Descriptor: "MESH: Epidemics" - Searchworks@Jio Institute Digital Library Search Results

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46 results on '"MESH: Epidemics"'

1. Monitoring sick leave data for early detection of influenza outbreaks

Author: David R M Smith, Jonathan Bastard, Pearl Anne Ante-Testard, Oumou Salama Daouda, Laura Temime, Tom Duchemin, Helene Neynaud, Kévin Jean, Audrey Duval, Mounia N. Hocine, Rania Assab, Narimane Nekkab, William Dab, Radowan Lounissi, Jérôme-Philippe Garsi, Laboratoire Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), 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), Malakoff Humanis, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris] (IP)-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, Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur [Paris] (IP), Malaria : parasites et hôtes - Malaria : parasites and hosts, TD PhD is funded by Association Nationale de la Recherche et de la Technologie and Malakoff Humanis. JB PhD is funded by the INCEPTION project (PIA/ANR-16-CONV-0005). PAAT PhD is funded by INSERM-ANRS (France Recherche Nord & Sud Sida-HIV Hépatites), grant number ANRS-12377 B104. DS PhD is funded by a Canadian Institutes of Health Research Doctoral Foreign Study Award (Funding Reference Number 164263) as well as the French government through its National Research Agency project SPHINX-17-CE36–0008-01., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-17-CE36-0008,SPHINx,Diffusion de pathogènes au sein des réseaux de soins : une étude de modélisation(2017), TD is supported by Association Nationale de la Recherche et de la Technologie and Malakoff Humanis. JB is supported by the INCEPTION project (PIA/ANR-16-CONV-0005) PAA is supported by INSERM-ANRS (France Recherche Nord & Sud Sida-HIV Hepatites), grant number ANRS-12377 B104 DS is supported by a Canadian Institutes of Health Research Doctoral Foreign Study Award (Funding Reference Number 164263) as well as the French government through its National Research Agency project SPHINX-17-CE36-0008-01., Institut Pasteur [Paris]-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], Hocine, Mounia N., 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 Diffusion de pathogènes au sein des réseaux de soins : une étude de modélisation - - SPHINx2017 - ANR-17-CE36-0008 - AAPG2017 - VALID
Subjects: Sick-leave, MESH: Influenza, Human / epidemiology, MESH: Public Health Surveillance / methods, 010501 environmental sciences, 01 natural sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Absenteeism, MESH: Sick Leave, Medicine, Public Health Surveillance, MESH: Epidemics, 030212 general & internal medicine, MESH: Incidence, Workplace, MESH: Sentinel Surveillance, MESH: Workplace, MESH: France / epidemiology, [STAT.ME] Statistics [stat]/Methodology [stat.ME], Surveillance, MESH: Middle Aged, Incidence, Middle Aged, Infectious Diseases, Sick leave, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, France, Sick Leave, 0305 other medical science, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Research Article, MESH: Absenteeism, Surveillance Methods, Early detection, Influenza epidemics, Primary care, MESH: Insurance, Health, Sensitivity and Specificity, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Environmental health, Outbreak detection, Influenza, Human, Health insurance, Humans, lcsh:RC109-216, Epidemics, MESH: Influenza, Human / virology, 0105 earth and related environmental sciences, Retrospective Studies, 030505 public health, Insurance, Health, Models, Statistical, MESH: Humans, business.industry, Outbreak, MESH: Retrospective Studies, Influenza, MESH: Sensitivity and Specificity, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Sentinel Surveillance, MESH: Models, Statistical
Abstract: Background Workplace absenteeism increases significantly during influenza epidemics. Sick leave records may facilitate more timely detection of influenza outbreaks, as trends in increased sick leave may precede alerts issued by sentinel surveillance systems by days or weeks. Sick leave data have not been comprehensively evaluated in comparison to traditional surveillance methods. The aim of this paper is to study the performance and the feasibility of using a detection system based on sick leave data to detect influenza outbreaks. Methods Sick leave records were extracted from private French health insurance data, covering on average 209,932 companies per year across a wide range of sizes and sectors. We used linear regression to estimate the weekly number of new sick leave spells between 2016 and 2017 in 12 French regions, adjusting for trend, seasonality and worker leaves on historical data from 2010 to 2015. Outbreaks were detected using a 95%-prediction interval. This method was compared to results from the French Sentinelles network, a gold-standard primary care surveillance system currently in place. Results Using sick leave data, we detected 92% of reported influenza outbreaks between 2016 and 2017, on average 5.88 weeks prior to outbreak peaks. Compared to the existing Sentinelles model, our method had high sensitivity (89%) and positive predictive value (86%), and detected outbreaks on average 2.5 weeks earlier. Conclusion Sick leave surveillance could be a sensitive, specific and timely tool for detection of influenza outbreaks.
Published: 2023

2. Hotspot or blind spot? Historical perspectives on surveillance and response to epidemics in the Central African Republic

Author: Emmanuel Nakouné, Pierre-Marie David, Tamara Giles-Vernick, Université de Montréal (UdeM), Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Anthropologie et écologie de l’émergence des maladies - Anthropology and Ecology of Disease Emergence, Institut Pasteur [Paris] (IP), This work was supported by Fonds de Recherche Québécois Société et Culture—FRQSC (2016-B3-189967), the Agence Nationale de la Recherche sur le SIDA et les Hépatites (12288), and the Agence Nationale de la Recherche (ANR 31-CE31-004-001)., ANR-14-CE31-0004,SHAPES,Une étude pluridisciplinaire de l'émergence des maladies: le regard des sciences humaines sur les relations hommes-singes en Afrique équatoriale(2014), Institut Pasteur [Paris], and Université de Montréal. Faculté de pharmacie
Subjects: History, Economic growth, medicine.medical_specialty, Health (social science), Psychological intervention, Population health, History, 21st Century, Archival research, MESH: Population Surveillance, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Politics, 0302 clinical medicine, medicine, Global health, Humans, 030212 general & internal medicine, Epidemics, MESH: Epidemics, Central Africa, Surveillance, MESH: Humans, 030505 public health, Blind spot, Public health, 1. No poverty, Public Health, Environmental and Occupational Health, History, 20th Century, Colonial period, Central African Republic, Pasteur, Geography, MESH: Central African Republic, Population Surveillance, Disease emergence, MESH: History, 20th Century, Public Health, MESH: History, 21st Century, MESH: Public Health, 0305 other medical science
Abstract: Objectives The Central African Republic (CAR), a site of recurrent disease emergence, developed a noteworthy epidemiological surveillance system from the colonial period, but its health measures have remained among the world’s lowest. To understand this disparity between surveillance and public health, we examined selected moments in its history of surveillance and changing relations with public health structures. Methods We conducted archival research in CAR and French archives and 18 semi-structured interviews with key researchers working in CAR. Results We find long-term continuities in privileging surveillance over the health system and population health, making the CAR a ‘‘hotspot’’ for emerging diseases and a ‘‘blind spot’’ of primary health care. From the colonial period, the country attracted considerable support for surveillance, without concomitant investment in public health system. Political disputes and financial constraints have obscured real primary care needs on the ground. Conclusions As both a hotspot and a blind spot for global health, the CAR signals the need to reorient health interventions to address the long-term health of Central African people.
Published: 2020

3. COVID-19 epidemic in remote areas of the French Amazon, March 2020 to May 2021: Another reality

Author: Loïc Epelboin, Tiphanie Succo, Céline Michaud, Margot Oberlis, Bastien Bidaud, Pauline Naudion, Lise Dudognon, Clara Fernandes, Charlène Cochet, Cécile Caspar, Estelle Jacoud, Sébastien Teissier, Maylis Douine, Dominique Rousset, Claude Flamand, Félix Djossou, Mathieu Nacher, Cyril Rousseau, Nicolas Vignier, Mélanie Gaillet, Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Centre d'Investigation Clinique Antilles-Guyane (CIC - Antilles Guyane), Université des Antilles et de la Guyane (UAG)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de Fort de France-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Santé publique France Guyane, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Croix rouge française, Centre Hospitalier de l'Ouest Guyanais Franck Joly [Saint-Laurent-du-Maroni, Guyane Française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), 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 FEDER European funding for the « AMAZCOV’N FEVER» project: FEADER /2020/AAP-FLASH COVID-19 /N°18 - GY0028034.
Subjects: Microbiology (medical), Adolescent, COVID-19 vaccines, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, MESH: French Guiana, Humans, MESH: COVID-19, Epidemics, MESH: Epidemics, MESH: Adolescent, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Humans, SARS-CoV-2, COVID-19, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, French Guiana, Europe, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Health promotion, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Parasitology, MESH: Europe, MESH: Brazil, Brazil
Abstract: International audience; Background:French Guiana (FG) is an ultra-peripheral European region in the Amazon, and the COVID-19 epidemic has had very different kinetics from both its giant neighbors, Brazil or mainland France.Methods:This study summarized the epidemics of COVID-19 in FG.Results:The tropical climate, multiethnicity, and remoteness of the population forced healthcare providers to accordingly adapt the management of the epidemic. Incidence and mortality have been lower than that in Europe and Latin America due to a combination of prevalence of the youth in the population and highly developed healthcare system.Conclusions:Currently, vaccine hesitancy hinders the rapid expansion of vaccine coverage.
Published: 2022

4. Enhanced mosquito vectorial capacity underlies the Cape Verde Zika epidemic

Author: Noah H. Rose, Stéphanie Dabo, Silvânia da Veiga Leal, Massamba Sylla, Cheikh T. Diagne, Oumar Faye, Ousmane Faye, Amadou A. Sall, Carolyn S. McBride, Louis Lambrechts, Princeton University, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Instituto Nacional de Saúde Pública [Cabo Verde] (INSP), Université du Sine Saloum El-Hadj Ibrahima NIASS (USSEIN), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), This work was supported by the European Union’s Horizon 2020 research and innovation programme under ZikaPLAN grant agreement no. 734584 (to LL), Agence Nationale de la Recherche (grant ANR-18-CE35-0003-01 to LL), the French Government’s Investissement d’Avenir program Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant ANR-10-LABX-62-IBEID to LL), and the US National Institutes of Health (grant NIDCD R00-DC012069 to CSM). NHR was supported by a Helen Hay Whitney Postdoctoral Fellowship. CSM is a New York Stem Cell Foundation – Robertson Investigator., ANR-18-CE35-0003,BAKOUMBA,Dissection de la base génétique d'un phénotype naturel de résistance à la dengue chez le moustique Aedes aegypti(2018), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and European Project: no. 734584
Subjects: MESH: Humans, General Immunology and Microbiology, Zika Virus Infection, General Neuroscience, MESH: Zika Virus, Zika Virus, Mosquito Vectors, MESH: Aedes, MESH: Cabo Verde, General Biochemistry, Genetics and Molecular Biology, MESH: Zika Virus Infection, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Aedes, Cabo Verde, Animals, Humans, MESH: Animals, MESH: Saliva, MESH: Mosquito Vectors, Saliva, Epidemics, General Agricultural and Biological Sciences, MESH: Epidemics
Abstract: The explosive emergence of Zika virus (ZIKV) across the Pacific and Americas since 2007 was associated with hundreds of thousands of human cases and severe outcomes, including congenital microcephaly caused by ZIKV infection during pregnancy. Although ZIKV was first isolated in Uganda, Africa has so far been exempt from large-scale ZIKV epidemics, despite widespread susceptibility among African human populations. A possible explanation for this pattern is natural variation among populations of the primary vector of ZIKV, the mosquito Aedes aegypti. Globally invasive populations of Ae. aegypti outside of Africa are considered effective ZIKV vectors because they are human specialists with high intrinsic ZIKV susceptibility, whereas African populations of Ae. aegypti across the species’ native range are predominantly generalists with low intrinsic ZIKV susceptibility, making them less likely to spread viruses in the human population. We test this idea by studying a notable exception to the patterns observed across most of Africa: Cape Verde experienced a large ZIKV outbreak in 2015 to 2016. We find that local Ae. aegypti in Cape Verde have substantial human-specialist ancestry, show a robust behavioral preference for human hosts, and exhibit increased susceptibility to ZIKV infection, consistent with a key role for variation among mosquito populations in ZIKV epidemiology. These findings suggest that similar human-specialist populations of Ae. aegypti in the nearby Sahel region of West Africa, which may be expanding in response to rapid urbanization, could serve as effective vectors for ZIKV in the future.
Published: 2022

5. Indirect protection from vaccinating children against influenza in households

Author: Vicky J. Fang, Benjamin J. Cowling, Ranawaka A.P.M. Perera, Gabriel M. Leung, J S Malik Peiris, Hau Chi So, Tim K. Tsang, Simon Cauchemez, Dennis K. M. Ip, The University of Hong Kong (HKU), University of Florida [Gainesville] (UF), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Génomique évolutive, modélisation et santé (CNRS-UMR2000), This study was supported by the Research Fund for the Control of Infectious Diseases of the Health, Welfare and Food Bureau of the Hong Kong SAR Government (grant CHP-CE-03), the Theme-based Research Scheme project no. T11-705/14N from the Hong Kong Government, the National Institute of General Medical Sciences (grant U54 GM088558 to the Harvard Center for Communicable Disease Dynamics to B.J.C, MIDAS initiative grant 1U01GM110721-01 to S.C., and U54 GM111274-01 to Center for Statistics and Quantitative Infectious Diseases to T.K.T.), L’Oreal Hong Kong (research scholarship to T.K.T), the Laboratory of Excellence Integrative Biology of Emerging Infectious Diseases (research funding to S.C.), and AXA Research Fund to S.C., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Génomique évolutive, modélisation et santé (GEMS)
Subjects: 0301 basic medicine, General Physics and Astronomy, 02 engineering and technology, law.invention, MESH: Influenza Vaccines, Randomized controlled trial, law, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], MESH: Child, Outcome Assessment, Health Care, Medicine, Child, lcsh:Science, MESH: Influenza B virus, Family Characteristics, Multidisciplinary, Transmission (medicine), MESH: Influenza, Human, Vaccination, 021001 nanoscience & nanotechnology, 3. Good health, Influenza Vaccines, Child, Preschool, Hong Kong, 0210 nano-technology, MESH: Hong Kong, Adolescent, Influenza vaccine, Science, Disease cluster, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Environmental health, Influenza, Human, MESH: Family Characteristics, Humans, MESH: Outcome Assessment, Health Care, Epidemics, MESH: Epidemics, MESH: Adolescent, MESH: Humans, business.industry, Extramural, Family characteristics, MESH: Child, Preschool, General Chemistry, MESH: Vaccination, Vaccine efficacy, Influenza B virus, 030104 developmental biology, lcsh:Q, business
Abstract: Vaccination is an important intervention to prevent influenza virus infection, but indirect protection of household members of vaccinees is not fully known. Here, we analyze a cluster household randomized controlled trial, with one child in each household randomized to receive influenza vaccine or placebo, for an influenza B epidemic in Hong Kong. We apply statistical models to estimate household transmission dynamics and quantify the direct and indirect protection of vaccination. Direct vaccine efficacy was 71%. The infection probability of unvaccinated household members in vaccinated households was only 5% lower than in control households, because only 10% of infections are attributed to household transmission. Even when that proportion rises to 30% and all children are vaccinated, we predict that the infection probability for unvaccinated household members would only be reduced by 20%. This suggests that benefits of individual vaccination remain important even when other household members are vaccinated., Relevance of indirect protection of household members of vaccinees is unclear. Here, Tsang et al. quantify the direct and indirect protection of vaccination in a randomized controlled trial and show that benefits of individual vaccination remain important even when other household members are vaccinated.
Published: 2019

6. Using serological studies to reconstruct the history of bluetongue epidemic in French cattle under successive vaccination campaigns

Author: Noémie Courtejoie, Gina Zanella, Simon Cauchemez, Benoit Durand, Henrik Salje, 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), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), This work was supported by 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 and the AXA Research Fund., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé
Subjects: 0301 basic medicine, Epidemiology, [SDV]Life Sciences [q-bio], MESH: Immunization Programs, MESH: Bluetongue virus, Serology, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], MESH: Cattle Diseases, MESH: Animals, 2. Zero hunger, Incidence (epidemiology), Vaccination, 3. Good health, MESH: Cattle, Infectious Diseases, Geography, France, medicine.medical_specialty, MESH: Bayes Theorem, 030106 microbiology, Cattle Diseases, Microbiology, Bluetongue, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Virology, medicine, Animals, lcsh:RC109-216, MESH: Bluetongue, Seroconversion, Epidemics, MESH: Epidemics, Immunization Programs, Public Health, Environmental and Occupational Health, Outbreak, Bayes Theorem, MESH: Vaccination, MESH: France, 030104 developmental biology, Immunization, Vaccination Campaigns, Cattle, Parasitology, Bluetongue virus, Demography
Abstract: Bluetongue virus is a vector-borne pathogen affecting ruminants that has caused major epidemics in France. Reconstructing the history of bluetongue in French cattle under control strategies such as vaccination has been hampered by the high level of sub-clinical infection, incomplete case data and poor understanding of vaccine uptake over time and space. To tackle these challenges, we used three age-structured serological surveys carried out in cattle (N = 22,342) from ten administrative subdivisions called departments. We fitted catalytic models within a Bayesian MCMC framework to reconstruct the force of seroconversion from infection or vaccination, and the population-level susceptibility per semester between 2007 and 2016. In the departments of the study area, we estimated that 36% of cattle had been infected prior to vaccine rollout that became compulsory from July 2008. The last outbreak case was notified in December 2009, at which time 83% of the animals were seropositive, under the cumulative effect of vaccination and infection. The probability of seroconversion per semester dropped below 10% after 2010 when vaccination became optional. Vaccine uptake was smaller during the 2012 campaign than during the one in 2011, with strong regional contrasts. Eighty four percent of cattle were susceptible when bluetongue re-emerged in 2015. Thus, serological surveys can be used to estimate vaccine uptake and the magnitude of infection, the relative effect of which can sometimes be inferred using prior knowledge on reported incidence and vaccination dates. Keywords: Bluetongue, Epidemiology, France, Immunization, Serology
Published: 2018

7. The methamphetamine epidemic among persons who inject heroin in Hai Phong, Vietnam

Author: Roselyne Vallo, Kamyar Arasteh, Jonathan Feelemyer, Don C. Des Jarlais, Pham Minh Khue, Laurent Michel, Catherine Quillet, Nicolas Nagot, Vu Hai Vinh, Hoang Thi Giang, Duong Thi Huong, Jean-Pierre Molès, Delphine Rapoud, Drive Study Team, Didier Laureillard, Khuat Thi Hai Oanh, Nham Thi Tuyet Thanh, College of Global Public Health [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Hai Phong University of Medicine and Pharmacy [Hai Phong, Vietnam], Supporting Community Development Initiatives [Hanoï, Vietnam], Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier], Viet Tiep Hospital [Hai Phong, Vietnam], Centre Pierre Nicole [Paris], 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, Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), and Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)
Subjects: Male, medicine.medical_specialty, Medicine (miscellaneous), HIV Infections, Persons who inject drugs, Article, MESH: Methamphetamine, Heroin, Methamphetamine, Hai Phong, Social support, Environmental health, medicine, Humans, Adverse effect, Epidemics, Substance Abuse, Intravenous, MESH: Epidemics, Harm reduction, MESH: Humans, business.industry, Public health, MESH: HIV Infections, Mental health, MESH: Male, Psychiatry and Mental health, Clinical Psychology, Vietnam, Viet Nam, Structured interview, MESH: Substance Abuse, Intravenous, MESH: Heroin, MESH: Vietnam, Pshychiatric Mental Health, business, Psychosocial, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, medicine.drug
Abstract: International audience; Aims: To describe the current methamphetamine (MA) use epidemic among persons who inject heroin (PWID) in Hai Phong, Vietnam, and consider possibilities for mitigating adverse effects of methamphetamine use.Methods: This study conducted surveys of PWID in 2016, 2017, and 2018 (N = 1383, 1451, and 1445, respectively). Trained interviewers administered structured interviews covering drug use histories, current drug use, and related risk behaviors. The study used urinalysis to confirm current drug use, and conducted HIV and HCV testing.Results: Participants were predominantly male (95%), mean age of 40, and all reported injecting heroin. Respondents' reports of initiating MA use were rare up through early 2000s but increased exponentially through the mid-2010s. MA use was predominantly "smoking," heating the drug and inhaling the vapor using a pipe; injecting MA was rare. Current (past 30 day) MA use appears to have plateaued in 2016-2018 with 53-58% of participants reporting no use in the last 30 days, 37-41% reporting low to moderate use (1 to 19 days in last 30 days), and 5-7% reporting very frequent use (20 or more days in last 30 days). This plateau reflects a rough balance between new users and individuals ceasing use.Conclusions: MA use has become a substantial public health problem among PWID in Hai Phong. Initiation into MA use rose exponentially from 2005 to about 2015. Use of MA will likely continue for a substantial number of PWID. Currently, no medication is approved for treating MA disorders in Vietnam. Current psychosocial treatment requires highly trained counselors and months of treatment, so that psychosocial treatment for all PWID with MA disorders is likely beyond the resources available in a middle-income country such as Vietnam. Harm reduction programs implemented by community-based organization staff may provide a way to rapidly address aspects of the current MA epidemic. Such programs could emphasize social support for reducing use where possible and for avoiding escalation of use among persons continuing to use.
Published: 2021

