1
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Langedijk AC, Vrancken B, Lebbink RJ, Wilkins D, Kelly EJ, Baraldi E, Mascareñas de Los Santos AH, Danilenko DM, Choi EH, Palomino MA, Chi H, Keller C, Cohen R, Papenburg J, Pernica J, Greenough A, Richmond P, Martinón-Torres F, Heikkinen T, Stein RT, Hosoya M, Nunes MC, Verwey C, Evers A, Kragten-Tabatabaie L, Suchard MA, Kosakovsky Pond SL, Poletto C, Colizza V, Lemey P, Bont LJ. The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus. Nat Commun 2024; 15:3083. [PMID: 38600104 PMCID: PMC11006891 DOI: 10.1038/s41467-024-47118-6] [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: 04/12/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection in young children and the second leading cause of infant death worldwide. While global circulation has been extensively studied for respiratory viruses such as seasonal influenza, and more recently also in great detail for SARS-CoV-2, a lack of global multi-annual sampling of complete RSV genomes limits our understanding of RSV molecular epidemiology. Here, we capitalise on the genomic surveillance by the INFORM-RSV study and apply phylodynamic approaches to uncover how selection and neutral epidemiological processes shape RSV diversity. Using complete viral genome sequences, we show similar patterns of site-specific diversifying selection among RSVA and RSVB and recover the imprint of non-neutral epidemic processes on their genealogies. Using a phylogeographic approach, we provide evidence for air travel governing the global patterns of RSVA and RSVB spread, which results in a considerable degree of phylogenetic mixing across countries. Our findings highlight the potential of systematic global RSV genomic surveillance for transforming our understanding of global RSV spread.
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Affiliation(s)
- Annefleur C Langedijk
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Deidre Wilkins
- Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA
| | - Elizabeth J Kelly
- Translational Medicine, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, 1 MedImmune Way, Gaithersburg, MD, USA
| | - Eugenio Baraldi
- Department of Woman's and Child's Health, University Hospital of Padova, Padova, Italy
- ReSViNET Foundation, Zeist, the Netherlands
- Institute of Pediatric Research "Città della Speranza", Padova, Italy
| | | | - Daria M Danilenko
- Smorodintsev Research Institute of Influenza, St. Petersburg, Russia
| | - Eun Hwa Choi
- Seoul National University Children's Hospital, Seoul, South Korea
| | | | - Hsin Chi
- MacKay Children's Hospital, New Taipei, Taiwan, ROC
| | - Christian Keller
- Institute of Virology, University Hospital Giessen and Marburg, Marburg, Germany
| | | | | | | | - Anne Greenough
- ReSViNET Foundation, Zeist, the Netherlands
- King's College London, London, UK
| | | | - Federico Martinón-Torres
- ReSViNET Foundation, Zeist, the Netherlands
- Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Terho Heikkinen
- ReSViNET Foundation, Zeist, the Netherlands
- University of Turku and Turku University Hospital, Turku, Finland
| | - Renato T Stein
- ReSViNET Foundation, Zeist, the Netherlands
- Pontificia Universidade Catolica de Rio Grande do Sul, Porto Alegre, Brazil
| | - Mitsuaki Hosoya
- Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Marta C Nunes
- ReSViNET Foundation, Zeist, the Netherlands
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, and 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
| | - Charl Verwey
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Hospices Civils de Lyon and the Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Anouk Evers
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | | | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, 801 N Broad St, Philadelphia, PA, 19122, USA
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Herestraat 49, 3000, Leuven, Belgium
| | - Louis J Bont
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands.
- ReSViNET Foundation, Zeist, the Netherlands.
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Parino F, Gustani-Buss E, Bedford T, Suchard MA, Trovão NS, Rambaut A, Colizza V, Poletto C, Lemey P. Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation. medRxiv 2024:2024.03.14.24303719. [PMID: 38559244 PMCID: PMC10980132 DOI: 10.1101/2024.03.14.24303719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Global seasonal influenza circulation involves a complex interplay between local (seasonality, demography, host immunity) and global factors (international mobility) shaping recurrent epidemic patterns. No studies so far have reconciled the two spatial levels, evaluating the coupling between national epidemics, considering heterogeneous coverage of epidemiological and virological data, integrating different data sources. We propose a novel combined approach based on a dynamical model of global influenza spread (GLEAM), integrating high-resolution demographic and mobility data, and a generalized linear model of phylogeographic diffusion that accounts for time-varying migration rates. Seasonal migration fluxes across global macro-regions simulated with GLEAM are tested as phylogeographic predictors to provide model validation and calibration based on genetic data. Seasonal fluxes obtained with a specific transmissibility peak time and recurrent travel outperformed the raw air-transportation predictor, previously considered as optimal indicator of global influenza migration. Influenza A subtypes supported autumn-winter reproductive number as high as 2.25 and an average immunity duration of 2 years. Similar dynamics were preferred by influenza B lineages, with a lower autumn-winter reproductive number. Comparing simulated epidemic profiles against FluNet data offered comparatively limited resolution power. The multiscale approach enables model selection yielding a novel computational framework for describing global influenza dynamics at different scales - local transmission and national epidemics vs. international coupling through mobility and imported cases. Our findings have important implications to improve preparedness against seasonal influenza epidemics. The approach can be generalized to other epidemic contexts, such as emerging disease outbreaks to improve the flexibility and predictive power of modeling.
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Affiliation(s)
- Francesco Parino
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidemiologie et de Santé Publique (IPLESP), Paris, France
| | - Emanuele Gustani-Buss
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, 3000 Leuven, Belgium
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Howard Hughes Medical Institute, Seattle, Washington 98109, USA
| | - Marc A. Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
| | | | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidemiologie et de Santé Publique (IPLESP), Paris, France
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, 3000 Leuven, Belgium
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3
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic. Cell 2024; 187:1374-1386.e13. [PMID: 38428425 PMCID: PMC10962340 DOI: 10.1016/j.cell.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I Paredes
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA
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4
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Faucher B, Sabbatini CE, Czuppon P, Kraemer MUG, Lemey P, Colizza V, Blanquart F, Boëlle PY, Poletto C. Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha. Nat Commun 2024; 15:2152. [PMID: 38461311 PMCID: PMC10925057 DOI: 10.1038/s41467-024-46345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) circulated cryptically before being identified as a threat, delaying interventions. Here we studied the drivers of such silent spread and its epidemic impact to inform future response planning. We focused on Alpha spread out of the UK. We integrated spatio-temporal records of international mobility, local epidemic growth and genomic surveillance into a Bayesian framework to reconstruct the first three months after Alpha emergence. We found that silent circulation lasted from days to months and decreased with the logarithm of sequencing coverage. Social restrictions in some countries likely delayed the establishment of local transmission, mitigating the negative consequences of late detection. Revisiting the initial spread of Alpha supports local mitigation at the destination in case of emerging events.
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Affiliation(s)
- Benjamin Faucher
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), F75012, Paris, France
| | - Chiara E Sabbatini
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), F75012, Paris, France
| | - Peter Czuppon
- Institute for Evolution and Biodiversity, University of Münster, Münster, 48149, Germany
| | - Moritz U G Kraemer
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), F75012, Paris, France
- Department of Biology, Georgetown University, Washington, DC, USA
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris, 75005, France
| | - Pierre-Yves Boëlle
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), F75012, Paris, France
| | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy.
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5
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Pouquet M, Decarreaux D, Di Domenico L, Sabbatini CE, Prévot-Monsacre P, Fourié T, Villarroel PMS, Priet S, Blanché H, Sebaoun JM, Deleuze JF, Turbelin C, Rossignol L, Werner A, Kochert F, Grosgogeat B, Rabiega P, Laupie J, Abraham N, Noël H, van der Werf S, Colizza V, Carrat F, Charrel R, de Lamballerie X, Blanchon T, Falchi A. SARS-CoV-2 infection prevalence and associated factors among primary healthcare workers in France after the third COVID-19 wave. Sci Rep 2024; 14:5418. [PMID: 38443618 PMCID: PMC10914718 DOI: 10.1038/s41598-024-55477-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
Data on the SARS-CoV-2 infection among primary health care workers (PHCWs) are scarce but essential to reflect on policy regarding prevention and control measures. We assessed the prevalence of PHCWs who have been infected by SARS-CoV-2 in comparison with modeling from the general population in metropolitan France, and associated factors. A cross-sectional study was conducted among general practitioners (GPs), pediatricians, dental and pharmacy workers in primary care between May and August 2021. Participants volunteered to provide a dried-blood spot for SARS-CoV-2 antibody assessment and completed a questionnaire. The primary outcome was defined as the detection of infection-induced antibodies (anti-nucleocapsid IgG, and for non-vaccinees: anti-Spike IgG and neutralizing antibodies) or previous self-reported infection (positive RT-qPCR or antigenic test, or positive ELISA test before vaccination). Estimates were adjusted using weights for representativeness and compared with prediction from the general population. Poisson regressions were used to quantify associated factors. The analysis included 1612 PHCWs. Weighted prevalences were: 31.7% (95% CI 27.5-36.0) for GPs, 28.7% (95% CI 24.4-33.0) for pediatricians, 25.2% (95% CI 20.6-31.0) for dentists, and 25.5% (95% CI 18.2-34.0) for pharmacists. Estimates were compatible with model predictions for the general population. PHCWs more likely to be infected were: GPs compared to pharmacist assistants (adjusted prevalence ratio [aPR] = 2.26; CI 95% 1.01-5.07), those living in Île-de-France (aPR = 1.53; CI 95% 1.14-2.05), South-East (aPR = 1.57; CI 95% 1.19-2.08), North-East (aPR = 1.81; CI 95% 1.38-2.37), and those having an unprotected contact with a COVID-19 case within the household (aPR = 1.48; CI 95% 1.22-1.80). Occupational factors were not associated with infection. In conclusion, the risk of SARS-CoV-2 exposure for PHCWs was more likely to have occurred in the community rather than at their workplace.
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Affiliation(s)
- Marie Pouquet
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France.
| | - Dorine Decarreaux
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
- Laboratoire de Virologie, Université de Corse Pascal Paoli, UR7310 Bioscope, 20250, Corte, France
- Unité Des Virus Emergents, Aix Marseille University, IRD 190, INSERM U1207, 13005, Marseille, France
| | - Laura Di Domenico
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
| | - Chiara E Sabbatini
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
| | - Pol Prévot-Monsacre
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
| | - Toscane Fourié
- Unité Des Virus Emergents, Aix Marseille University, IRD 190, INSERM U1207, 13005, Marseille, France
| | | | - Stephane Priet
- Unité Des Virus Emergents, Aix Marseille University, IRD 190, INSERM U1207, 13005, Marseille, France
| | | | | | | | - Clément Turbelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
| | - Louise Rossignol
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
| | - Andréas Werner
- Association Française de Pédiatrie Ambulatoire (AFPA), Zone de la Fouquetière, 155 Rue Edouard Branly, 44150, Ancenis-Saint-Géréon, France
| | - Fabienne Kochert
- Association Française de Pédiatrie Ambulatoire (AFPA), Zone de la Fouquetière, 155 Rue Edouard Branly, 44150, Ancenis-Saint-Géréon, France
| | - Brigitte Grosgogeat
- Faculté d'Odontologie, Université Claude Bernard Lyon 1, Université de Lyon, 69000, Lyon, France
- Laboratoire des Multimatériaux et Interfaces, UMR CNRS 5615, Université Claude Bernard Lyon 1, Université de Lyon, 69000, Lyon, France
- Réseau ReCOL, Association Dentaire Française, 75000, Paris, France
- Service d'Odontologie, Hospices Civils de Lyon, 69007, Lyon, France
| | | | - Julien Laupie
- Réseau ReCOL, Association Dentaire Française, 75000, Paris, France
| | | | - Harold Noël
- Infectious Diseases Division, Santé Publique France, 94410, Saint Maurice, France
| | - Sylvie van der Werf
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Molecular Genetics of RNA Viruses Unit, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, National Reference Center for Respiratory Viruses, 75015, Paris, France
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
| | - Fabrice Carrat
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
- Département de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine, Sorbonne Université, 75012, Paris, France
| | - Remi Charrel
- Unité Des Virus Emergents, Aix Marseille University, IRD 190, INSERM U1207, 13005, Marseille, France
- LE Service de Prévention du Risque Infectieux (LESPRI), CLIN AP-HM Hôpitaux Universitaires de Marseille, 13005, Marseille, France
| | - Xavier de Lamballerie
- Unité Des Virus Emergents, Aix Marseille University, IRD 190, INSERM U1207, 13005, Marseille, France
| | - Thierry Blanchon
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), 75012, Paris, France
| | - Alessandra Falchi
- Laboratoire de Virologie, Université de Corse Pascal Paoli, UR7310 Bioscope, 20250, Corte, France
- Unité Des Virus Emergents, Aix Marseille University, IRD 190, INSERM U1207, 13005, Marseille, France
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6
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Gräf T, Martinez AA, Bello G, Dellicour S, Lemey P, Colizza V, Mazzoli M, Poletto C, Cardoso VLO, da Silva AF, Motta FC, Resende PC, Siqueira MM, Franco L, Gresh L, Gabastou JM, Rodriguez A, Vicari A, Aldighieri S, Mendez-Rico J, Leite JA. Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean. Nat Commun 2024; 15:1837. [PMID: 38418815 PMCID: PMC10902334 DOI: 10.1038/s41467-024-46143-9] [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: 10/11/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.
