecology and Evolutionary Biology, Statistics & Data Science, Yale School of Management
| | | | - Don Olson
- Department of Health and Mental Hygiene, New York City, NY
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT
| | - Nicholas G Reich
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA
| | - Marcus Russi
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT
| | - Lone Simonsen
- Department of Science and Environment, Roskilde University, Denmark
| | - Anne Watkins
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD
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47
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Muniz-Rodriguez K, Chowell G, Cheung CH, Jia D, Lai PY, Lee Y, Liu M, Ofori SK, Roosa KM, Simonsen L, Viboud C, Chun-Hai Fung I. Doubling Time of the COVID-19 Epidemic by Chinese Province. medRxiv 2020:2020.02.05.20020750. [PMID: 32511421 PMCID: PMC7216847 DOI: 10.1101/2020.02.05.20020750] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
COVID-19 epidemic doubling time by Chinese province was increasing from January 20 through February 9, 2020. The harmonic mean of the arithmetic mean doubling time estimates ranged from 1.4 (Hunan, 95% CI, 1.2-2.0) to 3.1 (Xinjiang, 95% CI, 2.1-4.8), with an estimate of 2.5 days (95% CI, 2.4-2.6) for Hubei.
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Affiliation(s)
- Kamalich Muniz-Rodriguez
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Gerardo Chowell
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Chi-Hin Cheung
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Dongyu Jia
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Po-Ying Lai
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Yiseul Lee
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Manyun Liu
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Sylvia K Ofori
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Kimberlyn M Roosa
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Lone Simonsen
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Cecile Viboud
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
| | - Isaac Chun-Hai Fung
- Georgia Southern University, Statesboro, GA, USA (K. Muniz-Rodriguez, D. Jia, M. Liu, S. K. Ofori, I. C.-H. Fung); Georgia State University, Atlanta, GA, USA (G. Chowell, Y. Lee, K. M. Roosa); Independent researcher (C.-H. Cheung); Boston University, Boston, MA, USA (P.-Y. Lai); Roskilde University, Roskilde, Denmark (L. Simonsen); The National Institutes of Health, Bethesda, MD, USA (G. Chowell, C. Viboud)
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48
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Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, Schroeder A. Aggregated mobility data could help fight COVID-19. Science 2020; 368:145-146. [PMID: 32205458 DOI: 10.1126/science.abb8021] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Caroline O Buckee
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.
| | - Satchit Balsari
- Emergency Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer Chan
- Emergency Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.,NetHope, Inc., Fairfax, VA 22030, USA
| | - Mercè Crosas
- Institute for Quantitative Social Science, Harvard University, Boston, MA 02138, USA
| | - Francesca Dominici
- Harvard Data Science Initiative, Harvard University, Boston, MA 02138, USA
| | - Urs Gasser
- Berkman Klein Center for Internet and Society, Harvard University Harvard Law School, Boston, MA 02138, USA
| | - Yonatan H Grad
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | | | - M Elizabeth Halloran
- Center for Inference and Dynamics of Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,University of Washington, Seattle, WA 98195, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.,Boston Children's Hospital, Boston, MA 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | | | | | - T Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mauricio Santillana
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Boston Children's Hospital, Boston, MA 02115, USA
| | - Samuel V Scarpino
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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49
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Zhang J, Litvinova M, Liang Y, Wang Y, Wang W, Zhao S, Wu Q, Merler S, Viboud C, Vespignani A, Ajelli M, Yu H. Age profile of susceptibility, mixing, and social distancing shape the dynamics of the novel coronavirus disease 2019 outbreak in China. medRxiv 2020:2020.03.19.20039107. [PMID: 32511428 PMCID: PMC7217069 DOI: 10.1101/2020.03.19.20039107] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Strict interventions were successful to control the novel coronavirus (COVID-19) outbreak in China. As transmission intensifies in other countries, the interplay between age, contact patterns, social distancing, susceptibility to infection and disease, and COVID-19 dynamics remains unclear. To answer these questions, we analyze contact surveys data for Wuhan and Shanghai before and during the outbreak and contact tracing information from Hunan Province. Daily contacts were reduced 7-9 fold during the COVID-19 social distancing period, with most interactions restricted to the household. Children 0-14 years were 59% (95% CI 7-82%) less susceptible than individuals 65 years and over. A transmission model calibrated against these data indicates that social distancing alone, as implemented in China during the outbreak, is sufficient to control COVID-19. While proactive school closures cannot interrupt transmission on their own, they reduce peak incidence by half and delay the epidemic. These findings can help guide global intervention policies.
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Affiliation(s)
- Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | | | - Yuxia Liang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wei Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Shanlu Zhao
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Qianhui Wu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | | | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Alessandro Vespignani
- ISI Foundation, Turin, Italy
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | | | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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50
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Deng X, Yang J, Wang W, Wang X, Zhou J, Chen Z, Li J, Chen Y, Yan H, Zhang J, Zhang Y, Wang Y, Qiu Q, Gong H, Wei X, Wang L, Sun K, Wu P, Ajelli M, Cowling BJ, Viboud C, Yu H. Case fatality risk of novel coronavirus diseases 2019 in China. medRxiv 2020:2020.03.04.20031005. [PMID: 32511425 PMCID: PMC7217011 DOI: 10.1101/2020.03.04.20031005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE The outbreak of novel coronavirus disease 2019 (COVID-19) imposed a substanal health burden in mainland China and remains a global epidemic threat. Our objectives are to assess the case fatality risk (CFR) among CO VID-19 patients detected in mainland China, stratified by clinical category and age group. METHODS We collected individual information on laboratory-confirmed COVID-19 cases from publicly available official sources from December 29, 2019 to February 23, 2020. We explored the risk factors associated with mortality. We used methods accounting for right-censoring and survival analyses to estimatethe CFR among detected cases. RESULTS Of 12,863 cases reported outside Hubei, we obtained individual records for 9,651 cases, including 62 deaths and 1,449 discharged cases. The deceased were significantly older than discharged cases (median age: 77 vs 39 years, p<0.001). 58% (36/62) were male. Older age (OR 1.18 per year; 95% CI: 1.14 to 1.22), being male (OR 2.02; 95% CI: 1.02 to 4.03), and being treated in less developed economic regions (e.g., West and Northeast vs. East, OR 3.93; 95 %Cl:1.74 to 8.85) were mortality risk factors. The estimated CFR was 0.89-1.24% among all cases. The fatality risk among critical patients was 2-fold higher than that among severe and critical patients, and 24-fold higher than that among moderate, severe and critical patients. CONCLUSIONS Our estimates of CFR based on laboratory-confirmed cases ascertained outside of Hubei suggest that COVID-19 is not as severe as severe acute respiratory syndrome and Middle East respiratory syndrome, but more similar to the mortality risk of 2009 H1N1 influenza pandemic in hospitalized patients. The fatality risk of COVID-19 is higher in males and increases with age. Our study improves the severity assessment of the ongoing epidemic and can inform the COVID-19 outbreak response in China and beyond.
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Affiliation(s)
- Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wei Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiling Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiaxin Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jing Li
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yinzi Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Han Yan
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Juanjuan Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yongli Zhang
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Hui Gong
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xianglin Wei
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lili Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | | | - Benjamin J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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