8. Impact of mass testing during an epidemic rebound of SARS-CoV-2: a modelling study using the example of France

Author: Cécile Tran Kiem, Vittoria Colizza, Yazdan Yazdanpanah, Arnaud Fontanet, Bruno Lina, 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), Collège Doctoral, Sorbonne Université (SU), 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, 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), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Virology and human respiratory Pathologies - Virology and human respiratory Pathologies (VirPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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 programme under grants 101003589 (RECOVER) and 874735 (VEO), AXA., 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), Limouzin, Cécile, 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, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and European Project: 874735,VEO
Subjects: 2019-20 coronavirus outbreak, medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030204 cardiovascular system & hematology, epidemic, Very frequent, 03 medical and health sciences, 0302 clinical medicine, COVID-19 Testing, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Virology, MESH: COVID-19, Medicine, Humans, Mass Screening, MESH: Mass Screening, 030212 general & internal medicine, mass testing, MESH: Models, Theoretical, Intensive care medicine, Epidemics, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], MESH: Epidemics, Mass screening, MESH: Humans, business.industry, SARS-CoV-2, MESH: COVID-19 Testing, Public Health, Environmental and Occupational Health, COVID-19, Models, Theoretical, 3. Good health, MESH: France, France, Prevention control, business, Rapid Communication
Abstract: International audience; We used a mathematical model to evaluate the impact of mass testing in the control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Under optimistic assumptions, one round of mass testing may reduce daily infections by up to 20–30%. Consequently, very frequent testing would be required to control a quickly growing epidemic if other control measures were to be relaxed. Mass testing is most relevant when epidemic growth remains limited through a combination of interventions.
Published: 2021
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9. Using large-scale respondent driven sampling to monitor the end of an HIV epidemic among persons who inject drugs in Hai Phong, Viet Nam

Author: Roselyne Vallo, Pham Minh Khue, Laurent Michel, Kamyar Arasteh, Drive Study Team, Didier Laureillard, Vu Hai Vinh, Delphine Rapoud, Nicolas Nagot, Hoang Thi Giang, Don C. Des Jarlais, Sao Mai Le, Duong Thi Huong, Jonathan Feelemyer, Catherine Quillet, Khuat Thi Hai Oanh, Jean-Pierre Molès, Nham Thi Tuyet Thanh, College of Global Public Health [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Hai Phong University of Medicine and Pharmacy [Hai Phong, Vietnam], Supporting Community Development Initiatives [Hanoï, Vietnam], Viet Tiep Hospital [Hai Phong, Vietnam], Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier], Centre Pierre Nicole [Paris], 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, Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), and Herrada, Anthony
Subjects: RNA viruses, Male, Epidemiology, Hiv epidemic, HIV Infections, Surveys, Pathology and Laboratory Medicine, Geographical Locations, Cohort Studies, Immunodeficiency Viruses, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, Substance Abuse, Intravenous, MESH: Cohort Studies, Virus Testing, education.field_of_study, Multidisciplinary, Viet nam, Sampling (statistics), MESH: HIV Infections, Vietnam, HIV epidemiology, Medical Microbiology, Research Design, Viral Pathogens, Scale (social sciences), Viruses, Epidemiological Monitoring, Respondent, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Infectious diseases, Female, Pathogens, Research Article, Cohort study, Medical conditions, Adult, Asia, Science, HIV prevention, Population, Viral diseases, Research and Analysis Methods, Microbiology, Sampling Studies, MESH: Sampling Studies, Diagnostic Medicine, Retroviruses, Humans, Epidemics, education, Microbial Pathogens, MESH: Sample Size, MESH: Epidemics, Medicine and health sciences, Preventive medicine, MESH: Humans, Survey Research, business.industry, Lentivirus, Organisms, Biology and Life Sciences, HIV, MESH: Adult, MESH: Male, Public and occupational health, Snowball sampling, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Sample Size, People and Places, MESH: Substance Abuse, Intravenous, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, respondent driven sampling, MESH: Epidemiological Monitoring, MESH: Vietnam, business, MESH: Female, Demography
Abstract: Aims To describe the use of large-scale respondent driven sampling (RDS) surveys to demonstrate the “end of an HIV epidemic” (HIV incidence < 0.5/100 person-years) among persons who inject drugs (PWID) in a middle-income country. Large sample sizes are needed to convincingly demonstrate very low incidence rates. Methods 4 large surveys (Ns approximately 1500 each) were conducted among PWID in Hai Phong, Vietnam in 2016–2019. Respondent driven sampling (RDS) with a modification to add snowball sampling was used for recruiting participants. HIV incidence was measured through recency testing, repeat participants across multiple surveys and in a cohort study of PWID recruited from the surveys. RDS analytics (time to equilibria and homophilies for major variables) were used to assess similarities/differences in RDS only versus RDS plus snowball recruiting. Characteristics were compared among respondents recruited through standard RDS recruitment versus through snowball sampling. An overall assessment of the robustness of RDS to modification was made when adding a snowball sampling recruitment. Results RDS recruiting was very efficient in the first 5 weeks of each survey with approximately 180 respondents recruited per week. Recruiting then slowed considerably, and snowball sampling (permitting an individual respondent to recruit large numbers of new respondents) was added to the existing RDS recruiting. This led to recruiting within 13–14 weeks of 1383, 1451, 1444 and 1268 respondents, close to the target of 1500 respondents/survey. Comparisons of participants recruited through standard RDS method and respondents recruited through snowball methods showed very few significant differences. RDS analytics (quickly reaching equilibria, low homophilies) were favorable for both RDS recruited and total numbers of participants in each survey. DRug use and Infections in ViEtnam (DRIVE) methods have now been officially adopted in other provinces. Conclusions RDS appears to be quite robust with respect to adding a modest number of participants recruited through snowball sampling. Large sample sizes can provide compelling evidence for “ending an HIV epidemic” to policy makers in a PWID population in a middle income country setting.
Published: 2021

10. Characteristics of the delayed respiratory syncytial virus epidemic, 2020/2021, Rhône Loire, France

Author: Casalegno, Jean-Sebastien, Ploin, Dominique, Cantais, Aymeric, Masson, Elsa, Bard, Emilie, Valette, Martine, Fanget, Remi, Targe, Sandrine Couray, Myar-Dury, Anne-Florence, Doret-Dion, Muriel, Massoud, Mona, Queromes, Gregory, Vanhems, Philippe, Claris, Olivier, Butin, Marine, Pillet, Sylvie, Ader, Florence, Bin, Sylvie, Gaymard, Alexandre, Lina, Bruno, Morfin, Florence, Javouhey, Etienne, Gillet, Yves, Ouziel, Antoine, Tardy, Jean-claude, Gaucherand, Pascal, Panetta, Luc, Massardier, Jerome, Polazzi, Stephanie, Duclos, Antoine, Benchaib, Mehdi, Cartier, Regine, Jourdain, Marine, Ottmann, Michelle, Kramer, Rolf, Fiorini, Sylvie, Rivat, Nathalie, Mekki, Yahia, Fort-Jacquier, Julie, Barral, Maud-Catherine, Noelie, Vey, Haesebaert, Julie, Horvat, Come, Vidoni, Leo, Reynes, Jean-Marc, Eleouet, Jean-Francois, Josset, Laurence, Receveur, Matthieu, Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Virology and human respiratory Pathologies - Virology and human respiratory Pathologies (VirPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP), Université Jean Monnet - Saint-Étienne (UJM), Hôpital Edouard Herriot [CHU - HCL], Santé publique, épidémiologie et écologie évolutive des maladies infectieuses (PHE3ID), Pôle Information Médicale Evaluation Recherche (IMER), Hôpital de la Croix-Rousse [CHU - HCL], VRS study group in Lyon: Antoine Ouziel, Jean-claude Tardy, Pascal Gaucherand, Luc Panetta, Jerome Massardier, Stephanie Polazzi, Antoine Duclos, Mehdi Benchaib, Regine Cartier, Marine Jourdain, Michelle Ottmann, Rolf Kramer, Sylvie Fiorini, Nathalie Rivat, Yahia Mekki, Julie Fort-Jacquier, Maud-Catherine Barral, Vey Noelie, Julie Haesebaert, Come Horvat, Leo Vidoni, Jean-Marc Reynes, Jean-Francois Eleouet, Laurence Josset, Matthieu Receveur, Reynes, Jean-Marc, Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne)
Subjects: 0301 basic medicine, Pediatrics, Epidemiology, pharmacological interventions, MESH: Hospitalization, MESH: Respiratory Syncytial Virus, Human, disease burden, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Child, 030212 general & internal medicine, Respiratory system, Child, Respiratory Tract Infections, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Respiratory tract infections, Incidence (epidemiology), RSV, MESH: Infant, Hospitalization, non-pharmacological interventions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, bronchiolitis, France, Rapid Communication, Adult, medicine.medical_specialty, Respiratory Syncytial Virus Infections, Virus, MESH: Respiratory Syncytial Virus Infections, 03 medical and health sciences, Virology, Lower respiratory tract infection, medicine, Humans, Epidemics, MESH: Epidemics, Disease burden, MESH: Humans, business.industry, SARS-CoV-2, Public Health, Environmental and Occupational Health, Outbreak, COVID-19, Infant, MESH: Adult, medicine.disease, MESH: France, 030104 developmental biology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Bronchiolitis, Respiratory Syncytial Virus, Human, MESH: Respiratory Tract Infections, SARI, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract: International audience; The Rhône-Loire metropolitan areas’ 2020/21 respiratory syncytial virus (RSV) epidemic was delayed following the implementation of non-pharmaceutical interventions (NPI), compared with previous seasons. Very severe lower respiratory tract infection incidence among infants ≤ 3 months decreased twofold, the proportion of cases among children aged > 3 months to 5 years increased, and cases among adults > 65 years were markedly reduced. NPI appeared to reduce the RSV burden among at-risk groups, and should be promoted to minimise impact of future RSV outbreaks.
Published: 2021

11. Longitudinal monitoring in Cambodia suggests higher circulation of alpha and betacoronaviruses in juvenile and immature bats of three species

Author: Cappelle, Julien, Furey, Neil, Hoem, Thavry, Ou, Tey Putita, Lim, Thona, Hul, Vibol, Heng, Oudam, Chevalier, Véronique, Dussart, Philippe, Duong, Veasna, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Harrison Institute, Fauna and Flora International [Cambodia], Fauna and Flora International [Cambridge, UK], Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Free the Bears [Phnom Penh, Cambodia], Free the Bears [Australia], 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), This study was supported by the European Commission Innovate program (ComAcross project, Grant no. DCI-ASIE/2013/315-047) and the French ANR (ZooCov project, Flash COVID-19 call)., ANR-20-COVI-0055,ZooCov,Vers la mise en place d'un système de surveillance intégré des Betacorornavirus dans la filière de viande de brousse au Cambodge(2020), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur de Madagascar, and Réseau International des Instituts Pasteur (RIIP)
Subjects: Male, MESH: Geography, [SDV]Life Sciences [q-bio], MESH: Asia, Southeastern, L73 - Maladies des animaux, Chiroptera, MESH: COVID-19, MESH: Animals, Longitudinal Studies, MESH: Longitudinal Studies, MESH: Phylogeny, MESH: Evolution, Molecular, Asia, Southeastern, Phylogeny, Geography, Alphacoronavirus, MESH: Chiroptera, virus diseases, Épidémiologie, MESH: Betacoronavirus, Medicine, MESH: Genome, Viral, Cambodia, Science, Genome, Viral, Article, Evolution, Molecular, Betacoronavirus, Species Specificity, MESH: Alphacoronavirus, Coronavirus 2 du syndrome respiratoire aigu sévère, Virology, parasitic diseases, MESH: Species Specificity, Animals, Humans, MESH: SARS-CoV-2, Surveillance épidémiologique, Epidemics, MESH: Epidemics, Transmission des maladies, Ecological epidemiology, MESH: Humans, SARS-CoV-2, MESH: Cambodia, COVID-19, MESH: Male
Abstract: International audience; Abstract Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus . Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46–7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.
Published: 2021

12. Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus

Author: Lionel Almeras, Albin Fontaine, Sebastian Lequime, Séverine Matheus, Sébastien Briolant, Jean-Sébastien Dehecq, Franck de Laval, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, KU Leuven (KU Leuven), Agence Régionale de Santé Océan Indien, Agence Régionale de la Santé (ARS), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP), Centre National de Référence pour les Arbovirus - Laboratoire de Virologie [Cayenne, Guyane française] (CNR - laboratoire associé), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre d'épidémiologie et de santé publique des armées [Marseille] (CESPA), Service de Santé des Armées, 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), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Direction Générale de l’Armement grant no PDH-2-NRBC-2-B-2113Direction Centrale du Service de Santé des Armées grant agreement 2016RC10European Virus Archive goes Global (EVAg, project that has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 653316.)Fonds Wetenschappelijk Onderzoek – Vlaanderen (FWO, https://www.fwo.be)., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut Pasteur [Paris], Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), GUY, Charlotte, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Lequime lab
Subjects: Epidemiology, Pathology and Laboratory Medicine, Geographical locations, Zika virus, law.invention, Disease Outbreaks, 0302 clinical medicine, Medical Conditions, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Animals, Biology (General), MESH: Models, Theoretical, 0303 health sciences, Zika Virus Infection, Eukaryota, virus diseases, 3. Good health, Transmission (mechanics), Blood, Medical Microbiology, Viral Pathogens, Viral Vectors, QH301-705.5, Immunology, Viremia, MESH: Zika Virus, MESH: Disease Vectors, Microbiology, 03 medical and health sciences, Dose Prediction Methods, MESH: Zika Virus Infection, Genetics, Humans, MESH: Saliva, Epidemics, Saliva, Molecular Biology, Microbial Pathogens, MESH: Humans, Flaviviruses, fungi, Organisms, Outbreak, Models, Theoretical, medicine.disease, Virology, Invertebrates, Insect Vectors, Species Interactions, Vector (epidemiology), Parasitology, Immunologic diseases. Allergy, People and places, RNA viruses, Viral Diseases, Physiology, viruses, Disease Vectors, Mosquitoes, law, Aedes, Medicine and Health Sciences, MESH: Disease Outbreaks, biology, Pharmaceutics, MESH: Aedes, Viral Load, Body Fluids, Insects, Europe, Infectious Diseases, Viruses, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Mosquito Vectors, France, Pathogens, Anatomy, MESH: Viral Load, Research Article, Aedes albopictus, Arthropoda, 030231 tropical medicine, Aedes aegypti, Mosquito Vectors, Virus, medicine, Animals, European Union, MESH: Viremia, MESH: Epidemics, 030304 developmental biology, Biology and life sciences, Zika Virus, RC581-607, biology.organism_classification, Zoology, Entomology, Viral Transmission and Infection
Abstract: Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered until the end of 2019, when several autochthonous transmissions of the virus vectored by Ae. albopictus occurred in France. Aside from these few locally acquired ZIKV infections, most territories colonized by Ae. albopictus have been spared so far. The risk level of ZIKV emergence in these areas remains however an open question. To assess Ae. albopictus’ vector potential for ZIKV and identify key virus outbreak predictors, we built a complete framework using the complementary combination of (i) dose-dependent experimental Ae. albopictus exposure to ZIKV followed by time-dependent assessment of infection and systemic infection rates, (ii) modeling of intra-human ZIKV viremia dynamics, and (iii) in silico epidemiological simulations using an Agent-Based Model. The highest risk of transmission occurred during the pre-symptomatic stage of the disease, at the peak of viremia. At this dose, mosquito infection probability was estimated to be 20%, and 21 days were required to reach the median systemic infection rates. Mosquito population origin, either temperate or tropical, had no impact on infection rates or intra-host virus dynamic. Despite these unfavorable characteristics for transmission, Ae. albopictus was still able to trigger and yield large outbreaks in a simulated environment in the presence of sufficiently high mosquito biting rates. Our results reveal a low but existing epidemic potential of Ae. albopictus for ZIKV, that might explain the absence of large scale ZIKV epidemics so far in territories occupied only by Ae. albopictus. They nevertheless support active surveillance and eradication programs in these territories to maintain the risk of emergence to a low level., Author summary Zika virus (ZIKV) has emerged worldwide and triggered large outbreaks in human populations. While the yellow fever mosquito Aedes aegypti is considered the primary vector of ZIKV, the Asian tiger mosquito Aedes albopictus has been shown experimentally to transmit the virus and has been involved in a few autochthonous transmission in France in 2019. Here, we provide a comprehensive study on the ability of Ae. albopictus mosquitoes to transmit ZIKV by considering the within-host dynamics of ZIKV infection in humans and its impact on both mosquito infection probability and time to mosquito infectiousness. These empirical data were then leveraged by in silico simulations to embed them into their epidemiological context. Our study reveals a low but existing epidemic potential of Ae. albopictus for ZIKV, whatever their tropical or temperate origins. We identified mosquito density as a predictor for ZIKV outbreak occurrence when vectored by Ae. albopictus. Our findings help to explain the absence of large scale ZIKV epidemics in territories occupied by Ae. albopictus but call for active surveillance and eradication programs to maintain the risk of emergence to a low level.
Published: 2020

13. Instability of the NS1 Glycoprotein from La Reunion 2018 Dengue 2 Virus (Cosmopolitan-1 Genotype) in Huh7 Cells Is Due to Lysine Residues on Positions 272 and 324