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Affiliation(s)
- Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Brazil.
| | - Alexander A Martinez
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
- National Research System (SNI), National Secretary of Research, Technology and Innovation (SENACYT), Panama City, Panama
- Department of Microbiology and Immunology, University of Panama, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Mattia Mazzoli
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Vanessa Leiko Oikawa Cardoso
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, FIOCRUZ-Bahia, Salvador, Brazil
| | | | - Fernando Couto Motta
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leticia Franco
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Lionel Gresh
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jean-Marc Gabastou
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Angel Rodriguez
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Andrea Vicari
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Sylvain Aldighieri
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jairo Mendez-Rico
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Juliana Almeida Leite
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA.
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Sabbatini CE, Pullano G, Di Domenico L, Rubrichi S, Bansal S, Colizza V. The impact of spatial connectivity on NPIs effectiveness. BMC Infect Dis 2024; 24:21. [PMID: 38166649 PMCID: PMC10763474 DOI: 10.1186/s12879-023-08900-x] [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: 07/05/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND France implemented a combination of non-pharmaceutical interventions (NPIs) to manage the COVID-19 pandemic between September 2020 and June 2021. These included a lockdown in the fall 2020 - the second since the start of the pandemic - to counteract the second wave, followed by a long period of nighttime curfew, and by a third lockdown in the spring 2021 against the Alpha wave. Interventions have so far been evaluated in isolation, neglecting the spatial connectivity between regions through mobility that may impact NPI effectiveness. METHODS Focusing on September 2020-June 2021, we developed a regionally-based epidemic metapopulation model informed by observed mobility fluxes from daily mobile phone data and fitted the model to regional hospital admissions. The model integrated data on vaccination and variants spread. Scenarios were designed to assess the impact of the Alpha variant, characterized by increased transmissibility and risk of hospitalization, of the vaccination campaign and alternative policy decisions. RESULTS The spatial model better captured the heterogeneity observed in the regional dynamics, compared to models neglecting inter-regional mobility. The third lockdown was similarly effective to the second lockdown after discounting for immunity, Alpha, and seasonality (51% vs 52% median regional reduction in the reproductive number R0, respectively). The 6pm nighttime curfew with bars and restaurants closed, implemented in January 2021, substantially reduced COVID-19 transmission. It initially led to 49% median regional reduction of R0, decreasing to 43% reduction by March 2021. In absence of vaccination, implemented interventions would have been insufficient against the Alpha wave. Counterfactual scenarios proposing a sequence of lockdowns in a stop-and-go fashion would have reduced hospitalizations and restriction days for low enough thresholds triggering and lifting restrictions. CONCLUSIONS Spatial connectivity induced by mobility impacted the effectiveness of interventions especially in regions with higher mobility rates. Early evening curfew with gastronomy sector closed allowed authorities to delay the third wave. Stop-and-go lockdowns could have substantially lowered both healthcare and societal burdens if implemented early enough, compared to the observed application of lockdown-curfew-lockdown, but likely at the expense of several labor sectors. These findings contribute to characterize the effectiveness of implemented strategies and improve pandemic preparedness.
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Affiliation(s)
- Chiara E Sabbatini
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Pullano
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Laura Di Domenico
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Stefania Rubrichi
- Orange Labs, Sociology and Economics of Networks and Services (SENSE), Chatillon, France
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
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8
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Valdano E, Colombi D, Poletto C, Colizza V. Epidemic graph diagrams as analytics for epidemic control in the data-rich era. Nat Commun 2023; 14:8472. [PMID: 38123580 PMCID: PMC10733371 DOI: 10.1038/s41467-023-43856-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023] Open
Abstract
COVID-19 highlighted modeling as a cornerstone of pandemic response. But it also revealed that current models may not fully exploit the high-resolution data on disease progression, epidemic surveillance and host behavior, now available. Take the epidemic threshold, which quantifies the spreading risk throughout epidemic emergence, mitigation, and control. Its use requires oversimplifying either disease or host contact dynamics. We introduce the epidemic graph diagrams to overcome this by computing the epidemic threshold directly from arbitrarily complex data on contacts, disease and interventions. A grammar of diagram operations allows to decompose, compare, simplify models with computational efficiency, extracting theoretical understanding. We use the diagrams to explain the emergence of resistant influenza variants in the 2007-2008 season, and demonstrate that neglecting non-infectious prodromic stages of sexually transmitted infections biases the predicted epidemic risk, compromising control. The diagrams are general, and improve our capacity to respond to present and future public health challenges.
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Affiliation(s)
- Eugenio Valdano
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012, Paris, France
| | | | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012, Paris, France.
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9
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Paredes MI, Ahmed N, Figgins M, Colizza V, Lemey P, McCrone JT, Müller N, Tran-Kiem C, Bedford T. Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic. medRxiv 2023:2023.07.27.23293266. [PMID: 37577709 PMCID: PMC10418578 DOI: 10.1101/2023.07.27.23293266] [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] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case-reporting throughout the epidemic, and a large degree of transmission heterogeneity. We find that viral introductions played a limited role in prolonging spread after initial dissemination, suggesting that travel bans would have had only a minor impact. We find that mpox transmission in North America began declining before more than 10% of high-risk individuals in the USA had vaccine-induced immunity. Our findings highlight the importance of broader routine specimen screening surveillance for emerging infectious diseases and of joint integration of genomic and epidemiological information for early outbreak control.
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Affiliation(s)
- Miguel I. Paredes
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nashwa Ahmed
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - John T. McCrone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nicola Müller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Cécile Tran-Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Trevor Bedford
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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10
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Jit M, Ainslie K, Althaus C, Caetano C, Colizza V, Paolotti D, Beutels P, Willem L, Edmunds J, Nunes B, Namorado S, Faes C, Low N, Wallinga J, Hens N. Reflections On Epidemiological Modeling To Inform Policy During The COVID-19 Pandemic In Western Europe, 2020-23. Health Aff (Millwood) 2023; 42:1630-1636. [PMID: 38048502 DOI: 10.1377/hlthaff.2023.00688] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
We reflect on epidemiological modeling conducted throughout the COVID-19 pandemic in Western Europe, specifically in Belgium, France, Italy, the Netherlands, Portugal, Switzerland, and the United Kingdom. Western Europe was initially one of the worst-hit regions during the COVID-19 pandemic. Western European countries deployed a range of policy responses to the pandemic, which were often informed by mathematical, computational, and statistical models. Models differed in terms of temporal scope, pandemic stage, interventions modeled, and analytical form. This diversity was modulated by differences in data availability and quality, government interventions, societal responses, and technical capacity. Many of these models were decisive to policy making at key junctures, such as during the introduction of vaccination and the emergence of the Alpha, Delta, and Omicron variants. However, models also faced intense criticism from the press, other scientists, and politicians around their accuracy and appropriateness for decision making. Hence, evaluating the success of models in terms of accuracy and influence is an essential task. Modeling needs to be supported by infrastructure for systems to collect and share data, model development, and collaboration between groups, as well as two-way engagement between modelers and both policy makers and the public.
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Affiliation(s)
- Mark Jit
- Mark Jit , London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kylie Ainslie
- Kylie Ainslie, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Constantino Caetano
- Constantino Caetano, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | | | | | | | | | - John Edmunds
- John Edmunds, London School of Hygiene and Tropical Medicine
| | - Baltazar Nunes
- Baltazar Nunes, National Institute of Health Doutor Ricardo Jorge
| | - Sónia Namorado
- Sónia Namorado, National Institute of Health Doutor Ricardo Jorge
| | | | | | - Jacco Wallinga
- Jacco Wallinga, National Institute for Public Health and the Environment (RIVM)
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11
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Leblanc J, Dusserre-Telmon L, Chauvin A, Simon T, Sabbatini CE, Hemming K, Colizza V, Bérard L, Convert J, Lazazga S, Jegou C, Taibi N, Dautheville S, Zaghia D, Gerlier C, Domergue M, Larrouturou F, Bonnet F, Fontanet A, Salhi S, LeGoff J, Crémieux AC. Intensified screening for SARS-CoV-2 in 18 emergency departments in the Paris metropolitan area, France (DEPIST-COVID): A cluster-randomized, two-period, crossover trial. PLoS Med 2023; 20:e1004317. [PMID: 38060611 PMCID: PMC10735176 DOI: 10.1371/journal.pmed.1004317] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/21/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Asymptomatic and paucisymptomatic infections account for a substantial portion of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmissions. The value of intensified screening strategies, especially in emergency departments (EDs), in reaching asymptomatic and paucisymptomatic patients and helping to improve detection and reduce transmission has not been documented. The objective of this study was to evaluate in EDs whether an intensified SARS-CoV-2 screening strategy combining nurse-driven screening for asymptomatic/paucisymptomatic patients with routine practice (intervention) could contribute to higher detection of SARS-CoV-2 infections compared to routine practice alone, including screening for symptomatic or hospitalized patients (control). METHODS AND FINDINGS We conducted a cluster-randomized, two-period, crossover trial from February 2021 to May 2021 in 18 EDs in the Paris metropolitan area, France. All adults visiting the EDs were eligible. At the start of the first period, 18 EDs were randomized to the intervention or control strategy by balanced block randomization with stratification, with the alternative condition being applied in the second period. During the control period, routine screening for SARS-CoV-2 included screening for symptomatic or hospitalized patients. During the intervention period, in addition to routine screening practice, a questionnaire about risk exposure and symptoms and a SARS-CoV-2 screening test were offered by nurses to all remaining asymptomatic/paucisymptomatic patients. The primary outcome was the proportion of newly diagnosed SARS-CoV-2-positive patients among all adults visiting the 18 EDs. Primary analysis was by intention-to-treat. The primary outcome was analyzed using a generalized linear mixed model (Poisson distribution) with the center and center by period as random effects and the strategy (intervention versus control) and period (modeled as a weekly categorical variable) as fixed effects with additional adjustment for community incidence. During the intervention and control periods, 69,248 patients and 69,104 patients, respectively, were included for a total of 138,352 patients. Patients had a median age of 45.0 years [31.0, 63.0], and women represented 45.7% of the patients. During the intervention period, 6,332 asymptomatic/paucisymptomatic patients completed the questionnaire; 4,283 were screened for SARS-CoV-2 by nurses, leading to 224 new SARS-CoV-2 diagnoses. A total of 1,859 patients versus 2,084 patients were newly diagnosed during the intervention and control periods, respectively (adjusted analysis: 26.7/1,000 versus 26.2/1,000, adjusted relative risk: 1.02 (95% confidence interval (CI) [0.94, 1.11]; p = 0.634)). The main limitation of this study is that it was conducted in a rapidly evolving epidemiological context. CONCLUSIONS The results of this study showed that intensified screening for SARS-CoV-2 in EDs was unlikely to identify a higher proportion of newly diagnosed patients. TRIAL REGISTRATION Trial registration number: ClinicalTrials.gov NCT04756609.
