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1. Vaccine effectiveness and duration of protection of COVID-19 mRNA vaccines against Delta and Omicron BA.1 symptomatic and severe COVID-19 outcomes in adults aged 50 years and over in France

Author: Cynthia Raissa Tamandjou Tchuem, Vincent Auvigne, Sophie Vaux, Charline Montagnat, Juliette Paireau, Stéphanie Monnier Besnard, Amélie Gabet, Nabil Benhajkassen, Yann Le Strat, Isabelle Parent Du Chatelet, and Daniel Levy-Bruhl
Subjects: Infectious Diseases, General Veterinary, General Immunology and Microbiology, Public Health, Environmental and Occupational Health, Molecular Medicine
Published: 2023
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2. Impact of non-pharmaceutical interventions, weather, vaccination, and variants on COVID-19 transmission across departments in France

Author: Juliette Paireau, Marie-Laure Charpignon, Sophie Larrieu, Clémentine Calba, Nathanaël Hozé, Pierre-Yves Boëlle, Rodolphe Thiebaut, Mélanie Prague, Simon Cauchemez, Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice], Santé publique France - French National Public Health Agency [Saint-Maurice, France], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), MIT Institute for Data, Systems, and Society [Cambridge, MA] (IDSS), Massachusetts Institute of Technology (MIT), Boston Children's Hospital, Harvard Medical School [Boston] (HMS), Statistics In System biology and Translational Medicine (SISTM), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)- Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Santé publique France Nouvelle-Aquitaine [Bordeaux], Santé publique France Provence-Alpes-Côte d'azur et Corse - Provence-Alps-French Riviera and Corsica [Marseille], Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), We acknowledge financial support from the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (grant ANR-10-LABX-62-IBEID), Santé publique France, the INCEPTION project (PIA/ANR16-CONV-0005), the European Union’s Horizon 2020 research and innovation program under grants 101003589 (RECOVER) and 874735 (VEO), AXA, Groupama, the French Agency for Research on AIDS and Emerging Infectious Diseases via the EMERGEN project (ANRS0151), and the National Research Agency (ANR) through the ANR-Flash call for COVID-19 (grant ANR-20-COVI-0018)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-20-COVI-0018,TheraCoV,Dynamique virale au niveau individuel et populationnel : implications pour l'optimisation des stratégies antivirales(2020), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), and European Project: 874735,H2020-SC1-2019-Single-Stage-RTD,VEO(2020)
Subjects: variants, Infectious Diseases, SARS-CoV-2, COVID-19, reproduction number, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, vaccination, non-pharmaceutical interventions, climate, multivariable regression model
Abstract: Background Multiple factors shape the temporal dynamics of the COVID-19 pandemic. Quantifying their relative contributions is key to guide future control strategies. Our objective was to disentangle the individual effects of non-pharmaceutical interventions (NPIs), weather, vaccination, and variants of concern (VOC) on local SARS-CoV-2 transmission. Methods We developed a log-linear model for the weekly reproduction number (R) of hospital admissions in 92 French metropolitan departments. We leveraged (i) the homogeneity in data collection and NPI definitions across departments, (ii) the spatial heterogeneity in the timing of NPIs, and (iii) an extensive observation period (14 months) covering different weather conditions, VOC proportions, and vaccine coverage levels. Findings Three lockdowns reduced R by 72.7% (95% CI 71.3–74.1), 70.4% (69.2–71.6) and 60.7% (56.4–64.5), respectively. Curfews implemented at 6/7 pm and 8/9 pm reduced R by 34.3% (27.9–40.2) and 18.9% (12.04–25.3), respectively. School closures reduced R by only 4.9% (2.0–7.8). We estimated that vaccination of the entire population would have reduced R by 71.7% (56.4–81.6), whereas the emergence of VOC (mainly Alpha during the study period) increased transmission by 44.6% (36.1–53.6) compared with the historical variant. Winter weather conditions (lower temperature and absolute humidity) increased R by 42.2% (37.3–47.3) compared to summer weather conditions. Additionally, we explored counterfactual scenarios (absence of VOC or vaccination) to assess their impact on hospital admissions. Interpretation Our study demonstrates the strong effectiveness of NPIs and vaccination and quantifies the role of weather while adjusting for other confounders. It highlights the importance of retrospective evaluation of interventions to inform future decision-making.
Published: 2023
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3. Two-Dose Measles Vaccine Effectiveness Remains High Over Time: A French Observational Study, 2017-2019

Author: Léa Franconeri, Denise Antona, Simon Cauchemez, Daniel Lévy-Bruhl, and Juliette Paireau
Published: 2023
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4. Reconstructing Mayotte 2018–19 Rift Valley Fever outbreak in humans by combining serological and surveillance data

Author: Jonathan Bastard, Guillaume André Durand, Fanny Parenton, Youssouf Hassani, Laure Dommergues, Juliette Paireau, Nathanaël Hozé, Marc Ruello, Gilda Grard, Raphaëlle Métras, Harold Noël, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Groupement de Défense Sanitaire Mayotte (GDS 976), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), and This work was funded by internal resources of Santé Publique France.
Subjects: [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: Rift Valley Fever (RVF) is a zoonosis that affects large parts of Africa and the Arabian Peninsula. RVF virus (RVFV) is transmitted to humans through contacts with infected animals, animal products, mosquito bites or aerosols. Its pathogenesis in humans ranges from asymptomatic forms to potentially deadly haemorrhagic fevers, and the true burden of human infections during outbreaks is generally unknown.We build a model fitted to both passive surveillance data and serological data collected throughout a RVF epidemic that occurred in Mayotte Island in 2018-2019.We estimate that RVFV infected 10,797 (95% CrI 4,728-16,127) people aged ≥15 years old in Mayotte during the entire outbreak, among which only 1.2% (0.67%-2.2%) were reported to the syndromic surveillance system. RVFV IgG seroprevalence in people ≥15 years old was estimated to increase from 5.5% (3.6%-7.7%) before the outbreak to 12.9% (10.4%-16.3%) thereafter.Our results suggest that a large part of RVFV infected people present subclinical forms of the disease and/or do not reach medical care that could lead to their detection by the surveillance system. This may threaten the implementation of exhaustive RVF surveillance and adequate control programs in affected countries.Rift Valley Fever (RVF) is a disease caused by a virus transmitted from livestock animals to humans by mosquito bites, aerosols or direct contact with infected animals or animal products. In some parts of Africa and the Arabian Peninsula, the virus can lead to large outbreaks in both humans and animals. Despite some infected people developing severe forms of the disease, some experience no or mild symptoms. Therefore, infection is often not detected by surveillance systems based on the reporting of symptoms by patients. Here, we use data collected during a RVF outbreak that occurred in 2018–2019 in Mayotte Island, in the Indian Ocean, to model the course of the outbreak in humans. We estimate that, throughout the epidemic, only 1.2% of infected people were detected by the surveillance system. Our results highlight that most human cases may go unreported during RVF outbreaks, making it difficult to monitor the burden of infections.
Published: 2022
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5. Modelling the end of a Zero-COVID strategy using nirmatrelvir/ritonavir, vaccination and NPIs in Wallis and Futuna

Author: Antoine Brault, Cécile Tran-Kiem, Clément Couteaux, Valérie Olié, Juliette Paireau, Yazdan Yazdanpanah, Jade Ghosn, Guillaume Martin-Blondel, Paolo Bosetti, Simon Cauchemez, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège Doctoral, Sorbonne Université (SU), Agence de Santé des îles Wallis & Futuna, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Duchange, Nathalie, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), CHU Toulouse [Toulouse], and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: NPIs, SARS-CoV-2, Nirmatrelvir/ritonavir, Health Policy, Public Health, Environmental and Occupational Health, Paxlovid, Obstetrics and Gynecology, COVID-19, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Zero-COVID, Treatment, Psychiatry and Mental health, Infectious Diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Pediatrics, Perinatology and Child Health, Internal Medicine, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, Geriatrics and Gerontology, Antiviral, Vaccine
Abstract: International audience; Ending Zero-COVID is challenging, particularly when vaccine coverage is low. Considering Wallis and Futuna, a French Zero-COVID territory affected by reluctance to vaccination, low immunity and high levels of comorbidities, we investigate how targeted use of nirmatrelvir/ritonavir (brand name Paxlovid) can complement vaccination and non-pharmaceutical interventions (NPIs) and mitigate the epidemic rebound expected when Zero-COVID ends.We developed a discrete age-stratified compartmental model describing SARS-CoV-2 spread and healthcare impact once Wallis and Futuna reopens. It accounts for comorbidity risk groups (CRG), vaccine coverage (2 doses, 3 doses), the effectiveness of vaccines (recent or old injection), treatments and NPIs. In our baseline scenario, cases aged 65+ in intermediate/high CRG and 40+ in high CRG are eligible for treatment.FindingsThe epidemic is expected to start 13-20 days after reopening with a doubling time of 1·6-3·7 days. For medium transmission intensity (R0=5), 134 (115-156) hospital admissions are expected within 3 months, with no pharmaceutical measures. In our baseline scenario, admissions are reduced by 11%-21% if 50% of the target group receive treatment, with maximum impact when combined with NPIs and vaccination. The number of hospitalisations averted (HA) per patient treated (PT) is maximum when 65+ in high CRG are targeted (0·124 HA/PT), quickly followed by 65+ in intermediate/high CRG (0·097 HA/PT), and any 65+ (0·093 HA/PT). Expanding the target group increases both PT and HA, but marginal gains diminish.Modelling suggests that test and treat may contribute to the mitigation of epidemic rebounds at the end of Zero-COVID, particularly in populations with low immunity and high levels of comorbidities.
Published: 2022
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6. Association between the COVID-19 pandemic and pertussis derived from multiple nationwide data sources, France, 2013 to 2020

Author: Soraya Matczak, Corinne Levy, Camille Fortas, Jérémie F Cohen, Stéphane Béchet, Fatima Aït El Belghiti, Sophie Guillot, Sabine Trombert-Paolantoni, Véronique Jacomo, Yann Savitch, Juliette Paireau, Sylvain Brisse, Nicole Guiso, Daniel Lévy-Bruhl, Robert Cohen, Julie Toubiana, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Association Clinique et Thérapeutique Infantile du Val de Marne (ACTIV), Groupe de Pathologie Infectieuse Pédiatrique [Paris] (GPIP), Société Française de Pédiatrie (SFP), Centre de Recherche Clinique [Créteil] (CRC), Centre Hospitalier Intercommunal de Créteil (CHIC), Association Française de Pédiatrie Ambulatoire (AFPA), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Equipe 1 : EPOPé - Épidémiologie Obstétricale, Périnatale et Pédiatrique (CRESS - U1153), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre national de Référence de la Coqueluche et autres Bordetelloses - National Reference Center for Whooping Cough and other Bordetella infections (CNR), Institut Pasteur [Paris] (IP), Laboratoire CERBA [Saint Ouen l'Aumône], Eurofins Biomnis, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: Epidemiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Whooping Cough, Virology, Communicable Disease Control, Public Health, Environmental and Occupational Health, COVID-19, Humans, Information Storage and Retrieval, France, Child, Pandemics
Abstract: Background Interventions to mitigate the COVID-19 pandemic may impact other respiratory diseases. Aims We aimed to study the course of pertussis in France over an 8-year period including the beginning of the COVID-19 pandemic and its association with COVID-19 mitigation strategies, using multiple nationwide data sources and regression models. Methods We analysed the number of French pertussis cases between 2013 and 2020, using PCR test results from nationwide outpatient laboratories (Source 1) and a network of the paediatric wards from 41 hospitals (Source 2). We also used reports of a national primary care paediatric network (Source 3). We conducted a quasi-experimental interrupted time series analysis, relying on negative binomial regression models. The models accounted for seasonality, long-term cycles and secular trend, and included a binary variable for the first national lockdown (start 16 March 2020). Results We identified 19,039 pertussis cases from these data sources. Pertussis cases decreased significantly following the implementation of mitigation measures, with adjusted incidence rate ratios of 0.10 (95% CI: 0.04–0.26) and 0.22 (95% CI: 0.07–0.66) for Source 1 and Source 2, respectively. The association was confirmed in Source 3 with a median of, respectively, one (IQR: 0–2) and 0 cases (IQR: 0–0) per month before and after lockdown (p = 0.0048). Conclusions The strong reduction in outpatient and hospitalised pertussis cases suggests an impact of COVID-19 mitigation measures on pertussis epidemiology. Pertussis vaccination recommendations should be followed carefully, and disease monitoring should be continued to detect any resurgence after relaxation of mitigation measures.
Published: 2022
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7. An ensemble model based on early predictors to forecast COVID-19 health care demand in France

Author: Juliette Paireau, Alessio Andronico, Nathanaël Hozé, Maylis Layan, Pascal Crépey, Alix Roumagnac, Marc Lavielle, Pierre-Yves Boëlle, Simon Cauchemez, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice], Santé publique France - French National Public Health Agency [Saint-Maurice, France], Centre de Recherches sur l'Action Politique en Europe (ARENES), Université de Rennes (UR)-Institut d'Études Politiques [IEP] - Rennes-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Centre National de la Recherche Scientifique (CNRS), Recherche sur les services et le management en santé (RSMS), Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Predict Services [Castelnau-le-Lez], Modélisation en pharmacologie de population (XPOP), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut Polytechnique de Paris (IP Paris), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), We acknowledge financial support from the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (grant ANR-10-LABX-62- IBEID), Santé publique France, the INCEPTION project (PIA/ANR16-CONV-0005), the European Union’s Horizon 2020 research and innovation program under grants 101003589(RECOVER) and 874735 (VEO), AXA, Groupama, and EMERGEN, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), European Project: 874735,H2020-SC1-2019-Single-Stage-RTD,VEO(2020), Lassailly-Bondaz, Anne, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID, and Versatile Emerging infectious disease Observatory - VEO - - H2020-SC1-2019-Single-Stage-RTD2020-01-01 - 2024-12-31 - 874735 - VALID
Subjects: MESH: Health Services Needs and Demand, Health Services Needs and Demand, MESH: Pandemics, Multidisciplinary, MESH: Humans, MESH: Delivery of Health Care, COVID-19, forecasting, MESH: Retrospective Studies, MESH: France, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Humans, MESH: COVID-19, ensemble model, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, Delivery of Health Care, Pandemics, Retrospective Studies
Abstract: Short-term forecasting of the COVID-19 pandemic is required to facilitate the planning of COVID-19 health care demand in hospitals. Here, we evaluate the performance of 12 individual models and 19 predictors to anticipate French COVID-19-related health care needs from September 7, 2020, to March 6, 2021. We then build an ensemble model by combining the individual forecasts and retrospectively test this model from March 7, 2021, to July 6, 2021. We find that the inclusion of early predictors (epidemiological, mobility, and meteorological predictors) can halve the rms error for 14-d–ahead forecasts, with epidemiological and mobility predictors contributing the most to the improvement. On average, the ensemble model is the best or second-best model, depending on the evaluation metric. Our approach facilitates the comparison and benchmarking of competing models through their integration in a coherent analytical framework, ensuring that avenues for future improvements can be identified.
Published: 2022
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8. Early chains of transmission of COVID-19 in France, January to March 2020

Author: Juliette Paireau, Alexandra Mailles, Catherine Eisenhauer, Franck de Laval, François Delon, Paolo Bosetti, Henrik Salje, Valérie Pontiès, Simon Cauchemez, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'épidémiologie et de santé publique des armées [Marseille] (CESPA), Service de Santé des Armées, Institut des sciences de la santé publique [Marseille] (ISSPAM), University of Cambridge [UK] (CAM), Santé publique France, Haut-de-France [Lille, France], This work was supported by the LabEx Integrative Biology of Emerging Infectious Diseases (IBEID) (Grant Number ANR-10-LABX-62-IBEID), Santé Publique France, project Theracov, the INCEPTION project (PIA/ANR-16-CONV-0005), the European Union’s Horizon 2020 research and innovation program under grants 101003589 (RECOVER) and 874735 (VEO), and the National Research Agency (ANR) through the ANR-Flash call for COVID-19 (Grant ANR-20-COVI-0018)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-20-COVI-0018,TheraCoV,Dynamique virale au niveau individuel et populationnel : implications pour l'optimisation des stratégies antivirales(2020), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), European Project: 874735,H2020-SC1-2019-Single-Stage-RTD,VEO(2020), PAIREAU, Juliette, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Dynamique virale au niveau individuel et populationnel : implications pour l'optimisation des stratégies antivirales - - TheraCoV2020 - ANR-20-COVI-0018 - COVID-19 - VALID, Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID, and Versatile Emerging infectious disease Observatory - VEO - - H2020-SC1-2019-Single-Stage-RTD2020-01-01 - 2024-12-31 - 874735 - VALID
Subjects: MESH: Pandemics, MESH: Humans, SARS-CoV-2, Epidemiology, transmission, Public Health, Environmental and Occupational Health, COVID-19, MESH: Retrospective Studies, contact tracing, secondary clinical attack rate, MESH: Contact Tracing, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Virology, Humans, MESH: COVID-19, superspreading, MESH: SARS-CoV-2, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, cluster, Pandemics, Retrospective Studies
Abstract: Introduction SARS-CoV-2, the virus that causes COVID-19, has spread rapidly worldwide. In January 2020, a surveillance system was implemented in France for early detection of cases and their contacts to help limit secondary transmissions. Aim To use contact-tracing data collected during the initial phase of the COVID-19 pandemic to better characterise SARS-CoV-2 transmission. Methods We analysed data collected during contact tracing and retrospective epidemiological investigations in France from 24 January to 30 March 2020. We assessed the secondary clinical attack rate and characterised the risk of a contact becoming a case. We described chains of transmission and estimated key parameters of spread. Results During the study period, 6,082 contacts of 735 confirmed cases were traced. The overall secondary clinical attack rate was 4.1% (95% confidence interval (CI): 3.6–4.6), increasing with age of index case and contact. Compared with co-workers/friends, family contacts were at higher risk of becoming cases (adjusted odds ratio (AOR): 2.1, 95% CI: 1.4–3.0) and nosocomial contacts were at lower risk (AOR: 0.3, 95% CI: 0.1–0.7). Of 328 infector/infectee pairs, 49% were family members. The distribution of secondary cases was highly over-dispersed: 80% of secondary cases were caused by 10% of cases. The mean serial interval was 5.1 days (interquartile range (IQR): 2–8 days) in contact tracing pairs, where late transmission events may be censored, and 6.8 (3–8) days in pairs investigated retrospectively. Conclusion This study increases knowledge of SARS-CoV-2 transmission, including the importance of superspreading events during the onset of the pandemic.
Published: 2022
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9. Impact of booster vaccination on the control of COVID-19 Delta wave in the context of waning immunity: application to France in the winter 2021/22