Author: Philippe Desprès, Olivier Diaz, Pierre-Olivier Vidalain, Vincent Lotteau, Eva Ogire, Marjolaine Roche, 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), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Vidalain, Pierre-Olivier, Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Serotype, viruses, MESH: Dengue, Dengue virus, Viral Nonstructural Proteins, medicine.disease_cause, soluble viral protein, MESH: Dengue Virus, Tanzania, Dengue fever, lcsh:Chemistry, MESH: Recombinant Proteins, MESH: Genotype, MESH: Hepatocytes, Dengue, multimeric viral protein, flavivirus, Genotype, lcsh:QH301-705.5, Antigens, Viral, Spectroscopy, chemistry.chemical_classification, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology, MESH: Protein Multimerization, Protein Stability, virus diseases, General Medicine, MESH: Amino Acid Substitution, Recombinant Proteins, 3. Good health, Computer Science Applications, Flavivirus, MESH: HEK293 Cells, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Reunion, MESH: Antigens, Viral, MESH: Cell Line, Tumor, 030106 microbiology, Serogroup, Transfection, Arbovirus, Article, Catalysis, Virus, Inorganic Chemistry, 03 medical and health sciences, MESH: Tanzania, MESH: Protein Stability, Cell Line, Tumor, medicine, Humans, nonstructural protein 1, MESH: Lysine, Physical and Theoretical Chemistry, Epidemics, Molecular Biology, MESH: Epidemics, MESH: Humans, MESH: Transfection, Lysine, Organic Chemistry, MESH: Serogroup, biochemical phenomena, metabolism, and nutrition, Dengue Virus, biology.organism_classification, medicine.disease, Virology, 030104 developmental biology, arbovirus, HEK293 Cells, lcsh:Biology (General), lcsh:QD1-999, chemistry, Amino Acid Substitution, Hepatocytes, MESH: Viral Nonstructural Proteins, recombinant viral protein, Protein Multimerization, Glycoprotein, hepatoma cells, Reunion
Abstract: La Reunion island in the South West Indian Ocean is now endemic for dengue following the introduction of dengue virus serotype 2 (DENV-2) cosmopolitan-I genotype in 2017. DENV-2 infection causes a wide spectrum of clinical manifestations ranging from flu-like disease to severe dengue. The nonstructural glycoprotein 1 (NS1) has been identified as playing a key role in dengue disease severity. The intracellular NS1 exists as a homodimer, whereas a fraction is driven towards the plasma membrane or released as a soluble hexameric protein. Here, we characterized the NS1 glycoproteins from clinical isolates DES-14 and RUN-18 that were collected during the DENV-2 epidemics in Tanzania in 2014 and La Reunion island in 2018, respectively. In relation to hepatotropism of the DENV, expression of recombinant DES-14 NS1 and RUN-18 NS1 glycoproteins was compared in human hepatoma Huh7 cells. We observed that RUN-18 NS1 was poorly stable in Huh7 cells compared to DES-14 NS1. The instability of RUN-18 NS1 leading to a low level of NS1 secretion mostly relates to lysine residues on positions 272 and 324. Our data raise the issue of the consequences of a defect in NS1 stability in human hepatocytes in relation to the major role of NS1 in the pathogenesis of the DENV-2 infection.
Published: 2020

14. IMPact of the COVID-19 epidemic on the moRTAlity of kidney transplant recipients and candidates in a French Nationwide registry sTudy (IMPORTANT)

Author: Olivier Thaunat, Camille Legeai, Dany Anglicheau, Lionel Couzi, Gilles Blancho, Marc Hazzan, Myriam Pastural, Emilie Savoye, Florian Bayer, Emmanuel Morelon, Yann Le Meur, Olivier Bastien, Sophie Caillard, Charlene Levi, Fanny Buron, Alice Koenig, Thomas Barba, Bruno Moulin, Samira Fafi-Kremer, Anglicheau Dany, Alexandre Hertig, Jérôme Tourret, Benoit Barrou, Pierre Merville, Anna Kaminski, Valérie Moal, Tristan Legris, Pierre-François Westeel, Maïté Jaureguy, Luc Frimat, Didier Ducloux, Jamal Bamoulid, Dominique Bertrand, Michel Tsimaratos, Florentine Garaix-Gilardo, Jérôme Dumortier, Sacha Mussot, Antoine Roux, Laurent Sebbag, Yannick Le Meur, Christophe Masset, Nassim Kamar, Hélène Francois, Eric Rondeau, Nicolas Bouvier, Christiane Mousson, Matthias Buchler, Philippe Gatault, Jean-François Augusto, Agnès Duveau, Cécile Vigneau, Marie-Christine Morin, Jonathan Chemouny, Leonard Golbin, Philippe Grimbert, Marie Matignon, Antoine Durrbach, Clarisse Greze, Renaud Snanoudj, Charlotte Colosio, Betoul Schvartz, Paolo Malvezzi, Christophe Mariat, Antoine Thierry, Moglie Le Quintrec, Antoine Sicard, Jean Philippe Rerolle, Anne-Élisabeth Heng, Cyril Garrouste, Henri Vacher Coponat, Éric Epailly, Olivier Brugiere, Sébastien Dharancy, Éphrem Salame, Faouzi Saliba, Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Cellules B normales et pathogéniques - Normal and pathogenic B cell responses (NOPAB), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Agence de la biomédecine [Saint-Denis la Plaine], Service Néphrologie et transplantation rénale Adultes [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), Service de Néphrologie-transplantation-dialyse [Bordeaux], CHU Bordeaux [Bordeaux], Centre hospitalier universitaire de Nantes (CHU Nantes), Centre de Recherche en Transplantation et Immunologie (U1064 Inserm - CRTI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHRU Brest - Service de Nephrologie (CHU - BREST - Nephrologie), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Service de néphrologie et hémodialyse [CHU de Strasbourg], CHU Strasbourg, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Lille, French nationwide Registry of Solid Organ Transplant Recipients with COVID-19: Olivier Thaunat, Emmanuel Morelon, Charlene Levi, Fanny Buron, Alice Koenig, Thomas Barba, Sophie Caillard, Bruno Moulin, Samira Fafi-Kremer, Marc Hazzan, Anglicheau Dany, Alexandre Hertig, Jérôme Tourret, Benoit Barrou, Lionel Couzi, Pierre Merville, Anna Kaminski, Valérie Moal, Tristan Legris, Pierre-François Westeel, Maïté Jaureguy, Luc Frimat, Didier Ducloux, Jamal Bamoulid, Dominique Bertrand, Michel Tsimaratos, Florentine Garaix-Gilardo, Jérôme Dumortier, Sacha Mussot, Antoine Roux, Laurent Sebbag, Yannick Le Meur, Gilles Blancho, Christophe Masset, Nassim Kamar, Hélène Francois, Eric Rondeau, Nicolas Bouvier, Christiane Mousson, Matthias Buchler, Philippe Gatault, Jean-François Augusto, Agnès Duveau, Cécile Vigneau, Marie-Christine Morin, Jonathan Chemouny, Leonard Golbin, Philippe Grimbert, Marie Matignon, Antoine Durrbach, Clarisse Greze, Renaud Snanoudj, Charlotte Colosio, Betoul Schvartz, Paolo Malvezzi, Christophe Mariat, Antoine Thierry, Moglie Le Quintrec, Antoine Sicard, Jean Philippe Rerolle, Anne-Élisabeth Heng, Cyril Garrouste, Henri Vacher Coponat, Éric Epailly, Olivier Brugiere, Sébastien Dharancy, Éphrem Salame, Faouzi Saliba, CCSD, Accord Elsevier, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, 0301 basic medicine, Pediatrics, MESH: Registries, Registry study, 030232 urology & nephrology, Kidney transplant, [SDV.MHEP.UN]Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, MESH: Kidney Transplantation, Postoperative Complications, 0302 clinical medicine, MESH: Aged, 80 and over, MESH: Postoperative Complications, Pandemic, MESH: COVID-19, Registries, Wasting, Kidney transplantation, Aged, 80 and over, MESH: Aged, MESH: Middle Aged, Middle Aged, renal transplantation, 3. Good health, MESH: Waiting Lists, Nephrology, Female, France, medicine.symptom, Adult, medicine.medical_specialty, Waiting Lists, Coronavirus disease 2019 (COVID-19), 03 medical and health sciences, Intensive care, medicine, Humans, ESRD, Epidemics, MESH: Epidemics, Aged, Retrospective Studies, MESH: Humans, business.industry, SARS-CoV-2, COVID-19, Retrospective cohort study, MESH: Adult, MESH: Retrospective Studies, medicine.disease, Kidney Transplantation, [SDV.MHEP.UN] Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, mortality, MESH: Male, MESH: France, 030104 developmental biology, business, MESH: Female
Abstract: International audience; End stage kidney disease increase the risk of COVID-19 related death but how the kidney replacement strategy should be adapted during the pandemic is unknown. Chronic hemodialysis makes social distancing difficult to achieve. Alternatively, kidney transplantation could increase the severity of COVID-19 due to therapeutic immunosuppression and contribute to saturation of intensive care units. For these reasons, kidney transplantation was suspended in France during the first epidemic wave. Here, we retrospectively evaluated this strategy by comparing the overall and COVID-19 related mortality in kidney transplant recipients and candidates over the last three years. Cross-interrogation of two national registries for the period 1 March and 1 June 2020, identified 275 deaths among the 42812 kidney transplant recipients and 144 deaths among the 16210 candidates. This represents an excess of deaths for both populations, as compared with the same period the two previous years (mean of two previous years: 253 in recipients and 112 in candidates). This difference was integrally explained by COVID-19, which accounted for 44% (122) and 42% (60) of the deaths in recipients and candidates, respectively. Taking into account the size of the two populations and the geographical heterogeneity of virus circulation, we found that the excess of risk of death due to COVID-19 was similar for recipients and candidates in high viral risk area but four-fold higher for candidates in the low viral risk area. Thus, in case of a second epidemic wave, kidney transplantation should be suspended in high viral risk areas but maintained outside those areas, both to reduce the excess of deaths of candidates and avoid wasting precious resources.
Published: 2020

15. Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014

Author: Bernard Cazelles, Anavaj Sakuntabhai, Carlos J. Dommar, Henrik Salje, Xavier Rodó, Richard Paul, Maite Aubry, Van-Mai Cao-Lormeau, Yoann Teissier, Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), UFR Sciences Fondamentales et Biomédicales [Sciences] - Université Paris Cité, Université Paris Cité (UPCité), Génétique fonctionnelle des maladies infectieuses - Functional Genetics of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), ICREA Infection Biology Laboratory (Department of Experimental and Health Sciences), Universitat Pompeu Fabra [Barcelona] (UPF), Instituto de Salud Global - Institute For Global Health [Barcelona] (ISGlobal), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Sorbonne Université (SU)-Institut de Recherche pour le Développement (IRD [France-Nord]), Interdisciplinary and Global Environmental Studies (iGLOBES), University of Arizona-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The research leading to these results has received funding from the European Commission Seventh Framework Program [FP7/2007-2013] for the DENFREE project under Grant Agreement n ̊ 282378.Délégation à la Recherche de la Polynésie française, European Project: 282378,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,DENFREE(2012), Université de Paris - UFR Sciences Fondamentales et Biomédicales [Sciences], Université de Paris (UP), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Nord])-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Sorbonne Université (SU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - 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), Paul, Richard [0000-0002-0665-5089], and Apollo - University of Cambridge Repository
Subjects: Male, Serotype, Topography, Epidemiology, RC955-962, French Polynesia, Social Sciences, Dengue virus, Pathology and Laboratory Medicine, MESH: Dengue Virus, Geographical locations, 0302 clinical medicine, Arctic medicine. Tropical medicine, MESH: Child, MESH: Incidence, Child, Islands, Aged, 80 and over, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Middle Aged, Geography, Incidence, Eukaryota, Spatial epidemiology, MESH: Polynesia, Island hopping, MESH: Infant, Viral Persistence and Latency, 3. Good health, Medical Microbiology, MESH: Young Adult, Viral Pathogens, Child, Preschool, Public aspects of medicine, Zoology, MESH: Disease Transmission, Infectious, Human Geography, Serogroup, Microbiology, 03 medical and health sciences, Disease Transmission, Infectious, Humans, Epidemics, Microbial Pathogens, Aged, MESH: Adolescent, MESH: Humans, Flaviviruses, MESH: Child, Preschool, Organisms, Public Health, Environmental and Occupational Health, Infant, MESH: Adult, Dengue Virus, medicine.disease, Invertebrates, Insect Vectors, Species Interactions, 030104 developmental biology, Period (geology), Human Mobility, People and places, MESH: Female, RNA viruses, 0301 basic medicine, Spatial Epidemiology, MESH: Dengue, Disease Vectors, medicine.disease_cause, Mosquitoes, Dengue fever, Dengue, MESH: Aged, 80 and over, Medicine and Health Sciences, MESH: Aged, Population size, Incidence (epidemiology), MESH: Infant, Newborn, Middle Aged, Insects, Air Travel, Infectious Diseases, Viruses, Female, Pathogens, RA1-1270, Research Article, Adult, Arthropoda, Adolescent, Oceania, 030231 tropical medicine, Polynesia, Young Adult, Virology, medicine, Animals, MESH: Epidemics, Landforms, Biology and life sciences, Infant, Newborn, Geomorphology, MESH: Serogroup, MESH: Male, Earth Sciences, Viral Transmission and Infection
Abstract: Understanding the transition of epidemic to endemic dengue transmission remains a challenge in regions where serotypes co-circulate and there is extensive human mobility. French Polynesia, an isolated group of 117 islands of which 72 are inhabited, distributed among five geographically separated subdivisions, has recorded mono-serotype epidemics since 1944, with long inter-epidemic periods of circulation. Laboratory confirmed cases have been recorded since 1978, enabling exploration of dengue epidemiology under monotypic conditions in an isolated, spatially structured geographical location. A database was constructed of confirmed dengue cases, geolocated to island for a 35-year period. Statistical analyses of viral establishment, persistence and fade-out as well as synchrony among subdivisions were performed. Seven monotypic and one heterotypic dengue epidemic occurred, followed by low-level viral circulation with a recrudescent epidemic occurring on one occasion. Incidence was asynchronous among the subdivisions. Complete viral die-out occurred on several occasions with invasion of a new serotype. Competitive serotype replacement has been observed previously and seems to be characteristic of the South Pacific. Island population size had a strong impact on the establishment, persistence and fade-out of dengue cases and endemicity was estimated achievable only at a population size in excess of 175 000. Despite island remoteness and low population size, dengue cases were observed somewhere in French Polynesia almost constantly, in part due to the spatial structuration generating asynchrony among subdivisions. Long-term persistence of dengue virus in this group of island populations may be enabled by island hopping, although could equally be explained by a reservoir of sub-clinical infections on the most populated island, Tahiti., Author summary Dengue virus is the most significant arthropod-borne virus infecting man. Understanding how long dengue virus can persist in populations of varying size is key to understanding its epidemiology. This is, however, impossible to achieve in settings where dengue is endemic, because of continued human movement and is further complexified by the occurrence of several co-circulating serotypes. By contrast, French Polynesia, an isolated group of 72 inhabited islands in the South Pacific, has had intermittent majoritarily monotypic dengue epidemics since the 1940s and offers a unique opportunity to address questions of viral persistence, turnover and the importance of spatial sub-structure in determining dengue epidemiology. Collating and analyzing a database of laboratory-confirmed dengue cases from across French Polynesia over a 35 year period we were able to show that dengue virus die-out can occur with or without replacement by a new serotype, monotypic transmission of dengue viruses fails to be maintained within small island populations but can persist for years among isolated islands connected via air and sea links. This remarkable long-term persistence of dengue virus in French Polynesia could be maintained by asynchronous viral transmission among connected islands and/or by repeated seeding from a reservoir of sub-clinical infections in the most populated island, Tahiti.
Published: 2020

16. Systematic selection between age and household structure for models aimed at emerging epidemic predictions

Author: Lorenzo Pellis, Christophe Fraser, Neil M. Ferguson, Simon Cauchemez, University of Manchester [Manchester], University of Warwick [Coventry], Imperial College London, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, We acknowledge the MRC Methodology Grant G0800596. L.P. acknowledges the EPSRC (grant EP/J002437/1) and the Wellcome Trust and Royal Society (grant 202562/Z/16/Z), S.C. acknowledges funding from the NIGMS MIDAS initiative, the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant number ANR-10-LABX-62-IBEID), the AXA Research Fund and Grand Prix Robert Debré, and N.M.F. acknowledges Centre funding from the MRC and DFID, Health Protection Research Unit funding from NIHR, Institute funding from Community Jameel and grant funding from the Bill and Melinda Gates Foundation., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and University of Oxford [Oxford]
Subjects: 0301 basic medicine, Population dynamics, Computer science, Epidemics/statistics & numerical data, Science, Psychological intervention, General Physics and Astronomy, Communicable Diseases, Emerging/epidemiology, Communicable Diseases, Emerging, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Econometrics, MESH: Family Characteristics, Humans, MESH: Communicable Diseases, Emerging, 030212 general & internal medicine, Transmission risks and rates, Model choice, lcsh:Science, Epidemics, Selection (genetic algorithm), MESH: Epidemics, Structure (mathematical logic), MESH: Age Factors, Family Characteristics, Multidisciplinary, Models, Statistical, MESH: Humans, Model selection, Computational science, Age Factors, General Chemistry, Applied mathematics, Rule of thumb, 030104 developmental biology, Age stratification, Infectious diseases, lcsh:Q, MESH: Models, Statistical
Abstract: Numerous epidemic models have been developed to capture aspects of human contact patterns, making model selection challenging when they fit (often-scarce) early epidemic data equally well but differ in predictions. Here we consider the invasion of a novel directly transmissible infection and perform an extensive, systematic and transparent comparison of models with explicit age and/or household structure, to determine the accuracy loss in predictions in the absence of interventions when ignoring either or both social components. We conclude that, with heterogeneous and assortative contact patterns relevant to respiratory infections, the model’s age stratification is crucial for accurate predictions. Conversely, the household structure is only needed if transmission is highly concentrated in households, as suggested by an empirical but robust rule of thumb based on household secondary attack rate. This work serves as a template to guide the simplicity/accuracy trade-off in designing models aimed at initial, rapid assessment of potential epidemic severity., Models of emerging epidemics can be exceedingly helpful in planning the response, but early on model selection is a difficult task. Here, the authors explore the joint contribution of age stratification and household structure on epidemic spread, and provides a rule of thumb to guide model choice.
Published: 2020

17. Molecular characterization of measles virus strains circulating in Cameroon during the 2013-2016 epidemics

Author: Valérie Caro, Diane Ouapi, Frédy Brice Simo Nemg, Maurice Demanou, Franck-Martin Obam Mekanda, Gilde Martial Yonga, Véronique Penlap Beng, Christophe Batéjat, Jean-Claude Manuguerra, Chavely Gwladys Monamele, Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur (RIIP), Université de Yaoundé I, 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), The authors received no specific funding for this work., and Institut Pasteur [Paris] (IP)
Subjects: RNA viruses, Male, Viral Diseases, Genotyping Techniques, Artificial Gene Amplification and Extension, Pathology and Laboratory Medicine, 01 natural sciences, Polymerase Chain Reaction, Geographical Locations, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Reverse Transcriptase Polymerase Chain Reaction, MESH: Child, Genotype, Medicine and Health Sciences, 030212 general & internal medicine, Cameroon, Child, MESH: Phylogeny, Phylogeny, Data Management, Vaccines, Multidisciplinary, Reverse Transcriptase Polymerase Chain Reaction, Phylogenetic Analysis, MESH: Infant, 3. Good health, Phylogenetics, Infectious Diseases, Medical Microbiology, MESH: Young Adult, Viral Pathogens, Child, Preschool, Viruses, MESH: Measles, Medicine, Female, Pathogens, Research Article, medicine.medical_specialty, Computer and Information Sciences, Genotyping, Infectious Disease Control, Adolescent, Science, Measles Virus, Biology, Disease cluster, Research and Analysis Methods, Measles, Microbiology, Measles virus, 03 medical and health sciences, Young Adult, Extraction techniques, Molecular genetics, MESH: Genotyping Techniques, medicine, Humans, Evolutionary Systematics, 0101 mathematics, Molecular Biology Techniques, Epidemics, Microbial Pathogens, Molecular Biology, MESH: Epidemics, Taxonomy, MESH: Adolescent, Evolutionary Biology, MESH: Humans, Biology and life sciences, 010102 general mathematics, MESH: Child, Preschool, Organisms, Outbreak, Infant, Reverse Transcriptase-Polymerase Chain Reaction, MESH: Cameroon, biology.organism_classification, medicine.disease, Virology, RNA extraction, MESH: Male, Paramyxoviruses, People and Places, Africa, MESH: Measles virus, MESH: Female
Abstract: International audience; The first genotyping data on measles virus (MeV) strains in Cameroon dates from 1994, while other studies were realized in 2001 and 2011 with the establishment of MeV virological surveillance. However, the genetic data of MeV strains circulating in Cameroon remains fragmented and concentrated in certain regions, hence the need for an update. The objective of this study was to have recent data on MeV genotypes circulating in Cameroon. Ninety throat swabs collected during recent measles outbreaks were analyzed by MeV genotyping RT-PCR using the nucleoprotein gene N. The resulting sequences were analyzed on the basis of 450 nucleotides with MEGA 7 software. Overall genome analysis was performed on 40/90 sequences. The strains were from all ten regions and all belonged to cluster 1 of genotype B3. The genotype B3 has been circulating in Cameroon for long periods of time; efforts must be made in immunization for its elimination.
Published: 2019

18. Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis

Author: Eduardo Massad, Laura C. Rodrigues, Rosalind M Eggo, John Edmunds, Thomas Jaenisch, Kamran Khan, Moritz U. G. Kraemer, Patrícia Brasil, Annelies Wilder-Smith, Deepit Bhatia, Oliver J. Brady, Adam J. Kucharski, Rachel Lowe, Sebastian Funk, Philippe Mayaud, Simon Cauchemez, Kathleen M. O’Reilly, Laith Yakob, London School of Hygiene and Tropical Medicine (LSHTM), Instituto de Salud Global - Institute For Global Health [Barcelona] (ISGlobal), University of Toronto, St. Michael's Hospital, Harvard Medical School [Boston] (HMS), Boston Children's Hospital, University of Oxford [Oxford], Umeå University, Universität Heidelberg [Heidelberg], Instituto Nacional de Infectologia Evandro Chagas [Rio de Janeiro] (INI), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Fundacao Getulio Vargas [Rio de Janeiro] (FGV), Modélisation mathématique des maladies infectieuses, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was partially supported by the European Union’s Horizon 2020 Research and Innovation Programme under ZIKAlliance Grant Agreement no. 734548 and ZikaPLAN Grant Agreement No 734584. RL was funded by a Royal Society Dorothy Hodgkin Fellowship. AK was funded by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant Number 206250/Z/17/Z). OJB was funded by a Sir Henry Wellcome Fellowship funded by the Wellcome Trust (grant number 206471/Z/17/Z). SC was funded by 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, and the AXA Research Fund. MUGK is supported by The Branco Weiss Fellowship - Society in Science, administered by the ETH Zurich and acknowledges funding from a Training Grant from the National Institute of Child Health and Human Development (T32HD040128) and the National Library of Medicine of the National Institutes of Health (R01LM010812, R01LM011965)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 734548,ZIKAlliance(2016), European Project: 734584,ZikaPLAN, University of Oxford, Universität Heidelberg [Heidelberg] = Heidelberg University, Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, lcsh:Medicine, Infektionsmedicin, MESH: World Health Organization, law.invention, Zika virus, 0302 clinical medicine, 610 Medical sciences Medicine, law, MESH: Animals, MESH: Incidence, [MATH]Mathematics [math], MESH: Models, Theoretical, 0303 health sciences, education.field_of_study, Connectivity, biology, Mathematical modelling, Zika Virus Infection, Incidence, Incidence (epidemiology), Public Health, Global Health, Social Medicine and Epidemiology, General Medicine, Latin America and the Caribbean, 3. Good health, Geography, Transmission (mechanics), Research Article, medicine.medical_specialty, Infectious Medicine, 030231 tropical medicine, Population, Epidemic, MESH: Zika Virus, World Health Organization, Disease cluster, Herd immunity, 03 medical and health sciences, MESH: Zika Virus Infection, medicine, Animals, Humans, Epidemics, education, MESH: Epidemics, 030304 developmental biology, MESH: Latin America, MESH: Humans, business.industry, Public health, lcsh:R, Outbreak, Models, Theoretical, biology.organism_classification, Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi, 030104 developmental biology, Latin America, business, Demography
Abstract: Background Zika virus (ZIKV) emerged in Latin America & the Caribbean (LAC) region in 2013, and has had serious implications for population health in the region. In 2016, the World Health Organization declared the ZIKV outbreak a Public Health Emergency of International Concern following a cluster of associated neurological disorders and neonatal malformations. In 2017, Zika cases declined, but future incidence in LAC remains uncertain due to gaps in our understanding, considerable variation in surveillance and a lack of a comprehensive collation of data from affected countries.Methods Our analysis combines information on confirmed and suspected Zika cases across LAC countries and a spatio-temporal dynamic transmission model for ZIKV infection to determine key transmission parameters and projected incidence in 91 major cities within 35 countries. Seasonality was determined by spatio-temporal estimates of Aedes aegypti vector capacity. We used country and state-level data from 2015 to mid-2017 to infer key model parameters, country-specific disease reporting rates, and the 2018 projected incidence. A 10-fold cross-validation approach was used to validate parameter estimates to out-of-sample epidemic trajectories.Results There was limited transmission in 2015, but in 2016 and 2017 there was sufficient opportunity for wide-spread ZIKV transmission in most cities, resulting in the depletion of susceptible individuals. We predict that the highest number of cases in 2018 within some Brazilian States (Sao Paulo and Rio de Janeiro), Colombia and French Guiana, but the estimated number of cases were no more than a few hundred. Model estimates of the timing of the peak in incidence were correlated (pConclusions The findings suggest that the ZIKV epidemic is by and large over, with incidence projected to be low in most cities in LAC in 2018. Local low levels of transmission are probable but the estimated rate of infection suggests that most cities have a population with high levels of herd immunity.
Published: 2018

19. Spatio-temporal dynamics of dengue in Brazil: seasonal travelling waves and determinants of regional synchrony

Author: Christian Julian Villabona-Arenas, Moritz U. G. Kraemer, Simon Cauchemez, Mikhail Churakov, Henrik Salje, Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Harvard Medical School [Boston] (HMS), Boston Children's Hospital, University of Oxford, MC and SC received financial support from the National Institute of General Medical Sciences MIDAS grant 1U01GM110721-01. SC also acknowledges 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) and the INCEPTION project (PIA/ANR-16-CONV-0005). CJVA was supported by a fellowship from IRD and the Labex EpiGenMed/University of Montpellier, via the National Research Agency, Programme for Future Investment ANR-10-LABX-12-01. MUGK is supported by The Branco Weiss Fellowship - Society in Science, administered by the ETH Zurich and acknowledges funding from a Training Grant from the National Institute of Child Health and Human Development (T32HD040128) and the National Library of Medicine of the National Institutes of Health (R01LM010812, R01LM011965). HS was supported by the European Research Council (804744)., 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-10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010), Limouzin, Cécile, 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, Laboratoires d'excellence - From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow - - EpiGenMed2010 - ANR-10-LABX-0012 - LABX - VALID, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), University of Oxford [Oxford], Churakov, Mikhail [0000-0001-9707-6885], Apollo - University of Cambridge Repository, and Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI)
Subjects: 0301 basic medicine, Viral Diseases, Periodicity, Spatial Epidemiology, Mosquito Control, MESH: Periodicity, Disease occurrence, Epidemiology, RC955-962, Social Sciences, MESH: Dengue, Geographical locations, Dengue Fever, MESH: Linear Models, Dengue fever, Dengue, 0302 clinical medicine, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Arctic medicine. Tropical medicine, Medicine and Health Sciences, Traveling wave, Case Series, Acre, Socioeconomics, MESH: Travel, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], MESH: Mosquito Control, Travel, 0303 health sciences, Geography, Spatial structure, Physics, Spatial epidemiology, 3. Good health, Mosquito control, Infectious Diseases, Research Design, Physical Sciences, Viruses, Seasons, Public aspects of medicine, RA1-1270, Brazil, Research Article, Neglected Tropical Diseases, Clinical Research Design, 030231 tropical medicine, Human Geography, Research and Analysis Methods, 03 medical and health sciences, Spatio-Temporal Analysis, MESH: Spatio-Temporal Analysis, parasitic diseases, medicine, Humans, Epidemics, MESH: Epidemics, 030304 developmental biology, Traveling Waves, MESH: Humans, Organisms, Public Health, Environmental and Occupational Health, Biology and Life Sciences, South America, Seasonality, Tropical Diseases, medicine.disease, 030104 developmental biology, Vector (epidemiology), Earth Sciences, Waves, Linear Models, Spatial ecology, Human Mobility, People and places, MESH: Brazil, MESH: Seasons, Arboviruses
Abstract: Dengue continues to be the most important vector-borne viral disease globally and in Brazil, where more than 1.4 million cases and over 500 deaths were reported in 2016. Mosquito control programmes and other interventions have not stopped the alarming trend of increasingly large epidemics in the past few years. Here, we analyzed monthly dengue cases reported in Brazil between 2001 and 2016 to better characterise the key drivers of dengue epidemics. Spatio-temporal analysis revealed recurring travelling waves of disease occurrence. Using wavelet methods, we characterised the average seasonal pattern of dengue in Brazil, which starts in the western states of Acre and Rondônia, then travels eastward to the coast before reaching the northeast of the country. Only two states in the north of Brazil (Roraima and Amapá) did not follow the countrywide pattern and had inconsistent timing of dengue epidemics throughout the study period. We also explored epidemic synchrony and timing of annual dengue cycles in Brazilian regions. Using gravity style models combined with climate factors, we showed that both human mobility and vector ecology contribute to spatial patterns of dengue occurrence. This study offers a characterization of the spatial dynamics of dengue in Brazil and its drivers, which could inform intervention strategies against dengue and other arboviruses., Author summary In this paper we studied the synchronization of dengue epidemics in Brazilian regions. We found that a typical dengue season in Brazil can be described as a wave travelling from the western part of the country towards the east, with the exception of the two most northern equatorial states that experienced inconsistent seasonality of dengue epidemics. We found that the spatial structure of dengue cases is driven by both climate and human mobility patterns. In particular, precipitation was the most important factor for the seasonality of dengue at finer spatial resolutions. Our findings increase our understanding of large scale dengue patterns and could be used to enhance national control programs against dengue and other arboviruses.
Published: 2018

20. Maternal-fetal transmission and adverse perinatal outcomes in pregnant women infected with Zika virus: prospective cohort study in French Guiana

Author: Najeh Hcini, Véronique Lambert, Anne Jolivet, David Baud, C. Pomar, Manon Vouga, Alice Panchaud, Léo Pomar, Guillaume Benoist, Gustavo Malinger, Dominique Rousset, Séverine Matheus, Gabriel Carles, Centre Hospitalier de l'Ouest Guyanais Franck Joly [Saint-Laurent-du-Maroni, Guyane Française], Université de Lausanne (UNIL), Centre Hospitalier de l'Ouest Guyanais, Institut pluridisciplinaire de recherche appliquée dans le domaine du génie pétrolier (IPRADDGP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Tel Aviv University [Tel Aviv], University of Geneva [Switzerland], Gestionnaire, Hal Sorbonne Université, Université de Lausanne = University of Lausanne (UNIL), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre National de Référence pour les Arbovirus - Laboratoire de Virologie [Cayenne, Guyane française] (CNR - laboratoire associé), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Tel Aviv University (TAU), Tel Aviv Sourasky Medical Center [Te Aviv], Université de Genève = University of Geneva (UNIGE), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), We thank all involved personnel at the Centre Hospitalier de l'Ouest Guyannais (CHOG)., and Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: MESH: Pregnancy Complications, Infectious* / epidemiology, MESH: Risk Assessment, MESH: Zika Virus Infection / congenital, Zika virus, 0302 clinical medicine, MESH: Pregnancy, Pregnancy, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, 030212 general & internal medicine, Prospective Studies, Pregnancy Complications, Infectious, Prospective cohort study, ComputingMilieux_MISCELLANEOUS, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 030219 obstetrics & reproductive medicine, biology, Obstetrics, Zika Virus Infection, MESH: Infant, Newborn, MESH: Infectious Disease Transmission, Vertical, Pregnancy Outcome, General Medicine, MESH: Zika Virus Infection / transmission, 3. Good health, French Guiana, MESH: Young Adult, Cohort, [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, medicine.symptom, Cohort study, Adult, medicine.medical_specialty, Population, Prenatal diagnosis, [SDV.MHEP.GEO]Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, Asymptomatic, Risk Assessment, 03 medical and health sciences, Young Adult, MESH: French Guiana, medicine, Humans, education, Epidemics, MESH: Epidemics, MESH: Humans, business.industry, Research, Infant, Newborn, MESH: Adult, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, medicine.disease, MESH: Pregnancy Outcome, MESH: Prospective Studies, Infectious Disease Transmission, Vertical, [SDV.MHEP.GEO] Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Zika Virus Infection / epidemiology, MESH: Female
Abstract: ObjectivesTo estimate the rates of maternal-fetal transmission of Zika virus, adverse fetal/neonatal outcomes, and subsequent rates of asymptomatic/symptomatic congenital Zika virus infections up to the first week of life.DesignCohort study with prospective data collection and subsequent review of fetal/neonatal outcomes.SettingsReferral centre for prenatal diagnosis of the French Guiana Western Hospital.ParticipantsPregnant women at any stage of pregnancy with a laboratory confirmed symptomatic or asymptomatic Zika virus infection during the epidemic period in western French Guiana. The cohort enrolled 300 participants and prospectively followed their 305 fetuses/newborns.Main outcome measuresRate of maternal-fetal transmission of Zika virus (amniotic fluid, fetal and neonatal blood, urine, cerebrospinal fluid, and placentas); clinical, biological, and radiological outcomes (blindly reviewed); and adverse outcomes defined as moderate signs potentially related to congenital Zika syndrome (CZS), severe complications compatible with CZS, or fetal loss. Associations between a laboratory confirmed congenital Zika virus infection and adverse fetal/neonatal outcomes were evaluated.ResultsMaternal-fetal transmission was documented in 26% (76/291) of fetuses/newborns with complete data. Among the Zika virus positive fetuses/newborns, 45% (34/76) presented with no signs/complications at birth, 20% (15/76) with moderate signs potentially related to CZS, 21% (16/76) with severe complications compatible with CZS, and 14% (11/76) with fetal loss. Compared with the Zika virus positive fetuses/neonates, those that were identified as negative for Zika virus (215/291) were less likely to present with severe complications (5%; 10/215) or fetal loss (0.5%; 1/215; relative risk 6.9, 95% confidence interval 3.6 to 13.3). Association between a positive Zika virus test and any adverse fetal/neonatal outcome was also significant (relative risk 4.4, 2.9 to 6.6). The population attributable fraction estimates that a confirmed congenital Zika virus infection contributes to 47% of adverse outcomes and 61% of severe adverse outcomes observed.ConclusionIn cases of a known maternal Zika virus infection, approximately a quarter of fetuses will become congenitally infected, of which a third will have severe complications at birth or fetal loss. The burden of CZS might be lower than initially described in South America and may not differ from other congenital infections.
Published: 2018

21. Mosquitoes as vectors of arboviruses: an endless story

Author: Failloux, Anna-Bella, Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris], Les travaux sur Zika ont reçu un financement de l’Union Européenne (H2020, ZIKAlliance grant agreement no. 734548)., European Project: 734548,ZIKAlliance(2016), and Institut Pasteur [Paris] (IP)
Subjects: global changes, [SDV]Life Sciences [q-bio], changements globaux, Mosquito Vectors, Arbovirus Infections, Disease Vectors, MESH: Disease Vectors, Communicable Diseases, Emerging, émergence, Aedes, vector-borne diseases, MESH: Arboviruses, Animals, Humans, emergence, MESH: Animals, MESH: Communicable Diseases, Emerging, Bites and Stings, Epidemics, MESH: Epidemics, mosquitoes, moustiques, MESH: Humans, MESH: Aedes, MESH: Bites and Stings, Culicidae, arbovirus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, maladies à transmission vectorielle, MESH: Arbovirus Infections, MESH: Mosquito Vectors, MESH: Culicidae, Arboviruses
Abstract: International audience; The recent emergence or re-emergence of vector-borne diseases (VBD) and, more specifically, VBD associated with arboviruses such as dengue, chikungunya, Zika or yellow fever are not new events. The globalization of trade and travels as well as the unplanned urbanization of many tropical and subtropical cities have created the conditions suitable for the establishment of vector mosquitoes offering opportunities for arbovirus introduction. This review describes the major arboviruses important for human health and their epidemic vectors, and the conditions leading to their emergence.; L’émergence ou la ré-émergence récente des maladies à transmission vectorielle et plus précisément, celle associée aux arbovirus tels que la dengue, le chikungunya, le Zika ou encore la fièvre jaune ne sont pas des phénomènes nouveaux. Aujourd’hui, la mondialisation des échanges commerciaux, des déplacements des voyageurs ainsi que l’urbanisation anarchique de nombreuses villes tropicales et subtropicales créent les conditions propices à l’installation durable des moustiques vecteurs et par conséquent, à l’introduction des arbovirus. Cette revue décrit les principaux arbovirus importants en santé humaine et leurs vecteurs épidémiques, ainsi que les conditions facilitant leur émergence.
Published: 2018

22. Performances of statistical methods for the detection of seasonal influenza epidemics using a consensus-based gold standard

Author: Shirley Masse, R Jreich, Y. Le Strat, Cécile Souty, Caroline Guerrisi, Clément Turbelin, Pierre-Yves Boëlle, Camille Pelat, Thomas Hanslik, Thierry Blanchon, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Santé publique France - French National Public Health Agency [Saint-Maurice, France], CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire de Virologie [UNIV Corse-Inserm] (EA7310), Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Hôpital Ambroise Paré [AP-HP]
Subjects: Epidemiology, Computer science, Statistics as Topic, Influenza epidemics, Context (language use), MESH: Algorithms, Large range, 01 natural sciences, surveillance system, MESH: Regression Analysis, Seasonal influenza, 010104 statistics & probability, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Statistics, Influenza, Human, Humans, 030212 general & internal medicine, MESH: Incidence, 0101 mathematics, Epidemics, MESH: Epidemics, MESH: Statistics as Topic, [STAT.AP]Statistics [stat]/Applications [stat.AP], MESH: Humans, Incidence (epidemiology), MESH: Influenza, Human, Incidence, Expert consensus, Gold standard (test), Original Papers, MESH: France, Infectious Diseases, outbreaks, Epidemiological Monitoring, Regression Analysis, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Epidemiological Monitoring, France, Seasons, influenza, MESH: Seasons, Algorithms
Abstract: SUMMARYInfluenza epidemics are monitored using influenza-like illness (ILI) data reported by health-care professionals. Timely detection of the onset of epidemics is often performed by applying a statistical method on weekly ILI incidence estimates with a large range of methods used worldwide. However, performance evaluation and comparison of these algorithms is hindered by: (1) the absence of a gold standard regarding influenza epidemic periods and (2) the absence of consensual evaluation criteria. As of now, performance evaluations metrics are based only on sensitivity, specificity and timeliness of detection, since definitions are not clear for time-repeated measurements such as weekly epidemic detection. We aimed to evaluate several epidemic detection methods by comparing their alerts to a gold standard determined by international expert consensus. We introduced new performance metrics that meet important objective of influenza surveillance in temperate countries: to detect accurately the start of the single epidemic period each year. Evaluations are presented using ILI incidence in France between 1995 and 2011. We found that the two performance metrics defined allowed discrimination between epidemic detection methods. In the context of performance detection evaluation, other metrics used commonly than the standard could better achieve the needs of real-time influenza surveillance.
Published: 2017

23. Seroepidemiological Study of Interepidemic Rift Valley Fever Virus Infection among Persons with Intense Ruminant Exposure in Madagascar and Kenya