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Affiliation(s)
- Judith Leblanc
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health; Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital St Antoine, Clinical Research Platform Paris-East, Paris, France
| | | | - Anthony Chauvin
- AP-HP, Hôpital Lariboisière, Emergency department; Université Paris Cité, INSERM U942 MASCOT, Paris, France
| | - Tabassome Simon
- AP-HP, Hôpital St Antoine, Clinical Research Platform Paris-East; Sorbonne Université, Department of Clinical Pharmacology, Paris, France
| | - Chiara E. Sabbatini
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Karla Hemming
- University of Birmingham, Institute of Applied Health Research, Birmingham, United Kingdom
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Laurence Bérard
- AP-HP, Hôpital St Antoine, Clinical Research Platform Paris-East, Paris, France
| | - Jérome Convert
- AP-HP, Hôpital Lariboisière, Emergency department, Paris, France
| | - Sonia Lazazga
- Centre Hospitalier de Gonesse, Emergency department, Gonesse, France
| | - Carole Jegou
- AP-HP, Hôpital Avicenne, Emergency department, Bobigny, France
| | - Nabila Taibi
- AP-HP, Hôpital Pitié-Salpêtrière, Emergency department, Paris, France
| | | | - Damien Zaghia
- AP-HP, Hôpital Beaujon, Emergency department, Clichy, France
| | - Camille Gerlier
- Hôpital Paris St Joseph, Emergency department, Paris, France
| | - Muriel Domergue
- AP-HP, Hôpital Européen Georges Pompidou, Emergency department, Paris, France
| | | | - Florence Bonnet
- AP-HP, Hôpital St Antoine, Emergency department, Paris, France
| | - Arnaud Fontanet
- Institut Pasteur, Emerging Diseases Epidemiology Unit; PACRI unit, Conservatoire National des Arts et Métiers, Paris, France
| | - Sarah Salhi
- AP-HP, Hôpital St Antoine, Clinical Research Platform Paris-East, Paris, France
| | - Jérome LeGoff
- Université Paris Cité, INSERM U976, INSIGHT Team; AP-HP, Hôpital St Louis, Virology Department, Paris, France
| | - Anne-Claude Crémieux
- AP-HP, Hôpital St Louis, Infectious Diseases Department; Université Paris Cité, FHU PROTHEE, Paris, France
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12
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Leal Neto O, Paolotti D, Dalton C, Carlson S, Susumpow P, Parker M, Phetra P, Lau EHY, Colizza V, Jan van Hoek A, Kjelsø C, Brownstein JS, Smolinski MS. Enabling Multicentric Participatory Disease Surveillance for Global Health Enhancement: Viewpoint on Global Flu View. JMIR Public Health Surveill 2023; 9:e46644. [PMID: 37490846 PMCID: PMC10504624 DOI: 10.2196/46644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/21/2023] [Accepted: 07/25/2023] [Indexed: 07/27/2023] Open
Abstract
Participatory surveillance (PS) has been defined as the bidirectional process of transmitting and receiving data for action by directly engaging the target population. Often represented as self-reported symptoms directly from the public, PS can provide evidence of an emerging disease or concentration of symptoms in certain areas, potentially identifying signs of an early outbreak. The construction of sets of symptoms to represent various disease syndromes provides a mechanism for the early detection of multiple health threats. Global Flu View (GFV) is the first-ever system that merges influenza-like illness (ILI) data from more than 8 countries plus 1 region (Hong Kong) on 4 continents for global monitoring of this annual health threat. GFV provides a digital ecosystem for spatial and temporal visualization of syndromic aggregates compatible with ILI from the various systems currently participating in GFV in near real time, updated weekly. In 2018, the first prototype of a digital platform to combine data from several ILI PS programs was created. At that time, the priority was to have a digital environment that brought together different programs through an application program interface, providing a real time map of syndromic trends that could demonstrate where and when ILI was spreading in various regions of the globe. After 2 years running as an experimental model and incorporating feedback from partner programs, GFV was restructured to empower the community of public health practitioners, data scientists, and researchers by providing an open data channel among these contributors for sharing experiences across the network. GFV was redesigned to serve not only as a data hub but also as a dynamic knowledge network around participatory ILI surveillance by providing knowledge exchange among programs. Connectivity between existing PS systems enables a network of cooperation and collaboration with great potential for continuous public health impact. The exchange of knowledge within this network is not limited only to health professionals and researchers but also provides an opportunity for the general public to have an active voice in the collective construction of health settings. The focus on preparing the next generation of epidemiologists will be of great importance to scale innovative approaches like PS. GFV provides a useful example of the value of globally integrated PS data to help reduce the risks and damages of the next pandemic.
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Affiliation(s)
- Onicio Leal Neto
- Ending Pandemics, San Francisco, CA, United States
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | | | | | | | | | | | | | - Eric H Y Lau
- School of Public Health, University of Hong Kong, Hong Kong, China
| | - Vittoria Colizza
- Pierre Louis Institute of Epidemiology and Public Health, INSERM, Sorbonne Université, Paris, France
| | - Albert Jan van Hoek
- National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | | | - John S Brownstein
- Boston Children Hospital, Harvard University, Boston, MA, United States
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13
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Tsui JLH, McCrone JT, Lambert B, Bajaj S, Inward RP, Bosetti P, Tegally H, Hill V, Pena RE, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O’Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MU. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science 2023; 381:336-343. [PMID: 37471538 PMCID: PMC10866301 DOI: 10.1126/science.adg6605] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA.1 genomes, we identified >6,000 introductions of the antigenically distinct VOC into England and analyzed their local transmission and dispersal history. We find that six of the eight largest English Omicron lineages were already transmitting when Omicron was first reported in southern Africa (22 November 2021). Multiple datasets show that importation of Omicron continued despite subsequent restrictions on travel from southern Africa as a result of export from well-connected secondary locations. Initiation and dispersal of Omicron transmission lineages in England was a two-stage process that can be explained by models of the country's human geography and hierarchical travel network. Our results enable a comparison of the processes that drive the invasion of Omicron and other VOCs across multiple spatial scales.
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Affiliation(s)
| | - John T. McCrone
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- Helix, San Mateo, USA
| | - Ben Lambert
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Paolo Bosetti
- Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Verity Hill
- Helix, San Mateo, USA
- Yale University, New Haven, USA
| | | | | | - Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | - Neo Wu
- Google Research, Mountain View, USA
| | | | - Isaac I. Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | | | | | | | | | | | | | - Eduan Wilkinson
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Thomas R. Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, UK
- Pandemic Sciences Institute, University of Oxford, UK
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Xiang Ji
- Department of Mathematics, Tulane University, New Orleans, USA
| | | | | | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Simon Cauchemez
- Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Jayna Raghwani
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Marc A. Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Oliver G. Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Moritz U.G. Kraemer
- Department of Biology, University of Oxford, Oxford, UK
- Pandemic Sciences Institute, University of Oxford, UK
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14
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de Meijere G, Valdano E, Castellano C, Debin M, Kengne-Kuetche C, Turbelin C, Noël H, Weitz JS, Paolotti D, Hermans L, Hens N, Colizza V. Attitudes towards booster, testing and isolation, and their impact on COVID-19 response in winter 2022/2023 in France, Belgium, and Italy: a cross-sectional survey and modelling study. Lancet Reg Health Eur 2023; 28:100614. [PMID: 37131863 PMCID: PMC10035813 DOI: 10.1016/j.lanepe.2023.100614] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/25/2023] Open
Abstract
Background European countries are focusing on testing, isolation, and boosting strategies to counter the 2022/2023 winter surge due to SARS-CoV-2 Omicron subvariants. However, widespread pandemic fatigue and limited compliance potentially undermine mitigation efforts. Methods To establish a baseline for interventions, we ran a multicountry survey to assess respondents’ willingness to receive booster vaccination and comply with testing and isolation mandates. Integrating survey and estimated immunity data in a branching process epidemic spreading model, we evaluated the effectiveness and costs of current protocols in France, Belgium, and Italy to manage the winter wave. Findings The vast majority of survey participants (N = 4594) was willing to adhere to testing (>91%) and rapid isolation (>88%) across the three countries. Pronounced differences emerged in the declared senior adherence to booster vaccination (73% in France, 94% in Belgium, 86% in Italy). Epidemic model results estimate that testing and isolation protocols would confer significant benefit in reducing transmission (17–24% reduction, from R = 1.6 to R = 1.3 in France and Belgium, to R = 1.2 in Italy) with declared adherence. Achieving a mitigating level similar to the French protocol, the Belgian protocol would require 35% fewer tests (from 1 test to 0.65 test per infected person) and avoid the long isolation periods of the Italian protocol (average of 6 days vs. 11). A cost barrier to test would significantly decrease adherence in France and Belgium, undermining protocols’ effectiveness. Interpretation Simpler mandates for isolation may increase awareness and actual compliance, reducing testing costs, without compromising mitigation. High booster vaccination uptake remains key for the control of the winter wave. Funding The 10.13039/501100000780European Commission, ANRS–Maladies Infectieuses Émergentes, the Agence Nationale de la Recherche, the Chaires Blaise Pascal Program of the Île-de-France region.
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Affiliation(s)
- Giulia de Meijere
- Gran Sasso Science Institute (GSSI), L'Aquila, Italy
- Istituto dei Sistemi Complessi (ISC-CNR), Roma, Italy
| | - Eugenio Valdano
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Claudio Castellano
- Istituto dei Sistemi Complessi (ISC-CNR), Roma, Italy
- Centro Ricerche Enrico Fermi, Roma, Italy
| | - Marion Debin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Charly Kengne-Kuetche
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Clément Turbelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Harold Noël
- Santé Publique France, Saint-Maurice, France
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Institut de Biologie, École Normale Supérieure, Paris, France
| | | | - Lisa Hermans
- Data Science Institute, I-biostat, Hasselt University, Hasselt, Belgium
| | - Niel Hens
- Data Science Institute, I-biostat, Hasselt University, Hasselt, Belgium
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
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15
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Bonacina F, Boëlle PY, Colizza V, Lopez O, Thomas M, Poletto C. Global patterns and drivers of influenza decline during the COVID-19 pandemic. Int J Infect Dis 2023; 128:132-139. [PMID: 36608787 PMCID: PMC9809002 DOI: 10.1016/j.ijid.2022.12.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/02/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES The influenza circulation reportedly declined during the COVID-19 pandemic in many countries. The occurrence of this change has not been studied worldwide nor its potential drivers. METHODS The change in the proportion of positive influenza samples reported by country and trimester was computed relative to the 2014-2019 period using the FluNet database. Random forests were used to determine predictors of change from demographical, weather, pandemic preparedness, COVID-19 incidence, and pandemic response characteristics. Regression trees were used to classify observations according to these predictors. RESULTS During the COVID-19 pandemic, the influenza decline relative to prepandemic levels was global but heterogeneous across space and time. It was more than 50% for 311 of 376 trimesters-countries and even more than 99% for 135. COVID-19 incidence and pandemic preparedness were the two most important predictors of the decline. Europe and North America initially showed limited decline despite high COVID-19 restrictions; however, there was a strong decline afterward in most temperate countries, where pandemic preparedness, COVID-19 incidence, and social restrictions were high; the decline was limited in countries where these factors were low. The "zero-COVID" countries experienced the greatest decline. CONCLUSION Our findings set the stage for interpreting the resurgence of influenza worldwide.
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Affiliation(s)
- Francesco Bonacina
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012 Paris, France; Sorbonne Université, CNRS, Laboratoire de Probabilités, Statistique et Modélisation, F-75013 Paris, France
| | - Pierre-Yves Boëlle
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012 Paris, France
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012 Paris, France; Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Olivier Lopez
- Sorbonne Université, CNRS, Laboratoire de Probabilités, Statistique et Modélisation, F-75013 Paris, France
| | - Maud Thomas
- Sorbonne Université, CNRS, Laboratoire de Probabilités, Statistique et Modélisation, F-75013 Paris, France
| | - Chiara Poletto
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75012 Paris, France; Department of Molecular Medicine, University of Padova, 35121 Padova, Italy.
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16
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Colosi E, Bassignana G, Barrat A, Lina B, Vanhems P, Bielicki J, Colizza V. Minimising school disruption under high incidence conditions due to the Omicron variant in France, Switzerland, Italy, in January 2022. Euro Surveill 2023; 28:2200192. [PMID: 36729116 PMCID: PMC9896604 DOI: 10.2807/1560-7917.es.2023.28.5.2200192] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BackgroundAs record cases of Omicron variant were registered in Europe in early 2022, schools remained a vulnerable setting undergoing large disruption.AimThrough mathematical modelling, we compared school protocols of reactive screening, regular screening, and reactive class closure implemented in France, in Baselland (Switzerland), and in Italy, respectively, and assessed them in terms of case prevention, testing resource demand, and schooldays lost.MethodsWe used a stochastic agent-based model of SARS-CoV-2 transmission in schools accounting for within- and across-class contacts from empirical contact data. We parameterised it to the Omicron BA.1 variant to reproduce the French Omicron wave in January 2022. We simulated the three protocols to assess their costs and effectiveness for varying peak incidence rates in the range experienced by European countries.ResultsWe estimated that at the high incidence rates registered in France during the Omicron BA.1 wave in January 2022, the reactive screening protocol applied in France required higher test resources compared with the weekly screening applied in Baselland (0.50 vs 0.45 tests per student-week), but achieved considerably lower control (8% vs 21% reduction of peak incidence). The reactive class closure implemented in Italy was predicted to be very costly, leading to > 20% student-days lost.ConclusionsAt high incidence conditions, reactive screening protocols generate a large and unplanned demand in testing resources, for marginal control of school transmissions. Comparable or lower resources could be more efficiently used through weekly screening. Our findings can help define incidence levels triggering school protocols and optimise their cost-effectiveness.