Author: Paolo Bosetti, Cécile Tran Kiem, Alessio Andronico, Juliette Paireau, Daniel Levy-Bruhl, Lise Alter, Arnaud Fontanet, Simon Cauchemez, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège Doctoral, Sorbonne Université (SU), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Haute Autorité de Santé [Saint-Denis La Plaine] (HAS), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Université Paris Cité (UPCité)-Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Pasteur-Cnam Risques infectieux et émergents (PACRI), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Cité (UPCité), We acknowledge financial support from the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (grant ANR-10-LABX-62-IBEID), HAS, Santé Publique France, the EMERGEN project (ANRS0151), the INCEPTION project (PIA/ANR-16-CONV-0005), the European Union’s Horizon 2020 research and innovation program under grant 101003589 (RECOVER) and 874735 (VEO), AXA and Groupama., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), European Project: 874735,H2020-SC1-2019-Single-Stage-RTD,VEO(2020), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), European Project: 874735,VEO, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Université Paris Cité (UPC)-Pasteur-Cnam Risques infectieux et émergents (PACRI), HESAM Université (HESAM)-HESAM Université (HESAM)-Université Paris Cité (UPC)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM), and HESAM Université (HESAM)-HESAM Université (HESAM)-Université Paris Cité (UPC)
Subjects: 0303 health sciences, COVID-19 Vaccines, SARS-CoV-2, Epidemiology, Vaccination, Immunization, Secondary, Public Health, Environmental and Occupational Health, COVID-19, 3. Good health, modelling, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Humans, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, Seasons, 030212 general & internal medicine, Rapid Communication, 030304 developmental biology
Abstract: Europe has experienced a large COVID-19 wave caused by the Delta variant in winter 2021/22. Using mathematical models applied to Metropolitan France, we find that boosters administered to ≥ 65, ≥ 50 or ≥ 18 year-olds may reduce the hospitalisation peak by 25%, 36% and 43% respectively, with a delay of 5 months between second and third dose. A 10% reduction in transmission rates might further reduce it by 41%, indicating that even small increases in protective behaviours may be critical to mitigate the wave.
Published: 2022
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10. Analytical framework to evaluate and optimize the use of imperfect diagnostics to inform outbreak response : Application to the 2017 plague epidemic in Madagascar

Author: Quirine ten Bosch, Voahangy Andrianaivoarimanana, Beza Ramasindrazana, Guillain Mikaty, Rado J. L. Rakotonanahary, Birgit Nikolay, Soloandry Rahajandraibe, Maxence Feher, Quentin Grassin, Juliette Paireau, Soanandrasana Rahelinirina, Rindra Randremanana, Feno Rakotoarimanana, Marie Melocco, Voahangy Rasolofo, Javier Pizarro-Cerdá, Anne-Sophie Le Guern, Eric Bertherat, Maherisoa Ratsitorahina, André Spiegel, Laurence Baril, Minoarisoa Rajerison, Simon Cauchemez, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Wageningen University and Research [Wageningen] (WUR), Unité Peste - Plague Unit [Antananarivo, Madagascar], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Cellule d'Intervention Biologique d'Urgence (Centre National de Référence) - Laboratory for Urgent Response to Biological Threats (National Reference Center) (CIBU), Université Paris Cité (UPCité)-Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP), Unité d’Épidémiologie et de Recherche clinique [Antananarivo, Madagascar], Réseau International des Instituts Pasteur (RIIP), Yersinia, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence de la Peste et autres Yersinioses - National Reference Center Plague and Yersinioses (CNR), Centre collaborateur de l'OMS Yersinia - WHO Collaborating Center Yersinia (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)-Université Paris Cité (UPCité), and Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)
Subjects: Plague, General Immunology and Microbiology, Yersinia pestis, General Neuroscience, [SDV]Life Sciences [q-bio], Kwantitatieve Veterinaire Epidemiologie, Quantitative Veterinary Epidemiology, General Biochemistry, Genetics and Molecular Biology, Disease Outbreaks, Madagascar, WIAS, Humans, Life Science, Epidemics, General Agricultural and Biological Sciences
Abstract: During outbreaks, the lack of diagnostic “gold standard” can mask the true burden of infection in the population and hamper the allocation of resources required for control. Here, we present an analytical framework to evaluate and optimize the use of diagnostics when multiple yet imperfect diagnostic tests are available. We apply it to laboratory results of 2,136 samples, analyzed with 3 diagnostic tests (based on up to 7 diagnostic outcomes), collected during the 2017 pneumonic (PP) and bubonic plague (BP) outbreak in Madagascar, which was unprecedented both in the number of notified cases, clinical presentation, and spatial distribution. The extent of these outbreaks has however remained unclear due to nonoptimal assays. Using latent class methods, we estimate that 7% to 15% of notified cases were Yersinia pestis-infected. Overreporting was highest during the peak of the outbreak and lowest in the rural settings endemic to Y. pestis. Molecular biology methods offered the best compromise between sensitivity and specificity. The specificity of the rapid diagnostic test was relatively low (PP: 82%, BP: 85%), particularly for use in contexts with large quantities of misclassified cases. Comparison with data from a subsequent seasonal Y. pestis outbreak in 2018 reveal better test performance (BP: specificity 99%, sensitivity: 91%), indicating that factors related to the response to a large, explosive outbreak may well have affected test performance. We used our framework to optimize the case classification and derive consolidated epidemic trends. Our approach may help reduce uncertainties in other outbreaks where diagnostics are imperfect.
Published: 2022
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11. Evaluating and optimizing the use of diagnostics during epidemics: Application to the 2017 plague outbreak in Madagascar

Author: Quirine Bosch, Voahangy Andrianaivoarimanana, Beza Ramasindrazana, Guillain Mikaty, Rado JL Rakotonanahary, Birgit Nikolay, Soloandry Rahajandraibe, Maxence Feher, Quentin Grassin, Juliette Paireau, Soanandrasana Rahelinirina, Rindra Randremanana, Feno Rakotoarimanana, Marie Melocco, Voahangy Rasolofo, Javier Pizarro-Cerda, Anne-Sophie Le Guern, Eric Bertherat, Maherisoa Ratsitorahina, Andre Spiegel, Laurence Baril, Minoarisoa Rajerison, and Simon Cauchemez
Abstract: During outbreaks, the lack of diagnostic “gold standard” can mask the true burden of infection in the population and hamper the allocation of resources required for control. Here, we present an analytical framework to evaluate and optimize the use of diagnostics when multiple yet imperfect diagnostic tests are available. We apply it to laboratory results of 2,136 samples, analyzed with three diagnostic tests (based on up to seven diagnostic outcomes), collected during the 2017 pneumonic (PP) and bubonic plague (BP) outbreak in Madagascar, which was unprecedented both in the number of notified cases, clinical presentation, and spatial distribution. The extent of this outbreaks has however remained unclear due to non-optimal assays. Using latent class methods, we estimate that 7%-15% of notified cases were Yersinia pestis-infected. Overreporting was highest during the peak of the outbreak and lowest in the rural settings endemic to Yersinia pestis. Molecular biology methods offered the best compromise between sensitivity and specificity. The specificity of the rapid diagnostic test was relatively low (PP: 82%, BP: 85%), particularly for use in contexts with large quantities of misclassified cases. Comparison with data from a subsequent seasonal Yersinia pestis outbreak in 2018 reveal better test performance (BP: specificity 99%, sensitivity: 91%), indicating that factors related to the response to a large, explosive outbreak may well have affected test performance. We used our framework to optimize the case classification and derive consolidated epidemic trends. Our approach may help reduce uncertainties in other outbreaks where diagnostics are imperfect.
Published: 2021
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12. The epidemiology of hepatitis delta virus infection in Cameroon

Author: Juliette Paireau, Mathurin Cyrille Tejiokem, Jacques Pépin, Richard Njouom, Arnaud Fontanet, Guillaume Lachenal, Simon Cauchemez, Gaëtan Texier, Camille Besombes, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur (RIIP), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Médialab (Sciences Po) (Médialab), Sciences Po (Sciences Po), Université de Sherbrooke (UdeS), This study was funded by the Agence Nationale de Recherche sur le Sida et les Hépatites Virales (grant ANRS 12289) and got support from the INCEPTION project (PIA/ANR-16-CONV-0005)., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and médialab (Sciences Po) (médialab)
Subjects: Adult, Male, 0301 basic medicine, medicine.medical_specialty, HBsAg, Adolescent, viruses, Hepatitis C virus, medicine.disease_cause, Virus, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Epidemiology, Prevalence, medicine, Humans, Cameroon, Geography, Medical, Hepatitis B virus, Family Characteristics, biology, Transmission (medicine), business.industry, Gastroenterology, virus diseases, biochemical phenomena, metabolism, and nutrition, Middle Aged, medicine.disease, [SDE.ES]Environmental Sciences/Environmental and Society, Hepatitis D, Virology, 3. Good health, 030104 developmental biology, biology.protein, Female, 030211 gastroenterology & hepatology, Hepatitis Delta Virus, Antibody, business
Abstract: ObjectiveTo investigate the distribution and risk factors of hepatitis delta virus (HDV) infection in Cameroon.DesignWe tested for hepatitis B virus (HBV) surface antigen (HBsAg) and anti-HDV antibody 14 150 samples collected during a survey whose participants were representative of the Cameroonian adult population. The samples had already been tested for hepatitis C virus and HIV antibodies.ResultsOverall, 1621/14 150 (weighted prevalence=11.9%) participants were HBsAg positive, among whom 224/1621 (10.6%) were anti-HDV positive. In 2011, the estimated numbers of HBsAg positive and HDV seropositives were 1 160 799 and 122 910 in the 15–49 years age group, respectively. There were substantial regional variations in prevalence of chronic HBV infection, but even more so for HDV (from 1% to 54%). In multivariable analysis, HDV seropositivity was independently associated with living with an HDV-seropositive person (OR=8.80; 95% CI: 3.23 to 24.0), being HIV infected (OR=2.82; 95% CI: 1.32 to 6.02) and living in the South (latitude ConclusionWe found evidence for effective intra-household transmission of HDV in Cameroon. We also identified large differences in prevalence between regions, with cases concentrated in forested areas close to the Equator, as described in other tropical areas. The reasons underlying these geographical variations in HDV prevalence deserve further investigation.
Published: 2020
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13. Association between the COVID-19 pandemic and pertussis in France using multiple nationwide data sources

Author: Jérémie F. Cohen, Fatima Aït El Belghiti, Juliette Paireau, Camille Fortas, Yann Savitch, Sylvain Brisse, Soraya Matczak, Julie Toubiana, Stéphane Béchet, Nicole Guiso, Robert M. Cohen, Sophie Guillot, Daniel Levy Bruhl, Sabine Trombert, Véronique Jacomo, and Corinne Levy
Subjects: medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), business.industry, Pcr test, Environmental health, Epidemiology, Pandemic, medicine, Psychological intervention, Pertussis vaccination, Disease, Disease monitoring, business
Abstract: BackgroundInterventions to mitigate coronavirus disease 19 (COVID-19) pandemic may impact other respiratory diseases such as pertussis. We aimed to study the course of pertussis in France over an 8-year period and its association with COVID-19 mitigation strategies, using multiple nationwide data sources.MethodsWe analyzed the number of French pertussis cases between 2013 and 2020, using the PCR test results from nationwide outpatient laboratories (Source 1) and the pediatric network of 41 hospitals (Source 2), and using the reports of an office-based pediatric national network (Source 3). We conducted a quasi-experimental interrupted time-series analysis, relying on negative binomial regression models. The models accounted for seasonality, long-term cycles, and secular trend, and included a binary variable for the first national lockdown (ordered on March 16, 2021).ResultsWe identified 19,039 cases of pertussis from the three data sources during the study period. There was a significant decrease of pertussis cases following the implementation of mitigation measures, with adjusted incidence rate ratios of 0.102 (95% CI 0.040-0.256) and 0.216 (95% CI 0.071-0.656) for Source 1 and Source 2, respectively. The association was confirmed in Source 3 (median of 1 [IQR 0-2] vs. 0 [IQR 0-0] pertussis cases per month before and after lockdown, respectively, p=0.0048).ConclusionThe drastic reduction of outpatient and hospitalized cases of pertussis strongly suggests an impact of COVID-19 mitigation measures and their consequences on pertussis epidemiology. Pertussis vaccination recommendations should be carefully followed, and disease monitoring should be continued to detect any resurgence after relaxation of mitigation measures.FundingThere was no specific funding for the study.
Published: 2021
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14. Benefits and risks associated with different uses of the COVID-19 vaccine Vaxzevria: a modelling study, France, May to September 2021

Author: Lise Alter, Daniel Lévy-Bruhl, Cécile Tran Kiem, Pierre-Yves Boëlle, Paolo Bosetti, Simon Cauchemez, Juliette Paireau, Alessio Andronico, Arnaud Fontanet, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Haute Autorité de Santé [Saint-Denis La Plaine] (HAS), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), We acknowledge financial support from the Investissement d’Avenir programme, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases programme (grant ANR-10-LABX-62-IBEID), and the European Union’s Horizon 2020 research and innovation programme under grants 101003589 (RECOVER) and 874735 (VEO), AXA, Groupama, INCEPTION project (PIA/ANR-16-CONV-0005)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), European Project: 874735,H2020-SC1-2019-Single-Stage-RTD,VEO(2020), Gestionnaire, HAL Sorbonne Université 5, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID, Versatile Emerging infectious disease Observatory - VEO - - H2020-SC1-2019-Single-Stage-RTD2020-01-01 - 2024-12-31 - 874735 - VALID, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), and European Project: 874735,VEO
Subjects: 2019-20 coronavirus outbreak, COVID-19 Vaccines, Coronavirus disease 2019 (COVID-19), Epidemiology, Vaxzevria, 030204 cardiovascular system & hematology, Risk Assessment, Young Adult, 03 medical and health sciences, 0302 clinical medicine, vaccine, Virology, Environmental health, Humans, Medicine, benefit-risk balance, 030212 general & internal medicine, Young adult, Adverse effect, thrombosis, SARS-CoV-2, business.industry, Public Health, Environmental and Occupational Health, COVID-19, AstraZeneca, 3. Good health, Metropolitan France, Vaccination, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, Risk of death, business, Risk assessment, Rapid Communication
Abstract: International audience; Thrombosis with thrombocytopenia (TTS) has been identified as a rare adverse event following COVID-19 vaccination with Vaxzevria. We modelled the benefits and risks of Vaxzevria distribution from May to September 2021 in metropolitan France where other vaccines are available, considering French hospitalisation data and European data on TTS. Across different scenarios, benefits of Vaxzevria distribution in people 55 years and older exceeded the risk of death from COVID-19. In young adults, risks were at least of similar magnitude as benefits.
Published: 2021
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15. Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study