Author: Gray, Gregory C., Anderson, Benjamin D., LaBeaud, A. Desirée, Heraud, Jean-Michel, Fèvre, Eric M., Andriamandimby, Soa Fy, Cook, Elizabeth A. J., Dahir, Saidi, De Glanville, William A., Heil, Gary L., Khan, Salah U., Muiruri, Samuel, Olive, Marie-Marie, Thomas, Lian F., Merrill, Hunter R., Merrill, Mary L. M., Richt, Juergen A., Duke University [Durham], Stanford University, Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), University of Liverpool, International Livestock Research Institute [CGIAR, Nairobi] (ILRI), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Ministry of Health, University of Edinburgh, University of Florida [Gainesville] (UF), Animal et gestion intégrée des risques (UPR AGIRs), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Kansas State University
Subjects: Adult, Male, Adolescent, Rift Valley Fever, MESH: Kenya, Enzyme-Linked Immunosorbent Assay, Antibodies, Viral, MESH: Madagascar, Young Adult, MESH: Risk Factors, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Neutralization Tests, Risk Factors, Zoonoses, MESH: Rift Valley Fever, Madagascar, Animals, Humans, MESH: Animals, Epidemics, MESH: Epidemics, MESH: Adolescent, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Middle Aged, MESH: Humans, MESH: Neutralization Tests, MESH: Enzyme-Linked Immunosorbent Assay, MESH: Adult, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Articles, Ruminants, Middle Aged, Rift Valley fever virus, Kenya, MESH: Male, MESH: Immunoglobulin M, Immunoglobulin M, MESH: Ruminants, MESH: Young Adult, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Rift Valley fever virus, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Female, MESH: Zoonoses, MESH: Female, MESH: Antibodies, Viral
Abstract: International audience; In this cross-sectional seroepidemiological study we sought to examine the evidence for circulation of Rift Valley fever virus (RVFV) among herders in Madagascar and Kenya. From July 2010 to June 2012, we enrolled 459 herders and 98 controls (without ruminant exposures) and studied their sera (immunoglobulin G [IgG] and IgM through enzyme-linked immunosorbent assay [ELISA] and plaque reduction neutralization test [PRNT] assays) for evidence of previous RVFV infection. Overall, 59 (12.9%) of 459 herders and 7 (7.1%) of the 98 controls were positive by the IgG ELISA assay. Of the 59 ELISA-positive herders, 23 (38.9%) were confirmed by the PRNT assay (21 from eastern Kenya). Two of the 21 PRNT-positive study subjects also had elevated IgM antibodies against RVFV suggesting recent infection. Multivariate modeling in this study revealed that being seminomadic (odds ratio [OR] = 6.4, 95% confidence interval [CI] = 2.1–15.4) was most strongly associated with antibodies against RVFV. Although we cannot know when these infections occurred, it seems likely that some interepidemic RVFV infections are occurring among herders. As there are disincentives regarding reporting RVFV outbreaks in livestock or wildlife, it may be prudent to conduct periodic , limited, active seroepidemiological surveillance for RVFV infections in herders, especially in eastern Kenya.
Published: 2015

24. Analysing trends and forecasting malaria epidemics in Madagascar using a sentinel surveillance network: a web‑based application

Author: Florian Girond, Vincent Herbreteau, Sixte Zigiumugabe, Fanjasoa Rakotomanana, Judith Hedje, Lea Randriamampionona, Patrice Piola, Laurence Randrianasolo, Télesphore Yao Brou, Morgan Mangeas, Christophe Rogier, Maherisoa Ratsitorahina, Milijaona Randrianarivelojosia, Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Polytechnic of Namibia [Windhoek], Ministère de la Santé Publique [Antananarivo, Madagascar], U.S. President’s Malaria Initiative [Antananarivo] (PMI), U.S. President's Malaria Initiative [Atlanta, GA,], Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), 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, INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Institute for Biomedical Research of the French Armed Forces (IRBA), This research was supported by the USAID (Grant No. AID-687-G-13-00003). We thank administration authorities and health authorities from the Ministry of Health, the National Malaria Control Program and the President’s Malaria Initiative. We especially thank all the sentinel surveillance team of the Institut Pasteur de Madagascar., Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), Ministère de la Santé Publique - Ministry of Public Health [Antananarivo, Madagascar], Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-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), Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Solofoharivelo, Marie Chrystine, and Institut de Recherche Biomédicale des Armées (IRBA)
Subjects: Male, Veterinary medicine, MESH: Text Messaging, Indoor residual spraying, MESH: Madagascar, 0302 clinical medicine, MESH: Aged, 80 and over, MESH: Child, Medicine, Prospective Studies, 030212 general & internal medicine, Child, Aged, 80 and over, MESH: Aged, MESH: Middle Aged, MESH: Infant, Newborn, Middle Aged, MESH: Infant, 3. Good health, Infectious Diseases, MESH: Internet, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Young Adult, Child, Preschool, MESH: Sentinel Surveillance, Female, Adult, MESH: Forecasting, medicine.medical_specialty, Short Message Service, Adolescent, 030231 tropical medicine, MESH: Malaria, Young Adult, 03 medical and health sciences, MESH: Software, parasitic diseases, Madagascar, Humans, Web application, Epidemics, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Epidemics, Aged, Retrospective Studies, MESH: Adolescent, Internet, Text Messaging, MESH: Humans, business.industry, Research, Public health, MESH: Child, Preschool, Infant, Newborn, Infant, Outbreak, MESH: Adult, MESH: Retrospective Studies, medicine.disease, Data science, MESH: Male, MESH: Prospective Studies, Malaria, Mews, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Early warning system, Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Sentinel Surveillance, MESH: Female, Software, Forecasting
Abstract: Background : The use of a malaria early warning system (MEWS) to trigger prompt public health interventions is a key step in adding value to the epidemiological data routinely collected by sentinel surveillance systems. Methods : This study describes a system using various epidemic thresholds and a forecasting component with the support of new technologies to improve the performance of a sentinel MEWS. Malaria-related data from 21 sentinel sites collected by Short Message Service are automatically analysed to detect malaria trends and malaria outbreak alerts with automated feedback reports. Results : Roll Back Malaria partners can, through a user-friendly web-based tool, visualize potential outbreaks and generate a forecasting model. The system already demonstrated its ability to detect malaria outbreaks in Madagascar in 2014. Conclusion : This approach aims to maximize the usefulness of a sentinel surveillance system to predict and detect epidemics in limited-resource environments.
Published: 2017

25. The epidemiological signature of influenza B virus and its B/Victoria and B/Yamagata lineages in the 21st century

Author: John Paget, Olga Bessonova, Joseph S. Bresee, Norosoa Harline Razanajatovo, Saverio Caini, Binay Thapa, Francisco José de Paula Júnior, Jenny Lara Araya, Florette K. Treurnicht, Walquiria Aparecida Ferreira de Almeida, Brechla Moreno Arévalo, Zhibin Peng, Raquel Guiomar, Gabriela Kusznierz, Q. Sue Huang, Herman Kosasih, Antonino Bella, Doménica de Mora, Rakhee Palekar, Olha Holubka, Maria R. Castrucci, Rudevelinda Rivera, Phuong Vu Mai Hoang, Gideon O. Emukule, Rodrigo Fasce, Rocio Higueros, Sandra S. Chaves, Fatima el Falaki, Mai T. Q. Le, Herve A. Kadjo, Patricia Bustos, Luzhao Feng, Ainash Makusheva, Vernon J. Lee, Richard Njouom, Ana Paula Rodrigues, Coulibaly Daouda, Gé Donker, Alfredo Bruno, Alla Mironenko, Cheryl Cohen, Jean-Michel Heraud, Li Wei Ang, Sonam Wangchuk, Mónica Jeannette Barahona de Gámez, Maria Zambon, Clotilde El Guerche-Séblain, Angel Balmaseda, Lynnette Brammer, Amal Barakat, Richard Pebody, Adam Meijer, Verònica Vera Garate, Tim Wood, Netherlands Institute for Health Services Research [Utrecht] (NIVEL), Instituto Nacional de Enfermedades Respiratorias Dr. Emilio Coni [Santa Fe, Argentina] (INER), Ministry of Health [Bhoutan], Ministry of Health [Brasília, Brazil], Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur (RIIP), Instituto de Salud Pública de Chile (ISP), Chinese Center for Disease Control and Prevention, Ministry of Health [Costa Rica], Instituto Nacional de Investigación en Salud Pública [Guayaquil, Ecuador] (INSPI), Ministerio de Salud de El Salvador (MINSAL), Public Health England [London], Ministerio de Salud Publica y Asistencia Social [Guatemala] (MSPAS), Ministry of Health [Honduras] (SESAL), US Naval Medical Research Unit No.2 [Jakarta, Indonesia] (NAMRU-2), Naval Medical Research Center [Silver Spring, USA] (NMRC), Istituto Superiore di Sanita [Rome], Institut Pasteur de Côte d'Ivoire, Institut National de Santé Publique d'Abidjan-INSP, Ministry of Healthcare [Kazakhstan], Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Centers for Disease Control and Prevention [Kenya], Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut National d'Hygiène [Maroc], National Institute for Public Health and the Environment [Bilthoven] (RIVM), Institute of Environmental Science and Research (ESR), Ministry of Health [Nicaragua] (MINSA), Pan American Health Organization [Washington] (PAHO), Instituto Conmemorativo Gorgas de Estudios de la Salud [Panamá], Instituto Nacional de Saùde Dr Ricardo Jorge [Portugal] (INSA), Ministry of Health [Singapore], National Institute for Communicable Diseases [Johannesburg] (NICD), University of the Witwatersrand [Johannesburg] (WITS), National Academy of Sciences of Ukraine (NASU), National Institute of Hygiene and Epidemiology [Hanoi, Vietnam] (NIHE), Sanofi Pasteur [Lyon, France], The study is supported by a research grant from Sanofi Pasteur: the ‘Global Epidemiology of Influenza B’ research project. The funder provided support in the form of salaries for two authors (CEGS and JP) but did not have any additional role in the data collection, analysis, decision to publish, or preparation of the manuscript., The 'Global Influenza B Study team' (group authorship) includes the following scientists: Juan Manuel Rudi (jmrudi@anlis.gov.ar), National Institute of Respiratory Diseases 'Emilio Coni', Santa Fe, Argentina, Dorji Wangchuk (dorjiwangchuk@health.gov.bt) and Sangay Zangmo (szangmo@health.gov.bt), Royal Centre for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan, Daiana Araujo da Silva (daiana.silva@saude.gov.br), Ministry of Health, Department of Surveillance of Transmissible Diseases, Brasília/DF, Brazil, Winston Andrade (wandrade@ispch.cl), Sub-Department of Viral Diseases, Instituto de Salud Pública de Chile, Santiago, Chile, Jiandong Zheng (zhengjd@chinacdc.cn) and Ying Qin (qinying@chinacdc.cn), Division of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, P.R. China, Joanna Ellis (joanna.ellis@phe.gov.uk), Public Health England, London, United Kingdom, Simona Puzelli (simona.puzelli@iss.it), National Influenza Center, Department of Infectious Diseases, National Institute of Health, Rome, Italy, Caterina Rizzo (rizzocaterina@gmail.com), Bambino Gesù Children's Hospital, Rome, Italy, Linus Ndegwa (ikf7@cdc.gov), Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya, Marit MA de Lange (marit.de.lange@rivm.nl) and Anne C. Teirlinck (anne.teirlinck@rivm.nl), National Institute for Public Health and the Environment, Centre for Infectious Diseases, Epidemiology and Surveillance, Bilthoven, The Netherlands, Jeffery Cutter (jeffery_cutter@moh.gov.sg) and Raymond Tzer Pin Lin (raymond_lin@moh.gov.sg), Public Health Group, Ministry of Health, Singapore, Singapore, Than T. Le (lmot82@yahoo.com), National Institute of Hygiene and Epidemiology, Hanoi, Vietnam, and Peter Kinuthia 42 (polorien@gmail.com), IHRC Inc., Atlanta, USA.
Subjects: RNA viruses, Male, Infecções Respiratórias, 0301 basic medicine, Viral Diseases, medicine.disease_cause, MESH: Influenza Vaccines, Seasonal influenza, Influenza A Virus, H1N1 Subtype, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Epidemiology, Medicine and Health Sciences, Influenza A virus, 030212 general & internal medicine, MESH: Influenza B virus, Pathology and laboratory medicine, Northern Hemisphere, Vaccines, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, Geography, MESH: Influenza, Human, virus diseases, Medical microbiology, 3. Good health, Infectious Diseases, Influenza Vaccines, Population Surveillance, Viruses, Epidemiological Monitoring, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Medicine, Southern Hemisphere, Female, Age distribution, Seasons, Pathogens, MESH: History, 21st Century, Research Article, medicine.medical_specialty, Infectious Disease Control, Science, MESH: Influenza A virus, Biology, Microbiology, History, 21st Century, Virus, MESH: Population Surveillance, MESH: Influenza A Virus, H1N1 Subtype, 03 medical and health sciences, Age Distribution, Population Metrics, Influenza, Human, medicine, Influenza viruses, Humans, Epidemics, MESH: Epidemics, Disease burden, MESH: Humans, Biology and life sciences, Population Biology, Organisms, Viral pathogens, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Estados de Saúde e de Doença, Virology, Influenza, MESH: Male, Microbial pathogens, Earth sciences, Influenza B virus, Vaccine mismatch, 030104 developmental biology, Virus type, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Epidemiological Monitoring, Geographic areas, MESH: Seasons, MESH: Female, Orthomyxoviruses
Abstract: Free PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31513690/ We describe the epidemiological characteristics, pattern of circulation, and geographical distribution of influenza B viruses and its lineages using data from the Global Influenza B Study. We included over 1.8 million influenza cases occurred in thirty-one countries during 2000-2018. We calculated the proportion of cases caused by influenza B and its lineages; determined the timing of influenza A and B epidemics; compared the age distribution of B/Victoria and B/Yamagata cases; and evaluated the frequency of lineage-level mismatch for the trivalent vaccine. The median proportion of influenza cases caused by influenza B virus was 23.4%, with a tendency (borderline statistical significance, p = 0.060) to be higher in tropical vs. temperate countries. Influenza B was the dominant virus type in about one every seven seasons. In temperate countries, influenza B epidemics occurred on average three weeks later than influenza A epidemics; no consistent pattern emerged in the tropics. The two B lineages caused a comparable proportion of influenza B cases globally, however the B/Yamagata was more frequent in temperate countries, and the B/Victoria in the tropics (p = 0.048). B/Yamagata patients were significantly older than B/Victoria patients in almost all countries. A lineage-level vaccine mismatch was observed in over 40% of seasons in temperate countries and in 30% of seasons in the tropics. The type B virus caused a substantial proportion of influenza infections globally in the 21st century, and its two virus lineages differed in terms of age and geographical distribution of patients. These findings will help inform health policy decisions aiming to reduce disease burden associated with seasonal influenza. info:eu-repo/semantics/publishedVersion
Published: 2019

26. 'Epidemic Clones' of Listeria monocytogenes Are Widespread and Ancient Clonal Groups

Author: Lise Frézal, Thierry Wirth, Laure Diancourt, Viviane Chenal-Francisque, Alexandre Leclercq, Marc Lecuit, Sylvain Brisse, Thomas Cantinelli, Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Biologie des Infections - Biology of Infection, Génotypage des Pathogènes et Santé Publique (Plate-forme) (PF8), Institut Pasteur [Paris], Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, 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), 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 pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service des Maladies infectieuses et tropicales [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Institut Pasteur [Paris] (IP), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), DIAKITE, andrée, and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: Microbiology (medical), Genotype, [SDV]Life Sciences [q-bio], Biology, MESH: Listeria monocytogenes, MESH: Genotype, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylogenetics, Genetic variation, Pulsed-field gel electrophoresis, Cluster Analysis, Humans, MESH: Molecular Epidemiology, Listeriosis, MESH: Genetic Variation, Typing, Epidemics, MESH: Phylogeny, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Phylogeny, MESH: Epidemics, 030304 developmental biology, Genetics, Molecular Epidemiology, 0303 health sciences, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, MESH: Humans, Molecular epidemiology, Phylogenetic tree, 030306 microbiology, Genetic heterogeneity, Genetic Variation, Bacteriology, Listeria monocytogenes, MESH: Cluster Analysis, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Electrophoresis, Gel, Pulsed-Field, [SDV] Life Sciences [q-bio], MESH: Electrophoresis, Gel, Pulsed-Field, MESH: Multilocus Sequence Typing, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Listeriosis, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Multilocus sequence typing, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Multilocus Sequence Typing
Abstract: The food-borne pathogen Listeria monocytogenes is genetically heterogeneous. Although some clonal groups have been implicated in multiple outbreaks, there is currently no consensus on how “epidemic clones” should be defined. The objectives of this work were to compare the patterns of sequence diversity on two sets of genes that have been widely used to define L. monocytogenes clonal groups: multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MvLST). Further, we evaluated the diversity within clonal groups by pulsed-field gel electrophoresis (PFGE). Based on 125 isolates of diverse temporal, geographical, and source origins, MLST and MvLST genes (i) had similar patterns of sequence polymorphisms, recombination, and selection, (ii) provided concordant phylogenetic clustering, and (iii) had similar discriminatory power, which was not improved when we combined both data sets. Inclusion of representative strains of previous outbreaks demonstrated the correspondence of epidemic clones with previously recognized MLST clonal complexes. PFGE analysis demonstrated heterogeneity within major clones, most of which were isolated decades before their involvement in outbreaks. We conclude that the “epidemic clone” denominations represent a redundant but largely incomplete nomenclature system for MLST-defined clones, which must be regarded as successful genetic groups that are widely distributed across time and space.
Published: 2013

27. What is AIDS in Guadeloupe? A descriptive and comparative study

Author: Narcisse Elenga, I Lamaury, Mathieu Nacher, Gilles Beaucaire, Thierry Messiaen, Marie-Thérèse Georger-Sow, Isabelle Favre, Service de Pédiatrie, Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Coordination Régionale de la lutte contre le Virus de L'Immunodéficience Humaine [Pointe-à-Pitre] (COREVIH), CHU Pointe-à-Pitre/Abymes [Guadeloupe], Service des maladies infectieuses, Centre d'investigation clinique Antilles-Guyane (CIC - Antilles Guyane), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU de la Martinique [Fort de France]-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Coordination Régionale de la lutte contre le Virus de L'Immunodéficience Humaine [Cayenne] (COREVIH), and ADENIS, ANTOINE
Subjects: Male, MESH: Sexual Behavior, Pediatrics, Urban Population, MESH: Aged, 80 and over, MESH: Cross-Cultural Comparison, Hiv infected patients, Pharmacology (medical), Guadeloupe, Aged, 80 and over, MESH: Aged, MESH: Middle Aged, MESH: AIDS-Related Opportunistic Infections, Middle Aged, French Guiana, AIDS, MESH: Urban Population, Infectious Diseases, Sexual behavior, MESH: Young Adult, Population Surveillance, Female, France, HIV-infected patients, Adult, Cross-Cultural Comparison, medicine.medical_specialty, Mandatory reporting, Adolescent, Sexual Behavior, Ecology (disciplines), Dermatology, MESH: Population Surveillance, Young Adult, Acquired immunodeficiency syndrome (AIDS), MESH: French Guiana, medicine, Humans, MESH: Guadeloupe, Epidemics, MESH: Epidemics, Aged, Retrospective Studies, MESH: Acquired Immunodeficiency Syndrome, MESH: Adolescent, Acquired Immunodeficiency Syndrome, MESH: Humans, AIDS-Related Opportunistic Infections, business.industry, Public Health, Environmental and Occupational Health, MESH: Retrospective Studies, MESH: Adult, Retrospective cohort study, Mandatory Reporting, medicine.disease, Cross-cultural studies, MESH: Male, MESH: France, Metropolitan France, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Mandatory Reporting, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, MESH: Female, Demography
Abstract: International audience; Since the pathogen ecology differs between Caribbean regions, specific differences in the most frequent clinical presentations of acquired immunodeficiency syndrome (AIDS) may be expected. We therefore conducted the present retrospective cohort study in order to describe the main AIDS-defining events in Guadeloupe and to compare them with those observed in Metropolitan France and in French Guiana. We discuss the local pathogen ecology, the diagnostic limitations of hospitals in overseas territories and the drivers of the epidemic.
Published: 2013

28. Whole-Genome Characterization of Epidemic Neisseria meningitidis Serogroup C and Resurgence of Serogroup W, Niger, 2015