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Affiliation(s)
- Elisabetta Colosi
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Bassignana
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Alain Barrat
- Aix Marseille Univ, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
| | - Bruno Lina
- National Reference Center for Respiratory Viruses, Department of Virology, Infective Agents Institute, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France,Centre International de Recherche en Infectiologie (CIRI), Virpath Laboratory, INSERM U1111, CNRS—UMR 5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon University, Lyon, France
| | - Philippe Vanhems
- Service d'Hygiène, Épidémiologie, Infectiovigilance et Prévention, Hospices Civils de Lyon, Lyon, France,Centre International de Recherche en Infectiologie (CIRI), Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases (PHE3ID) – Inserm - U1111 - UCBL Lyon 1 - CNRS –UMR5308 - ENS de Lyon, Lyon, France
| | - Julia Bielicki
- Paediatric Infectious Diseases, University of Basel Children's Hospital, Basel, Switzerland
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
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17
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Abstract
Several countries have implemented lockdowns to control their COVID-19 epidemic. However, questions like "where" and "when" still require answers. We assessed the impact of national and regional lockdowns considering the French first epidemic wave of COVID-19 as a case study. In a regional lockdown scenario aimed at preventing intensive care units (ICU) saturation, almost all French regions would have had to implement a lockdown within 10 days and 96% of ICU capacities would have been used. For slowly growing epidemics, with a lower reproduction number, the expected delays between regional lockdowns increase. However, the public health costs associated with these delays tend to grow with time. In a quickly growing pandemic wave, defining the timing of lockdowns at a regional rather than national level delays by a few days the implementation of a nationwide lockdown but leads to substantially higher morbidity, mortality, and stress on the healthcare system.
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Affiliation(s)
- Jonathan Roux
- RSMS-U 1309, ARENES-UMR 6051, EHESP, CNRS, Inserm, Université de Rennes, 15, Avenue du Professeur Léon-Bernard, CS 74312, 35043, Rennes Cedex, France
| | - Clément R Massonnaud
- RSMS-U 1309, ARENES-UMR 6051, EHESP, CNRS, Inserm, Université de Rennes, 15, Avenue du Professeur Léon-Bernard, CS 74312, 35043, Rennes Cedex, France
- Department of Biomedical Informatics, Rouen University Hospital, 76000, Rouen, France
| | - Vittoria Colizza
- Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Sorbonne Université, Inserm, 75012, Paris, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Pascal Crépey
- RSMS-U 1309, ARENES-UMR 6051, EHESP, CNRS, Inserm, Université de Rennes, 15, Avenue du Professeur Léon-Bernard, CS 74312, 35043, Rennes Cedex, France.
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18
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Roux J, Massonnaud CR, Colizza V, Cauchemez S, Crépey P. Modeling the impact of national and regional lockdowns on the 2020 spring wave of COVID-19 in France. Sci Rep 2023; 13:1834. [PMID: 36725962 PMCID: PMC9890427 DOI: 10.1038/s41598-023-28687-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Several countries have implemented lockdowns to control their COVID-19 epidemic. However, questions like "where" and "when" still require answers. We assessed the impact of national and regional lockdowns considering the French first epidemic wave of COVID-19 as a case study. In a regional lockdown scenario aimed at preventing intensive care units (ICU) saturation, almost all French regions would have had to implement a lockdown within 10 days and 96% of ICU capacities would have been used. For slowly growing epidemics, with a lower reproduction number, the expected delays between regional lockdowns increase. However, the public health costs associated with these delays tend to grow with time. In a quickly growing pandemic wave, defining the timing of lockdowns at a regional rather than national level delays by a few days the implementation of a nationwide lockdown but leads to substantially higher morbidity, mortality, and stress on the healthcare system.
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Affiliation(s)
- Jonathan Roux
- RSMS-U 1309, ARENES-UMR 6051, EHESP, CNRS, Inserm, Université de Rennes, 15, Avenue du Professeur Léon-Bernard, CS 74312, 35043, Rennes Cedex, France
| | - Clément R Massonnaud
- RSMS-U 1309, ARENES-UMR 6051, EHESP, CNRS, Inserm, Université de Rennes, 15, Avenue du Professeur Léon-Bernard, CS 74312, 35043, Rennes Cedex, France.,Department of Biomedical Informatics, Rouen University Hospital, 76000, Rouen, France
| | - Vittoria Colizza
- Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Sorbonne Université, Inserm, 75012, Paris, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Pascal Crépey
- RSMS-U 1309, ARENES-UMR 6051, EHESP, CNRS, Inserm, Université de Rennes, 15, Avenue du Professeur Léon-Bernard, CS 74312, 35043, Rennes Cedex, France.
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19
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Valdano E, Okano JT, Colizza V, Mitonga HK, Blower S. Use of mobile phone data in HIV epidemic control. Lancet HIV 2022; 9:e820-e821. [PMID: 36460021 PMCID: PMC9762893 DOI: 10.1016/s2352-3018(22)00332-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 07/25/2022] [Revised: 09/27/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Eugenio Valdano
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, F75012, Paris, France
| | - Justin T Okano
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, F75012, Paris, France
| | - Honore K Mitonga
- Department of Epidemiology and Biostatistics, School of Public Health, University of Namibia, Private Bag 13301, Windhoek, Namibia
| | - Sally Blower
- Center for Biomedical Modeling, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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20
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Torneri A, Willem L, Colizza V, Kremer C, Meuris C, Darcis G, Hens N, Libin PJK. Controlling SARS-CoV-2 in schools using repetitive testing strategies. eLife 2022; 11:75593. [PMID: 35787310 PMCID: PMC9255973 DOI: 10.7554/elife.75593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 06/15/2022] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 remains a worldwide emergency. While vaccines have been approved and are widely administered, there is an ongoing debate whether children should be vaccinated or prioritized for vaccination. Therefore, in order to mitigate the spread of more transmissible SARS-CoV-2 variants among children, the use of non-pharmaceutical interventions is still warranted. We investigate the impact of different testing strategies on the SARS-CoV-2 infection dynamics in a primary school environment, using an individual-based modelling approach. Specifically, we consider three testing strategies: (1) symptomatic isolation, where we test symptomatic individuals and isolate them when they test positive, (2) reactive screening, where a class is screened once one symptomatic individual was identified, and (3) repetitive screening, where the school in its entirety is screened on regular time intervals. Through this analysis, we demonstrate that repetitive testing strategies can significantly reduce the attack rate in schools, contrary to a reactive screening or a symptomatic isolation approach. However, when a repetitive testing strategy is in place, more cases will be detected and class and school closures are more easily triggered, leading to a higher number of school days lost per child. While maintaining the epidemic under control with a repetitive testing strategy, we show that absenteeism can be reduced by relaxing class and school closure thresholds.
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Affiliation(s)
- Andrea Torneri
- Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium.,Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Lander Willem
- Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium.,Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.,Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Cécile Kremer
- Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Christelle Meuris
- Department of Infectious Diseases, Liège University Hospital, Liège, Belgium
| | - Gilles Darcis
- Department of Infectious Diseases, Liège University Hospital, Liège, Belgium
| | - Niel Hens
- Centre for Health Economic Research and Modelling Infectious Diseases, University of Antwerp, Antwerp, Belgium.,Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Pieter J K Libin
- Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium.,Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium.,KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
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21
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Colosi E, Bassignana G, Contreras DA, Poirier C, Boëlle PY, Cauchemez S, Yazdanpanah Y, Lina B, Fontanet A, Barrat A, Colizza V. Screening and vaccination against COVID-19 to minimise school closure: a modelling study. Lancet Infect Dis 2022; 22:977-989. [PMID: 35378075 PMCID: PMC8975262 DOI: 10.1016/s1473-3099(22)00138-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/26/2022] [Accepted: 02/15/2022] [Indexed: 12/18/2022]
Abstract
BACKGROUND Schools were closed extensively in 2020-21 to counter SARS-CoV-2 spread, impacting students' education and wellbeing. With highly contagious variants expanding in Europe, safe options to maintain schools open are urgently needed. By estimating school-specific transmissibility, our study evaluates costs and benefits of different protocols for SARS-CoV-2 control at school. METHODS We developed an agent-based model of SARS-CoV-2 transmission in schools. We used empirical contact data in a primary and a secondary school and data from pilot screenings in 683 schools during the alpha variant (B.1.1.7) wave in March-June, 2021, in France. We fitted the model to observed school prevalence to estimate the school-specific effective reproductive number for the alpha (Ralpha) and delta (B.1.617.2; Rdelta) variants and performed a cost-benefit analysis examining different intervention protocols. FINDINGS We estimated Ralpha to be 1·40 (95% CI 1·35-1·45) in the primary school and 1·46 (1·41-1·51) in the secondary school during the spring wave, higher than the time-varying reproductive number estimated from community surveillance. Considering the delta variant and vaccination coverage in Europe as of mid-September, 2021, we estimated Rdelta to be 1·66 (1·60-1·71) in primary schools and 1·10 (1·06-1·14) in secondary schools. Under these conditions, weekly testing of 75% of unvaccinated students (PCR tests on saliva samples in primary schools and lateral flow tests in secondary schools), in addition to symptom-based testing, would reduce cases by 34% (95% CI 32-36) in primary schools and 36% (35-39) in secondary schools compared with symptom-based testing alone. Insufficient adherence was recorded in pilot screening (median ≤53%). Regular testing would also reduce student-days lost up to 80% compared with reactive class closures. Moderate vaccination coverage in students would still benefit from regular testing for additional control-ie, weekly testing 75% of unvaccinated students would reduce cases compared with symptom-based testing only, by 23% in primary schools when 50% of children are vaccinated. INTERPRETATION The COVID-19 pandemic will probably continue to pose a risk to the safe and normal functioning of schools. Extending vaccination coverage in students, complemented by regular testing with good adherence, are essential steps to keep schools open when highly transmissible variants are circulating. FUNDING EU Framework Programme for Research and Innovation Horizon 2020, Horizon Europe Framework Programme, Agence Nationale de la Recherche, ANRS-Maladies Infectieuses Émergentes.
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Affiliation(s)
- Elisabetta Colosi
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Bassignana
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Diego Andrés Contreras
- Aix-Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, Turing Center for Living Systems, Marseille, France
| | - Canelle Poirier
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Yazdan Yazdanpanah
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Université de Paris, Paris, France; Bichat Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Bruno Lina
- National Reference Center for Respiratory Viruses, Department of Virology, Infective Agents Institute, Croix-Rousse Hospital, Hospices Civils de Lyon, Lyon, France; Virpath Laboratory, International Center of Research in Infectiology, INSERM U1111, CNRS-UMR 5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon University, Lyon, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France; PACRI Unit, Conservatoire National des Arts et Metiers, Paris, France
| | - Alain Barrat
- Aix-Marseille Univ, Université de Toulon, CNRS, Centre de Physique Théorique, Turing Center for Living Systems, Marseille, France; Tokyo Tech World Research Hub Initiative, Tokyo Institute of Technology, Tokyo, Japan
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France; Tokyo Tech World Research Hub Initiative, Tokyo Institute of Technology, Tokyo, Japan.
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22
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Contreras DA, Colosi E, Bassignana G, Colizza V, Barrat A. Impact of contact data resolution on the evaluation of interventions in mathematical models of infectious diseases. J R Soc Interface 2022; 19:20220164. [PMID: 35730172 PMCID: PMC9214285 DOI: 10.1098/rsif.2022.0164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Computational models offer a unique setting to test strategies to mitigate the spread of infectious diseases, providing useful insights to applied public health. To be actionable, models need to be informed by data, which can be available at different levels of detail. While high-resolution data describing contacts between individuals are increasingly available, data gathering remains challenging, especially during a health emergency. Many models thus use synthetic data or coarse information to evaluate intervention protocols. Here, we evaluate how the representation of contact data might affect the impact of various strategies in models, in the realm of COVID-19 transmission in educational and work contexts. Starting from high-resolution contact data, we use detailed to coarse data representations to inform a model of SARS-CoV-2 transmission and simulate different mitigation strategies. We find that coarse data representations estimate a lower risk of superspreading events. However, the rankings of protocols according to their efficiency or cost remain coherent across representations, ensuring the consistency of model findings to inform public health advice. Caution should be taken, however, on the quantitative estimations of those benefits and costs triggering the adoption of protocols, as these may depend on data representation.
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Affiliation(s)
- Diego Andrés Contreras
- Aix Marseille University, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
| | - Elisabetta Colosi
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Bassignana
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Alain Barrat
- Aix Marseille University, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
- Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
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23
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Lee EC, Arab A, Colizza V, Bansal S. Spatial aggregation choice in the era of digital and administrative surveillance data. PLOS Digit Health 2022; 1:e0000039. [PMID: 36812505 PMCID: PMC9931313 DOI: 10.1371/journal.pdig.0000039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 04/11/2022] [Indexed: 11/18/2022]
Abstract
Traditional disease surveillance is increasingly being complemented by data from non-traditional sources like medical claims, electronic health records, and participatory syndromic data platforms. As non-traditional data are often collected at the individual-level and are convenience samples from a population, choices must be made on the aggregation of these data for epidemiological inference. Our study seeks to understand the influence of spatial aggregation choice on our understanding of disease spread with a case study of influenza-like illness in the United States. Using U.S. medical claims data from 2002 to 2009, we examined the epidemic source location, onset and peak season timing, and epidemic duration of influenza seasons for data aggregated to the county and state scales. We also compared spatial autocorrelation and tested the relative magnitude of spatial aggregation differences between onset and peak measures of disease burden. We found discrepancies in the inferred epidemic source locations and estimated influenza season onsets and peaks when comparing county and state-level data. Spatial autocorrelation was detected across more expansive geographic ranges during the peak season as compared to the early flu season, and there were greater spatial aggregation differences in early season measures as well. Epidemiological inferences are more sensitive to spatial scale early on during U.S. influenza seasons, when there is greater heterogeneity in timing, intensity, and geographic spread of the epidemics. Users of non-traditional disease surveillance should carefully consider how to extract accurate disease signals from finer-scaled data for early use in disease outbreaks.