Author: Cassandre Von Platen, Simon Galmiche, Alexandra Maurizot, Sophie Martin, Faïza Omar, Laura Schaeffer, Olivia Chény, Juliette Paireau, Annika Dinis, Alexandra Septfons, Rebecca Grant, Fabrice Carrat, Carole Blanc, Simon Cauchemez, Arnaud Fontanet, Alexandra Mailles, Christophe David, Tiffany Charmet, Daniel Lévy-Bruhl, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Sorbonne Université (SU), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris], Caisse Nationale d'Assurance Maladie des Travailleurs salariés (CNAMTS), Ministère de l'économie et des finances, Ipsos, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance' Tous unis contre le virus')., We would like to thank the AC transmission group of REACTing (Research & Action Emerging Infectious Diseases) for helpful discussions about the study design, Xavier Duval and Sarah Tubiana for pilot testing the questionnaire, and Nathalie Bajos and Dominique Costagliola for their critical review of an earlier version of the manuscript., Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and Limouzin, Cécile
Subjects: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], 030231 tropical medicine, Computer-assisted web interviewing, 03 medical and health sciences, 0302 clinical medicine, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Environmental health, Internal Medicine, Medicine, Infection control, 030212 general & internal medicine, Sports activity, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], business.industry, Health Policy, Risk of infection, Case-control study, 3. Good health, [SDV] Life Sciences [q-bio], Increased risk, Oncology, Public aspects of medicine, RA1-1270, business, Research Paper
Abstract: Summary: Background: We aimed to assess the role of different setting and activities in acquiring SARS-CoV-2 infection. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 27 October and 30 November 2020. Controls were individuals from the Ipsos market research database matched to cases by age, sex, region, population density and time period. Participants completed an online questionnaire on recent activity-related exposures. Findings: Among 3426 cases and 1713 controls, in multivariable analysis, we found an increased risk of infection associated with any additional person living in the household (adjusted-OR: 1•16; 95%CI: 1•11-1•21); having children attending day-care (aOR: 1•31; 95%CI: 1•02-1•62), kindergarten (aOR: 1•27; 95%CI: 1•09-1•45), middle school (aOR: 1•30; 95%CI: 1•15-1•47), or high school (aOR: 1•18; 95%CI: 1•05-1•34); with attending professional (aOR: 1•15; 95%CI: 1•04-1•26) or private gatherings (aOR: 1•57; 95%CI: 1•45-1•71); and with having frequented bars and restaurants (aOR: 1•95; 95%CI: 1•76-2•15), or having practiced indoor sports activities (aOR: 1•36; 95%CI: 1•15-1•62). We found no increase in risk associated with frequenting shops, cultural or religious gatherings, or with transportation, except for carpooling (aOR: 1•47; 95%CI: 1•28-1•69). Teleworking was associated with decreased risk of infection (aOR: 0•65; 95%CI: 0•56-0•75). Interpretation: Places and activities during which infection prevention and control measures may be difficult to fully enforce were those with increased risk of infection. Children attending day-care, kindergarten, middle and high schools, but not primary schools, were potential sources of infection for the household. Funding: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance” Tous unis contre le virus”).
Published: 2021
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16. Do not neglect SARS-CoV-2 hospitalization and fatality risks in the middle-aged adult population

Author: Xavier de Lamballerie, Daniel Lévy-Bruhl, Mathilde Touvier, Simon Cauchemez, Juliette Paireau, Gianluca Severi, Fabrice Carrat, Nathanael Lapidus, Marie Zins, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Paris (UP), Cohortes épidémiologiques en population (CONSTANCES), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université de Paris (UP), The SAPRIS-SERO study was supported by Agence Nationale de la Recherche, #ANR-10-COHO-06, Fondation pour la Recherche Médicale (#20RR052-00), Inserm (Institut National de la Santé et de la Recherche Médicale), #C20-26., The SAPRIS-SERO study group Sofiane Kab, Adeline Renuy, Stephane Le-Got, Celine Ribet, Emmanuel Wiernik, Marcel Goldberg, Marie Zins (Constances cohort). Fanny Artaud, Pascale Gerbouin-Rérolle, Mélody Enguix, Camille Laplanche, Roselyn Gomes-Rima, Lyan Hoang, Emmanuelle Correia, Alpha Amadou Barry, Nadège Senina, Gianluca Severi (E3N-E4 N cohort). Fabien Szabo de Edelenyi, Nathalie Druesne-Pecollo, Younes Esseddik, Serge Hercberg, Mathilde Touvier (NutriNet-Santé cohort). Marie-Aline Charles, Pierre-Yves Ancel, Valérie Benhammou, Anass Ritmi, Laetitia Marchand, Cecile Zaros, Elodie Lordmi, Adriana Candea, Sophie de Visme, Thierry Simeon, Xavier Thierry, Bertrand Geay, Marie-Noelle Dufourg, Karen Milcent (Epipage2 and Elfe child cohorts). Clovis Lusivika-Nzinga, Gregory Pannetier, Nathanael Lapidus, Frédéric Chau, Isabelle Goderel, Céline Dorival, Jérôme Nicol, Fabrice Carrat (IPLESP–methodology and coordinating data center). Cindy Lai, Hélène Esperou, Sandrine Couffin-Cadiergues (Inserm). Jean-Marie Gagliolo (Institut de Santé Publique). Hélène Blanché, Jean-Marc Sébaoun, Jean-Christophe Beaudoin, Laetitia Gressin, Valérie Morel, Ouissam Ouili, Jean-François Deleuze (Fondation Jean-Dausset, CEPH-Biobank). Stéphane Priet, Paola Mariela Saba Villarroel, Toscane Fourié, Souand Mohamed Ali, Abdenour Amroun, Morgan Seston, Nazli Ayhan, Boris Pastorino, Xavier de Lamballerie (Unité des Virus Émergents)., ANR-10-COHO-0006,E4N,Etude Epidémiologique des Enfants de femmes de l'Education Nationale(2010), HAL-SU, Gestionnaire, Cohortes - Etude Epidémiologique des Enfants de femmes de l'Education Nationale - - E4N2010 - ANR-10-COHO-0006 - COHO - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Firenze = University of Florence (UniFI), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris Cité (UPCité), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université Paris Cité (UPCité)
Subjects: Male, Adult, Age-Specific Death Rate, Short Communication, media_common.quotation_subject, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Population, Risk Assessment, Neglect, Young Adult, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Pandemic, Humans, Medicine, 030212 general & internal medicine, Young adult, education, Aged, 030304 developmental biology, media_common, Aged, 80 and over, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, SARS-CoV-2, Incidence (epidemiology), COVID-19, Middle Aged, 3. Good health, Hospitalization, Infectious Diseases, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Relative risk, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Age Specific Death Rate, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, business, Risk assessment, Demography
Abstract: Highlights • During the first wave of the pandemic in France, the estimated overall infection hospitalization ratio (IHR, probability of hospitalization in infected adults) was 2.7%. • At that time, the estimated overall infection fatality ratio (IFR, probability of death in infected adults) was 0.49%. • Both IHR and IFR were higher in men. • IHR approximately doubled every 10 years while IFR doubled every 5 years. • IFR should not be neglected, even in young and middle-aged adults (0.042% in individuals aged 40-50 years)., Objectives This study aimed at estimating the SARS-CoV-2 infection hospitalization (IHR) and infection fatality ratios (IFR) in France. Patients and methods A serosurvey was conducted in 9782 subjects from the two French regions with the highest incidence of COVID-19 during the first wave of the pandemic and coupled with surveillance data. Results IHR and IFR were 2.7% and 0.49% overall. Both were higher in men and increased exponentially with age. The relative risks of hospitalization and death were 2.1 (95% CI: 1.9-2.3) and 3.8 (2.4-4.2) per 10-year increase, meaning that IHR and IFR approximately doubled every 10 and 5 years, respectively. They were dramatically high in the very elderly (80-90 years: IHR: 26%, IFR: 9.2%), and also substantial in younger adults (40-50 years: IHR: 0.98%, IFR: 0.042%). Conclusions These findings support the need for comprehensive preventive measures to help reduce the spread of the virus, even in young or middle-aged adults.
Published: 2021
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17. Monitoring the proportion of the population infected by SARS-CoV-2 using age-stratified hospitalisation and serological data: a modelling study

Author: Nathanaël Hozé, PhD, Juliette Paireau, PhD, Nathanaël Lapidus, MD, Cécile Tran Kiem, MSc, Henrik Salje, PhD, Gianluca Severi, PhD, Mathilde Touvier, PhD, Marie Zins, ProfMD, Xavier de Lamballerie, ProfMD, Daniel Lévy-Bruhl, MPH, Fabrice Carrat, ProfMD, and Simon Cauchemez, PhD
Subjects: Public aspects of medicine, RA1-1270
Abstract: Summary: Background: Regional monitoring of the proportion of the population who have been infected by SARS-CoV-2 is important to guide local management of the epidemic, but is difficult in the absence of regular nationwide serosurveys. We aimed to estimate in near real time the proportion of adults who have been infected by SARS-CoV-2. Methods: In this modelling study, we developed a method to reconstruct the proportion of adults who have been infected by SARS-CoV-2 and the proportion of infections being detected, using the joint analysis of age-stratified seroprevalence, hospitalisation, and case data, with deconvolution methods. We developed our method on a dataset consisting of seroprevalence estimates from 9782 participants (aged ≥20 years) in the two worst affected regions of France in May, 2020, and applied our approach to the 13 French metropolitan regions over the period March, 2020, to January, 2021. We validated our method externally using data from a national seroprevalence study done between May and June, 2020. Findings: We estimate that 5·7% (95% CI 5·1–6·4) of adults in metropolitan France had been infected with SARS-CoV-2 by May 11, 2020. This proportion remained stable until August, 2020, and increased to 14·9% (13·2–16·9) by Jan 15, 2021. With 26·5% (23·4–29·8) of adult residents having been infected in Île-de-France (Paris region) compared with 5·1% (4·5–5·8) in Brittany by January, 2021, regional variations remained large (coefficient of variation [CV] 0·50) although less so than in May, 2020 (CV 0·74). The proportion infected was twice as high (20·4%, 15·6–26·3) in 20–49-year-olds than in individuals aged 50 years or older (9·7%, 6·9–14·1). 40·2% (34·3–46·3) of infections in adults were detected in June to August, 2020, compared with 49·3% (42·9–55·9) in November, 2020, to January, 2021. Our regional estimates of seroprevalence were strongly correlated with the external validation dataset (coefficient of correlation 0·89). Interpretation: Our simple approach to estimate the proportion of adults that have been infected with SARS-CoV-2 can help to characterise the burden of SARS-CoV-2 infection, epidemic dynamics, and the performance of surveillance in different regions. Funding: EU RECOVER, Agence Nationale de la Recherche, Fondation pour la Recherche Médicale, Institut National de la Santé et de la Recherche Médicale (Inserm).
Published: 2021

18. Adherence and sustainability of interventions informing optimal control against COVID-19 pandemic

Author: Vittoria Colizza, Juliette Paireau, Harold Noel, Simon Cauchemez, Laura Di Domenico, François Beck, Daniel Lévy-Bruhl, Pascal Crépey, Pierre-Yves Boëlle, Chiara Poletto, and Chiara E. Sabbatini
Subjects: Distress, Coronavirus disease 2019 (COVID-19), High intensity, Social distance, Sustainability, Development economics, Pandemic, Psychological intervention, Duration (project management), Psychology
Abstract: After one year of stop-and-go COVID-19 mitigation, some European countries still experience sustained viral circulation due to the B.1.1.7 variant. As the prospect of phasing out this stage through vaccination draws closer, it is critical to balance the efficacy of long-lasting interventions and their impact on the quality of life. Focusing on the current situation in France, we show that moderate interventions require a much longer time to achieve the same result as high intensity lockdowns, with the additional risk of deteriorating control as adherence wanes. Integrating intensity and duration of social distancing in a data-driven “distress” index, we show that shorter strict lockdowns are largely more performant than longer moderate lockdowns, for similar intermediate distress and infringement on individual freedom. 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.
Published: 2021
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19. Effect of change in vaccine schedule on pertussis epidemiology in France: a modelling and serological study

Author: Julie Toubiana, Muhamed-Kheir Taha, Soraya Matczak, Daniel Lévy-Bruhl, Simon Cauchemez, Juliette Paireau, Henrik Salje, Sophie Guillot, Sylvain Brisse, Véronique Jacomo, Fatima Aït El Belghiti, and Sabine Trombert-Paolantoni
Subjects: Pertussis Vaccine, Schedule, Pediatrics, medicine.medical_specialty, Booster (rocketry), business.industry, Whooping Cough, Immunization, Secondary, Bayes Theorem, Diphtheria-Tetanus-acellular Pertussis Vaccines, Antibodies, Bacterial, Serology, Clinical trial, Vaccination, Infectious Diseases, Pertussis Toxin, Immunity, Relative risk, Epidemiology, medicine, Humans, business, Child
Abstract: Summary Background In April–May, 2013, France modified its pertussis vaccination schedule, which uses the acellular pertussis vaccine, from three primary doses at 2, 3, and 4 months of age and a first booster at 16–18 months of age (former schedule) to two primary doses at 2 and 4 months of age and a first booster at 11 months of age (new schedule). We aimed to assess the subsequent effect of the vaccine schedule change on pertussis epidemiology in France. Methods In this modelling study, using data collected between Jan 1, 2012, and Dec 31, 2019, from French national surveillance sources, we analysed the PCR test results of nasopharyngeal swabs collected from symptomatic outpatients aged 2–20 years with suspected pertussis. We developed a negative binomial regression model for the number of confirmed pertussis cases by year and age to assess the relative risks of pertussis depending on vaccine schedule. The linear predictor included the year, the age group, the population size, and a proxy of waning immunity. We tested different models in which waning immunity could vary with vaccine schedule and type of primary vaccine. The models were fitted to the 2012–18 data via Bayesian Markov chain Monte Carlo sampling, and the 2019 data were left out for external model validation. We also compared the anti-pertussis toxin (PT) antibody concentrations in leftover sera from children not tested for pertussis or recent respiratory tract infection aged 2–5 years born before and after the vaccine schedule change. Findings We collected data on 7493 confirmed cases of pertussis. The model that best fitted the 2012–18 epidemiological data supported a faster waning of immunity following vaccination with the new vaccine schedule. 3 years after vaccination, the risk of developing pertussis was 1·7 (95% CI 1·4–2·0) times higher for children vaccinated according to the new schedule than those vaccinated according to the former schedule. The model correctly predicted the age distribution of cases in 2019. Geometric mean concentrations (GMC) of anti-PT IgG were 50% lower in children aged 2 years vaccinated with the new schedule (GMC=5·85 IU/mL [95% CI 4·08–8·39]) than in children of the same age vaccinated with the former schedule (GMC=11·62 IU/mL [95% CI 9·05–14·92]; p=0·0016), and 43% lower in children aged 3 years vaccinated with the new schedule (GMC=3·88 IU/mL [95% CI 2·82–5·34]) than those with the former schedule (GMC=6·80 IU/mL [95% CI 4·77–9·70]; p=0·026). Interpretation A shorter-lived protection induced by the new vaccine schedule recommended in France since 2013 is associated with an increase of pertussis cases in children aged 2–5 years. If similar findings are observed in other countries and clinical trials, these findings should be considered in future pertussis vaccination policies. Funding INCEPTION, Labex-IBEID, Institut Pasteur, and Sante Publique France.
Published: 2021

20. Colder and drier winter conditions are associated with greater SARS-CoV-2 transmission: a regional study of the first epidemic wave in north-west hemisphere countries

Author: Eva Legendre, Jordi Landier, Stanislas Rebaudet, Arnaud Fontanet, Laurent Le Hot, Simon Cauchemez, Juliette Paireau, and Jean Gaudart
Subjects: Geography, Transmission (mechanics), law, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pandemic, Humidity, Context (language use), Population density, Basic reproduction number, Transmissibility (vibration), Demography, law.invention
Abstract: Higher transmissibility of SARS-CoV-2 in cold and dry weather conditions has been hypothesized since the onset of the COVID-19 pandemic but the level of epidemiological evidence remains low.During the first wave of the pandemic, Spain, Italy, France, Portugal, Canada and USA presented an early spread, a heavy COVID-19 burden, and low initial public health response until lockdowns. In a context when testing was limited, we calculated the basic reproduction number (R0) in 63 regions from the growth in regional death counts. After adjusting for population density, early spread of the epidemic, and age structure, temperature and humidity were negatively associated to SARS-CoV-2 transmissibility. A reduction of mean absolute humidity by 1g/m3 was associated with a 0.15-unit increase of R0. Below 10°C, a temperature reduction of 1°C was associated with a 0.16-unit increase of R0.Our results confirm a dependency of SARS-CoV-2 transmissibility to weather conditions in the absence of control measures during the first wave. The transition from summer-to winter-like conditions likely contributed to the intensification of the second wave in north-west hemisphere countries. Adjustments of the levels of social mobility restrictions need to account for increased SARS-CoV-2 transmissibility in winter conditions.
Published: 2021
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21. Monitoring the proportion infected by SARS-CoV-2 from age-stratified hospitalisation and serological data

Author: Daniel Lévy-Bruhl, Mathilde Touvier, Marie Zins, Juliette Paireau, Henrik Salje, Cécile Tran Kiem, Gianluca Severi, Fabrice Carrat, Xavier de Lamballerie, Nathanaël Hozé, Simon Cauchemez, and Nathanael Lapidus
Subjects: Metropolitan France, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Seroprevalence, Medicine, Joint analysis, business, Demography, Serology
Abstract: BackgroundRegional monitoring of the proportion infected by SARS-CoV-2 is important to guide local management of the epidemic, but is difficult in the absence of regular nationwide serosurveys.MethodsWe developed a method to reconstruct in real-time the proportion infected by SARS-CoV-2 and the proportion of infections being detected from the joint analysis of age-stratified seroprevalence, hospitalisation and case data. We applied our approach to the 13 French metropolitan regions.FindingsWe estimate that 5.7% [5.1%-6.4%] of adults in metropolitan France had been infected by SARS-CoV-2 by May 2020. This proportion remained stable until August and increased to 12.6% [11.2%-14.3%] by the end of November. With 23.8% [21.2%-26.8%] infected in the Paris region compared to 4.0% [3.5% - 4.6%] in Brittany, regional variations remained large (Coefficient of Variation CV: 0.53) although less so than in May (CV: 0.74). The proportion infected was twice higher (17.6% [13.4%-22.7%]) in 20-49 y.o. than in 50+ y.o (8.0% [5.7% - 11.5%]). Forty percent [33.7% - 45.4%] of infections in adults were detected in June-August compared to 55.7% [48.7% - 63.1%] in September-November. Our method correctly predicted seroprevalence in 11 regions in which only hospitalisation data were used.InterpretationIn the absence of contemporary serosurvey, our real-time monitoring indicates that the proportion infected by SARS-CoV-2 may be above 20% in some French regions.FundingEU RECOVER, ANR, Fondation pour la Recherche Médicale, Inserm.
Published: 2021
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22. Comparing the age and sex trajectories of SARS-CoV-2 morbidity with other respiratory pathogens points to potential immune mechanisms