Author: Cecilia B, Kretz, Adam C, Retchless, Fati, Sidikou, Bassira, Issaka, Sani, Ousmane, Stephanie, Schwartz, Ashley H, Tate, Assimawè, Pana, Berthe-Marie, Njanpop-Lafourcade, Innocent, Nzeyimana, Ricardo Obama, Nse, Ala-Eddine, Deghmane, Eva, Hong, Ola Brønstad, Brynildsrud, Ryan T, Novak, Sarah A, Meyer, Odile Ouwe Missi, Oukem-Boyer, Olivier, Ronveaux, Dominique A, Caugant, Muhamed-Kheir, Taha, Xin, Wang, Goumbi, Kadade, Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), World Health Organization [Niamey], Agence de Médecine Préventive, Institut Pasteur [Paris] (IP), Norwegian Institute of Public Health [Oslo] (NIPH), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), This work was funded by CDC., Members of the Niger Response Team who contributed to this study: Jennifer D. Thomas, Fang Hu, Brian H. Harcourt, Melissa J. Whaley, How-Yi Chang, Laurel Thompson Jenkins, Susanna E. Schmink (CDC), Didier Mounkoro, Oubote Abodji (Agence de Médecine Préventive), Jibir Zanguina, Aichatou Moussa, Mariama Sambo (CERMES), and Maman Zaneidou and Goumbi Kadade (Direction de la Surveillance et de la Riposte aux Epidémies)., and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, MESH: Neisseria meningitidis, Serogroup C/genetics, MESH: Meningitis, Meningococcal/microbiology, MESH: Sequence Analysis, DNA, Epidemiology, MESH: Neisseria meningitidis, Serogroup C/isolation & purification, lcsh:Medicine, MESH: Antigens, Bacterial/genetics, Neisseria meningitidis, Serogroup C, Neisseria meningitidis, Meningococcal meningitis, MESH: Genome, Bacterial, Genome, Communicable Diseases, Emerging, meningitis belt, MESH: Drug Resistance, Bacterial/genetics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Communicable Diseases, Emerging, Niger, MESH: Genetic Variation, bacteria, MESH: Phylogeny, Phylogeny, Phylogenetic tree, MESH: Molecular Typing, Epidemic season, Neisseria meningitidis serogroup C, 3. Good health, Infectious Diseases, whole-genome sequencing, MESH: Neisseria meningitidis/genetics, Microbiology (medical), DNA, Bacterial, Whole-Genome Characterization of Epidemic Neisseria meningitidis Serogroup C and Resurging Serogroup W, Niger, 2015, MESH: Meningitis, Meningococcal/epidemiology, Biology, Meningitis, Meningococcal, lcsh:Infectious and parasitic diseases, Microbiology, 03 medical and health sciences, Genetic Evolution, Drug Resistance, Bacterial, parasitic diseases, Humans, lcsh:RC109-216, Serotyping, Epidemics, MESH: Epidemics, Antigens, Bacterial, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, Research, lcsh:R, MESH: Niger/epidemiology, Outbreak, Genetic Variation, MESH: Serotyping, Sequence Analysis, DNA, Virology, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Typing, 030104 developmental biology, MESH: Neisseria meningitidis/isolation & purification, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Genome, Bacterial
Abstract: International audience; In 2015, Niger reported the largest epidemic of Neisseria meningitidis serogroup C (NmC) meningitis in sub-Saharan Africa. The NmC epidemic coincided with serogroup W (NmW) cases during the epidemic season, resulting in a total of 9,367 meningococcal cases through June 2015. To clarify the phylogenetic association, genetic evolution, and antibiotic determinants of the meningococcal strains in Niger, we sequenced the genomes of 102 isolates from this epidemic, comprising 81 NmC and 21 NmW isolates. The genomes of 82 isolates were completed, and all 102 were included in the analysis. All NmC isolates had sequence type 10217, which caused the outbreaks in Nigeria during 2013-2014 and for which a clonal complex has not yet been defined. The NmC isolates from Niger were substantially different from other NmC isolates collected globally. All NmW isolates belonged to clonal complex 11 and were closely related to the isolates causing recent outbreaks in Africa.
Published: 2016

29. A Seroepidemiological Study of Serogroup A Meningococcal Infection in the African Meningitis Belt

Author: Manigart, Olivier, Trotter, Caroline, Findlow, Helen, Assefa, Abraham, Mihret, Wude, Moti Demisse, Tesfaye, Yeshitela, Biruk, Osei, Isaac, Hodgson, Abraham, Quaye, Stephen Laryea, Sow, Samba, Coulibaly, Mamadou, Diallo, Kanny, Traore, Awa, Collard, Jean-Marc, Moustapha Boukary, Rahamatou, Djermakoye, Oumarou, Mahamane, Ali Elhaji, Jusot, Jean-François, Sokhna, Cheikh, Alavo, Serge, Doucoure, Souleymane, Ba, El Hadj, Dieng, Mariétou, Diallo, Aldiouma, Daugla, Doumagoum Moto, Omotara, Babatunji, Chandramohan, Daniel, Hassan-King, Musa, Nascimento, Maria, Woukeu, Arouna, Borrow, Ray, Stuart, James M, Greenwood, Brian, London School of Hygiene and Tropical Medicine (LSHTM), Medical Research Council Unit The Gambia (MRC), University of Cambridge [UK] (CAM), Public Health England North West [Manchester] (PHE), Public Health England [London], Armauer Hansen Research Institute (AHRI), Navrongo Health Research Centre [Navrongo, Ghana] (NHRC), Centre pour les Vaccins en Développement [Bamako] (CVD), Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), Institut de recherche pour le développement (IRD [Sénégal]), Centre de Support en Santé Internationale [N'Djamena, Tchad] (CSSI), University of Maiduguri, This work was supported by Wellcome Trust (grant no. 086546/Z/08/Z), www.wellcome.ac.uk, Bill & Melinda Gates Foundation (grant no. 51251), www.gatesfoundation.org., Trotter, Caroline [0000-0003-4000-2708], and Apollo - University of Cambridge Repository
Subjects: Male, Bacterial Diseases, Physiology, lcsh:Medicine, Meningococcal Disease, Neisseria meningitidis, MESH: Africa, Biochemistry, Ghana, MESH: Meningococcal Vaccines, Geographical Locations, Seroepidemiologic Studies, Infectious Diseases of the Nervous System, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Immune Physiology, MESH: Child, MESH: Antibodies, Bacterial, Medicine and Health Sciences, Public and Occupational Health, Enzyme-Linked Immunoassays, lcsh:Science, Child, MESH: Aged, MESH: Immunoglobulin G, Immune System Proteins, MESH: Middle Aged, Vaccination, MESH: Meningitis, Meningococcal, MESH: Enzyme-Linked Immunosorbent Assay, Middle Aged, Antibodies, Bacterial, Vaccination and Immunization, MESH: Infant, Senegal, Infectious Diseases, Neurology, Child, Preschool, Carrier State, MESH: Immunologic Memory, Female, MESH: Carrier State, Research Article, Adult, Adolescent, Inflammatory Diseases, Immunology, Enzyme-Linked Immunosorbent Assay, Meningococcal Vaccines, Meningitis, Meningococcal, Serogroup, Research and Analysis Methods, Antibodies, MESH: Neisseria meningitidis, MESH: Cross-Sectional Studies, Humans, Meningitis, Epidemics, Immunoassays, MESH: Epidemics, Aged, MESH: Adolescent, MESH: Seroepidemiologic Studies, MESH: Humans, lcsh:R, MESH: Child, Preschool, Infant, Biology and Life Sciences, Proteins, MESH: Adult, MESH: Serogroup, MESH: Vaccination, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Male, Cross-Sectional Studies, Immunoglobulin G, People and Places, Africa, Immunologic Techniques, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Ethiopia, Preventive Medicine, Immunologic Memory, MESH: Female
Abstract: International audience; The pattern of epidemic meningococcal disease in the African meningitis belt may be influenced by the background level of population immunity but this has been measured infrequently. A standardised enzyme-linked immunosorbent assay (ELISA) for measuring meningococcal serogroup A IgG antibodies was established at five centres within the meningitis belt. Antibody concentrations were then measured in 3930 individuals stratified by age and residence from six countries. Seroprevalence by age was used in a catalytic model to determine the force of infection. Meningococcal serogroup A IgG antibody concentrations were high in each country but showed heterogeneity across the meningitis belt. The geometric mean concentration (GMC) was highest in Ghana (9.09 μg/mL [95% CI 8.29, 9.97]) and lowest in Ethiopia (1.43 μg/mL [95% CI 1.31, 1.57]) on the margins of the belt. The force of infection was lowest in Ethiopia (λ = 0.028). Variables associated with a concentration above the putative protective level of 2 μg/mL were age, urban residence and a history of recent vaccination with a meningococcal vaccine. Prior to vaccination with the serogroup A meningococcal conjugate vaccine, meningococcal serogroup A IgG antibody concentrations were high across the African meningitis belt and yet the region remained susceptible to epidemics.
Published: 2016

30. New introduction and spread of rabies among dog population in Bangui

Author: M. Digol, Benjamin Selekon, Xavier Konamna, Emmanuel Nakouné, A. Le Faou, Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Faculté de Médecine, Université de Bangui, Université de Bangui, and Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)
Subjects: Veterinary medicine, medicine.medical_specialty, Rabies, MESH: Dog Diseases, Veterinary (miscellaneous), 030231 tropical medicine, Notifiable disease, Population, Prevalence, Animals, Wild, medicine.disease_cause, Virus, MESH: Dogs, 03 medical and health sciences, Dogs, MESH: Rabies, 0302 clinical medicine, Epidemiology, medicine, Animals, MESH: Animals, MESH: Animals, Wild, Dog Diseases, Epidemics, education, MESH: Epidemics, 030304 developmental biology, 0303 health sciences, education.field_of_study, Vaccination, Rabies virus, MESH: Rabies Vaccines, MESH: Vaccination, medicine.disease, Virology, MESH: Rabies virus, 3. Good health, Central African Republic, Infectious Diseases, Geography, Rabies Vaccines, MESH: Central African Republic, Insect Science, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Parasitology
Abstract: International audience; Rabies is endemic in the Central African Republic (CAR) and a neglected enzootic disease which represents a serious public health problem. Before April 2009, rabies was not a notifiable disease in CAR. Vaccination of animals is expensive and not commonly done. In 2005, none rabies case was recorded in Bangui. To understand how rabies was introduced and propagated in the city of Bangui from 2006 to 2008, we analyzed samplings of dog brain as well as reviewed the records of dog owners. A total of 86 out of 101 samples (84.8%) tested positive for rabies virus during this period. Previous phylogenetic analysis of some strains circulating in Bangui between 2006 and 2008 indicated that virus of cosmopolitan and Africa 2 clade are found. Given the time frame and location of these samples, one possible explanation for this alarming result may be that two different strains of rabies virus were introduced at different times in Bangui. Stray dogs are solely responsible for the spread of the epidemic.
Published: 2012

31. Value of Routine Dengue Diagnostic Tests in Urine and Saliva Specimens

Author: Anavaj Sakuntabhai, Anne-Claire Andries, Patrich Lorn Try, Sopheaktra Ros, Kim Srorn Kim, Paul F. Horwood, Julien Cappelle, Marie Flamand, Sowath Ly, Veasna Duong, Arnaud Tarantola, Philippe Buchy, Sivuth Ong, Rekol Huy, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Animal et gestion intégrée des risques (UPR AGIRs), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Pediatric Department [Cambodia], Kampong Cham Provincial hospital [Cambodia], Centre National de Malariologie (CNM), Virologie Structurale - Structural Virology, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génétique fonctionnelle des Maladies infectieuses - Functional Genetics of Infectious Diseases, GlaxoSmithKline Vaccines [Singapore], GlaxoSmithKline [Headquarters, London, UK] (GSK), The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007/2011) under Grant Agreement n°282378., European Project: 282378,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,DENFREE(2012), Institut Pasteur du Cambodge-Réseau International des Instituts Pasteur ( RIIP ), Animal et gestion intégrée des risques ( Agirs ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ), Kampong Cham Provincial hospital, National Center of Parasitology ( CNM ), National Malaria Center [Phnom Penh], Département de Virologie, Institut Pasteur [Paris], Génétique fonctionnelle des Maladies infectieuses, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007/2011) under Grant Agreement n°282 378., European Project : 282378,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,DENFREE ( 2012 ), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, MESH: Viral Nonstructural Proteins/urine, Urine, Dengue virus, Antibodies, Viral, MESH: Immunoglobulin Isotypes/analysis, Santé publique, Polymerase Chain Reaction, Gastroenterology, MESH: Antibodies, Viral/blood, Plasma, MESH : Child, MESH: Child, MESH : Dengue Virus, Child, MESH : Viral Nonstructural Proteins, MESH: Dengue Virus/isolation & purification, MESH : Diagnostic Tests, Routine, Blood proteins, MESH : Enzyme-Linked Immunosorbent Assay, 3. Good health, Immunoglobulin Isotypes, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH : Urine, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Child, Preschool, Disease Progression, MESH: Disease Progression, MESH: Dengue/urine, Antibody, Genre humain, medicine.medical_specialty, lcsh:RC955-962, MESH: Dengue/epidemiology, MESH: Saliva/virology, MESH: Urine/chemistry, MESH: Plasma/immunology, MESH: RNA, Viral/isolation & purification, MESH : Adolescent, Humans, Epidemics, Saliva, Technique analytique, MESH: Diagnostic Tests, Routine, Test biologique, MESH: Adolescent, MESH: Humans, MESH: Viral Nonstructural Proteins/blood, [ SDV ] Life Sciences [q-bio], MESH: Dengue/blood, Diagnostic Tests, Routine, MESH : Cambodia, MESH : Humans, MESH: Child, Preschool, Public Health, Environmental and Occupational Health, lcsh:RA1-1270, MESH: Polymerase Chain Reaction, MESH : Disease Progression, Dengue Virus, medicine.disease, Immunology, MESH: Antibodies, Viral/urine, MESH : Saliva, MESH: Female, MESH: Dengue Virus/immunology, Sang, Viral Nonstructural Proteins, MESH : Child, Preschool, medicine.disease_cause, MESH: Immunoglobulin Isotypes/blood, Serology, Dengue fever, Dengue, Blood plasma, MESH : Female, MESH : Polymerase Chain Reaction, Salive, MESH: Dengue/diagnosis, MESH : Epidemics, lcsh:Public aspects of medicine, MESH: Enzyme-Linked Immunosorbent Assay, MESH : Immunoglobulin Isotypes, MESH: Viral Nonstructural Proteins/analysis, MESH: Immunoglobulin Isotypes/urine, Infectious Diseases, S50 - Santé humaine, MESH: Urine/virology, RNA, Viral, Female, MESH: Genome, Viral, Cambodia, MESH: Dengue Virus/genetics, MESH : Genome, Viral, Research Article, MESH : Antibodies, Viral, MESH: Saliva/immunology, lcsh:Arctic medicine. Tropical medicine, Adolescent, MESH : Male, MESH : Dengue, Enzyme-Linked Immunosorbent Assay, Genome, Viral, Biology, Diagnostic de laboratoire, MESH: Antibodies, Viral/analysis, Internal medicine, medicine, MESH : RNA, Viral, MESH: Epidemics, MESH: Plasma/chemistry, MESH : Plasma, MESH: Urine/physiology, Flavivirus, MESH: Cambodia, MESH: Male, biology.protein, MESH: Saliva/chemistry, U30 - Méthodes de recherche, MESH: Plasma/virology
Abstract: Background Dengue laboratory diagnosis is essentially based on detection of the virus, its components or antibodies directed against the virus in blood samples. Blood, however, may be difficult to draw in some patients, especially in children, and sampling during outbreak investigations or epidemiological studies may face logistical challenges or limited compliance to invasive procedures from subjects. The aim of this study was to assess the possibility of using saliva and urine samples instead of blood for dengue diagnosis. Methodology/Principal Findings Serial plasma, urine and saliva samples were collected at several time-points between the day of admission to hospital until three months after the onset of fever in children with confirmed dengue disease. Quantitative RT-PCR, NS1 antigen capture and ELISA serology for anti-DENV antibody (IgG, IgM and IgA) detection were performed in parallel on the three body fluids. RT-PCR and NS1 tests demonstrated an overall sensitivity of 85.4%/63.4%, 41.6%/14.5% and 39%/28.3%, in plasma, urine and saliva specimens, respectively. When urine and saliva samples were collected at the same time-points and tested concurrently, the diagnostic sensitivity of RNA and NS1 detection assays was 69.1% and 34.4%, respectively. IgG/IgA detection assays had an overall sensitivity of 54.4%/37.4%, 38.5%/26.8% and 52.9%/28.6% in plasma, urine and saliva specimens, respectively. IgM were detected in 38.1% and 36% of the plasma and saliva samples but never in urine. Conclusions Although the performances of the different diagnostic methods were not as good in saliva and urine as in plasma specimens, the results obtained by qRT-PCR and by anti-DENV antibody ELISA could well justify the use of these two body fluids to detect dengue infection in situations when the collection of blood specimens is not possible., Author Summary Dengue is the most important arthropod-borne disease affecting humans and represents a huge public health burden in affected countries. Symptoms are often non-specific hence the need for an early, sensitive and specific diagnosis of dengue for appropriate management as well as for early epidemic detection. Currently, almost all laboratory diagnostic methods require a blood specimen that may be sometimes be difficult or inconvenient to obtain. In this study, we assessed the possibility to use saliva and urine samples as alternatives to blood specimens in dengue diagnosis. We demonstrated that the performances of the different diagnostic methods (RT-PCR, NS1 antigen detection and anti-DENV IgM/IgG/IgA ELISAs) were in general not as good in saliva and urine as in plasma, but that the use of these body fluids obtained by non-invasive methods could be of value in certain circumstances such as outbreak investigations or in young children (once they are old enough to comply to instructions), in addition to the situations when blood cannot be easily collected (e.g., lack of phlebotomist, refusal of the procedure, etc.).
Published: 2015

32. Challenges in Antimalarial Drug Treatment for Vivax Malaria Control

Author: Didier Menard, Jean Popovici, Institut Pasteur du Cambodge, and Réseau International des Instituts Pasteur (RIIP)
Subjects: Plasmodium vivax, MESH: Disease Eradication, Biology, Models, Biological, Drug treatment, Antimalarials, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, medicine, Malaria, Vivax, Humans, Severe Malaria, Disease Eradication, Epidemics, Molecular Biology, MESH: Epidemics, MESH: Humans, Benign disease, MESH: Models, Biological, MESH: Malaria, Vivax, Neglected Diseases, Plasmodium falciparum, medicine.disease, biology.organism_classification, MESH: Antimalarials, 3. Good health, Vivax malaria, Immunology, Molecular Medicine, MESH: Neglected Diseases, Malaria
Abstract: International audience; Plasmodium vivax is the most widespread human malaria parasite, but has received much less attention than Plasmodium falciparum during the past 50 years of research. Plasmodium vivax was historically seen as causing only benign disease, but this view has recently changed, with increased recognition of the burden of vivax malaria, as well as numerous case reports of severe malaria or death caused by this parasite. The complexity of P. vivax biology is characteristic of specific features of the parasite, and recent years have seen major progress in our understanding of this complexity. In this review, we analyze the latest advances in the field, describing the constraints that the unique features of P. vivax place on drug treatments aimed at controlling or eliminating it.
Published: 2015

33. West Nile Virus: High Transmission Rate in North-Western European Mosquitoes Indicates Its Epidemic Potential and Warrants Increased Surveillance