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Affiliation(s)
- Elizabeth C. Lee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Ali Arab
- Department of Mathematics and Statistics, Georgetown University, Washington, District of Columbia, United States of America
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Paris, France
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, District of Columbia, United States of America
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24
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Affiliation(s)
- Elisabetta Colosi
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Bassignana
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Alain Barrat
- Aix Marseille Univ, Université de Toulon, CNRS, CPT, Turing Centre for Living Systems, Marseille, France; Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France; Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan.
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25
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Bosetti P, Tran Kiem C, Andronico A, Colizza V, Yazdanpanah Y, Fontanet A, Benamouzig D, Cauchemez S. Epidemiology and control of SARS-CoV-2 epidemics in partially vaccinated populations: a modeling study applied to France. BMC Med 2022; 20:33. [PMID: 35078469 PMCID: PMC8789481 DOI: 10.1186/s12916-022-02235-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vaccination is expected to change the epidemiology and management of SARS-CoV-2 epidemics. METHODS We used an age-stratified compartmental model calibrated to French data to anticipate these changes and determine implications for the control of an autumn epidemic. We assumed vaccines reduce the risk of hospitalization, infection, and transmission if infected by 95%, 60%, and 50%, respectively. RESULTS In our baseline scenario characterized by basic reproduction number R0=5 and a vaccine coverage of 70-80-90% among 12-17, 18-59, and ≥ 60 years old, important stress on healthcare is expected in the absence of measures. Unvaccinated adults ≥60 years old represent 3% of the population but 43% of hospitalizations. Given limited vaccine coverage, children aged 0-17 years old represent a third of infections and are responsible for almost half of transmissions. Unvaccinated individuals have a disproportionate contribution to transmission so that measures targeting them may help maximize epidemic control while minimizing costs for society compared to non-targeted approaches. Of all the interventions considered including repeated testing and non-pharmaceutical measures, vaccination of the unvaccinated is the most effective. CONCLUSIONS With the Delta variant, vaccinated individuals are well protected against hospitalization but remain at risk of infection and should therefore apply protective behaviors (e.g., mask-wearing). Targeting non-vaccinated individuals may maximize epidemic control while minimizing costs for society. Vaccinating children protects them from the deleterious effects of non-pharmaceutical measures. Control strategies should account for the changing SARS-CoV-2 epidemiology.
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Affiliation(s)
- Paolo Bosetti
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université de Paris, UMR2000, CNRS, Paris, France
| | - Cécile Tran Kiem
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université de Paris, UMR2000, CNRS, Paris, France.,Collège Doctoral, Sorbonne Université, Paris, France
| | - Alessio Andronico
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université de Paris, UMR2000, CNRS, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Yazdan Yazdanpanah
- Université of Paris, INSERM UMR 1137 IAME, Paris, France.,Department of Infectious Diseases, Assistance Publique-Hôpitaux de Paris, Bichat-Claude-Bernard University Hospital, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Université de Paris, Institut Pasteur, Paris, France.,PACRI Unit, Conservatoire National des Arts et Métiers, Paris, France
| | - Daniel Benamouzig
- Sciences Po - Centre de sociologie des organisations and Chaire santé - CNRS, Paris, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université de Paris, UMR2000, CNRS, Paris, France.
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McColl K, Debin M, Souty C, Guerrisi C, Turbelin C, Falchi A, Bonmarin I, Paolotti D, Obi C, Duggan J, Moreno Y, Wisniak A, Flahault A, Blanchon T, Colizza V, Raude J. Are People Optimistically Biased about the Risk of COVID-19 Infection? Lessons from the First Wave of the Pandemic in Europe. Int J Environ Res Public Health 2021; 19:436. [PMID: 35010707 PMCID: PMC8744599 DOI: 10.3390/ijerph19010436] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022]
Abstract
Unrealistic optimism, the underestimation of one's risk of experiencing harm, has been investigated extensively to understand better and predict behavioural responses to health threats. Prior to the COVID-19 pandemic, a relative dearth of research existed in this domain regarding epidemics, which is surprising considering that this optimistic bias has been associated with a lack of engagement in protective behaviours critical in fighting twenty-first-century, emergent, infectious diseases. The current study addresses this gap in the literature by investigating whether people demonstrated optimism bias during the first wave of the COVID-19 pandemic in Europe, how this changed over time, and whether unrealistic optimism was negatively associated with protective measures. Taking advantage of a pre-existing international participative influenza surveillance network (n = 12,378), absolute and comparative unrealistic optimism were measured at three epidemic stages (pre-, early, peak), and across four countries-France, Italy, Switzerland and the United Kingdom. Despite differences in culture and health response, similar patterns were observed across all four countries. The prevalence of unrealistic optimism appears to be influenced by the particular epidemic context. Paradoxically, whereas absolute unrealistic optimism decreased over time, comparative unrealistic optimism increased, suggesting that whilst people became increasingly accurate in assessing their personal risk, they nonetheless overestimated that for others. Comparative unrealistic optimism was negatively associated with the adoption of protective behaviours, which is worrying, given that these preventive measures are critical in tackling the spread and health burden of COVID-19. It is hoped these findings will inspire further research into sociocognitive mechanisms involved in risk appraisal.
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Affiliation(s)
- Kathleen McColl
- Unite des Virus Emergents, Institut de Recherche pour le Développement 190, Institut National de la Santé Et de la Recherche Médicale (INSERM) 1207, Health, Aix-Marseille University, 13009 Marseille, France;
- École des Hautes Études en Santé Publique (EHESP) French School of Public Health, 35043 Rennes, France
| | - Marion Debin
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Sorbonne Université, F-75012 Paris, France; (M.D.); (C.S.); (C.G.); (C.T.); (T.B.); (V.C.)
| | - Cecile Souty
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Sorbonne Université, F-75012 Paris, France; (M.D.); (C.S.); (C.G.); (C.T.); (T.B.); (V.C.)
| | - Caroline Guerrisi
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Sorbonne Université, F-75012 Paris, France; (M.D.); (C.S.); (C.G.); (C.T.); (T.B.); (V.C.)
| | - Clement Turbelin
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Sorbonne Université, F-75012 Paris, France; (M.D.); (C.S.); (C.G.); (C.T.); (T.B.); (V.C.)
| | - Alessandra Falchi
- Laboratoire de Virologie, Unité de Recherche 7310, Université de Corse, 20250 Corte, France;
| | | | - Daniela Paolotti
- Istituto per l’Interscambio Scientifico, ISI Foundation, 10126 Turin, Italy;
| | | | - Jim Duggan
- School of Computer Science, National University of Ireland, H91 TK33 Galway, Ireland;
| | - Yamir Moreno
- Institute for Biocomputation and Physics and Complex Systems, University of Zaragoza, 50001 Zaragoza, Spain;
| | - Ania Wisniak
- Faculty of Medicine, Institute of Global Health, University of Geneva, 1202 Geneva, Switzerland; (A.W.); (A.F.)
| | - Antoine Flahault
- Faculty of Medicine, Institute of Global Health, University of Geneva, 1202 Geneva, Switzerland; (A.W.); (A.F.)
| | - Thierry Blanchon
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Sorbonne Université, F-75012 Paris, France; (M.D.); (C.S.); (C.G.); (C.T.); (T.B.); (V.C.)
| | - Vittoria Colizza
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Institut Pierre Louis d’Épidémiologie et de Santé Publique (IPLESP), Sorbonne Université, F-75012 Paris, France; (M.D.); (C.S.); (C.G.); (C.T.); (T.B.); (V.C.)
| | - Jocelyn Raude
- Unite des Virus Emergents, Institut de Recherche pour le Développement 190, Institut National de la Santé Et de la Recherche Médicale (INSERM) 1207, Health, Aix-Marseille University, 13009 Marseille, France;
- École des Hautes Études en Santé Publique (EHESP) French School of Public Health, 35043 Rennes, France
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27
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Lavergne J, Debin M, Blanchon T, Colizza V, Dassieu L, Gimenez L, Kengne-Kuetche C, Lapeyre-Mestre M, Dupouy J. Perceived risk of opioid use disorder secondary to opioid analgesic medication use by the general population in France. Eur J Pain 2021; 26:729-739. [PMID: 34958720 DOI: 10.1002/ejp.1901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/15/2021] [Accepted: 12/19/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND In Europe and France, the use of opioid analgesic drugs has become widespread as an option for pain management. However, their use can lead to nonmedical use and/or opioid use disorder (OUD). This work aimed to assess the perceived risk of OUD secondary to opioid analgesic drugs use by the general population. METHODS We conducted a cross-sectional observational study using the GrippeNet web-based cohort, comprising about 10,000 French volunteers from the general population, using a self-administered questionnaire. The main outcome was the perceived risk of OUD secondary to opioid analgesic drugs use, assessed by a 4-item scale and modeled using logistic regression (backward procedure). RESULTS Among 5,046 French respondents, after adjustment, 65% believed that the use of analgesic drugs could likely or very likely lead to OUD. Factors associated with perception of a higher risk were being over 50 and having heard about opioids in the media. Previous opioid use and a high level of education decreased the perception of the risk. Among those having used opioids in the past two years (N = 1770), 71.1% reported being not at all concerned by this risk. The majority of the sample perceived the risk of OUD but those having already used opioid analgesics drugs expressed no concern about this risk for themselves. CONCLUSIONS This finding highlight the need to reinforce warning on the package insert documents, therapeutic education and collaborative care between the prescribing general practitioners and pharmacists to increase awareness of opioid medications users on the risk of OUD.
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Affiliation(s)
- Justine Lavergne
- Département Universitaire de Médecine Générale, Université de Toulouse; Faculté de Médecine, 133 route de Narbonne, 31063, Toulouse, France
| | - Marion Debin
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, F-75012, Paris, France
| | - Thierry Blanchon
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, F-75012, Paris, France
| | - Vittoria Colizza
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, F-75012, Paris, France
| | - Lise Dassieu
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, 850 rue Saint Denis, Montréal, QC, H2X0A9, Canada
| | - Laetitia Gimenez
- Département Universitaire de Médecine Générale, Université de Toulouse; Faculté de Médecine, 133 route de Narbonne, 31063, Toulouse, France.,CERPOP, Université de Toulouse, Inserm, UPS, Toulouse, France
| | - Charly Kengne-Kuetche
- Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, F-75012, Paris, France
| | - Maryse Lapeyre-Mestre
- CEIP-Addictovigilance, CIC 1436, Service de Pharmacologie Médicale et Clinique, Faculté de Médecine, 37 allées Jules Guesde, 31000, Toulouse, France
| | - Julie Dupouy
- Département Universitaire de Médecine Générale, Université de Toulouse; Faculté de Médecine, 133 route de Narbonne, 31063, Toulouse, France.,CERPOP, Université de Toulouse, Inserm, UPS, Toulouse, France
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28
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Briand SC, Cinelli M, Nguyen T, Lewis R, Prybylski D, Valensise CM, Colizza V, Tozzi AE, Perra N, Baronchelli A, Tizzoni M, Zollo F, Scala A, Purnat T, Czerniak C, Kucharski AJ, Tshangela A, Zhou L, Quattrociocchi W. Infodemics: A new challenge for public health. Cell 2021; 184:6010-6014. [PMID: 34890548 PMCID: PMC8656270 DOI: 10.1016/j.cell.2021.10.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/15/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022]
Abstract
The COVID-19 information epidemic, or "infodemic," demonstrates how unlimited access to information may confuse and influence behaviors during a health emergency. However, the study of infodemics is relatively new, and little is known about their relationship with epidemics management. Here, we discuss unresolved issues and propose research directions to enhance preparedness for future health crises.