Author: Bruno Hubert, Simon Cauchemez, C. Jessica E. Metcalf, Juliette Paireau, Megan O'Driscoll, Henrik Salje, Isabelle Pontais, Mathilde Pivette, and Derek A. T. Cummings
Subjects: Adult life, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Immunology, Medicine, Immunosenescence, Age and sex, business, Health outcomes, Acquired immune system, Immune mechanisms, Respiratory pathogens
Abstract: Comparing age and sex differences in SARS-CoV-2 hospitalization and mortality with influenza and other health outcomes opens the way to generating hypotheses as to the underlying mechanisms, building on the extraordinary advances in immunology and physiology that have occurred over the last year. Notable departures in health outcomes starting around puberty suggest that burdens associated with influenza and other causes are reduced relative to the two emergent coronaviruses over much of adult life. Two possible hypotheses could explain this: protective adaptive immunity for influenza and other infections, or greater sensitivity to immunosenescence in the coronaviruses. Comparison of sex differences suggest an important role for adaptive immunity; but immunosenescence might also be relevant, if males experience faster immunosenescence. Involvement of the renin-angiotensin-system in SARS-CoV-2 infection might drive high sensitivity to disruptions of homeostasis. Overall, these results highlight the long tail of vulnerability in the age profile relevant to the emergent coronaviruses, which more transmissible variants have the potential to uncover at the younger end of the scale, and aging populations will expose at the other end of the scale.
Published: 2021
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23. Monitoring the Proportion Infected by SARS-CoV-2 from Age-Stratified Hospitalisation and Serological Data

Author: Juliette Paireau, Mathilde Touvier, Gianluca Severi, Fabrice Carrat, Nathanael Lapidus, Marie Zins, Henrik Salje, Daniel Lévy-Bruhl, Simon Cauchemez, Nathanaël Hozé, Xavier de Lamballerie, and Cécile Tran Kiem
Subjects: Competing interests, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Medicine, Seroprevalence, Joint analysis, business, Serology, Demography
Abstract: Background: Regional monitoring of the proportion infected by SARS-CoV-2 is important to guide local management of the epidemic, but is difficult in the absence of regular nationwide serosurveys. Methods: We developed a method to reconstruct in real-time the proportion infected by SARS-CoV-2 and the proportion of infections being detected from the joint analysis of age-stratified seroprevalence, hospitalisation and case data. We applied our approach to the 13 French metropolitan regions. Findings: We estimate that 5.7% [5.1%-6.4%] of adults in metropolitan France had been infected by SARS-CoV-2 by May 2020. This proportion remained stable until August and increased to 12.6% [11.2%-14.3%] by the end of November. With 23.8% [21.2%-26.8%] infected in the Paris region compared to 4.0% [3.5% - 4.6%] in Brittany, regional variations remained large (Coefficient of Variation CV: 0.53) although less so than in May (CV: 0.74). The proportion infected was twice higher (17.6% [13.4%-22.7%]) in 20-49 y.o. than in 50+ y.o (8.0% [5.7% - 11.5%]). Forty percent [33.7% - 45.4%] of infections in adults were detected in June-August compared to 55.7% [48.7% - 63.1%] in September-November. Our method correctly predicted seroprevalence in 11 regions in which only hospitalisation data were used. Interpretation: In the absence of contemporary serosurvey, our real-time monitoring indicates that the proportion infected by SARS-CoV-2 may be above 20% in some French regions. Funding Statement: EU RECOVER, ANR, Fondation pour la Recherche Medicale, Inserm. Declaration of Interests: Prof Fabrice Carrat reports personal fees from Imaxio and Sanofi, outside the submitted work. The other authors declare no competing interests.
Published: 2021
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24. Impact of Vaccine Schedule Change on Pertussis Epidemiology in France: A Modelling and Serological Study

Author: Henrik Salje, Sophie Guillot, Daniel Lévy-Bruhl, Julie Toubiana, Sylvain Brisse, Muhamed-Kheir Taha, Soraya Matczak, Sabine Trombert-Paolantoni, Fatima Aït El Belghiti, Véronique Jacomo, Simon Cauchemez, Juliette Paireau, Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice], Santé publique France - French National Public Health Agency [Saint-Maurice, France], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Centre national de Référence de la Coqueluche et autres Bordetelloses - National Reference Center for Whooping Cough and other Bordetella infections (CNR), Infections respiratoires et vaccination [Saint-Maurice], Département de Pédiatrie et maladies infectieuses [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire CERBA [Saint Ouen l'Aumône], Eurofins Biomnis, Infections Bactériennes Invasives - Invasive Bacterial Infections, Centre National de Référence des Méningocoques et Haemophilus influenzae - National Reference Center Meningococci and Haemophilus influenzae (CNR), University of Cambridge [UK] (CAM), This project was funded by the INCEPTION interdisciplinary project at Institut Pasteur, Understanding whooping cough resurgence in Europe by combining genomic, epidemiological, and sociological approaches (French Government Investissements d'Avenir grant ANR-16-CONV-0005). This work also received financial support from the French Government's Investissement d'Avenir programme, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases (grant n_ANR-10-LABX-62-IBEID). Institutional support was provided by an Institut Pasteur and Santé publique France grant to SB. SM was supported by a PhD grant from Fondation pour la Recherche Médicale. We thank Martin Chalumeau (CRESS, INSERM, Paris, France), for his contributions to the serological study., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), and Institut Pasteur [Paris]-Université Paris Cité (UPC)
Subjects: medicine.medical_specialty, Booster dose, medicine.disease, Institutional review board, Helsinki declaration, [STAT]Statistics [stat], Vaccination, Schedule (workplace), Informed consent, Family medicine, Epidemiology, medicine, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Whooping cough
Abstract: Background: In 2013, France modified its pertussis vaccination schedule to remove one dose at 3 months of age and change the age of the booster dose from 16 to 11 months. We aimed to assess the subsequent impact on pertussis epidemiology in France. Methods: We analysed the PCR test results of nasopharyngeal swabs (N=7493) collected from symptomatic outpatients aged 2-20 years old between 2012 and 2019 in France. We developed a Poisson regression model in which the number of positive cases by year and age depended on the year, age group, population size of each age group and a proxy of waning immunity that could vary with vaccine schedule. We also compared the anti-pertussis toxin (PT) antibody levels of 315 children born before and after the vaccine schedule change. Findings: The model that best fitted the 2012-2018 epidemiological data supported a faster waning of immunity following vaccination with the new vaccine schedule. Four years after vaccination, the risk of developing pertussis was 2.1 (95% CI, 1.7-2.2) times higher for children vaccinated according to the new schedule than those vaccinated according to the previous schedule. The model correctly predicted the age distribution of cases in 2019. Anti-PT IgG levels were significantly lower in children born after implementation of the new schedule, compared to children born before. Interpretation: A shorter-lived protection induced by the 2/4+11 vaccine schedule recommended in France since 2013 is associated with an increase of pertussis cases in 2-5-year olds. Funding Statement: This project was funded by the INCEPTION interdisciplinary project at Institut Pasteur, “Understanding whooping cough resurgence in Europe by combining genomic, epidemiological and sociological approaches” (French Government Investissements d’Avenir grant ANR-16-CONV-0005). This work received financial support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant n_ANR-10-LABX-62-IBEID). Institutional support was provided by Institut Pasteur and Sante publique France. Declaration of Interests: None to declare. Ethics Approval Statement: The data collection received approval by French supervisory ethics authority (CNIL, n°1474593), and was approved by the local Institutional Review board (N° 2020 1028160733). All data processing and storage comply with the General Data Protection Regulation (GDPR) and ethical standards of the National Research Committee. This study was conducted in accordance with the Helsinki Declaration, with informed consent obtained from each patient’s guardians.
Published: 2021
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25. Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic

Author: Laura Di Domenico, Chiara E. Sabbatini, Pierre-Yves Boëlle, Chiara Poletto, Pascal Crépey, Juliette Paireau, Simon Cauchemez, François Beck, Harold Noel, Daniel Lévy-Bruhl, Vittoria Colizza, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), École des Hautes Études en Santé Publique [EHESP] (EHESP), Recherche en Pharmaco-épidémiologie et Recours aux Soins (REPERES), Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Tokyo Institute of Technology [Tokyo] (TITECH), This study is partially funded by: ANR projects DATAREDUX (ANR-19-CE46-0008-03), EVALCOVID-19 (ANR-20-COVI-0007), and SPHINX (ANR-17-CE36-0008-05), EU H2020 grants MOOD (H2020-874850) and RECOVER (H2020-101003589)., ANR-19-CE46-0008,DataRedux,Réduction de données massives pour la simulation numérique prédictive(2019), ANR-20-COVI-0007,EVALCOVID-19,Modélisation mathématique et numérique intégrant des données de téléphonie mobile en temps réel pour évaluer les interventions contre la pandémie de COVID-19 en France.(2020), ANR-17-CE36-0008,SPHINx,Diffusion de pathogènes au sein des réseaux de soins : une étude de modélisation(2017), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), Jonchère, Laurent, Réduction de données massives pour la simulation numérique prédictive - - DataRedux2019 - ANR-19-CE46-0008 - AAPG2019 - VALID, Modélisation mathématique et numérique intégrant des données de téléphonie mobile en temps réel pour évaluer les interventions contre la pandémie de COVID-19 en France. - - EVALCOVID-192020 - ANR-20-COVI-0007 - COVID-19 - VALID, Diffusion de pathogènes au sein des réseaux de soins : une étude de modélisation - - SPHINx2017 - ANR-17-CE36-0008 - AAPG2017 - VALID, and Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID
Subjects: 0303 health sciences, Public health, Computational biology and bioinformatics, Infectious diseases, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Medicine, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 030212 general & internal medicine, 030304 developmental biology
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.
Published: 2021
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26. Early chains of transmission of COVID-19 in France

Author: Alexandra Mailles, Paolo Bosetti, Henrik Salje, Catherine Eisenhauer, Juliette Paireau, Franck de Laval, Valerie Ponties, François Delon, and Simon Cauchemez
Subjects: medicine.medical_specialty, business.industry, Attack rate, Odds ratio, law.invention, Transmission (mechanics), law, Epidemiology, medicine, media_common.cataloged_instance, European union, business, Index case, Contact tracing, Demography, media_common, Serial interval
Abstract: IntroductionSARS-CoV-2, which causes COVID-19, has spread rapidly across the world. A dedicated surveillance system was implemented in France in January 2020 to improve early detection of cases and their contacts and limit secondary transmission. Our objective was to use contact-tracing data collected during this initial phase of the epidemic to better characterize SARS-CoV-2 transmission.MethodsWe analysed data collected during contact tracing and retrospective epidemiological investigations in France from 24 January to 30 March 2020. We assessed the secondary clinical attack rate and characterized the risk of a contact becoming a case. We described chains of transmission and estimated key parameters of spread.ResultsOver the study period, 6,082 contacts of 735 confirmed cases were traced. The overall secondary clinical attack rate was 4.1% (95%CI 3.6-4.6) and increased with age of the index case and of the contact. Family contacts were at higher risk of becoming cases (adjusted odds ratio 2.1 (95%CI 1.4-3.0)) while nosocomial contacts were at lower risk (adjusted odds ratio 0.3 (95%CI 0.1-0.7)), compared to coworkers/friends. We identified 328 infector/infectee pairs, 49% of which were family members. The distribution of secondary cases was highly over-dispersed with 80% of secondary cases being caused by 10% of cases. The mean serial interval was 5.1 days (interquartile range 2-8 days) in contact-tracing pairs where late transmission events may be censored, and 6.8 (3-8) days in pairs investigated retrospectively.ConclusionThis study contributes to improving our knowledge of SARS-CoV-2 transmission, such as the importance of superspreading events. Contact-tracing data are challenging to collect but are key to better understand emerging pathogens.Funding statementThis work was supported by the LabEx “Integrative Biology of Emerging Infectious Diseases (IBEID)” (Grant Number ANR-10-LABX-62-IBEID), Santé Publique France, the INCEPTION project (PIA/ANR-16-CONV-0005), and the European Union’s Horizon 2020 research and innovation program under grants 101003589 (RECOVER) and 874735 (VEO).
Published: 2020
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27. Ready for a BASE jump? Do not neglect SARS-CoV-2 hospitalization and fatality risks in the middle-aged adult population

Author: Daniel Lévy-Bruhl, Xavier de Lamballerie, Mathilde Touvier, Nathanael Lapidus, Gianluca Severi, Fabrice Carrat, Juliette Paireau, Simon Cauchemez, and Marie Zins
Subjects: education.field_of_study, 2019-20 coronavirus outbreak, Surveillance data, Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, Population, Neglect, Medicine, Seroprevalence, Middle-aged adult, business, education, Demography, media_common
Abstract: Seroprevalence results coupled with surveillance data were used to estimate the SARS-CoV-2 infection hospitalization (IHR) and infection fatality ratios (IFR) in France. IHR and IFR were dramatically high in the very elderly (80-90 years: IHR: 30%, IFR: 11%), but also substantial in middle-aged adults (40-50 years: IHR: 1.2%, IFR: 0.05%).
Published: 2020
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28. Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana

Author: Noémie Lefrancq, Alessio Andronico, Alice Sanna, Mathieu Nacher, Cyril Rousseau, Henrik Salje, Cécile Tran Kiem, Félix Djossou, Simon Cauchemez, Claude Flamand, Tiphanie Succo, Paolo Bosetti, and Juliette Paireau
Subjects: 0303 health sciences, education.field_of_study, business.industry, Population, Psychological intervention, Context (language use), 3. Good health, law.invention, Metropolitan France, 03 medical and health sciences, 0302 clinical medicine, Geography, Transmission (mechanics), law, Environmental health, Health care, 030212 general & internal medicine, Economic impact analysis, business, education, Basic reproduction number, 030304 developmental biology
Abstract: While general lockdowns have proven effective to control SARS-CoV-2 epidemics, they come with enormous costs for society. It is therefore essential to identify control strategies with lower social and economic impact. Here, we report and evaluate the control strategy implemented during a large SARS-CoV-2 epidemic in June-July 2020 in French Guiana that relied on curfews, targeted lockdowns and other measures. We find that the combination of these interventions reduced the basic reproduction number of SARS-CoV-2 from 1.7 to 1.1, which was sufficient to avoid saturation of hospitals. We estimate that thanks to the young demographics across the territory, the risk of hospitalisation following infection was 0.3 times that of metropolitan France and that about 20% of the population was infected by July. Our model projections are consistent with a recent seroprevalence study. The study showcases how mathematical modeling can be used to support healthcare planning and decision making in a context of high uncertainty.
Published: 2020
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29. Lockdown impact on COVID-19 epidemics in regions across metropolitan France

Author: Patrick Rolland, Simon Cauchemez, Juliette Paireau, Cécile Tran Kiem, Arnaud Fontanet, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), We acknowledge financial support from the Investissement d'Avenir programme, the Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases programme (grant ANR-10-LABX-62-IBEID), the INCEPTION project (PIA/ANR-16-CONV-0005), and the European Union's Horizon 2020 research and innovation programme under grant 101003589 (RECOVER)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], and Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)
Subjects: MESH: Social Isolation, MESH: Pandemics, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), MESH: Coronavirus Infections, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Pneumonia, Viral, 030204 cardiovascular system & hematology, Betacoronavirus, MESH: Communicable Disease Control, 03 medical and health sciences, 0302 clinical medicine, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Pandemic, Correspondence, Humans, MESH: COVID-19, MESH: SARS-CoV-2, 030212 general & internal medicine, Socioeconomics, Pandemics, ComputingMilieux_MISCELLANEOUS, MESH: Humans, SARS-CoV-2, COVID-19, General Medicine, Metropolitan area, 3. Good health, MESH: France, Metropolitan France, Geography, Social Isolation, MESH: Pneumonia, Viral, Communicable Disease Control, MESH: Betacoronavirus, France, Coronavirus Infections
Abstract: Lockdowns have been used by most European countries in response to the COVID-19 pandemic. In France, a national lockdown was implemented on March 17, 2020. Some have questioned the need for a nationwide implementation given that most hospital admissions were concentrated in two of 13 regions; others have even questioned the impact of the lockdown on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread, arguing that the natural epidemic peak was about to be reached. Here we discuss the impact of lockdown on COVID-19 epidemics in regions across metropolitan France.
Published: 2020
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30. Age-specific mortality and immunity patterns of SARS-CoV-2 infection in 45 countries