Author: Just M. Vlak, Willem Takken, Jelke J. Fros, Gorben P. Pijlman, Corinne Geertsema, Constantianus J. M. Koenraadt, Anna-Bella Failloux, P.P.J. Roosjen, Chantal B.F. Vogels, Wageningen University and Research [Wageningen] (WUR), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), This work is supported by the European 195 Community’s Seventh Framework Programme (FP7 VECTORIE project number 261466)., We thank Els Roode for technical support concerning the BSL3 laboratory, Byron Martina for sharing the WNV isolates, Aaron Brault for the Culex tarsalis cells, the Cell Biology and Immunology group of Wageningen University for the Hela and DF-1 cells, Laura Kramer for providing egg rafts of the North American Culex pipiens mosquitoes, and Roy Hall for antibodies against the WNV envelope protein. We acknowledge the E-OBS dataset from the EU-FP6 project ENSEMBLES and the data providers in the ECA&D project., European Project: 261466,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,VECTORIE(2010), and Institut Pasteur [Paris]
Subjects: animal diseases, differential virulence, encephalitis, viruses, Laboratory of Virology, medicine.disease_cause, Mosquitoes, Laboratory of Geo-information Science and Remote Sensing, High transmission, MESH: Animals, Laboratory of Entomology, vector competence, biology, Transmission (medicine), lcsh:Public aspects of medicine, experimental-infection, Temperature, virus diseases, PE&RC, MESH: Temperature, 3. Good health, Europe, Culex, Infectious Diseases, Blood, Population Surveillance, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, circulation, Pathogens, West Nile virus, Encephalitis, Research Article, lcsh:Arctic medicine. Tropical medicine, Lineage (genetic), lcsh:RC955-962, united-states, Early detection, lineage 1, MESH: Culex, Cell Line, MESH: Population Surveillance, strains, Laboratorium voor Virologie, Birds, Culex pipiens, medicine, Vector-borne diseases, Animals, Humans, Laboratorium voor Geo-informatiekunde en Remote Sensing, MESH: Saliva, Epidemics, Saliva, MESH: West Nile virus, MESH: Epidemics, MESH: West Nile Fever, disease, MESH: Humans, outbreak, Public Health, Environmental and Occupational Health, Outbreak, lcsh:RA1-1270, biology.organism_classification, medicine.disease, Laboratorium voor Entomologie, Virology, nervous system diseases, MESH: Cell Line, MESH: Europe, West Nile Fever
Abstract: Background West Nile virus (WNV) is a highly pathogenic flavivirus transmitted by Culex spp. mosquitoes. In North America (NA), lineage 1 WNV caused the largest outbreak of neuroinvasive disease to date, while a novel pathogenic lineage 2 strain circulates in southern Europe. To estimate WNV lineage 2 epidemic potential it is paramount to know if mosquitoes from currently WNV-free areas can support further spread of this epidemic. Methodology/Principal Findings We assessed WNV vector competence of Culex pipiens mosquitoes originating from north-western Europe (NWE) in direct comparison with those from NA. We exposed mosquitoes to infectious blood meals of lineage 1 or 2 WNV and determined the infection and transmission rates. We explored reasons for vector competence differences by comparing intrathoracic injection versus blood meal infection, and we investigated the influence of temperature. We found that NWE mosquitoes are highly competent for both WNV lineages, with transmission rates up to 25%. Compared to NA mosquitoes, transmission rates for lineage 2 WNV were significantly elevated in NWE mosquitoes due to better virus dissemination from the midgut and a shorter extrinsic incubation time. WNV infection rates further increased with temperature increase. Conclusions/Significance Our study provides experimental evidence to indicate markedly different risk levels between both continents for lineage 2 WNV transmission and suggests a degree of genotype-genotype specificity in the interaction between virus and vector. Our experiments with varying temperatures explain the current localized WNV activity in southern Europe, yet imply further epidemic spread throughout NWE during periods with favourable climatic conditions. This emphasizes the need for intensified surveillance of virus activity in current WNV disease-free regions and warrants increased awareness in clinics throughout Europe., Author Summary West Nile virus (WNV) is on the rise in Europe, with increasing numbers of human cases of neurological disease and death since 2010. However, it is currently unknown whether or not WNV will continue to spread to north-western Europe (NWE), in a fashion similar to the WNV epidemic sweep in the United States (1999–2004). The presence of competent mosquitoes is a strict requirement for WNV transmission, but no laboratory studies have been conducted with the new European lineage 2 WNV outbreak strain. Our study is the first to investigate transmissibility in NWE Culex pipiens for lineage 2 WNV in a systematic, direct comparison with North American Culex pipiens and with the lineage 1 WNV strain. We demonstrate that European mosquitoes are highly competent for both WNV lineages, which underscores the epidemic potential of WNV in Europe. However, the transmission rate for lineage 2 WNV was significantly lower in North American mosquitoes, which indicates different risk levels between both continents for lineage 2 but not lineage 1 WNV. Based on our result, we propose that WNV surveillance in mosquitoes and birds must be intensified in Europe to allow early detection, timely intervention strategies and prevent outbreaks of WNV neurological disease.
Published: 2015

34. Influenza seasonality in Madagascar: the mysterious African free-runner

Author: Steven Zhixiang Zhou, Laurence Randrianasolo, Cécile Viboud, Wladimir J. Alonso, Jean-Michel Heraud, Julia Guillebaud, Norosoa Harline Razanajatovo, Arnaud Orelle, National Institutes of Health [Bethesda] (NIH), Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), London School of Hygiene and Tropical Medicine (LSHTM), and Unité d'Epidémiologie [Antananarivo, Madagascar] (IPM)
Subjects: Time Factors, Epidemiology, Climate, viruses, MESH: Influenza Vaccines, MESH: Madagascar, Influenza A Virus, H1N1 Subtype, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, 030212 general & internal medicine, MESH: Travel, MESH: Influenza B virus, Travel, 0303 health sciences, Ecology, seasonality, MESH: Influenza, Human, virus diseases, MESH: Climate, Infectious Diseases, Geography, Influenza Vaccines, MESH: Sentinel Surveillance, Seasons, Pulmonary and Respiratory Medicine, MESH: Influenza A Virus, H3N2 Subtype, MESH: Influenza A Virus, H1N1 Subtype, 03 medical and health sciences, Influenza, Human, Situated, medicine, Madagascar, Humans, Epidemics, viral migration, population connectivity, MESH: Epidemics, 030304 developmental biology, MESH: Humans, Influenza A Virus, H3N2 Subtype, MESH: Time Factors, Public Health, Environmental and Occupational Health, Tropics, Original Articles, biochemical phenomena, metabolism, and nutrition, Seasonality, medicine.disease, Virology, Influenza, Influenza B virus, time series, Sentinel Surveillance, MESH: Seasons
Abstract: International audience; BACKGROUND:The seasonal drivers of influenza activity remain debated in tropical settings where epidemics are not clearly phased. Antananarivo is a particularly interesting case study because it is in Madagascar, an island situated in the tropics and with quantifiable connectivity levels to other countries.OBJECTIVES:We aimed at disentangling the role of environmental forcing and population fluxes on influenza seasonality in Madagascar.METHODS:We compiled weekly counts of laboratory-confirmed influenza-positive specimens for the period 2002 to 2012 collected in Antananarivo, with data available from sub-Saharan countries and countries contributing most foreign travelers to Madagascar. Daily climate indicators were compiled for the study period.RESULTS:Overall, influenza activity detected in Antananarivo predated that identified in temperate Northern Hemisphere locations. This activity presented poor temporal matching with viral activity in other countries from the African continent or countries highly connected to Madagascar excepted for A(H1N1)pdm09. Influenza detection in Antananarivo was not associated with travel activity and, although it was positively correlated with all climatic variables studied, such association was weak.CONCLUSIONS:The timing of influenza activity in Antananarivo is irregular, is not driven by climate, and does not align with that of countries in geographic proximity or highly connected to Madagascar. This work opens fresh questions regarding the drivers of influenza seasonality globally particularly in mid-latitude and less-connected regions to tailor vaccine strategies locally.
Published: 2015

35. Recent Epidemiological Trends of Dengue in the French Territories of the Americas (2000–2012): A Systematic Literature Review

Author: Claude Flamand, Anne-Frieda Taurel, Philippe Quénel, Maïna L’Azou, Sanofi Pasteur [Lyon, France], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), and Sanofi Pasteur sponsored this survey and analysis. The authors (including members of Sanofi Pasteur) were responsible for the conception of the literature analysis, development of the protocol, data collection, analysis and interpretation of data, provision of critical comments, writing the paper and approving the final version to be published.
Subjects: lcsh:Arctic medicine. Tropical medicine, MESH: West Indies, lcsh:RC955-962, 030231 tropical medicine, MESH: Dengue, Dengue virus, medicine.disease_cause, MESH: Dengue Virus, Dengue fever, MESH: Sex Ratio, 03 medical and health sciences, 0302 clinical medicine, Environmental health, MESH: Severity of Illness Index, MESH: French Guiana, Medicine, Seroprevalence, 030212 general & internal medicine, MESH: Incidence, MESH: Disease Outbreaks, MESH: Age Distribution, Dengue vaccine, MESH: Epidemics, Disease surveillance, MESH: Humans, MESH: Seroepidemiologic Studies, business.industry, lcsh:Public aspects of medicine, MESH: Sex Distribution, Public Health, Environmental and Occupational Health, Outbreak, lcsh:RA1-1270, MESH: Serogroup, medicine.disease, 3. Good health, Infectious Diseases, 2009 Bolivian dengue fever epidemic, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Martinique
Abstract: International audience; Dengue is a public health concern across the globe, and an escalating problem in the Americas. As part of a wider programme (covering Latin America and South East Asia) to characterize the epidemiology of dengue in dengue endemic areas, we undertook a systematic literature review to assess epidemiological trends (incidence, timing and duration of outbreaks/epidemics, age and sex distribution, serotype distribution, seroprevalence and disease severity) for dengue across the French Territories of the Americas (FTA), in French Guiana, Guadeloupe, Martinique, Saint Martin and Saint Barthélemy between 2000 and 2012 (CRD42012002341: http://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42012002341). Of 413 relevant data sources identified, 45 were eligible for inclusion. A large proportion of the available data were from national surveillance reports, and 12 publications were from peer-reviewed journals. During the review period, 3-5 epidemics were identified in each of the island territories and French Guiana, and epidemics were often associated with a shift in the predominant circulating dengue virus serotype. Substantial gaps in epidemiological knowledge were identified. In particular, information regarding dengue virus genotype distribution, seroprevalence and age distribution of dengue were lacking. Additionally, much of the available data were from epidemic years; data from inter-epidemic periods were sparse. Nevertheless, the available epidemiological data showed that dengue is endemic across the FTA and suggest an evolution towards hyperendemicity, highlighting the need to continue the efforts with the existing surveillance programmes to assist in planning an effective vaccination programme once a dengue vaccine is deployed.
Published: 2014

36. Dengue epidemics and adverse obstetrical outcomes in French Guiana: a semi-ecological study

Author: Hanf, Matthieu, Friedman, Eleanor, Basurko, Celia, Roger, Amaury, Bruncher, Pascal, Dussart, Philippe, Flamand, Claude, Carles, Gabriel, Buekens, Pierre, Breart, Gerard, Carme, Bernard, Nacher, Mathieu, Centre d'investigation clinique Antilles-Guyane ( CIC - Antilles Guyane ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de la Martinique-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Department of Epidemiology, Tulane University, Protection Maternelle et Infantile, Conseil Général de la Guyane, Centre National de Référence des Arboviroses, Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur ( RIIP ) -Réseau International des Instituts Pasteur ( RIIP ), Cellule de l'InVS en Région Antilles Guyane, Institut de Veille Sanitaire (INVS), Service de Gynécologie Obstétrique, Centre Hospitalier de l'Ouest Guyanais, Recherche Epidémiologique en Santé Périnatale et Santé des Femmes et des Enfants ( UMR_S 953 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Sud - Paris 11 ( UP11 ), INSERM (Institut National de la Santé et de la Recherche Médicale) and the Cayenne General Hospital., Centre d'investigation clinique Antilles-Guyane (CIC - Antilles Guyane), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de la Martinique [Fort de France]-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Centre National de Référence pour les Arbovirus - Laboratoire de Virologie [Cayenne, Guyane française] (CNR - laboratoire associé), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Recherche Epidémiologique en Santé Périnatale et Santé des Femmes et des Enfants (UMR_S 953), Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU de la Martinique [Fort de France]-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Sud - Paris 11 (UP11)
Subjects: MESH : French Guiana, MESH: Premature Birth, MESH : Prevalence, MESH : Dengue, MESH : Pregnancy Trimester, First, MESH: Dengue, MESH: Dengue Virus, MESH : Postpartum Hemorrhage, MESH: Pregnancy, MESH: French Guiana, MESH : Dengue Virus, MESH : Female, MESH: Prevalence, MESH: Epidemics, MESH : Pregnancy Outcome, MESH: Humans, MESH : Epidemics, MESH : Humans, preterm birth, [ SDV.SPEE ] Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Pregnancy Outcome, Dengue fever, MESH: Postpartum Hemorrhage, French Guiana, MESH : Premature Birth, MESH : Pregnancy, postpartum hemorrhage, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, pregnancy, MESH: Pregnancy Trimester, First, MESH: Female
Abstract: International audience; OBJECTIVE: To determine whether dengue epidemics are associated with an increase in adverse obstetrical outcomes. METHODS: Semi-ecological study combining individual data on obstetrical events from the perinatal registry and aggregated exposure data from the epidemiologic surveillance of dengue in Cayenne, French Guiana between 2004 and 2007. RESULTS: After adjustment for individual risk factors, analysis showed that an epidemic level of dengue transmission during the first trimester was associated with an increased risk of post-partum haemorrhage and preterm birth. The associated risks seemed to depend on the epidemic level. CONCLUSIONS: Despite its limitations, this study suggests that dengue in the first trimester may be related to preterm birth and to post-partum bleeding, thus leading to specific hypotheses that should be tested in prospective studies.
Published: 2014

37. Dengue epidemics and adverse obstetrical outcomes in French Guiana: a semi-ecological study.: Dengue and adverse obstetrical outcomes

Author: Hanf, Matthieu, Friedman, Eleanor, Basurko, Celia, Roger, Amaury, Bruncher, Pascal, Dussart, Philippe, Flamand, Claude, Carles, Gabriel, Buekens, Pierre, Breart, Gerard, Carme, Bernard, Nacher, Mathieu, Centre d'investigation clinique Antilles-Guyane (CIC - Antilles Guyane), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de la Martinique [Fort de France]-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Department of Epidemiology, Tulane University, Protection Maternelle et Infantile, Conseil Général de la Guyane, Centre National de Référence pour les Arbovirus - Laboratoire de Virologie [Cayenne, Guyane française] (CNR - laboratoire associé), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Cellule de l'InVS en Région Antilles Guyane, Institut de Veille Sanitaire (INVS), Service de Gynécologie Obstétrique, Centre Hospitalier de l'Ouest Guyanais, Recherche Epidémiologique en Santé Périnatale et Santé des Femmes et des Enfants (UMR_S 953), Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), INSERM (Institut National de la Santé et de la Recherche Médicale) and the Cayenne General Hospital., and ADENIS, ANTOINE
Subjects: MESH: Humans, MESH: Premature Birth, preterm birth, MESH: Dengue, Dengue fever, MESH: Dengue Virus, MESH: Pregnancy Outcome, MESH: Postpartum Hemorrhage, French Guiana, MESH: Pregnancy, postpartum hemorrhage, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: French Guiana, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, pregnancy, MESH: Pregnancy Trimester, First, MESH: Female, MESH: Prevalence, MESH: Epidemics
Abstract: International audience; OBJECTIVE: To determine whether dengue epidemics are associated with an increase in adverse obstetrical outcomes. METHODS: Semi-ecological study combining individual data on obstetrical events from the perinatal registry and aggregated exposure data from the epidemiologic surveillance of dengue in Cayenne, French Guiana between 2004 and 2007. RESULTS: After adjustment for individual risk factors, analysis showed that an epidemic level of dengue transmission during the first trimester was associated with an increased risk of post-partum haemorrhage and preterm birth. The associated risks seemed to depend on the epidemic level. CONCLUSIONS: Despite its limitations, this study suggests that dengue in the first trimester may be related to preterm birth and to post-partum bleeding, thus leading to specific hypotheses that should be tested in prospective studies.
Published: 2014

38. Ebola virus disease in the Democratic Republic of Congo

Author: Sylvie Briand, Vital Mondonge, Jean-Marie Okwo-Bele, Felix Kabange, Nicolas Berthet, Eric Bertherat, Joseph Cabore, Gary P. Kobinger, Jean-Jacques Muyembe, Jean-Claude Manuguerra, Placide Mbala Kingebeni, Abstr Act, D. Phil, Alain Epelboin, Benoit Kebela Ilunga, Jimmy Kapetshi, Licé González-Angulo, Eric M. Leroy, Gael Darren Maganga, Christopher Dye, Centre International de Recherches Médicales de Franceville (CIRMF), Institut National de Recherche Biomédicale [Kinshasa] (INRB), Epidémiologie et Physiopathologie des Virus Oncogènes (EPVO (UMR_3569 / U-Pasteur_3)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Ministry of Health, Kinshasa, Democratic Republic of the Congo, World Health Organization [Kinshasa, Democratic Republic of Congo] (WHO-DRC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Public Health Agency of Canada (PHAC), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP), 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]), Supported by Centre International de Recherches Médicales de Franceville (CIRMF), which is funded by the Gabonese government, Total Gabon, and the French Foreign Ministry, and by Metabiota, which is funded by the U.S. Department of Defense Armed Forces Health Surveillance Center, Division of Global Emerging Infections, Surveillance Operations (AFHSC GEIS), the Henry M. Jackson Foundation for the Advancement of Military Medicine, the Defense Threat Reduction Agency Cooperative Biological Engagement Program (DTRA-CBEP), Google.org, the Skoll Foundation, the U.S. Agency for International Development (USAID) Emerging Pandemic Threats Program, and the PREDICT project (cooperative agreement number GHN-A-OO-09-00010-00)., We thank Philippe Engandja (CIRMF Gabon) and Valérie Caro and Laure Diancourt (Institut Pasteur de Paris) for their technical assistance, Ravi Santhana Gopala Krishna (WHO) and Hugh Keegan (ESRI [Environmental Systems Research Institute]) for providing the original version of the map in Figure 1, Jens H. Kuhn for assistance in the preparation of the manuscript, and and Joseph Fair for continuing support.
Subjects: Male, [SDV]Life Sciences [q-bio], Disease, medicine.disease_cause, West africa, MESH: Child, Geography, Medical, MESH: Phylogeny, Child, Letter to the Editor, Phylogeny, media_common, MESH: Aged, MESH: Middle Aged, General Medicine, Middle Aged, Ebolavirus, MESH: Infant, Democracy, Hemorrhagic Fevers, Africa, Western, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Child, Preschool, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Democratic Republic of the Congo, Female, Adult, Adolescent, media_common.quotation_subject, World health, MESH: Africa, Western, MESH: Geography, Medical, parasitic diseases, medicine, Humans, MESH: Ebolavirus, Epidemics, Viral isolation, MESH: Epidemics, Aged, MESH: Adolescent, Ebola virus, MESH: Humans, business.industry, MESH: Child, Preschool, Outbreak, Infant, MESH: Adult, MESH: Democratic Republic of the Congo, Hemorrhagic Fever, Ebola, Virology, MESH: Male, MESH: Hemorrhagic Fever, Ebola, business, MESH: Female
Abstract: International audience; BackgroundThe seventh reported outbreak of Ebola virus disease (EVD) in the equatorial African country of the Democratic Republic of Congo (DRC) began on July 26, 2014, as another large EVD epidemic continued to spread in West Africa. Simultaneous reports of EVD in equatorial and West Africa raised the question of whether the two outbreaks were linked.MethodsWe obtained data from patients in the DRC, using the standard World Health Organization clinical-investigation form for viral hemorrhagic fevers. Patients were classified as having suspected, probable, or confirmed EVD or a non-EVD illness. Blood samples were obtained for polymerase-chain-reaction–based diagnosis, viral isolation, sequencing, and phylogenetic analysis.ResultsThe outbreak began in Inkanamongo village in the vicinity of Boende town in Équateur province and has been confined to that province. A total of 69 suspected, probable, or confirmed cases were reported between July 26 and October 7, 2014, including 8 cases among health care workers, with 49 deaths. As of October 7, there have been approximately six generations of cases of EVD since the outbreak began. The reported weekly case incidence peaked in the weeks of August 17 and 24 and has since fallen sharply. Genome sequencing revealed Ebola virus (EBOV, Zaire species) as the cause of this outbreak. A coding-complete genome sequence of EBOV that was isolated during this outbreak showed 99.2% identity with the most closely related variant from the 1995 outbreak in Kikwit in the DRC and 96.8% identity to EBOV variants that are currently circulating in West Africa.ConclusionsThe current EVD outbreak in the DRC has clinical and epidemiologic characteristics that are similar to those of previous EVD outbreaks in equatorial Africa. The causal agent is a local EBOV variant, and this outbreak has a zoonotic origin different from that in the 2014 epidemic in West Africa. (Funded by the Centre International de Recherches Médicales de Franceville and others.)
Published: 2014