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Affiliation(s)
- Sylvie C Briand
- Global Infectious Hazards Preparedness Department, World Health Organization, Geneva, Switzerland
| | - Matteo Cinelli
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, 30172 Venice, Italy
| | - Tim Nguyen
- Impact Events Preparedness Unit, Global Infectious Hazards Preparedness Department, World Health Organization, Geneva, Switzerland
| | - Rosamund Lewis
- Infodemic Management Group. Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Dimitri Prybylski
- Global Immunization Division, Center for Global Health, U.S. Centers for Disease Control and Prevention, Atlanta, GA 30030, USA
| | - Carlo M Valensise
- Enrico Fermi Research Center, Piazza del Viminale, 1 - 00184, Roma, Italy
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Alberto Eugenio Tozzi
- Multifactorial and Complex Diseases research Area, Bambino Gesù Children's Hospital, Rome, Italy
| | - Nicola Perra
- Networks and Urban Systems Centre, University of Greenwich, London, UK
| | - Andrea Baronchelli
- Department of Mathematics, City University of London & The Alan Turing Institute, London, UK
| | | | - Fabiana Zollo
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, 30172 Venice, Italy
| | - Antonio Scala
- Applico Lab, CNR-ISC, Roma, Italy; Big Data in Health Society, Roma, Italy
| | - Tina Purnat
- Impact Events Preparedness Unit, Global Infectious Hazards Preparedness Department, World Health Organization, Geneva, Switzerland
| | - Christine Czerniak
- Global Infectious Hazards Preparedness Department, World Health Organization, Geneva, Switzerland
| | - Adam J Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Akhona Tshangela
- Africa Centers for Disease Control and Prevention, African Union Headquarters, Addis Ababa, Ethiopia
| | - Lei Zhou
- Public Health Emergency Center, Chinese Center for Disease Control and Prevention, Beijing, China
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29
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Di Domenico L, Sabbatini CE, Boëlle PY, Poletto C, Crépey P, Paireau J, Cauchemez S, Beck F, Noel H, Lévy-Bruhl D, Colizza V. Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic. Commun Med (Lond) 2021; 1:57. [PMID: 35602184 PMCID: PMC9053235 DOI: 10.1038/s43856-021-00057-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Background After one year of stop-and-go COVID-19 mitigation, in the spring of 2021 European countries still experienced sustained viral circulation due to the Alpha variant. As the prospect of entering a new pandemic phase through vaccination was drawing closer, a key challenge remained on how to balance the efficacy of long-lasting interventions and their impact on the quality of life. Methods Focusing on the third wave in France during spring 2021, we simulate intervention scenarios of varying intensity and duration, with potential waning of adherence over time, based on past mobility data and modeling estimates. We identify optimal strategies by balancing efficacy of interventions with a data-driven "distress" index, integrating intensity and duration of social distancing. Results We show that moderate interventions would require a much longer time to achieve the same result as high intensity lockdowns, with the additional risk of deteriorating control as adherence wanes. Shorter strict lockdowns are largely more effective than longer moderate lockdowns, for similar intermediate distress and infringement on individual freedom. Conclusions Our study shows that favoring milder interventions over more stringent short approaches on the basis of perceived acceptability could be detrimental in the long term, especially with waning adherence.
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Affiliation(s)
- Laura Di Domenico
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara E. Sabbatini
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pascal Crépey
- Univ Rennes, EHESP, REPERES « Recherche en Pharmaco-Epidémiologie et Recours aux Soins »—EA 7449, 35043 Rennes, France
| | - Juliette Paireau
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Santé Publique France, French National Public Health Agency, Saint-Maurice, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - François Beck
- Santé Publique France, French National Public Health Agency, Saint-Maurice, France
| | - Harold Noel
- Santé Publique France, French National Public Health Agency, Saint-Maurice, France
| | - Daniel Lévy-Bruhl
- Santé Publique France, French National Public Health Agency, Saint-Maurice, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
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30
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De Meijere G, Colizza V, Valdano E, Castellano C. Effect of delayed awareness and fatigue on the efficacy of self-isolation in epidemic control. Phys Rev E 2021; 104:044316. [PMID: 34781485 DOI: 10.1103/physreve.104.044316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/26/2021] [Indexed: 12/12/2022]
Abstract
The isolation of infectious individuals is a key measure of public health for the control of communicable diseases. However, involving a strong perturbation of daily life, it often causes psychosocial distress, and severe financial and social costs. These may act as mechanisms limiting the adoption of the measure in the first place or the adherence throughout its full duration. In addition, difficulty of recognizing mild symptoms or lack of symptoms may impact awareness of the infection and further limit adoption. Here we study an epidemic model on a network of contacts accounting for limited adherence and delayed awareness to self-isolation, along with fatigue causing overhasty termination. The model allows us to estimate the role of each ingredient and analyze the tradeoff between adherence and duration of self-isolation. We find that the epidemic threshold is very sensitive to an effective compliance that combines the effects of imperfect adherence, delayed awareness and fatigue. If adherence improves for shorter quarantine periods, there exists an optimal duration of isolation, shorter than the infectious period. However, heterogeneities in the connectivity pattern, coupled to a reduced compliance for highly active individuals, may almost completely offset the effectiveness of self-isolation measures on the control of the epidemic.
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Affiliation(s)
- Giulia De Meijere
- Gran Sasso Science Institute, Viale F. Crispi 7, 67100 L'Aquila, Italy.,Istituto dei Sistemi Complessi (ISC-CNR), Via dei Taurini 19, I-00185 Rome, Italy
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, 27, rue Chaligny, 75012 Paris, France.,Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori Ward, Yokohama, Kanagawa 226-0026, Japan
| | - Eugenio Valdano
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, 27, rue Chaligny, 75012 Paris, France
| | - Claudio Castellano
- Istituto dei Sistemi Complessi (ISC-CNR), Via dei Taurini 19, I-00185 Rome, Italy
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31
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Mazzoli M, Valdano E, Colizza V. Projecting the COVID-19 epidemic risk in France for the summer 2021. J Travel Med 2021; 28:6355057. [PMID: 34414436 PMCID: PMC8499767 DOI: 10.1093/jtm/taab129] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/14/2022]
Abstract
The next weeks will be critical in determining the conditions and timing of the 4th wave of COVID-19 in France. We assessed epidemic risk to assist spatially targeted surveillance and control. Southwest is estimated to be at highest risk, due to summer crowding, low acquired immunity and Delta variant hotspots.
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Affiliation(s)
- Mattia Mazzoli
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Eugenio Valdano
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.,Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
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32
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Launay T, Souty C, Vilcu AM, Turbelin C, Blanchon T, Guerrisi C, Hanslik T, Colizza V, Bardoulat I, Lemaître M, Boëlle PY. Common communicable diseases in the general population in France during the COVID-19 pandemic. PLoS One 2021; 16:e0258391. [PMID: 34634090 PMCID: PMC8504745 DOI: 10.1371/journal.pone.0258391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/26/2021] [Indexed: 12/02/2022] Open
Abstract
In France, social distancing measures have been adopted to contain the spread of COVID-19, culminating in national Lockdowns. The use of hand washing, hydro-alcoholic rubs and mask-wearing also increased over time. As these measures are likely to impact the transmission of many communicable diseases, we studied the changes in common infectious diseases incidence in France during the first year of COVID-19 circulation. We examined the weekly incidence of acute gastroenteritis, chickenpox, acute respiratory infections and bronchiolitis reported in general practitioner networks since January 2016. We obtained search engine query volume for French terms related to these diseases and sales data for relevant drugs over the same period. A periodic regression model was fit to disease incidence, drug sales and search query volume before the COVID-19 period and extrapolated afterwards. We compared the expected values with observations made in 2020. During the first lockdown period, incidence dropped by 67% for gastroenteritis, by 79% for bronchiolitis, by 49% for acute respiratory infection and 90% for chickenpox compared to the past years. Reductions with respect to the expected incidence reflected the strength of implemented measures. Incidence in children was impacted the most. Reduction in primary care consultations dropped during a short period at the beginning of the first lockdown period but remained more than 95% of the expected value afterwards. In primary care, the large decrease in reported gastroenteritis, chickenpox or bronchiolitis observed during the period where many barrier measures were implemented imply that the circulation of common viruses was reduced and informs on the overall effect of these measures.
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Affiliation(s)
- Titouan Launay
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Cécile Souty
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Ana-Maria Vilcu
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Clément Turbelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Thierry Blanchon
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Caroline Guerrisi
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Thomas Hanslik
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | | | | | - Pierre-Yves Boëlle
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
- Hôpital Saint-Antoine, Assistance Publique–Hôpitaux de Paris, Paris, France
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33
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Tennant WSD, Cardinale E, Cêtre-Sossah C, Moutroifi Y, Le Godais G, Colombi D, Spencer SEF, Tildesley MJ, Keeling MJ, Charafouddine O, Colizza V, Edmunds WJ, Métras R. Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape. Nat Commun 2021; 12:5593. [PMID: 34552082 PMCID: PMC8458460 DOI: 10.1038/s41467-021-25833-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/25/2021] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
The persistence mechanisms of Rift Valley fever (RVF), a zoonotic arboviral haemorrhagic fever, at both local and broader geographical scales have yet to be fully understood and rigorously quantified. We developed a mathematical metapopulation model describing RVF virus transmission in livestock across the four islands of the Comoros archipelago, accounting for island-specific environments and inter-island animal movements. By fitting our model in a Bayesian framework to 2004-2015 surveillance data, we estimated the importance of environmental drivers and animal movements on disease persistence, and tested the impact of different control scenarios on reducing disease burden throughout the archipelago. Here we report that (i) the archipelago network was able to sustain viral transmission in the absence of explicit disease introduction events after early 2007, (ii) repeated outbreaks during 2004-2020 may have gone under-detected by local surveillance, and (iii) co-ordinated within-island control measures are more effective than between-island animal movement restrictions.
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Affiliation(s)
- Warren S D Tennant
- The Zeeman Institute: SBIDER, University of Warwick, Coventry, CV4 7AL, UK.
- Mathematics Institute, University of Warwick, Coventry, CV4 7AL, UK.
| | - Eric Cardinale
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Animal, Santé, Territoires, Risques, et Écosystèmes, F-97490, Sainte Clotilde, La Réunion, France
- Animal, Santé, Territoires, Risques, et Écosystèmes, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, INRAE, Montpellier, France
| | - Catherine Cêtre-Sossah
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Animal, Santé, Territoires, Risques, et Écosystèmes, F-97490, Sainte Clotilde, La Réunion, France
- Animal, Santé, Territoires, Risques, et Écosystèmes, Université de Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, INRAE, Montpellier, France
| | - Youssouf Moutroifi
- Vice-Présidence en charge de l'Agriculture, l'Elevage, la Pêche, l'Industrie, l'Energie et l'Artisanat, B.P. 41 Mdé, Moroni, Union of the Comoros
| | - Gilles Le Godais
- Direction de l'Alimentation, de l'Agriculture et de la Forêt de Mayotte, Service de l'Alimentation, 97600, Mamoudzou, France
| | - Davide Colombi
- Aizoon Technology Consulting, Str. del Lionetto 6, Torino, Italy
| | - Simon E F Spencer
- The Zeeman Institute: SBIDER, University of Warwick, Coventry, CV4 7AL, UK
- Department of Statistics, University of Warwick, Coventry, CV4, 7AL, UK
| | - Mike J Tildesley
- The Zeeman Institute: SBIDER, University of Warwick, Coventry, CV4 7AL, UK
- Mathematics Institute, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Matt J Keeling
- The Zeeman Institute: SBIDER, University of Warwick, Coventry, CV4 7AL, UK
- Mathematics Institute, University of Warwick, Coventry, CV4 7AL, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Onzade Charafouddine
- Vice-Présidence en charge de l'Agriculture, l'Elevage, la Pêche, l'Industrie, l'Energie et l'Artisanat, B.P. 41 Mdé, Moroni, Union of the Comoros
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Épidémiologie et de Santé Publique (Unité Mixte de Recherche en Santé 1136), 75012, Paris, France
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Raphaëlle Métras
- INSERM, Sorbonne Université, Institut Pierre Louis d'Épidémiologie et de Santé Publique (Unité Mixte de Recherche en Santé 1136), 75012, Paris, France
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
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Susswein Z, Valdano E, Brett T, Rohani P, Colizza V, Bansal S. Ignoring spatial heterogeneity in drivers of SARS-CoV-2 transmission in the US will impede sustained elimination. medRxiv 2021:2021.08.09.21261807. [PMID: 34401885 PMCID: PMC8366803 DOI: 10.1101/2021.08.09.21261807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To dissect the transmission dynamics of SARS-CoV-2 in the United States, we integrate parallel streams of high-resolution data on contact, mobility, seasonality, vaccination and seroprevalence within a metapopulation network. We find the COVID-19 pandemic in the US is characterized by a geographically localized mosaic of transmission along an urban-rural gradient, with many outbreaks sustained by between-county transmission. We detect a dynamic tension between the spatial scale of public health interventions and population susceptibility as pre-pandemic contact is resumed. Further, we identify regions rendered particularly at risk from invasion by variants of concern due to spatial connectivity. These findings emphasize the public health importance of accounting for the hierarchy of spatial scales in transmission and the heterogeneous impacts of mobility on the landscape of contagion risk.