Author: Arnaud Fontanet, Megan O'Driscoll, Gabriel Ribeiro Dos Santos, Juliette Paireau, Lin Wang, Simon Cauchemez, Andrew S. Azman, Derek A. T. Cummings, and Henrik Salje
Subjects: Coronavirus disease 2019 (COVID-19), Immunity, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Age specific mortality, Medicine, Nursing homes, business, Demography
Abstract: The number of COVID-19 deaths is often used as a key indicator of SARS-CoV-2 epidemic size. However, heterogeneous burdens in nursing homes and variable reporting of deaths in elderly individuals can hamper comparisons of deaths and the number of infections associated with them across countries. Using age-specific death data from 45 countries, we find that relative differences in the number of deaths by age amongst individuals aged
Published: 2020
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31. Estimating the burden of SARS-CoV-2 in France

Author: Lulla Opatowski, Jehanne Richet, Juliette Paireau, Justin Lessler, Arnaud Fontanet, Noémie Lefrancq, Paolo Bosetti, Alessio Andronico, Nathanaël Hozé, Claire Lise Dubost, Pierre-Yves Boëlle, Henrik Salje, Cécile Tran Kiem, Noémie Courtejoie, Daniel Levy Bruhl, Yann Le Strat, Simon Cauchemez, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Department of Genetics [Cambridge], University of Cambridge [UK] (CAM), Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), Collège Doctoral, Sorbonne Université (SU), Centre de Recherche du DREES (DREES), Ministère de l'Emploi et de la Solidarité, Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice], Santé publique France - French National Public Health Agency [Saint-Maurice, France], Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM), Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), We acknowledge financial support from the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (grant ANR-10-LABX-62-IBEID), Santé Publique France, the INCEPTION project (PIA/ANR-16-CONV-0005), and the European Union’s Horizon 2020 research and innovation program under grants 101003589 (RECOVER) and 874735 (VEO). H.S. acknowledges support from the European Research Council (grant 804744) and a University of Cambridge COVID-19 Rapid Response Grant., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), European Project: 874735,H2020-SC1-2019-Single-Stage-RTD,VEO(2020), European Project: 804744,H2020-EU.1.1.,ARBODYNAMIC(2019), Department of Epidemiology [Baltimore], Johns Hopkins University (JHU)-Johns Hopkins University (JHU), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Conservatoire National des Arts et Métiers [CNAM] (CNAM), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris], HESAM Université (HESAM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Male, Epidemiology, Psychological intervention, law.invention, 0302 clinical medicine, Cost of Illness, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Pandemic, 030212 general & internal medicine, Young adult, Aged, 80 and over, 0303 health sciences, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, Middle Aged, 3. Good health, Hospitalization, [STAT]Statistics [stat], Severe acute respiratory syndrome-related coronavirus, Quarantine, Female, France, Coronavirus Infections, Adult, medicine.medical_specialty, Adolescent, Critical Care, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Population, Pneumonia, Viral, Herd immunity, 03 medical and health sciences, Young Adult, Intensive care, medicine, Humans, education, Pandemics, 030304 developmental biology, Aged, business.industry, SARS-CoV-2, Immunity, COVID-19, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030104 developmental biology, Modeling Method, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Demography
Abstract: COVID-19 pandemic in France Coronavirus disease 2019 (COVID-19) exacted a heavy toll in France during March and April 2020. Quarantine measures were effective in reducing transmission by 84%, and some relaxation of social isolation was expected in May. Salje et al. fit transmission models for the epidemic in France to hospital admissions. The authors forecast that 2.9 million people will have been infected by 11 May, representing 4.4% of the population—a value inadequate for herd immunity. Daily critical care hospitalizations should reduce from several hundreds to tens of cases, but control will remain a delicate balancing act. Any relaxation of lockdown in France will have to be carefully controlled and monitored to avoid undermining more optimistic forecasts. Science , this issue p. 208
Published: 2020
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32. Erratum for the Report: 'Estimating the burden of SARS-CoV-2 in France,' by H. Salje, C. Tran Kiem, N. Lefrancq, N. Courtejoie, P. Bosetti, J. Paireau, A. Andronico, N. Hozé, J. Richet, C.-L. Dubost, Y. Le Strat, J. Lessler, D. Levy-Bruhl, A. Fontanet, L. Opatowski, P.-Y. Boelle, S. Cauchemez

Author: Alessio Andronico, Lulla Opatowski, Juliette Paireau, Jehanne Richet, Daniel Lévy-Bruhl, Paolo Bosetti, Pierre-Yves Boëlle, Claire-Lise Dubost, Noémie Courtejoie, Y. Le Strat, Arnaud Fontanet, Tran Kiem, Noémie Lefrancq, Nathanaël Hozé, Simon Cauchemez, and Justin Lessler
Subjects: Multidisciplinary, Geography, Epidemiology, Report, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Virology, Reports
Abstract: France has been heavily affected by the SARS-CoV-2 epidemic and went into lockdown on the 17 March 2020. Using models applied to hospital and death data, we estimate the impact of the lockdown and current population immunity. We find 3.6% of infected individuals are hospitalized and 0.7% die, ranging from 0.001% in those 80ya. Across all ages, men are more likely to be hospitalized, enter intensive care, and die than women. The lockdown reduced the reproductive number from 2.90 to 0.67 (77% reduction). By 11 May 2020, when interventions are scheduled to be eased, we project 2.8 million (range: 1.8–4.7) people, or 4.4% (range: 2.8–7.2) of the population, will have been infected. Population immunity appears insufficient to avoid a second wave if all control measures are released at the end of the lockdown.
Published: 2020
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33. Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France

Author: Tiffany Charmet, Faïza Omar, Laura Schaeffer, Cassandre Von Platen, Alexandra Rogoff, Simon Cauchemez, Alexandra Septfons, Juliette Paireau, Fabrice Carrat, Olivia Chény, Simon Galmiche, Alexandra Mailles, Yoann Madec, Daniel Lévy-Bruhl, Rebecca Grant, Christophe David, Arnaud Fontanet, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Université Paris Cité (UPCité)-Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Sorbonne Université (SU), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Ipsos, Caisse primaire d'assurance maladie (CPAM), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), The study was funded by Institut Pasteur and Research, Action Emerging Infectious Diseases (REACTing), and the French Agency ANRS- Maladies Infectieuses Emergentes (ComCor project). AF's laboratory receives support from the Labex IBEID (ANR-10-LABX-62-IBEID) and the INCEPTION project (PIA/ANR-16-CONV-0005) for studies on emerging viruses. TC is funded by the Fondation de France (Alliance 'Tous unis contre le virus')., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Schaeffer, Laura, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, and Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID
Subjects: Delta, medicine.medical_specialty, business.industry, Transmission (medicine), [SDV]Life Sciences [q-bio], Health Policy, Public health, Case-control study, Context (language use), Logistic regression, Article, [SDV] Life Sciences [q-bio], Vaccination, Oncology, Internal medicine, Internal Medicine, Medicine, Observational study, Public aspects of medicine, RA1-1270, business
Abstract: Summary Background We aimed to assess the settings and activities associated with SARS-CoV-2 infection in the context of B.1.617.2 (Delta) variant circulation in France, as well as the protection against symptomatic Delta infection. Methods In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 23 May and 13 August 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire and multivariable logistic regression analysis was used to determine the association between acute SARS-CoV-2 infection and recent activity-related exposures, past history of SARS-CoV-2 infection, and COVID-19 vaccination. Findings We did not find any differences in the settings and activities associated with Delta versus non-Delta infections and grouped them for subsequent analyses. In multivariable analysis involving 12634 cases (8644 Delta and 3990 non-Delta) and 5560 controls, we found individuals under 40 years and attending bars (aOR:1.9; 95%CI:1.6-2.2) or parties (aOR:3.4; 95%CI:2.8-4.2) to be at increased risk of infection. In those aged 40 years and older, having children attend daycare (aOR:1.9; 95%CI:1.1-3.3), kindergarten (aOR:1.6; 95%CI:1.2-2.1), primary school (aOR:1.4; 95%CI:1.2-1.6) or middle school (aOR:1.3; 95%CI:1.2-1.6) were associated with increased risk of infection. We found strong protection against symptomatic Delta infection for those with prior infection whether it was recent (2-6 months) (95%; 95%CI:90-97) or associated with one dose (85%; 95%CI:78-90) or two doses of mRNA vaccine (96%; 95%CI:87-99). For those without past infection, protection was lower with two doses of mRNA vaccine (67%; 95%CI:63-71). Interpretation In line with other observational studies, we find reduced vaccine effectiveness against symptomatic Delta infections. The settings and activities at increased risk of infection indicate where efforts to reinforce individual and public health measures need to be concentrated.
Published: 2022
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34. Mapping influenza activity in emergency departments in France using Bayesian model‐based geostatistics

Author: Camille Pelat, Céline Caserio-Schönemann, Juliette Paireau, Daniel Lévy-Bruhl, Isabelle Pontais, Yann Le Strat, Simon Cauchemez, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Santé publique France - French National Public Health Agency [Saint-Maurice, France], This work was supported by the LabEx 'Integrative Biology of Emerging Infectious Diseases (IBEID)' (Grant Number ANR-10-LABX-62-IBEID)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Pulmonary and Respiratory Medicine, MESH: Topography, Medical, spatial analysis, Epidemiology, Computer science, geographic mapping, MESH: Bayes Theorem, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Population, Multivariate normal distribution, Bayesian inference, Generalized linear mixed model, 03 medical and health sciences, 0302 clinical medicine, Public health surveillance, Kriging, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Influenza, Human, Humans, 030212 general & internal medicine, education, education.field_of_study, MESH: Humans, MESH: Influenza, Human, Public Health, Environmental and Occupational Health, Bayes Theorem, Original Articles, Random effects model, public health surveillance, 3. Good health, Data set, MESH: France, Infectious Diseases, MESH: Emergency Service, Hospital, Original Article, Topography, Medical, France, influenza, Emergency Service, Hospital, Cartography
Abstract: International audience; BackgroundMaps of influenza activity are important tools to monitor influenza epidemics and inform policymakers. In France, the availability of a high-quality data set from the Oscour® surveillance network, covering 92% of hospital emergency department (ED) visits, offers new opportunities for disease mapping. Traditional geostatistical mapping methods such as Kriging ignore underlying population sizes, are not suited to non-Gaussian data and do not account for uncertainty in parameter estimates.ObjectiveOur objective was to create reliable weekly interpolated maps of influenza activity in the ED setting, to inform Santé publique France (the French national public health agency) and local healthcare authorities.MethodsWe used Oscour® data of ED visits covering the 2016-2017 influenza season. We developed a Bayesian model-based geostatistical approach, a class of generalized linear mixed models, with a multivariate normal random field as a spatially autocorrelated random effect. Using R-INLA, we developed an algorithm to create maps of the proportion of influenza-coded cases among all coded visits. We compared our results with maps obtained by Kriging.ResultsOver the study period, 45 565 (0.82%) visits were coded as influenza cases. Maps resulting from the model are presented for each week, displaying the posterior mean of the influenza proportion and its associated uncertainty. Our model performed better than Kriging.ConclusionsOur model allows producing smoothed maps where the random noise has been properly removed to reveal the spatial risk surface. The algorithm was incorporated into the national surveillance system to produce maps in real time and could be applied to other diseases.
Published: 2018
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35. Des conditions hivernales froides et sèches favorisent la transmission du SARS-CoV-2 : une analyse régionale de la première vague dans six pays occidentaux

Author: Arnaud Fontanet, Stanislas Rebaudet, Jordi Landier, L. Lehot, Juliette Paireau, Eva Legendre, Simon Cauchemez, and Jean Gaudart
Subjects: 2019-20 coronavirus outbreak, Infectious Diseases, Geography, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Col5-05, Humanities
Abstract: Introduction Une plus forte transmissibilité du SARS-CoV-2 lorsque les conditions météorologiques sont plus froides et sèches a été envisagée dès le début de la pandémie, mais les démonstrations rigoureuses et la quantification de ces effets sont restées peu nombreuses. Matériels et méthodes Pendant la première vague de l’épidémie, l’Espagne, l’Italie, la France, le Portugal, le Canada et les États-Unis ont présenté une propagation précoce, une mortalité/morbidité élevée, et une réponse de santé publique initiale limitée, jusqu’à des mesures de confinement national ou régional. Dans un contexte où l’accès aux tests était limité, nous avons estimé le nombre de reproduction de base (R0) régional à partir de la croissance des nombres de décès quotidiens enregistrés tels que rapportés par les autorités sanitaires nationales. Les données météorologiques ont été extraites à partir des données mises à disposition par l’US National Oceanic and Atmospheric Administration via le package R {worldmet}. La relation entre R0 et les paramètres météorologiques a été analysée par un modèle généralisé additif (GAM) sous l’hypothèse d’une relation linéaire ou non linéaire (splines) en ajustant sur la densité de population, la proximité avec la première région touchée du pays et la proportion de personnes > 80 ans. Résultats Après exclusion des régions n’ayant pas présenté une phase de croissance exponentielle, 63 régions ont été analysées sur les 128 régions/états des 6 pays étudiés. Le R0 a été estimé sur une durée médiane de 11 jours (interquartile = 9–14). La valeur médiane de R0 était de 2,58 (interquartile = 2,08–2,66). L’humidité absolue médiane était de 4,98 g/m3 (min-max: 2,26, 11,32) et la température 9.8 °C (min-max: −2, 19,9). Dans le modèle multivarié, la température et l’humidité étaient négativement associées à la transmissibilité du SARS-CoV-2. Une diminution de 1 g/m3 était associée à une augmentation de 0,15 du R0 (p-value = 0,034, déviance expliquée 33,6 %). La température était également négativement associée au R0, mais avec une relation non linéaire : en dessous de 10 °C, la baisse d’1 °C de la température était associée à une augmentation de 0,16 du R0 (p-value = 0,00655, devance expliquée 41,5 %). Conclusion Nos résultats confirment que la transmissibilité du SARS-CoV-2 dépendait des conditions météorologiques/climatiques en l’absence de mesures de contrôle, durant la première vague, et quantifient cet écart. Il existait un écart de près d’une unité de R0 entre les régions ayant un climat hivernal doux (humidité ∼8 g/m3, températures ∼10 °C et plus) et celle ayant un climat rigoureux (humidité 3 g/m3, températures
Published: 2021

36. Epidemiological characteristics of an urban plague epidemic in Madagascar, August–November, 2017: an outbreak report

Author: Beza Ramasindrazana, Rindra Randremanana, André Spiegel, Vaoary Razafimbia, Maherisoa Ratsitorahina, Lamina Arthur Rakotonjanabelo, Mamy Jean de Dieu Randria, Jean Marius Rakotondramanga, Simon Cauchemez, Eric Bertherat, Mihaja Raberahona, Minoarisoa Rajerison, Birgit Nikolay, Feno Manitra Jacob Rakotoarimanana, Soanandrasana Rahelinirina, Laurence Baril, Anne Sophie Le Guern, Charlotte Faty Ndiaye, Quirine A. ten Bosch, Fanjasoa Rakotomanana, Guillain Mikaty, Juliette Paireau, Soloandry Rahajandraibe, Lea Randriamampionona, Voahangy Rasolofo, Voahangy Andrianaivoarimanana, Unité d'Epidémiologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Unité Peste - Plague Unit [Antananarivo, Madagascar], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Ministère de la Santé Publique [Antananarivo, Madagascar], Hôpital Joseph Raseta Befelatanana, CHU d’Antananarivo, Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris], Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Yersinia, Organisation Mondiale de la Santé - World Health Organization [Madagascar] (OMS/WHO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Réseau International des Instituts Pasteur (RIIP), World Health Organisation (WHO), US Agency for International Development, WHO, Institut Pasteur, US Department of Health and Human Services, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases, Models of Infectious Disease Agent Study of the National Institute of General Medical Sciences, AXA Research Fund, and the INCEPTION programme., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ministère de la Santé Publique - Ministry of Public Health [Antananarivo, Madagascar], and Institut Pasteur [Paris] (IP)
Subjects: Pneumonic plague, Adult, Male, medicine.medical_specialty, Adolescent, Yersinia pestis, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Prevalence, Bubonic plague, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Environmental health, 11. Sustainability, Epidemiology, medicine, Madagascar, Urban plague, Humans, Life Science, 030212 general & internal medicine, Cities, Child, Epidemics, Rapid diagnostic test, Plague, Incidence, Infant, Newborn, Outbreak, Infant, Middle Aged, medicine.disease, 3. Good health, Infectious Diseases, Geography, Infectious disease (medical specialty), Child, Preschool, Female
Abstract: Background: Madagascar accounts for 75% of global plague cases reported to WHO, with an annual incidence of 200–700 suspected cases (mainly bubonic plague). In 2017, a pneumonic plague epidemic of unusual size occurred. The extent of this epidemic provides a unique opportunity to better understand the epidemiology of pneumonic plagues, particularly in urban settings. Methods: Clinically suspected plague cases were notified to the Central Laboratory for Plague at Institut Pasteur de Madagascar (Antananarivo, Madagascar), where biological samples were tested. Based on cases recorded between Aug 1, and Nov 26, 2017, we assessed the epidemiological characteristics of this epidemic. Cases were classified as suspected, probable, or confirmed based on the results of three types of diagnostic tests (rapid diagnostic test, molecular methods, and culture) according to 2006 WHO recommendations. Findings: 2414 clinically suspected plague cases were reported, including 1878 (78%) pneumonic plague cases, 395 (16%) bubonic plague cases, one (
Published: 2019
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37. Seasonal dynamics of bacterial meningitis: a time-series analysis