39. Meningococcal carriage in the African meningitis belt

Author: Odile Harrison, Abraham Aseffa, Martin Maiden, Kanny Diallo, Caroline Trotter, Dan Dano Ibrahim, Centre de Recherche Médicale et Sanitaire (Niamey, Niger) (CERMES), Réseau International des Instituts Pasteur (RIIP), Bill & Melinda Gates Foundation and the Wellcome Trust, The MenAfriCar consortium : Armauer Hansen Research Institute, Addis Ababa, Ethiopia: Oumer Ali, Abraham Aseffa (PI), Ahmed Bedru, Tsehaynesh Lemma, Tesfaye Moti, Alemayehu Worku, Haimanot Guebre Xabher, Lawrence Yamuah. Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger (Member of the International Network of Pasteur Institutes): Rahamatou Moustapha Boukary, Jean-Marc Collard (PI), Ibrahim Dan Dano, Ibrahim Habiboulaye, Bassira Issaka, Jean-François Jusot, Sani Ousmane, Issoufa Rabe. Centers for Disease Control, Atlanta, USA: Tom Clark, Leonard Mayer. Centre de Support en Santé International (CSSI), N'Djamena, Chad: Jean Pierre Gami, Kadidja Gamougam, Boulotigam Kodbesse, Nathan Naibei, Cyriaque Ngadoua, Lodoum Mbainadji, Daugla Doumagoum Moto (PI), Maxime Narbé, Jacques Toralta. Centre pour les Vaccins en Développement, Bamako, Mali: Abdoulaye Berthe, Mahamadou Keita, Kanny Diallo, Uma Onwuchekwa, Samba O Sow (PI), Boubou Tamboura, Awa Traore, Alou Toure. Department of Community Medicine, University of Maiduguri, Maiduguri, Nigeria: Mary Amodu, Omeiza Beida, Galadima Gadzama, Babatunji Omotara (PI), Zailani Sambo, Shuaibu Yahya. Faculty of Infectious Disease, London School of Hygiene & Tropical Medicine, London, UK: Daniel Chandramohan, Brian Greenwood, Musa Hassan-King, Olivier Manigart, Maria Nascimento, James Stuart, Arouna Woukeu. Health Protection Agency Vaccine Evaluation Unit, Manchester, UK: Xilian Bai, Ray Borrow, Helen Findlow. Institut de Recherche pour le Développement, Dakar, Senegal: Serge Avalo, Hubert Bassene, Aldiouma Diallo (PI), Marietou Dieng, Souleymane Doucouré, Jules François Gomis, Assane Ndiaye, Cheikh Sokhna, Jean François Trape. Navrongo Health Research Centre, Navrongo, Ghana: Bugri Akalifa, Abudulai Forgor, Abrahan Hodgson (PI), Isaac Osei, Stephen Quaye, John Williams, Peter Wontuo. Princeton University USA: Nicole Basta (Formerly University of Washington)(supported by NIH grants 2R37A1032042 and R03A1092121). School of Social and Community Medicine, University of Bristol, Bristol, UK: Thomas Irving, and Caroline Trotter. University of Oxford, UK: Julia Bennett, Marietou Dieng, Dorothea Hill, Odile Harrison, Lisa Rebbetts, Martin Maiden, Yenenesh Tekletsion, Eleanor Watkins.
Subjects: MESH: Vaccines, Conjugate, International Cooperation, Pilot Projects, Meningococcal Disease, MESH: Pharynx, Neisseria meningitidis, MESH: Africa, MESH: Immunization Programs, Polymerase Chain Reaction, MESH: Meningococcal Vaccines, 0302 clinical medicine, Neisseria meningitidis, Serogroup A, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Child, 030212 general & internal medicine, Child, 0303 health sciences, MESH: Program Evaluation, MESH: Meningitis, Meningococcal, MESH: Enzyme-Linked Immunosorbent Assay, MESH: Infant, 3. Good health, Infectious Diseases, MESH: Young Adult, Child, Preschool, meningococcus, Carrier State, MESH: Carrier State, Adult, Adolescent, MenAfriCar, Enzyme-Linked Immunosorbent Assay, Meningitis, Meningococcal, Specimen Handling, 03 medical and health sciences, Young Adult, MESH: Cross-Sectional Studies, meningococcal carriage, MESH: Neisseria meningitidis, Serogroup A, Humans, MESH: Specimen Handling, Epidemics, MESH: Epidemics, 030304 developmental biology, MESH: Adolescent, Vaccines, Conjugate, MESH: Humans, Immunization Programs, MESH: Child, Preschool, Public Health, Environmental and Occupational Health, Infant, MESH: Adult, MESH: Polymerase Chain Reaction, meningococcal vaccines, MESH: Pilot Projects, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: International Cooperation, Cross-Sectional Studies, Africa, Pharynx, Parasitology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Program Evaluation
Abstract: A meningococcal serogroup A polysaccharide/tetanus toxoid conjugate vaccine (PsA-TT) (MenAfriVac#x2122;) is being deployed in countries of the African meningitis belt. Experience with other polysaccharide/protein conjugate vaccines has shown that an important part of their success has been their ability to prevent the acquisition of pharyngeal carriage and hence to stop transmission and induce herd immunity. If PsA-TT is to achieve the goal of preventing epidemics, it must be able to prevent the acquisition of pharyngeal carriage as well as invasive meningococcal disease and whether PsA-TT can prevent pharyngeal carriage needs to be determined. To address this issue, a consortium (the African Meningococcal Carriage (MenAfriCar) consortium) was established in 2009 to investigate the pattern of meningococcal carriage in countries of the African meningitis belt prior to and after the introduction of PsA-TT. This article describes how the consortium was established, its objectives and the standardised field and laboratory methods that were used to achieve these objectives. The experience of the MenAfriCar consortium will help in planning future studies on the epidemiology of meningococcal carriage in countries of the African meningitis belt and elsewhere. Un vaccin conjugué contenant un polysaccharide du sérogroupe A méningococcique et une anatoxine du tétanos (PsA-TT) (MenAfriVac™) est en cours de déploiement dans les pays de la ceinture africaine de la méningite. L’ expérience avec d’ autres vaccins conjugués polysaccharide/protéine a montré qu’ une partie importante de leur succès a été leur capacité à empêcher l’ acquisition du portage pharyngé et donc à arrêter la transmission et à induire une immunité de group. Si PsA-TT doit d’ atteindre l’ objectif de prévenir les épidémies, il devrait être en mesure d’ empêcher l’ acquisition du portage pharyngé ainsi que la méningococcie invasive et le fait que PsA-TT puisse empêcher le portage pharyngé devrait être déterminé. Pour résoudre ce problème, le consortium MenAfriCar (Consortium Africain du Portage Méningococcique) a été établi en 2009 pour étudier le mode de portage du méningocoque dans les pays de la ceinture africaine de la méningite avant et après l’ introduction de PsA-TT. Cet article décrit comment le consortium a été établi, ses objectifs et les méthodes de laboratoire et de terrain standardisées qui ont été utilisées pour atteindre ces objectifs. L’ expérience du consortium MenAfriCar aidera à planifier les futures études sur l’ épidémiologie du portage du méningocoque dans les pays de la ceinture africaine de la méningite et d’ ailleurs. Se está utilizando una vacuna meningocócica conjugada (MenAfriVac™) de polisacárido del serogrupo A / tétano toxoide (PsA-TT) en países del cinturón Africano de meningitis. Las experiencias obtenidas con otras vacunas conjugadas polisacárido/proteína han demostrado que una parte importante de su éxito se debe a su habilidad para prevenir la colonización faríngea de los portadores, acabando por lo tanto con la transmisión, y a la de inducir la protección de rebaño. Si PsA-TT ha de cumplir el objetivo de prevenir epidemias, debe ser capaz de prevenir el estado de portador faríngeo, al igual que la enfermedad invasiva por meningococo, y para ello es necesario determinar si la PsA-TT puede prevenir la colonización faríngea. Con el fin de abordar esta cuestión se estableció un consorcio africano en el 2009 - el MenAfriCar (African Meningococcal Carriage Consortium) – para investigar los patrones del estado de portador de meningococo en países del cinturón Africano de la meningitis, antes y después de la introducción de PsA-TT. Este artículo describe como se estableció el consorcio, sus objetivos y los métodos estandarizados de campo y de laboratorio que se utilizaron para alcanzarlos. La experiencia del consorcio MenAfriCar ayudará en la planificación de estudios futuros sobre la epidemiología del estado de portador de meningococo, tanto en países del cinturón Africano de la meningitis como en otros lugares del mundo.
Published: 2013

40. Is harm reduction profitable? An analytical framework for corporate social responsibility based on an epidemic model of addictive consumption

Author: Sophie Massin, Centre d'économie de la Sorbonne (CES), Université Paris 1 Panthéon-Sorbonne (UP1)-Centre National de la Recherche Scientifique (CNRS), and Massin, Sophie
Subjects: MESH: Smoking, Health (social science), media_common.quotation_subject, Sincerity, Tobacco Industry, 03 medical and health sciences, 0302 clinical medicine, Harm Reduction, History and Philosophy of Science, MESH: Social Responsibility, 0502 economics and business, Economics, MESH: Harm Reduction, Humans, 030212 general & internal medicine, MESH: Marketing, 050207 economics, Epidemics, MESH: Models, Theoretical, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, health care economics and organizations, MESH: Epidemics, MESH: Tobacco Industry, media_common, Marketing, Consumption (economics), Social Responsibility, Harm reduction, MESH: Humans, Public economics, business.industry, Social cost, Smoking, 05 social sciences, Models, Theoretical, Public relations, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Product (business), MESH: France, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Corporate social responsibility, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, business, Social responsibility, Reputation
Abstract: International audience; This article aims to help resolve the apparent paradox of producers of addictive goods who claim to be socially responsible while marketing a product clearly identified as harmful. It advances that reputation effects are crucial in this issue and that determining whether harm reduction practices are costly or profitable for the producers can help to assess the sincerity of their discourse. An analytical framework based on an epidemic model of addictive consumption that includes a deterrent effect of heavy use on initiation is developed. This framework enables us to establish a clear distinction between a simple responsible discourse and genuine harm reduction practices and, among harm reduction practices, between use reduction practices and micro harm reduction practices. Using simulations based on tobacco sales in France from 1950 to 2008, we explore the impact of three corresponding types of actions: communication on damage, restraining selling practices and development of safer products on total sales and on the social cost. We notably find that restraining selling practices toward light users, that is, preventing light users from escalating to heavy use, can be profitable for the producer, especially at early stages of the epidemic, but that such practices also contribute to increase the social cost. These results suggest that the existence of a deterrent effect of heavy use on the initiation of the consumption of an addictive good can shed new light on important issues, such as the motivations for corporate social responsibility and the definition of responsible actions in the particular case of harm reduction.
Published: 2012

41. Virulence factors and TEM-type β-lactamases produced by two isolates of an epidemic Klebsiella pneumoniae strain

Author: Joanna Empel, Frédéric Robin, Claire Hennequin, Richard Bonnet, Marek Gniadkowski, Lucie Gibold, Racha Beyrouthy, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), National Medicines Institute - Narodowy Instytut Leków [Warsaw] (NIL), Faculty of Public Health [Lebanese University] (FSP III), Lebanese University [Beirut] (LU), Institut National de la Recherche Agronomique (INRA), Laboratoire de bactériologie, CHU Clermont-Ferrand, LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), National Medicines Institute, National Medicines Institute of Warsaw, Faculty of Public Health [Tripoli, Liban] (FSP III), Lebanese University [Beirut], Evolution des bactéries pathogènes et susceptibilité génétique de l'hôte (JE2526), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA), and LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs)
Subjects: Klebsiella pneumoniae, MESH: Klebsiella pneumoniae, MESH: beta-Lactamases, MESH: Virulence, medicine.disease_cause, Pharmacology (medical), Overproduction, chemistry.chemical_classification, 0303 health sciences, Mutation, Cross Infection, MESH: Microbial Sensitivity Tests, Strain (chemistry), Virulence, β lactamases, MESH: Amino Acid Substitution, 3. Good health, Infectious Diseases, MESH: Klebsiella Infections, MESH: Poland, MESH: Mutation, Virulence Factors, Microbial Sensitivity Tests, Biology, beta-Lactamases, Microbiology, 03 medical and health sciences, Mechanisms of Resistance, medicine, Potency, Humans, Epidemics, MESH: Epidemics, 030304 developmental biology, MESH: Virulence Factors, Pharmacology, MESH: Humans, 030306 microbiology, MESH: Cross Infection, biology.organism_classification, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Klebsiella Infections, Enzyme, chemistry, Amino Acid Substitution, Poland
Abstract: Two Klebsiella pneumoniae isolates of the same strain, identified in Poland, produced either TEM-47 or TEM-68, which differed by the Arg275Leu substitution. They harbored a few virulence factors, including an iron-chelating factor and capsule overproduction, suggesting that these factors were sufficient to enhance their nosocomial potency. TEM-68 and TEM-47 had similar enzymatic activities, but TEM-68 was less susceptible to inhibitors than TEM-47. These results confirm the role of the Arg275Leu substitution in the evolution of TEM enzymes.
Published: 2012

42. [Sleeping sickness: end of the epidemic outbreak?]

Author: Bisser, Sylvie, Courtioux, Bertrand, Neuroépidémiologie Tropicale (NET), Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-CHU Limoges-Institut d'Epidémiologie Neurologique et de Neurologie Tropicale-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université de Limoges (UNILIM)
Subjects: Trypanosoma brucei rhodesiense, MESH: Humans, Trypanosoma brucei gambiense, MESH: Polymerase Chain Reaction, MESH: Africa, Polymerase Chain Reaction, MESH: Trypanosoma brucei gambiense, MESH: Trypanosomiasis, African, Trypanosomiasis, African, Africa, Animals, Humans, MESH: Animals, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Epidemics, MESH: Trypanosoma brucei rhodesiense, MESH: Epidemics
Abstract: International audience; Sleeping sickness or human African trypanosomiasis is a parasitic disease transmitted by tsetse flies and therefore confined to its habitat, the central part of the African continent. Two disease forms are linked to two different parasites: T. b. gambiense and T. b. rhodesiense. Actual epidemiological data and precise and dynamic mapping of foci are in favor of a real decrease of the disease. Not all areas are under control and resurgence can still not be avoided from the remote areas where the disease is endemic. However, recent advances in knowledge in parasite genetics are giving hope of control. In 2009, for the first time since 50 years, less than 10,000 cases were declared to the World Health Organization. Clinical trials allowed revising some clinical concepts and linking them with parasite genetics: both disease forms can show variations from asymptomatic, chronic to acute and are linked to genetic differences in the host or the parasite. Parasitological diagnosis may be facilitated by the introduction of individual rapid tests and PCR-based field tests. Knowledge in mechanisms of brain invasion and screenings of inflammatory molecules allow new marker combinations for staging but they do not avoid lumbar puncture. Therapeutic options remain limited but there is hope to develop a new drug orally available in a near future.
Published: 2011

43. Emergence of Epidemic Neisseria meningitidis Serogroup X Meningitis in Togo and Burkina Faso

Author: Aly Drabo, Judith E. Mueller, Tsidi Agbeko Tamekloe, Bradford D. Gessner, Berthe Marie Njanpop-Lafourcade, Macaire S. Ouedraogo, Philippe Jaillard, Oumarou Sanou, Seydou Yaro, Kossi Badziklou, Isabelle Delrieu, Jean Ludovic Kambou, Haoua Tall, Agence de Médecine Préventive, École des Hautes Études en Santé Publique [EHESP] (EHESP), and Département Méthodes quantitatives en santé publique (METIS)
Subjects: Serotype, Bacterial Diseases, Veterinary medicine, Etiology, Epidemiology, lcsh:Medicine, Meningococcal Disease, Neisseria meningitidis, medicine.disease_cause, Global Health, Polymerase Chain Reaction, Disease Outbreaks, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, Cumulative incidence, MESH: Incidence, 030212 general & internal medicine, MESH: Disease Outbreaks, lcsh:Science, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, Disease surveillance, Incidence (epidemiology), Incidence, MESH: Meningitis, Meningococcal, 3. Good health, Infectious Diseases, Population Surveillance, Togo, Public Health, African meningitis belt, Meningitis, Research Article, Infectious Disease Control, 030231 tropical medicine, Meningitis, Meningococcal, Microbiology, MESH: Neisseria meningitidis, Infectious Disease Epidemiology, MESH: Population Surveillance, 03 medical and health sciences, Bacterial Meningitis, parasitic diseases, Burkina Faso, Humans, MESH: Burkina Faso, Serotyping, Epidemics, Biology, MESH: Epidemics, MESH: Humans, business.industry, lcsh:R, MESH: Serotyping, Outbreak, MESH: Polymerase Chain Reaction, medicine.disease, Virology, MESH: DNA, Viral, Emerging Infectious Diseases, MESH: Togo, DNA, Viral, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Preventive Medicine, business, MenAfriVac
Abstract: International audience; Serogroup X meningococci (NmX) historically have caused sporadic and clustered meningitis cases in sub-Saharan Africa. To study recent NmX epidemiology, we analyzed data from population-based, sentinel and passive surveillance, and outbreak investigations of bacterial meningitis in Togo and Burkina Faso during 2006-2010. Cerebrospinal fluid specimens were analyzed by PCR. In Togo during 2006-2009, NmX accounted for 16% of the 702 confirmed bacterial meningitis cases. Kozah district experienced an NmX outbreak in March 2007 with an NmX seasonal cumulative incidence of 33/100,000. In Burkina Faso during 2007-2010, NmX accounted for 7% of the 778 confirmed bacterial meningitis cases, with an increase from 2009 to 2010 (4% to 35% of all confirmed cases, respectively). In 2010, NmX epidemics occurred in northern and central regions of Burkina Faso; the highest district cumulative incidence of NmX was estimated as 130/100,000 during March-April. Although limited to a few districts, we have documented NmX meningitis epidemics occurring with a seasonal incidence previously only reported in the meningitis belt for NmW135 and NmA, which argues for development of an NmX vaccine.
Published: 2011

44. Clonal spread of Streptococcus pyogenes emm44 among homeless persons, Rennes, France

Author: Céline Plainvert, Matthieu Revest, Anne Cady, Samer Kayal, Pierre-Yves Donnio, Anne Bouvet, Didier Huguenet, Pascaline Loury, Alain Briand, Microbiologie : Risques Infectieux, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes]-Faculté de Chirurgie Dentaire de Rennes-Faculté d'Odontologie-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Service des maladies infectieuses et réanimation médicale [Rennes] = Infectious Disease and Intensive Care [Rennes], CHU Pontchaillou [Rennes], Université de Rennes (UR)-CHU Pontchaillou [Rennes]-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Université de Rennes - UFR d'Odontologie (UR Odontologie), Université de Rennes (UR)-Université de Rennes (UR), Université de Rennes (UR)-CHU Pontchaillou [Rennes]-Faculté de Chirurgie Dentaire de Rennes-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Brébion, Alice
Subjects: MESH: Tetracycline Resistance, Male, Epidemiology, medicine.medical_treatment, lcsh:