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Tran Kiem C, Massonnaud CR, Levy-Bruhl D, Poletto C, Colizza V, Bosetti P, Fontanet A, Gabet A, Olié V, Zanetti L, Boëlle PY, Crépey P, Cauchemez S. A modelling study investigating short and medium-term challenges for COVID-19 vaccination: From prioritisation to the relaxation of measures. EClinicalMedicine 2021; 38:101001. [PMID: 34278284 PMCID: PMC8278244 DOI: 10.1016/j.eclinm.2021.101001] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The roll-out of COVID-19 vaccines is a multi-faceted challenge whose performance depends on pace of vaccination, vaccine characteristics and heterogeneities in individual risks. METHODS We developed a mathematical model accounting for the risk of severe disease by age and comorbidity, and transmission dynamics. We compared vaccine prioritisation strategies in the early roll-out stage and quantified the extent to which measures could be relaxed as a function of the vaccine coverage achieved in France. FINDINGS Prioritizing at-risk individuals reduces morbi-mortality the most if vaccines only reduce severity, but is of less importance if vaccines also substantially reduce infectivity or susceptibility. Age is the most important factor to consider for prioritization; additionally accounting for comorbidities increases the performance of the campaign in a context of scarce resources. Vaccinating 90% of ≥65 y.o. and 70% of 18-64 y.o. before autumn 2021 with a vaccine that reduces severity by 90% and susceptibility by 80%, we find that control measures reducing transmission rates by 15-27% should be maintained to remain below 1000 daily hospital admissions in France with a highly transmissible variant (basic reproduction number R0 = 4). Assuming 90% of ≥65 y.o. are vaccinated, full relaxation of control measures might be achieved with a vaccine coverage of 89-100% in 18-64 y.o or 60-69% of 0-64 y.o. INTERPRETATION Age and comorbidity-based vaccine prioritization strategies could reduce the burden of the disease. Very high vaccination coverage may be required to completely relax control measures. Vaccination of children, if possible, could lower coverage targets necessary to achieve this objective.
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Affiliation(s)
- Cécile Tran Kiem
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 25-28 rue du Dr Roux, 75015 Paris, France
- Sorbonne Université, Paris, France
| | - Clément R. Massonnaud
- Univ Rennes, EHESP, REPERES « Recherche en Pharmaco-Epidémiologie et Recours aux Soins », EA 7449 Rennes, France
- Centre Hospitalier Universitaire de Rouen, Département d'Informatique Médicale, D2IM, Rouen, France
| | | | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Paolo Bosetti
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France
- PACRI Unit, Conservatoire National des Arts et Métiers, Paris, France
| | | | | | - Laura Zanetti
- Haute Autorité de Santé, Saint-Denis La plaine Stade de France, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Pascal Crépey
- Univ Rennes, EHESP, REPERES « Recherche en Pharmaco-Epidémiologie et Recours aux Soins », EA 7449 Rennes, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, 25-28 rue du Dr Roux, 75015 Paris, France
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Colman E, Colizza V, Hanks EM, Hughes DP, Bansal S. Social fluidity mobilizes contagion in human and animal populations. eLife 2021; 10:62177. [PMID: 34328080 PMCID: PMC8324292 DOI: 10.7554/elife.62177] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Humans and other group-living animals tend to distribute their social effort disproportionately. Individuals predominantly interact with a small number of close companions while maintaining weaker social bonds with less familiar group members. By incorporating this behavior into a mathematical model, we find that a single parameter, which we refer to as social fluidity, controls the rate of social mixing within the group. Large values of social fluidity correspond to gregarious behavior, whereas small values signify the existence of persistent bonds between individuals. We compare the social fluidity of 13 species by applying the model to empirical human and animal social interaction data. To investigate how social behavior influences the likelihood of an epidemic outbreak, we derive an analytical expression of the relationship between social fluidity and the basic reproductive number of an infectious disease. For species that form more stable social bonds, the model describes frequency-dependent transmission that is sensitive to changes in social fluidity. As social fluidity increases, animal-disease systems become increasingly density-dependent. Finally, we demonstrate that social fluidity is a stronger predictor of disease outcomes than both group size and connectivity, and it provides an integrated framework for both density-dependent and frequency-dependent transmission.
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Affiliation(s)
- Ewan Colman
- Department of Biology, Georgetown University, Washington, United States.,Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75012, Paris, France
| | - Ephraim M Hanks
- Department of Statistics, Eberly College of Science, Penn State University, State College, United States
| | - David P Hughes
- Department of Entomology, College of Agricultural Sciences, Penn State University, State College, United States
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, United States
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Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Oude Munnink BB, Koopmans M, Sadilek A, Lai S, Tatem AJ, Baele G, Suchard MA, Dellicour S. Untangling introductions and persistence in COVID-19 resurgence in Europe. Nature 2021; 595:713-717. [PMID: 34192736 PMCID: PMC8324533 DOI: 10.1038/s41586-021-03754-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [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: 02/04/2021] [Accepted: 06/22/2021] [Indexed: 11/09/2022]
Abstract
After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.
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Affiliation(s)
- Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
- Global Virus Network (GVN), Baltimore, MD, USA.
| | - Nick Ruktanonchai
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
- Population Health Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, Paris, France
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | - Anthony Levasseur
- UMR MEPHI (Microbes, Evolution, Phylogeny and Infections), Aix-Marseille Université (AMU) and Institut Universitaire de France (IUF), Marseille, France
| | - Bas B Oude Munnink
- Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus MC, Rotterdam, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus MC, Rotterdam, The Netherlands
| | | | - Shengjie Lai
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - Andrew J Tatem
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.
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38
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Valdano E, Lee J, Bansal S, Rubrichi S, Colizza V. Highlighting socio-economic constraints on mobility reductions during COVID-19 restrictions in France can inform effective and equitable pandemic response. J Travel Med 2021; 28:6225375. [PMID: 33851703 PMCID: PMC8083287 DOI: 10.1093/jtm/taab045] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Eugenio Valdano
- Pierre Louis Institute of Epidemiology and Public Health, INSERM, Sorbonne Université, Paris, France
| | - Jonggul Lee
- Pierre Louis Institute of Epidemiology and Public Health, INSERM, Sorbonne Université, Paris, France
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Stefania Rubrichi
- Orange Labs, Sociology and Economics of Networks and Services (SENSE), Chatillon, France
| | - Vittoria Colizza
- Pierre Louis Institute of Epidemiology and Public Health, INSERM, Sorbonne Université, Paris, France.,Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
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39
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Zipfel CM, Colizza V, Bansal S. The missing season: The impacts of the COVID-19 pandemic on influenza. Vaccine 2021; 39:3645-3648. [PMID: 34078554 DOI: 10.1016/j.vaccine.2021.05.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022]
Abstract
Throughout the COVID-19 pandemic, many have worried that the additional burden of seasonal influenza would create a devastating scenario, resulting in overwhelmed healthcare capacities and further loss of life. However, many were pleasantly surprised: the 2020 Southern Hemisphere and 2020-2021 Northern Hemisphere influenza seasons were entirely suppressed. The potential causes and impacts of this drastic public health shift are highly uncertain, but provide lessons about future control of respiratory diseases, especially for the upcoming influenza season.
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Affiliation(s)
- Casey M Zipfel
- Department of Biology, Georgetown University, Washington DC, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington DC, USA.
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40
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Valdano E, Okano JT, Colizza V, Mitonga HK, Blower S. Using mobile phone data to reveal risk flow networks underlying the HIV epidemic in Namibia. Nat Commun 2021; 12:2837. [PMID: 33990578 PMCID: PMC8121904 DOI: 10.1038/s41467-021-23051-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 04/08/2021] [Indexed: 12/22/2022] Open
Abstract
Twenty-six million people are living with HIV in sub-Saharan Africa; epidemics are widely dispersed, due to high levels of mobility. However, global elimination strategies do not consider mobility. We use Call Detail Records from 9 billion calls/texts to model mobility in Namibia; we quantify the epidemic-level impact by using a mathematical framework based on spatial networks. We find complex networks of risk flows dispersed risk countrywide: increasing the risk of acquiring HIV in some areas, decreasing it in others. Overall, 40% of risk was mobility-driven. Networks contained multiple risk hubs. All constituencies (administrative units) imported and exported risk, to varying degrees. A few exported very high levels of risk: their residents infected many residents of other constituencies. Notably, prevalence in the constituency exporting the most risk was below average. Large-scale networks of mobility-driven risk flows underlie generalized HIV epidemics in sub-Saharan Africa. In order to eliminate HIV, it is likely to become increasingly important to implement innovative control strategies that focus on disrupting risk flows.
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Affiliation(s)
- Eugenio Valdano
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Justin T Okano
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Honore K Mitonga
- Department of Epidemiology and Biostatistics, School of Public Health, University of Namibia, Windhoek, Namibia
| | - Sally Blower
- Center for Biomedical Modeling, The Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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41
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Moreno López JA, Arregui García B, Bentkowski P, Bioglio L, Pinotti F, Boëlle PY, Barrat A, Colizza V, Poletto C. Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection. Sci Adv 2021; 7:eabd8750. [PMID: 33712416 PMCID: PMC8034853 DOI: 10.1126/sciadv.abd8750] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/22/2021] [Indexed: 05/12/2023]
Abstract
The efficacy of digital contact tracing against coronavirus disease 2019 (COVID-19) epidemic is debated: Smartphone penetration is limited in many countries, with low coverage among the elderly, the most vulnerable to COVID-19. We developed an agent-based model to precise the impact of digital contact tracing and household isolation on COVID-19 transmission. The model, calibrated on French population, integrates demographic, contact and epidemiological information to describe exposure and transmission of COVID-19. We explored realistic levels of case detection, app adoption, population immunity, and transmissibility. Assuming a reproductive ratio R = 2.6 and 50% detection of clinical cases, a ~20% app adoption reduces peak incidence by ~35%. With R = 1.7, >30% app adoption lowers the epidemic to manageable levels. Higher coverage among adults, playing a central role in COVID-19 transmission, yields an indirect benefit for the elderly. These results may inform the inclusion of digital contact tracing within a COVID-19 response plan.
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Affiliation(s)
- Jesús A Moreno López
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Beatriz Arregui García
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Piotr Bentkowski
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Livio Bioglio
- Department of Computer Science, University of Turin, Turin, Italy
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Alain Barrat
- Aix-Marseille Univ, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
- Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
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42
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Moreno López JA, Arregui García B, Bentkowski P, Bioglio L, Pinotti F, Boëlle PY, Barrat A, Colizza V, Poletto C. Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection. Sci Adv 2021; 7:sciadv.abd8750. [PMID: 33712416 DOI: 10.1101/2020.07.22.20158352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/22/2021] [Indexed: 05/21/2023]
Abstract
The efficacy of digital contact tracing against coronavirus disease 2019 (COVID-19) epidemic is debated: Smartphone penetration is limited in many countries, with low coverage among the elderly, the most vulnerable to COVID-19. We developed an agent-based model to precise the impact of digital contact tracing and household isolation on COVID-19 transmission. The model, calibrated on French population, integrates demographic, contact and epidemiological information to describe exposure and transmission of COVID-19. We explored realistic levels of case detection, app adoption, population immunity, and transmissibility. Assuming a reproductive ratio R = 2.6 and 50% detection of clinical cases, a ~20% app adoption reduces peak incidence by ~35%. With R = 1.7, >30% app adoption lowers the epidemic to manageable levels. Higher coverage among adults, playing a central role in COVID-19 transmission, yields an indirect benefit for the elderly. These results may inform the inclusion of digital contact tracing within a COVID-19 response plan.
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Affiliation(s)
- Jesús A Moreno López
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Beatriz Arregui García
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), CSIC-UIB, Palma de Mallorca, Spain
| | - Piotr Bentkowski
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Livio Bioglio
- Department of Computer Science, University of Turin, Turin, Italy
| | - Francesco Pinotti
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Alain Barrat
- Aix-Marseille Univ, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
- Tokyo Tech World Research Hub Initiative (WRHI), Tokyo Institute of Technology, Tokyo, Japan
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
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43
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Di Domenico L, Sabbatini CE, Pullano G, Lévy-Bruhl D, Colizza V. Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France. Euro Surveill 2021; 26:2100272. [PMID: 33860748 PMCID: PMC8167415 DOI: 10.2807/1560-7917.es.2021.26.15.2100272] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/14/2021] [Indexed: 12/27/2022] Open
Abstract
Following the spread of the SARS-CoV-2 B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a two-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalisations to plateau by decreasing transmission of the historical strains while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalisations is expected, despite the foreseen increase in vaccination rhythm.