Author: Hélène Broutin, Bryan T. Grenfell, Juliette Paireau, Nicole E. Basta, Angelica Chen, Princeton University, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Fogarty International Center, and National Institutes of Health [Bethesda] (NIH)
Subjects: Male, 0301 basic medicine, Pediatrics, medicine.medical_specialty, 030106 microbiology, Disease, Neisseria meningitidis, Global Health, medicine.disease_cause, Article, Meningitis, Bacterial, Haemophilus influenzae, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Streptococcus pneumoniae, Epidemiology, medicine, Global health, Humans, 030212 general & internal medicine, business.industry, Incidence, General Medicine, medicine.disease, 3. Good health, Infectious disease (medical specialty), Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Seasons, business, Meningitis, Demography
Abstract: Summary Background Bacterial meningitis, which is caused mainly by Neisseria meningitidis, Haemophilus influenzae , and Streptococcus pneumoniae , inflicts a substantial burden of disease worldwide. Yet, the temporal dynamics of this disease are poorly characterised and many questions remain about the ecology of the disease. We aimed to comprehensively assess seasonal trends in bacterial meningitis on a global scale. Methods We developed the first bacterial meningitis global database by compiling monthly incidence data as reported by country-level surveillance systems. Using country-level wavelet analysis, we identified whether a 12 month periodic component (annual seasonality) was detected in time-series that had at least 5 years of data with at least 40 cases reported per year. We estimated the mean timing of disease activity by computing the centre of gravity of the distribution of cases and investigated whether synchrony exists between the three pathogens responsible for most cases of bacterial meningitis. Findings We used country-level data from 66 countries, including from 47 countries outside the meningitis belt in sub-Saharan Africa. A persistent seasonality was detected in 49 (96%) of the 51 time-series from 38 countries eligible for inclusion in the wavelet analyses. The mean timing of disease activity had a latitudinal trend, with bacterial meningitis seasons peaking during the winter months in countries in both the northern and southern hemispheres. The three pathogens shared similar seasonality, but time-shifts differed slightly by country. Interpretation Our findings provide key insight into the seasonal dynamics of bacterial meningitis and add to knowledge about the global epidemiology of meningitis and the host, environment, and pathogen characteristics driving these patterns. Comprehensive understanding of global seasonal trends in meningitis could be used to design more effective prevention and control strategies. Funding Princeton University Health Grand Challenge, US National Institutes of Health (NIH), NIH Fogarty International Center Research and Policy for Infectious Disease Dynamics programme (RAPIDD), Bill & Melinda Gates Foundation.
Published: 2016
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38. Impact of Zika Virus Emergence in French Guiana: A Large General Population Seroprevalence Survey

Author: Dominique Rousset, Juliette Paireau, Sarah Bailly, Félix Djossou, Antoine Enfissi, Jean-François Carod, Claude Flamand, Mirdad Kazanji, Séverine Matheus, Camille Fritzell, Henrik Salje, Léna Berthelot, J.-C. Manuguerra, Sandrine Fernandes-Pellerin, Simon Cauchemez, Sébastien Linares, Jessica Vanhomwegen, Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris] (IP), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Unité des Maladies Infectieuses et Tropicales (UMIT), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Centre Hospitalier de l'Ouest Guyanais Franck Joly [Saint-Laurent-du-Maroni, Guyane Française], This study was supported by the European Regional Development Fund under EPI-ARBO grant agreement GY0008695, the Regional Health Agency of French Guiana, and the National Center of Spatial Studies. C. Fl. acknowledges financial support from the Centre National d’Etudes Spatiales-Terre solide, Océan, Surfaces Continentales, Atmosphère fund (grant number CNES-TOSCA-4800000720) and funding from Calmette and Yersin allocated by the Pasteur Institut Department of International Affairs. S. C. acknowledges financial support from the AXA Research Fund, the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (grant number ANR-10-LABX-62-IBEID), the Models of Infectious Disease Agent Study of the National Institute of General Medical Sciences, the INCEPTION project (PIA/ANR-16-CONV-0005), and the European Union’s Horizon 2020 research and innovation program under ZIKAlliance grant agreement number 734548., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 734548,ZIKAlliance(2016), Salje, Henrik [0000-0003-3626-4254], Apollo - University of Cambridge Repository, Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), ROUSSET, Dominique, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, and A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID
Subjects: 0301 basic medicine, Male, Recombinant antigen, Communicable Diseases, Emerging, Serology, Zika virus, 0302 clinical medicine, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Child, Immunology and Allergy, MESH: Communicable Diseases, Emerging, Geography, Medical, Child, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Aged, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Middle Aged, Zika Virus Infection, Middle Aged, 3. Good health, French Guiana, Infectious Diseases, MESH: Young Adult, Child, Preschool, Population Surveillance, Viruses, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Adult, Adolescent, 030231 tropical medicine, Population, Biology, Virus, MESH: Population Surveillance, Major Articles and Brief Reports, 03 medical and health sciences, Young Adult, MESH: Zika Virus Infection, MESH: Cross-Sectional Studies, MESH: Geography, Medical, MESH: French Guiana, Seroprevalence, Humans, Serologic Tests, General population survey, education, Aged, MESH: Adolescent, MESH: Humans, MESH: Seroepidemiologic Studies, seroprevalence study, general population survey, MESH: Serologic Tests, MESH: Child, Preschool, MESH: Adult, Serum samples, biology.organism_classification, MESH: Male, 030104 developmental biology, Cross-Sectional Studies, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Female, Demography
Abstract: Background Since the identification of Zika virus (ZIKV) in Brazil in May 2015, the virus has spread throughout the Americas. However, ZIKV burden in the general population in affected countries remains unknown. Methods We conducted a general population survey in the different communities of French Guiana through individual interviews and serologic survey during June–October 2017. All serum samples were tested for anti-ZIKV immunoglobulin G antibodies using a recombinant antigen-based SGERPAxMap microsphere immunoassay, and some of them were further evaluated through anti-ZIKV microneutralization tests. Results The overall seroprevalence was estimated at 23.3% (95% confidence interval [CI], 20.9%–25.9%) among 2697 participants, varying from 0% to 45.6% according to municipalities. ZIKV circulated in a large majority of French Guiana but not in the most isolated forest areas. The proportion of reported symptomatic Zika infection was estimated at 25.5% (95% CI, 20.3%–31.4%) in individuals who tested positive for ZIKV. Conclusions This study described a large-scale representative ZIKV seroprevalence study in South America from the recent 2015–2016 Zika epidemic. Our findings reveal that the majority of the population remains susceptible to ZIKV, which could potentially allow future reintroductions of the virus., This study provides a consistent overview of a large-scale representative Zika virus (ZIKV) seroprevalence study in French Guiana, revealing that the majority of the population remains susceptible to ZIKV, which could potentially allow future reintroductions of the virus.
Published: 2019
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39. Hypoglycemic Toxins and Enteroviruses as Causes of Outbreaks of Acute Encephalitis-Like Syndrome in Children, Bac Giang Province, Northern Vietnam

Author: Marc Eloit, Meriadeg Ar Gouilh, Nghia D. Ngu, Johannes Sander, Charles Hebert, Nils Janzen, Paul T. Brey, Laura Tondeur, Juliette Paireau, Hien Tran Nguyen, Olivier Lortholary, Tuan Hai Nguyen, Arnaud Fontanet, Loan Phuong, Jean-Claude Manuguerra, Robert Barouki, Justine Cheval, Nga Thi Phan, National Institute of Hygiene and Epidemiology [Hanoi, Vietnam] (NIHE), Réseau International des Instituts Pasteur (RIIP), Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris] (IP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), PathoQuest, Régulation de l'expression génétique (REG), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre d'infectiologie Necker-Pasteur [CHU Necker], Institut Pasteur [Paris] (IP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Génétique Moléculaire des Virus Respiratoires, Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire (T3S - UMR_S 1124), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hannover Medical School [Hannover] (MHH), Institut Pasteur du Laos, Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Découverte de Pathogènes - Pathogen Discovery, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Le Gouil, Meriadeg, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Institut Pasteur [Paris], Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut Pasteur [Paris]-CHU Necker - Enfants Malades [AP-HP], Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], and Environnement et Risques infectieux - Environment and Infectious Risks (ERI)
Subjects: 0301 basic medicine, Male, Epidemiology, encephalitis, Physiology, lcsh:Medicine, medicine.disease_cause, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 0302 clinical medicine, Cerebrospinal fluid, methylenecyclopropylglycine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, litchi, Acute Febrile Encephalopathy, Child, Enterovirus, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.TOX.ECO] Life Sciences [q-bio]/Toxicology/Ecotoxicology, biology, acute encephalitis syndrome, Bac Giang Province, 3. Good health, Infectious Diseases, Vietnam, Child, Preschool, outbreaks, litchi cultivation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Seasons, meningitis/encephalitis, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Encephalitis, Microbiology (medical), [SDE.MCG]Environmental Sciences/Global Changes, 030231 tropical medicine, Aspartate transaminase, Hypoglycemia, hypoglycins, enteroviruses, hypoglycemic toxins, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, children, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, medicine, Enterovirus Infections, Humans, lcsh:RC109-216, viruses, Retrospective Studies, Hypoglycemic Toxins and Enteroviruses as Causes of Outbreaks of Acute Encephalitis-Like Syndrome in Children, Bac Giang Province, Northern Vietnam, business.industry, Viral encephalitis, Research, lcsh:R, Outbreak, Infant, medicine.disease, acute encephalitis-like syndrome, [SDE.MCG] Environmental Sciences/Global Changes, 030104 developmental biology, hypoglycemia, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, biology.protein, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract: International audience; We investigated the cause of seasonal outbreaks of pediatric acute encephalitis-like syndrome associated with litchi harvests (May-July) in northern Vietnam since 2008. Nineteen cerebrospinal fluid samples were positive for human enterovirus B, and 8 blood samples were positive for hypoglycemic toxins present in litchi fruits. Patients who were positive for hypoglycemic toxins had shorter median times between disease onset and admission, more reports of seizures, more reports of hypoglycemia (glucose level
Published: 2018
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40. Timeliness of Yellow Fever Surveillance, Central African Republic

Author: Julie Bouscaillou, Benjamin Selekon, Arnaud Fontanet, Mirdad Kazanji, Juliette Paireau, Emmanuel Nakouné, Dominique Senekian, and Antoine Rachas
Subjects: Adult, Male, Microbiology (medical), Pediatrics, medicine.medical_specialty, Delayed Diagnosis, Disease onset, Adolescent, Epidemiology, Population, lcsh:Medicine, lcsh:Infectious and parasitic diseases, yellow fever, medicine, Humans, lcsh:RC109-216, viruses, Child, education, Retrospective Studies, education.field_of_study, business.industry, Incidence, Incidence (epidemiology), Public health, lcsh:R, public health, Yellow fever, Dispatch, Retrospective cohort study, Jaundice, medicine.disease, Survival Analysis, Central African Republic, Infectious Diseases, Epidemiological Monitoring, Immunology, surveillance, RNA, Viral, Female, timeliness, Yellow fever virus, medicine.symptom, business
Abstract: During January 2007–July 2012, a total of 3,220 suspected yellow fever cases were reported in the Central African Republic; 55 were confirmed and 11 case-patients died. Mean delay between onset of jaundice and case confirmation was 16.6 days. Delay between disease onset and blood collection could be reduced by increasing awareness of the population.
Published: 2014
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41. Response Strategies against Meningitis Epidemics after Elimination of Serogroup A Meningococci, Niger

Author: Issa Idi, Juliette Paireau, Jean-Paul Moulia Pelat, Odile Ouwe Missi Oukem-Boyer, Halima Boubacar Maïnassara, Judith E. Mueller, Arnaud Fontanet, Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pasteur [Paris] (IP), Chaire de Santé et développement, Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), École des Hautes Études en Santé Publique [EHESP] (EHESP), Département Méthodes quantitatives en santé publique (METIS), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)
Subjects: Microbiology (medical), Pediatrics, medicine.medical_specialty, Epidemiology, Vaccine response, 030231 tropical medicine, lcsh:Medicine, Meningitis, Meningococcal, epidemics, Disease Outbreaks, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 0302 clinical medicine, Neisseria meningitidis, Serogroup A, Conjugate vaccine, Humans, Medicine, Meningitis, lcsh:RC109-216, 030212 general & internal medicine, Niger, bacteria, Response Strategies against Meningitis Epidemics after Elimination of Serogroup A Meningococci, Niger, business.industry, Research, lcsh:R, vaccines, medicine.disease, 3. Good health, Vaccination, Infectious Diseases, Population Surveillance, Immunology, surveillance, African meningitis belt, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Surveillance and epidemic vaccine response would be most effective at the health area level., To inform epidemic response strategies for the African meningitis belt after a meningococcal serogroup A conjugate vaccine was introduced in 2010, we compared the effectiveness and efficiency of meningitis surveillance and vaccine response strategies at district and health area levels using various thresholds of weekly incidence rates. We analyzed reports of suspected cases from 3 regions in Niger during 2002–2012 (154,392 health area weeks), simulating elimination of serogroup A meningitis by excluding health area years with identification of such cases. Effectiveness was highest for health area surveillance and district vaccination (58–366 cases; thresholds 7–20 cases/100,000 doses), whereas efficiency was optimized with health area vaccination (5.6–7.7 cases/100,000 doses). District-level intervention prevented
Published: 2015
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42. Cost-effectiveness of rabies post-exposure prophylaxis in the context of very low rabies risk: A decision-tree model based on the experience of France

Author: Yazdan Yazdanpanah, Dieynaba S. N’Diaye, Claude Le Pen, Florence Ribadeau Dumas, Juliette Paireau, Hervé Bourhy, Philippe Gautret, Centre National de Référence de la Rage-Dynamique des Lyssavirus et adaptation à l'hôte (CNR), Institut Pasteur [Paris] (IP), Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Santé publique : épidémiologie & sciences de l'information biomédicale (ED 393), Université Pierre et Marie Curie - Paris 6 (UPMC), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Cellule Pasteur UPMC, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre Collaborateur de l'OMS pour la Rage - Dynamique des lyssavirus et adaptation à l'hôte (CC-OMS), Service des maladies infectieuses et tropicales, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), No specific funding was provided for this study. The DGS (French Ministry of Health) and the Institut de Veille Sanitaire (a French governmental agency) are supporting the National Reference Center for Rabies, and ARS Ile de France (a French regional health agency) the Paris regional ARC. DSN was funded by a three-year doctoral contract from the ED 393 'Public health: Epidemiology and biomedical information science' graduate school., Institut Pasteur [Paris], Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Bourhy, Hervé
Subjects: MESH: Accidents, Traffic, MESH: Decision Trees, Time Factors, Cost effectiveness, medicine.medical_treatment, Cost-Benefit Analysis, MESH: Risk Assessment, MESH: Dogs, 0302 clinical medicine, Rabies vaccine, Prevalence, Medicine, MESH: Animals, 030212 general & internal medicine, Bites and Stings, education.field_of_study, Road accident, Accidents, Traffic, MESH: Rabies Vaccines, 3. Good health, MESH: Bites and Stings, Infectious Diseases, Cohort, Molecular Medicine, France, medicine.drug, Adverse event, medicine.medical_specialty, Rabies, 030231 tropical medicine, Population, Context (language use), Risk Assessment, Post-exposure prophylaxis, 03 medical and health sciences, Dogs, MESH: Rabies, Animals, Humans, education, Adverse effect, MESH: Prevalence, MESH: Humans, General Veterinary, General Immunology and Microbiology, business.industry, Decision Trees, MESH: Time Factors, Public Health, Environmental and Occupational Health, medicine.disease, Virology, MESH: France, Rabies Vaccines, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Emergency medicine, Cost-effectiveness, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Post-Exposure Prophylaxis, MESH: Cost-Benefit Analysis
Abstract: International audience; INTRODUCTION:Benefit-risk of different anti-rabies post-exposure prophylaxis (PEP) strategies after scratches or bites from dogs with unknown rabies status is unknown in very low rabies risk settings.DESIGN AND SETTING:A cost-effectiveness analysis in metropolitan France using a decision-tree model and input data from 2001 to 2011.POPULATION:A cohort of 2807 patients, based on the mean annual number of patients exposed to category CII (minor scratches) or CIII (transdermal bite) dog attacks in metropolitan France between 2001 and 2011.INTERVENTIONS:Five PEP strategies: (A) no PEP for CII and CIII; (B) vaccine only for CIII; (C) vaccine for CII and CIII; (D) vaccine+ rabies immunoglobulin (RIG) only for CIII; and (E) vaccine for CII and vaccine+ RIG for CIII.MAIN OUTCOMES MEASURES:The number of deaths related to rabies and to traffic accidents on the way to anti-rabies centers (ARC), effectiveness in terms of years of life gained by reducing rabies cases and avoiding traffic accidents, costs, and incremental cost-effectiveness ratios (ICER) associated with each strategy.RESULTS:Strategy E led to the fewest rabies cases (3.6 × 10(-8)) and the highest costs (€ 1,606,000) but also to 1.7 × 10(-3) lethal traffic accidents. Strategy A was associated with the most rabies cases (4.8 × 10(-6)), but the risk of traffic accidents and costs were null; therefore, strategy A was the most effective and the least costly. The sensitivity analysis showed that, when the probability that a given dog is rabid a given day (PA) was > 1.4 × 10(-6), strategy D was more effective than strategy A; strategy B became cost-effective (i.e. ICER vs strategy A < 3 × French Gross Domestic Product per capita) when PA was > 1 .4 × 10(-4).CONCLUSIONS:In the metropolitan France's very low rabies prevalence context, PEP with rabies vaccine, administered alone or with RIG, is associated with significant and unnecessary costs and unfavourable benefit-risk ratios regardless to exposure category.
Published: 2015
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43. Spatio-Temporal Factors Associated with Meningococcal Meningitis Annual Incidence at the Health Centre Level in Niger, 2004–2010