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Affiliation(s)
- Laura Di Domenico
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Chiara E Sabbatini
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Pullano
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Orange Labs, Sociology and Economics of Networks and Services (SENSE), Chatillon, France
| | | | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
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44
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Abstract
The lower an individual’s socioeconomic position, the higher their risk of poor health in low-, middle-, and high-income settings alike. As health inequities grow, it is imperative that we develop an empirically-driven mechanistic understanding of the determinants of health disparities, and capture disease burden in at-risk populations to prevent exacerbation of disparities. Past work has been limited in data or scope and has thus fallen short of generalizable insights. Here, we integrate empirical data from observational studies and large-scale healthcare data with models to characterize the dynamics and spatial heterogeneity of health disparities in an infectious disease case study: influenza. We find that variation in social and healthcare-based determinants exacerbates influenza epidemics, and that low socioeconomic status (SES) individuals disproportionately bear the burden of infection. We also identify geographical hotspots of influenza burden in low SES populations, much of which is overlooked in traditional influenza surveillance, and find that these differences are most predicted by variation in susceptibility and access to sickness absenteeism. Our results highlight that the effect of overlapping factors is synergistic and that reducing this intersectionality can significantly reduce inequities. Additionally, health disparities are expressed geographically, and targeting public health efforts spatially may be an efficient use of resources to abate inequities. The association between health and socioeconomic prosperity has a long history in the epidemiological literature; addressing health inequities in respiratory-transmitted infectious disease burden is an important step towards social justice in public health, and ignoring them promises to pose a serious threat. Health inequities, or increased morbidity and mortality due to social factors, have been demonstrated for respiratory-transmitted infectious diseases, most recently highlighted by disparities in COVID-19 severe cases and deaths. Many potential causes of these inequities have been proposed, but they have not been compared, and we do not understand their population-scale impacts. Our understanding of these issues is further hindered by epidemiological surveillance, which has been shown to overlook areas of low socioeconomic status. Here, we combine mechanistic and statistical modeling with high volume datasets to disentangle the drivers of respiratory-transmitted disease disparities, and to estimate locations where these health inequities are most severe, using influenza as a case study. We show that low socioeconomic status individuals disproportionately bear the burden of influenza infection, and that all proposed factors are synergistic in their effect. Additionally we identify geographical hotspots of poor disease surveillance among populations of low socioeconomic status, which contribute to an underestimation of health disparities. As the divide in health inequities, driven by income inequality and systemic racism, grows wider across the United States, we highlight the need to understand the mechanisms that may be at the root of disparities, and we advocate for the prioritization of capabilities to monitor outbreaks in at-risk populations so that we may prevent exacerbation of inequities.
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Affiliation(s)
- Casey M. Zipfel
- Department of Biology, Georgetown University, Washington DC, United States of America
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, F75012 Paris, France
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington DC, United States of America
- * E-mail:
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45
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Di Domenico L, Pullano G, Sabbatini CE, Boëlle PY, Colizza V. Modelling safe protocols for reopening schools during the COVID-19 pandemic in France. Nat Commun 2021; 12:1073. [PMID: 33594076 PMCID: PMC7887250 DOI: 10.1038/s41467-021-21249-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
As countries in Europe implement strategies to control the COVID-19 pandemic, different options are chosen regarding schools. Through a stochastic age-structured transmission model calibrated to the observed epidemic in Île-de-France in the first wave, we explored scenarios of partial, progressive, or full school reopening. Given the uncertainty on children's role, we found that reopening schools after lockdown may increase COVID-19 cases, yet protocols exist to keep the epidemic controlled. Under a scenario with stable epidemic activity if schools were closed, reopening pre-schools and primary schools would lead to up to 76% [67, 84]% occupation of ICU beds if no other school level reopened, or if middle and high schools reopened later. Immediately reopening all school levels may overwhelm the ICU system. Priority should be given to pre- and primary schools allowing younger children to resume learning and development, whereas full attendance in middle and high schools is not recommended for stable or increasing epidemic activity. Large-scale test and trace is required to keep the epidemic under control. Ex-post assessment shows that progressive reopening of schools, limited attendance, and strong adoption of preventive measures contributed to a decreasing epidemic after lifting the first lockdown.
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Affiliation(s)
- Laura Di Domenico
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Pullano
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Orange Labs, Sociology and Economics of Network and Services (SENSE), Chatillon, France
| | - Chiara E Sabbatini
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
- Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.
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46
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Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Sadilek A, Lai S, Tatem AJ, Baele G, Suchard MA, Dellicour S. SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data. Res Sq 2021:rs.3.rs-208849. [PMID: 33594355 PMCID: PMC7885927 DOI: 10.21203/rs.3.rs-208849/v1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Following the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting late summer that was deadlier and more difficult to contain. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave. Here, we build a phylogeographic model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the COVID-19 resurgence in Europe. We inform this model using genomic, mobility and epidemiological data from 10 West European countries and estimate that in many countries more than 50% of the lineages circulating in late summer resulted from new introductions since June 15th. The success in onwards transmission of these lineages is predicted by SARS-CoV-2 incidence during this period. Relatively early introductions from Spain into the United Kingdom contributed to the successful spread of the 20A.EU1/B.1.177 variant. The pervasive spread of variants that have not been associated with an advantage in transmissibility highlights the threat of novel variants of concern that emerged more recently and have been disseminated by holiday travel. Our findings indicate that more effective and coordinated measures are required to contain spread through cross-border travel.
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Affiliation(s)
- Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Global Virus Network (GVN), Baltimore, MD, USA
| | - Nick Ruktanonchai
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
- Population Health Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012 Paris, France
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012 Paris, France
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | - Anthony Levasseur
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université and Marseille Institut Universitaire de France, Marseille, France
| | | | - Shengjie Lai
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
| | - Andrew J Tatem
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, UK
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, 1050 Bruxelles, Belgium
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47
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Abstract
As healthcare capacities in the US and Europe reach their limits due to a surge in the COVID-19 pandemic, both regions enter the 2020-2021 influenza season. Southern hemisphere countries that had suppressed influenza seasons provide a hopeful example, but the lack of reduction in influenza in the 2019-2020 influenza season and heterogeneity in nonpharmaceutical and pharmaceutical interventions show that we cannot assume the same effect will occur globally. The US and Europe must promote the implementation and continuation of these measures in order to prevent additional burden to healthcare systems due to influenza.
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Affiliation(s)
- Casey Zipfel
- Department of Biology, Georgetown University, Washington DC, USA
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Shweta Bansal
- Department of Biology, Georgetown University, Washington DC, USA
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48
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Schirdewahn F, Lentz HHK, Colizza V, Koher A, Hövel P, Vidondo B. Early warning of infectious disease outbreaks on cattle-transport networks. PLoS One 2021; 16:e0244999. [PMID: 33406156 PMCID: PMC7787438 DOI: 10.1371/journal.pone.0244999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/19/2020] [Indexed: 11/18/2022] Open
Abstract
Surveillance of infectious diseases in livestock is traditionally carried out at the farms, which are the typical units of epidemiological investigations and interventions. In Central and Western Europe, high-quality, long-term time series of animal transports have become available and this opens the possibility to new approaches like sentinel surveillance. By comparing a sentinel surveillance scheme based on markets to one based on farms, the primary aim of this paper is to identify the smallest set of sentinel holdings that would reliably and timely detect emergent disease outbreaks in Swiss cattle. Using a data-driven approach, we simulate the spread of infectious diseases according to the reported or available daily cattle transport data in Switzerland over a four year period. Investigating the efficiency of surveillance at either market or farm level, we find that the most efficient early warning surveillance system [the smallest set of sentinels that timely and reliably detect outbreaks (small outbreaks at detection, short detection delays)] would be based on the former, rather than the latter. We show that a detection probability of 86% can be achieved by monitoring all 137 markets in the network. Additional 250 farm sentinels—selected according to their risk—need to be placed under surveillance so that the probability of first hitting one of these farm sentinels is at least as high as the probability of first hitting a market. Combining all markets and 1000 farms with highest risk of infection, these two levels together will lead to a detection probability of 99%. We conclude that the design of animal surveillance systems greatly benefits from the use of the existing abundant and detailed animal transport data especially in the case of highly dynamic cattle transport networks. Sentinel surveillance approaches can be tailored to complement existing farm risk-based and syndromic surveillance approaches.
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Affiliation(s)
- Frederik Schirdewahn
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
| | - Hartmut H. K. Lentz
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Vittoria Colizza
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d’épidémiologie et de Santé Publique, Paris, France
| | - Andreas Koher
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
| | - Philipp Hövel
- Institut für Theoretische Physik, Technische Universität Berlin, Berlin, Germany
- School of Mathematical Sciences, University College Cork, Cork, Ireland
| | - Beatriz Vidondo
- Veterinary Public Health Institute, University of Bern, Bern-Liebefeld, Switzerland
- * E-mail:
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49
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Bosetti P, Kiem CT, Yazdanpanah Y, Fontanet A, Lina B, Colizza V, Cauchemez S. Impact of mass testing during an epidemic rebound of SARS-CoV-2: a modelling study using the example of France. Euro Surveill 2021; 26:2001978. [PMID: 33413741 PMCID: PMC7791601 DOI: 10.2807/1560-7917.es.2020.26.1.2001978] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 11/23/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022] Open
Abstract
We used a mathematical model to evaluate the impact of mass testing in the control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Under optimistic assumptions, one round of mass testing may reduce daily infections by up to 20-30%. Consequently, very frequent testing would be required to control a quickly growing epidemic if other control measures were to be relaxed. Mass testing is most relevant when epidemic growth remains limited through a combination of interventions.
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Affiliation(s)
- Paolo Bosetti
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Cécile Tran Kiem
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Yazdan Yazdanpanah
- Infections Antimicrobials Modelling Evolution (IAME) UMR 1137, University of Paris, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France
- PACRI Unit, Conservatoire National des Arts et Métiers, Paris, France
| | - Bruno Lina
- National Reference Center for Respiratory Viruses, Department of Virology, Infective Agents Institute, North Hospital Network, Lyon, France
- Virpath Laboratory, International Center of Research in Infectiology, INSERM U1111, CNRS-UMR 5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon University, Lyon, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
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50
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Pullano G, Di Domenico L, Sabbatini CE, Valdano E, Turbelin C, Debin M, Guerrisi C, Kengne-Kuetche C, Souty C, Hanslik T, Blanchon T, Boëlle PY, Figoni J, Vaux S, Campèse C, Bernard-Stoecklin S, Colizza V. Underdetection of cases of COVID-19 in France threatens epidemic control. Nature 2020; 590:134-139. [PMID: 33348340 DOI: 10.1038/s41586-020-03095-6] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/08/2020] [Indexed: 01/17/2023]
Abstract
As countries in Europe gradually relaxed lockdown restrictions after the first wave, test-trace-isolate strategies became critical to maintain the incidence of coronavirus disease 2019 (COVID-19) at low levels1,2. Reviewing their shortcomings can provide elements to consider in light of the second wave that is currently underway in Europe. Here we estimate the rate of detection of symptomatic cases of COVID-19 in France after lockdown through the use of virological3 and participatory syndromic4 surveillance data coupled with mathematical transmission models calibrated to regional hospitalizations2. Our findings indicate that around 90,000 symptomatic infections, corresponding to 9 out 10 cases, were not ascertained by the surveillance system in the first 7 weeks after lockdown from 11 May to 28 June 2020, although the test positivity rate did not exceed the 5% recommendation of the World Health Organization (WHO)5. The median detection rate increased from 7% (95% confidence interval, 6-8%) to 38% (35-44%) over time, with large regional variations, owing to a strengthening of the system as well as a decrease in epidemic activity. According to participatory surveillance data, only 31% of individuals with COVID-19-like symptoms consulted a doctor in the study period. This suggests that large numbers of symptomatic cases of COVID-19 did not seek medical advice despite recommendations, as confirmed by serological studies6,7. Encouraging awareness and same-day healthcare-seeking behaviour of suspected cases of COVID-19 is critical to improve detection. However, the capacity of the system remained insufficient even at the low epidemic activity achieved after lockdown, and was predicted to deteriorate rapidly with increasing incidence of COVID-19 cases. Substantially more aggressive, targeted and efficient testing with easier access is required to act as a tool to control the COVID-19 pandemic. The testing strategy will be critical to enable partial lifting of the current restrictive measures in Europe and to avoid a third wave.
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Affiliation(s)
- Giulia Pullano
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France.,Orange Labs, Sociology and Economics of Network and Services (SENSE), Chatillon, France
| | - Laura Di Domenico
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Chiara E Sabbatini
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Eugenio Valdano
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Clément Turbelin
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Marion Debin
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Caroline Guerrisi
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Charly Kengne-Kuetche
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Cécile Souty
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Thomas Hanslik
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France.,UFR des Sciences de la Santé Simone-Veil, Université Versailles-Saint-Quentin-en-Yvelines, Versailles, France.,AP-HP, Service de Médecine Interne, Hôpital Ambroise Paré, Boulogne Billancourt, France
| | - Thierry Blanchon
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France
| | - Julie Figoni
- Santé publique France, Direction des maladies infectieuses, Saint-Maurice, France
| | - Sophie Vaux
- Santé publique France, Direction des maladies infectieuses, Saint-Maurice, France
| | - Christine Campèse
- Santé publique France, Direction des maladies infectieuses, Saint-Maurice, France
| | | | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, IPLESP, Paris, France. .,Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.
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