Author: Jean-François Jusot, Jean-Marc Collard, Juliette Paireau, Judith E. Mueller, Issa Idi, Arnaud Fontanet, J.P. Moulia-Pelat, Halima Boubacar Maïnassara, Cellule Pasteur UPMC, Institut Pasteur [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), École des Hautes Études en Santé Publique [EHESP] (EHESP), Département Méthodes quantitatives en santé publique (METIS), Institut Pasteur [Paris], Conservatoire National des Arts et Métiers [CNAM] (CNAM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Institut Pasteur [Paris] (IP), and HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)
Subjects: Bacterial Diseases, Atmospheric Science, Spatial Epidemiology, Epidemiology, Population Modeling, Meningococcal Disease, Rate ratio, 0302 clinical medicine, Infectious Diseases of the Nervous System, Geoinformatics, Credible interval, Medicine and Health Sciences, Public and Occupational Health, 030212 general & internal medicine, Niger, 2. Zero hunger, Climatology, Geography, Incidence (epidemiology), lcsh:Public aspects of medicine, Incidence, Spatial epidemiology, Spatial Autocorrelation, 3. Good health, Infectious Diseases, Physical Sciences, Public Health, African meningitis belt, Meningitis, Statistics (Mathematics), Research Article, Cartography, medicine.medical_specialty, Computer and Information Sciences, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, 030231 tropical medicine, Biology, Meningitis, Meningococcal, Human Geography, 03 medical and health sciences, Spatio-Temporal Analysis, medicine, Humans, Retrospective Studies, Spatial Analysis, Public Health, Environmental and Occupational Health, Outbreak, Biology and Life Sciences, Computational Biology, lcsh:RA1-1270, Bayes Theorem, medicine.disease, Geographic Information Systems, Earth Sciences, Infectious Disease Modeling, Mathematics, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Demography
Abstract: Background Epidemics of meningococcal meningitis (MM) recurrently strike the African Meningitis Belt. This study aimed at investigating factors, still poorly understood, that influence annual incidence of MM serogroup A, the main etiologic agent over 2004–2010, at a fine spatial scale in Niger. Methodology/Principal Findings To take into account data dependencies over space and time and control for unobserved confounding factors, we developed an explanatory Bayesian hierarchical model over 2004–2010 at the health centre catchment area (HCCA) level. The multivariate model revealed that both climatic and non-climatic factors were important for explaining spatio-temporal variations in incidence: mean relative humidity during November–June over the study region (posterior mean Incidence Rate Ratio (IRR) = 0.656, 95% Credible Interval (CI) 0.405–0.949) and occurrence of early rains in March in a HCCA (IRR = 0.353, 95% CI 0.239–0.502) were protective factors; a higher risk was associated with the percentage of neighbouring HCCAs having at least one MM A case during the same year (IRR = 2.365, 95% CI 2.078–2.695), the presence of a road crossing the HCCA (IRR = 1.743, 95% CI 1.173–2.474) and the occurrence of cases before 31 December in a HCCA (IRR = 6.801, 95% CI 4.004–10.910). At the study region level, higher annual incidence correlated with greater geographic spread and, to a lesser extent, with higher intensity of localized outbreaks. Conclusions Based on these findings, we hypothesize that spatio-temporal variability of MM A incidence between years and HCCAs result from variations in the intensity or duration of the dry season climatic effects on disease risk, and is further impacted by factors of spatial contacts, representing facilitated pathogen transmission. Additional unexplained factors may contribute to the observed incidence patterns and should be further investigated., Author Summary Meningococcal meningitis (MM) is a severe infection of the meninges caused by a bacterium transmitted through respiratory droplets. During January–May, epidemics of MM recurrently strike sub-Saharan countries, including Niger. Understanding why epidemics occur in a particular place at a particular time would help public health authorities to develop more efficient prevention strategies. To date, factors that govern the occurrence of localized outbreaks are still poorly understood and epidemics remain unpredictable. In this retrospective study (2004–2010), we developed a statistical model in order to investigate the influence of various factors (climatic, demographic, epidemiologic, etc.) on the annual incidence of MM serogroup A at a fine spatial scale (the health centre catchment area) in Niger. We found that mean relative humidity and occurrence of early rains were protective climatic factors and that a higher risk was associated with the presence of a road, the percentage of neighbouring areas having cases and the occurrence of early cases before January. These findings contribute to improve our understanding of MM epidemics in Africa and the associated factors, and might be used in the future for the subsequent development of an early warning system.
Published: 2014
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44. Serogroup-Specific Characteristics of Localized Meningococcal Meningitis Epidemics in Niger 2002–2012 and 2015: Analysis of Health Center Level Surveillance Data

Author: Arnaud Fontanet, Judith E. Mueller, Odile Ouwe Missi Oukem-Boyer, Halima Boubacar Maïnassara, Jean-Paul Moulia Pelat, Jean-François Jusot, Juliette Paireau, Issa Idi, Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Cellule Pasteur UPMC, Institut Pasteur [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Princeton University, Conservatoire National des Arts et Métiers [CNAM] (CNAM), École des Hautes Études en Santé Publique [EHESP] (EHESP), Département Méthodes quantitatives en santé publique (METIS), Institut Pasteur [Paris], Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and Institut Pasteur [Paris] (IP)
Subjects: Bacterial Diseases, Pediatrics, Spatial Epidemiology, Epidemiology, Physiology, [SDV]Life Sciences [q-bio], lcsh:Medicine, Artificial Gene Amplification and Extension, Nervous System, Polymerase Chain Reaction, Geographical Locations, 0302 clinical medicine, Infectious Diseases of the Nervous System, Geoinformatics, Medicine and Health Sciences, Niger, 030212 general & internal medicine, lcsh:Science, Cerebrospinal Fluid, Multidisciplinary, Geography, Spatial Autocorrelation, Body Fluids, 3. Good health, Infectious Diseases, Neurology, Anatomy, Meningitis, Research Article, Computer and Information Sciences, medicine.medical_specialty, Surveillance data, Inflammatory Diseases, 030231 tropical medicine, Research and Analysis Methods, Infectious Disease Epidemiology, 03 medical and health sciences, Bacterial Meningitis, medicine, Molecular Biology Techniques, Molecular Biology, business.industry, lcsh:R, Biology and Life Sciences, medicine.disease, People and Places, Africa, Earth Sciences, Meningococcal meningitis, lcsh:Q, business, District level
Abstract: International audience; To compare dynamics of localized meningitis epidemics (LE) by meningococcal (Nm) ser-ogroup, we analyzed a surveillance database of suspected and laboratory-confirmed Nm cases from 373 health areas (HA) of three regions in Niger during 2002–2012 and one region concerned by NmC epidemics during 2015. We defined LE as HA weekly incidence rates of !20 suspected cases per 100,000 during !2 weeks and assigned the predominant serogroup based on polymerase chain reaction testing of cerebrospinal fluid. Among the 175 LE, median peak weekly incidence rate in LE due to NmA, W, X and C were 54, 39, 109 and 46 per 100,000, respectively. These differences impacted ability of the epidemic to be detected at the district level. While this analysis is limited by the small number of LE due to NmX (N = 4) and NmW (N = 5), further research should explore whether strategies for prevention and response to meningitis epidemics need to be adapted according to predominant meningococcal serogroups.
Published: 2016
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45. Analysing Spatio-Temporal Clustering of Meningococcal Meningitis Outbreaks in Niger Reveals Opportunities for Improved Disease Control

Author: Halima Boubacar Maïnassara, Juliette Paireau, Jean-Marc Collard, Florian Girond, Jean-François Jusot, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), This work was financially supported by French Ministry of Foreign Affairs (FSP 2005-174), Sanofi Pasteur (contract Men07), the Belgian Technical Cooperation and the Office of International Cooperation of the Principality of Monaco. The internship of JP in CERMES was financially supported by the Fondation Pierre-Ledoux Jeunesse Internationale. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), and HESAM Université (HESAM)-HESAM Université (HESAM)
Subjects: Bacterial Diseases, Male, Pediatrics, Time Factors, MESH: Geography, Epidemiology, RC955-962, Disease Outbreaks, MESH: Communicable Disease Control, 0302 clinical medicine, Arctic medicine. Tropical medicine, MESH: Child, Geoinformatics, Cluster Analysis, 030212 general & internal medicine, Niger, MESH: Disease Outbreaks, Child, Disease surveillance, Geography, MESH: Meningitis, Meningococcal, Spatial epidemiology, MESH: Niger, 3. Good health, Infectious Diseases, Child, Preschool, Medicine, Female, Public Health, Public aspects of medicine, RA1-1270, African meningitis belt, Meningitis, Research Article, medicine.medical_specialty, Adolescent, 030231 tropical medicine, Meningitis, Meningococcal, Human Geography, 03 medical and health sciences, Environmental health, medicine, Humans, Spatial analysis, Retrospective Studies, MESH: Adolescent, MESH: Humans, Public health, MESH: Time Factors, MESH: Child, Preschool, Public Health, Environmental and Occupational Health, Outbreak, MESH: Retrospective Studies, medicine.disease, MESH: Cluster Analysis, MESH: Male, Communicable Disease Control, Spatial ecology, Earth Sciences, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Female
Abstract: Background Meningococcal meningitis is a major health problem in the “African Meningitis Belt” where recurrent epidemics occur during the hot, dry season. In Niger, a central country belonging to the Meningitis Belt, reported meningitis cases varied between 1,000 and 13,000 from 2003 to 2009, with a case-fatality rate of 5–15%. Methodology/Principal Findings In order to gain insight in the epidemiology of meningococcal meningitis in Niger and to improve control strategies, the emergence of the epidemics and their diffusion patterns at a fine spatial scale have been investigated. A statistical analysis of the spatio-temporal distribution of confirmed meningococcal meningitis cases was performed between 2002 and 2009, based on health centre catchment areas (HCCAs) as spatial units. Anselin's local Moran's I test for spatial autocorrelation and Kulldorff's spatial scan statistic were used to identify spatial and spatio-temporal clusters of cases. Spatial clusters were detected every year and most frequently occurred within nine southern districts. Clusters most often encompassed few HCCAs within a district, without expanding to the entire district. Besides, strong intra-district heterogeneity and inter-annual variability in the spatio-temporal epidemic patterns were observed. To further investigate the benefit of using a finer spatial scale for surveillance and disease control, we compared timeliness of epidemic detection at the HCCA level versus district level and showed that a decision based on threshold estimated at the HCCA level may lead to earlier detection of outbreaks. Conclusions/Significance Our findings provide an evidence-based approach to improve control of meningitis in sub-Saharan Africa. First, they can assist public health authorities in Niger to better adjust allocation of resources (antibiotics, rapid diagnostic tests and medical staff). Then, this spatio-temporal analysis showed that surveillance at a finer spatial scale (HCCA) would be more efficient for public health response: outbreaks would be detected earlier and reactive vaccination would be better targeted., Author Summary Meningococcal meningitis (MM) is an infection of the meninges caused by a bacterium, Neisseria meningitidis, transmitted through respiratory and throat secretions. It can cause brain damage and results in death in 5–15% of cases. Large epidemics of MM occur almost every year in sub-Saharan Africa during the hot, dry season. Understanding how epidemics emerge and spread in time and space would help public health authorities to develop more efficient strategies for the prevention and the control of meningitis. We studied the spatio-temporal distribution of MM cases in Niger from 2002 to 2009 at the scale of the health centre catchment areas (HCCAs). We found that spatial clusters of cases most frequently occurred within nine districts out of 42, which can assist public health authorities to better adjust allocation of resources such as antibiotics or rapid diagnostic tests. We also showed that the epidemics break out in different HCCAs from year to year and did not follow a systematic geographical direction. Finally, this analysis showed that surveillance at a finer spatial scale (health centre catchment area rather than district) would be more efficient for public health response: outbreaks would be detected earlier and reactive vaccination would be better targeted.
Published: 2012
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46. Evolution of outcomes for patients hospitalised during the first 9 months of the SARS-CoV-2 pandemic in France: A retrospective national surveillance data analysis

Author: Henrik Salje, Pierre-Yves Boëlle, Juliette Paireau, Fanny Chereau, Noémie Lefrancq, Yazdan Yazdanpanah, Nathanaël Hozé, Lila Bouadma, Simon Cauchemez, Noémie Courtejoie, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Direction de la recherche, des études, de l’évaluation et des statistiques [Paris] (DREES), Ministère des Solidarités et de la Santé [Paris, France], Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), We acknowledge financial support from the INCEPTION project (PIA/ANR-16-CONV-0005), the Investissement d'Avenir program, the Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases program (grant ANR-10-LABX-62-IBEID), Santé Publique France, the European Union's Horizon 2020 research and innovation program under grants 101003589 (RECOVER), AXA and Groupama. H.S. and N.L. acknowledge support from the European Research Council (grant 804744) and the EPSRC Impact Acceleration Grant (RG90413)., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), HAL-SU, Gestionnaire, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Lefrancq, Noemie [0000-0001-5991-6169], Salje, Henrik [0000-0003-3626-4254], and Apollo - University of Cambridge Repository
Subjects: Surveillance data, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), MEDLINE, Age and sex, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Health care, Pandemic, Internal Medicine, Medicine, In patient, 030212 general & internal medicine, Probabilistic framework, 030304 developmental biology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, Health Policy, Prevention, lcsh:Public aspects of medicine, 3 Good Health and Well Being, lcsh:RA1-1270, 3. Good health, Oncology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Patient Safety, business, Demography, Research Paper
Abstract: Background As SARS-CoV-2 continues to spread, a thorough characterisation of healthcare needs and patient outcomes, and how they have changed over time, is essential to inform planning. Methods We developed a probabilistic framework to analyse detailed patient trajectories from 198,846 hospitalisations in France during the first nine months of the pandemic. Our model accounts for the varying age- and sex- distribution of patients, and explore changes in outcome probabilities as well as length of stay. Findings We found that there were marked changes in the age and sex of hospitalisations over the study period. In particular, the proportion of hospitalised individuals that were >80y varied between 27% and 48% over the course of the epidemic, and was lowest during the inter-peak period. The probability of hospitalised patients entering ICU dropped from 0·25 (0·24–0·26) to 0·13 (0·12–0·14) over the four first months as case numbers fell, before rising to 0·19 (0·19–0·20) during the second wave. The probability of death followed a similar trajectory, falling from 0·25 (0·24–0·26) to 0·10 (0·09–0·11) after the first wave before increasing again during the second wave to 0·19 (0·18–0·19). Overall, we find both the probability of death and the probability of entering ICU were significantly correlated with COVID-19 ICU occupancy. Interpretation There are large scale trends in patients outcomes by age, sex and over time. These need to be considered in ongoing healthcare planning efforts. Funding INCEPTION.
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47. Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers

Author: Antoine Enfissi, Matthieu Najm, Sarah Bailly, Nathanaël Hozé, Dominique Rousset, Jessica Vanhomwegen, Jean-Claude Manuguerra, Camille Fritzell, Claude Flamand, Simon Cauchemez, Henrik Salje, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence pour les Arbovirus - Laboratoire associé de Virologie [Cayenne, Guyane] (CNR), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Unité d'Epidémiologie, Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris], This study was supported by the 'European Regional Development Fund' under EPI-ARBO grant agreement (GY0008695), the 'Regional Health Agency of French Guiana', the 'National Center of Spatial Studies'. C.Fl. and C. Fr. acknowledge funding from Calmette and Yersin allocated by the 'Pasteur Institut Department of International Affairs'. N.H. and S.C. acknowledge financial support from the AXA Research Fund, the Investissement d’Avenir program, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases program (Grant ANR-10-LABX-62-IBEID), the Models of Infectious Disease Agent Study of the National Institute of General Medical Sciences, the INCEPTION project (PIA/ANR-16-CONV-0005), the European Union’s Horizon 2020 research and innovation programme under ZIKAlliance grant agreement No. 734548., We wish to thank Mirdad Kazanji (Institut Pasteur in French Guiana), Félix Djossou (Cayenne hospital center), Sandrine Fernandes-Pellerin (Institut Pasteur - CRT), and Léna Berthelot, Séverine Matheus, Laetitia Bremand, Bhety Labeau, David Moua, and Marine Rangon from the Arbovirus National Reference Center for their valuable contribution in the laboratory analyses. We thank Juliette Paireau and Quirine ten Bosch for insightful discussions., ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l’étude de l’Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 734548,ZIKAlliance(2016), University of Cambridge [UK] (CAM), Centre National de Référence pour les Arbovirus - Laboratoire de Virologie [Cayenne, Guyane française] (CNR - laboratoire associé), Réseau International des Instituts Pasteur (RIIP), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Hozé, Nathanaël [0000-0002-3977-8966], Salje, Henrik [0000-0003-3626-4254], Rousset, Dominique [0000-0002-1473-3147], Manuguerra, Jean-Claude [0000-0002-5202-6531], Flamand, Claude [0000-0002-8064-445X], and Apollo - University of Cambridge Repository
Subjects: Male, 0301 basic medicine, Statistical methods, Epidemiology, [SDV]Life Sciences [q-bio], viruses, General Physics and Astronomy, Rural Health, Antibodies, Viral, medicine.disease_cause, Communicable Diseases, Emerging, Viral infection, MESH: Cross Reactions, 13/1, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Arboviruses, MESH: Child, MESH: Communicable Diseases, Emerging, 692/308/174, Chikungunya, [MATH]Mathematics [math], Child, MESH: Alphavirus Infections, lcsh:Science, MESH: Immunoglobulin G, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, MESH: Middle Aged, article, virus diseases, Middle Aged, 631/114/2415, MESH: Infant, French Guiana, 3. Good health, [STAT]Statistics [stat], Geography, MESH: Young Adult, Child, Preschool, Epidemiological Monitoring, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Sylvatic cycle, Chikungunya virus, Adult, Adolescent, Science, 030106 microbiology, Cross Reactions, Arbovirus, General Biochemistry, Genetics and Molecular Biology, Virus, Young Adult, 03 medical and health sciences, MESH: Cross-Sectional Studies, 692/699/255/2514, Environmental health, MESH: French Guiana, medicine, Humans, Natural reservoir, Viral immunology, MESH: Adolescent, MESH: Seroepidemiologic Studies, MESH: Humans, Alphavirus Infections, MESH: Child, Preschool, Infant, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Adult, MESH: Chikungunya virus, General Chemistry, MESH: Rural Health, biochemical phenomena, metabolism, and nutrition, medicine.disease, MESH: Male, Cross-Sectional Studies, 030104 developmental biology, Immunoglobulin G, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, lcsh:Q, MESH: Epidemiological Monitoring, MESH: Female, Arboviruses, MESH: Antibodies, Viral
Abstract: Characterizing the circulation of Mayaro virus (MAYV), an emerging arbovirus threat, is essential for risk assessment but challenging due to cross-reactivity with other alphaviruses such as chikungunya virus (CHIKV). Here, we develop an analytical framework to jointly assess MAYV epidemiology and the extent of cross-reactivity with CHIKV from serological data collected throughout French Guiana (N = 2697). We find strong evidence of an important sylvatic cycle for MAYV with most infections occurring near the natural reservoir in rural areas and in individuals more likely to go to the forest (i.e., adult males) and with seroprevalences of up to 18% in some areas. These findings highlight the need to strengthen MAYV surveillance in the region and showcase how modeling can improve interpretation of cross-reacting assays., Mayaro virus (MAYV) is an emerging arbovirus, but cross-reactivity with other alphaviruses makes analysis of its epidemiology difficult. Here, the authors develop an analytical framework to assess MAYV epidemiology and find evidence for an important sylvatic cycle and seroprevalences of up to 18% in some areas of French Guiana.
Published: 2020
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48. Prevalence of SARS-CoV-2 antibodies in France: results from nationwide serological surveillance

Author: Louise Perrin de Facci, Virgile Monnet, Pierre Charneau, Caroline Demeret, Jean-Baptiste Richard, Nicolas Escriou, Daniel Lévy-Bruhl, Gabrielle Jones, Thierry Rose, François Anna, Yvonnick Guillois, Marion Gransagne, Corinne Robin, Sophie Goyard, Stéphane Petres, Stéphane Le Vu, Marie-Noëlle Ungeheuer, Lucie Léon, Laurent Filleul, Sylvie van der Werf, Sibylle Bernard-Stoecklin, Olivier Helynck, Harold Noel, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Virologie Moléculaire et Vaccinologie / Molecular Virology and Vaccinology, Institut Pasteur [Paris], Laboratoire commun Pasteur-TheraVectys, Institut Pasteur [Paris]-TheraVectys, Biologie Cellulaire des Lymphocytes - Lymphocyte Cell Biology, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Chimie et Biocatalyse, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire CERBA [Saint Ouen l'Aumône], Biomnis Sample Library (BSL), Eurofins Biomnis, Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), We thank Christine Larsen, Bruno Coignard and Jean-Claude Desenclos (Santé publiqueFrance) for their helpful contribution at setting up the study, from Institut Pasteur,Isabelle Cailleau for support in the funding process, Hélène Munier-Lehmann for accessto automate and supply management at the Unit of Chemistry and Biocatalysis, Yves L.Janin for providing the luciferase prosubstrate hikarazine 108, Philippe Souque forproduction of the lentiviral pseudo-types, the whole ICAReB team and COVID-19support staff for sample management at Institut Pasteur, Juliette Paireau (Institut Pas-teur, Santé publique France), Rodolphe Thiébaut (Bordeaux Université) and Xavier deLamballerie (Aix-Marseille Université) for valuable comments onfirst results. We alsothank the team from the Eurofins Biomnis Sample Library and from CerbaHealthcareBenedicte Roquebert (Laboratoire Cerba) and Marie Pierre Guerra (CerbaXpert) forcontributing to sample collection. Santé publique France provided funding to the NRCand to the two centralising biobanks to cover sample collection, preparation, transportand analysis costs. The funder had no role in analysis, interpretation of data or writing ofthe report. S.L.V., G.J. and H.N. had full access to all the data and had responsibility tosubmit for publication., Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-TheraVectys, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Lassailly-Bondaz, Anne, Santé publique France - French National Public Health Agency, Centre National de Référence des virus des infections respiratoires (dont la grippe) [Paris] (CNR), Santé publique France, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: 0301 basic medicine, Male, Epidemiology, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Antibodies, Viral, Serology, 0302 clinical medicine, Seroepidemiologic Studies, Case fatality rate, Prevalence, Cumulative incidence, 030212 general & internal medicine, Child, Aged, 80 and over, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Transmission (medicine), Middle Aged, 3. Good health, [SDV] Life Sciences [q-bio], [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Child, Preschool, Female, France, medicine.symptom, Antibody, Adult, medicine.medical_specialty, Adolescent, Science, Population, Asymptomatic, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Young Adult, medicine, Seroprevalence, Humans, education, Epidemics, 030304 developmental biology, Aged, business.industry, SARS-CoV-2, Public health, Infant, Newborn, COVID-19, Infant, General Chemistry, 030104 developmental biology, Viral infection, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, biology.protein, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Demography
Abstract: Assessment of the cumulative incidence of SARS-CoV-2 infections is critical for monitoring the course and extent of the COVID-19 epidemic. Here, we report estimated seroprevalence in the French population and the proportion of infected individuals who developed neutralising antibodies at three points throughout the first epidemic wave. Testing 11,000 residual specimens for anti-SARS-CoV-2 IgG and neutralising antibodies, we find nationwide seroprevalence of 0.41% (95% CI: 0.05–0.88) mid-March, 4.14% (95% CI: 3.31–4.99) mid-April and 4.93% (95% CI: 4.02–5.89) mid-May 2020. Approximately 70% of seropositive individuals have detectable neutralising antibodies. Infection fatality rate is 0.84% (95% CI: 0.70–1.03) and increases exponentially with age. These results confirm that the nationwide lockdown substantially curbed transmission and that the vast majority of the French population remained susceptible to SARS-CoV-2 in May 2020. Our study shows the progression of the first epidemic wave and provides a framework to inform the ongoing public health response as viral transmission continues globally., The percentage of national populations infected during the first stages of the COVID-19 pandemic are unclear owing to limited early testing. Here the authors provide a nation-wide prevalence study of SARS-CoV-2 antibodies in France from the first wave of COVID-19 in 2020, including stratification based on age, sex and region.
Published: 2021
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49. Human plague: An old scourge that needs new answers

Author: Steven R. Belmain, Minoarisoa Rajerison, Oswaldo Cabanillas, Nils Chr. Stenseth, Peter Horby, Christian E. Demeure, Sandra Telfer, Xavier Vallès, Beza Ramasindrazana, Ratsitorahina M, Inès Vigan-Womas, Voahangy Andrianaivoarimanana, Pablo Tortosa, Yazdan Yazdanpanah, Laurence Baril, Javier Pizarro-Cerdá, David M. Wagner, Arnaud Fontanet, Eric D'Ortenzio, Jane Lynda Deuve, Romain Girod, Paul S. Mead, Holger C. Scholz, B. Joseph Hinnebusch, Guia Carrara, Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Tsinghua University [Beijing] (THU), Yersinia, Institut Pasteur [Paris] (IP), University of Oxford, Centers for Disease Control and Prevention, Oficina General de Epidemiologia [Lima, Peru], Ministerio de Salud de Perú [Lima], Unité Peste - Plague Unit [Antananarivo, Madagascar], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Bundeswehr Institute of Microbiology, Unité d'Entomologie Médicale [Antananarivo, Madagascar] (IPM), Rocky Mountain Laboratories, Unité d'immunologie des maladies infectieuses [Antananarivo, Madagascar] (IPM), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Northern Arizona University [Flagstaff], University of Aberdeen, REACTing, Institut National de la Santé et de la Recherche Médicale (INSERM), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IRD-Centre National de la Recherche Scientifique (CNRS), Natural Resources Institute [Chatham], University of Greenwich, The workshop meeting where the contents of this article were developed was hosted by the Institut Pasteur (Paris, France) with financial and organizational support from the Department of International Affairs, the Emerging Disease Epidemiology Unit, the Mathematical Modelling of Infectious Diseases Unit and REACTing-Inserm. Oswaldo Cabanillas’s travel was financed by the Department of International Affairs at the Institut Pasteur (Paris, France). Travel costs for Laurence Baril and Maherisoa Ratsitorahina were financially supported by USAID (Grant n° AID-687-G-13-00003), and for Voahangy Andrianaivoarimanan and Minoarisoa Rajerison by Northern Arizona University (through HDTRA1-11-16-BRCWMD-BAA). Attendance of Steven Belmain was supported by the African Union (Grant AURGII/1/006/2016). Travel and accommodation for Feno Rakotoarimanana, and accommodation for Romain Girod, Beza Ramasindrazana, Voahangy Andrianaivoarimanana, and Minoarisoa Rajerison, were financially supported by the Wellcome Trust/UK Department for International Development (Grant 211309/Z/18/Z) and REACTing-Inserm. All other participants financially supported travel and accommodation through their own institutional funding. The preparation and editing of the manuscript was financially supported by Wellcome Trust/UK Department for International Development (Grant 211309/Z/18/Z)., List of the other participants to the Plague Workshop (by alphabetical order): Fabrice Biot, Institut de Recherche Biomédicale des Armées, France, Carine Brouat, IRD, France, Simon Cauchemez, Infectious Diseases Mathematical Modelling Unit, Institut Pasteur, Paris, France, Rob Cohen, USAID, Washington, DC, USA, Koussay Dellagy, Department of International Affairs, Institut Pasteur, Paris, France, Nathalie Denoyes, Institut Pasteur, Paris, France, Hebert Echenique-Rivera, Yersinia Unit, Institut Pasteur, Paris, France, Florence Fouque, TDR, WHO, Lyon, France, Stephen Francesconi, Defence Threat Reduction Agency, Washington, DC, USA, Anna Funk, Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France, Finnian Hanrahan, DG Research, European Commission, Brussels, Belgium, Mireille Harimalala, Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Nadia Khellef, Institut Pasteur, Paris, France, Anne-Sophie Le Guern, Yersinia Unit, Institut Pasteur, Paris, France, Nadine Lemaitre, Bacteriology Department, CHU Lille, France, Jean-Claude Manuguerra, CIBU, Institut Pasteur, Paris, France, Jodie Mac Vernon, GLoPID-R, University of Melbourne, Australia, Serge Morand, CIRAD, Bangkok, Thailand, Birgit Nikolay, Infectious Diseases Mathematical Modelling Unit, Institut Pasteur, Paris, France, Juliette Paireau, Infectious Diseases Mathematical Modelling Unit, Institut Pasteur, Paris, France, Anna Paoletti, Ministry for Higher Education and Research, Paris, France, Feno MJ Rakotoarimanana, Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Zely Randriamanatany, Ministry of Public Health, Antananarivo, Madagascar, Laurent Raskine, Fondation Mérieux, Stéphanie Simon, CEA de Saclay, France, Cathy Roth, Department for International Development, London, UK, Alex Salam, Epidemic Diseases Research Group Oxford (ERGO), Nuffield Department of Medicine, University of Oxford, Oxford, UK, Florent Sebbane, Institut Pasteur de Lille, France, Christophe Shako, Department of Disease Control, Ministry of Health, Democratic Republic of Congo, Quirine Ten Bosch, Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Kathleen Victoir, Department of International Affairs, Institut Pasteur, Paris, France., Demeure, Christian E., Institut Pasteur [Paris], University of Oxford [Oxford], Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), and Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR)
Subjects: Epidemiology, RC955-962, MESH: Rodentia, Review, Pathology and Laboratory Medicine, Disease Outbreaks, Medical Conditions, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Arctic medicine. Tropical medicine, Case fatality rate, Public and Occupational Health, MESH: Animals, media_common, Mammals, Eukaryota, Neglected Diseases, Bacterial Pathogens, 3. Good health, One Health, Geography, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Medical Microbiology, Public aspects of medicine, S1, Yersinia Pestis, media_common.quotation_subject, Immunology, MESH: Yersinia pestis, Rodentia, Microbiology, 03 medical and health sciences, Vaccine Development, Madagascar, Humans, Microbial Pathogens, MESH: Disease Reservoirs, MESH: Humans, Bacteria, Organisms, Public Health, Environmental and Occupational Health, Biology and Life Sciences, Outbreak, medicine.disease, Invertebrates, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Insect Vectors, 030104 developmental biology, Vector (epidemiology), Africa, Preventive Medicine, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, Bacterial Diseases, 0301 basic medicine, Economic growth, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Geographical Locations, MESH: Madagascar, Medicine and Health Sciences, MESH: Disease Outbreaks, biology, Vaccination and Immunization, Yersinia, Insects, Infectious Diseases, Fleas, [SDV.IMM.IA] Life Sciences [q-bio]/Immunology/Adaptive immunology, Vertebrates, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Siphonaptera, Psychological resilience, RA1-1270, Pathogens, Pneumonic plague, Arthropoda, Pneumonic Plagues, 030231 tropical medicine, MESH: Insect Vectors, Plague (disease), Rodents, MESH: Plague, [SDV.IMM.VAC] Life Sciences [q-bio]/Immunology/Vaccinology, medicine, Animals, [SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity, Disease Reservoirs, Plague, MESH: Siphonaptera, biology.organism_classification, Plagues, Yersinia pestis, 13. Climate action, People and Places, Amniotes, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Neglected Diseases, Zoology, Entomology
Abstract: Yersinia pestis, the bacterial causative agent of plague, remains an important threat to human health. Plague is a rodent-borne disease that has historically shown an outstanding ability to colonize and persist across different species, habitats, and environments while provoking sporadic cases, outbreaks, and deadly global epidemics among humans. Between September and November 2017, an outbreak of urban pneumonic plague was declared in Madagascar, which refocused the attention of the scientific community on this ancient human scourge. Given recent trends and plague’s resilience to control in the wild, its high fatality rate in humans without early treatment, and its capacity to disrupt social and healthcare systems, human plague should be considered as a neglected threat. A workshop was held in Paris in July 2018 to review current knowledge about plague and to identify the scientific research priorities to eradicate plague as a human threat. It was concluded that an urgent commitment is needed to develop and fund a strong research agenda aiming to fill the current knowledge gaps structured around 4 main axes: (i) an improved understanding of the ecological interactions among the reservoir, vector, pathogen, and environment; (ii) human and societal responses; (iii) improved diagnostic tools and case management; and (iv) vaccine development. These axes should be cross-cutting, translational, and focused on delivering context-specific strategies. Results of this research should feed a global control and prevention strategy within a “One Health” approach., Author summary The historical aspect of plague makes for fascinating reading, due to its capacity to disrupt human society and its socioeconomic and cultural impacts throughout human history. We argue that the Madagascar outbreak in 2017 is a tipping point in human plague epidemiology and a call to elevate research priorities on plague as a matter of some urgency. In contrast with what occurred with the Ebola virus disease crisis in West Africa between 2013 and 2015 and the new coronaviruses (the emergence of severe acute respiratory syndrome coronavirus [SARS-CoV] and Middle East respiratory syndrome coronavirus [MERS-CoV] as early warnings of the current severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] pandemic), we have an opportunity to act preventively and enable evidence-based measures to avoid major health crises due to plague outbreaks in the near future.
Published: 2020
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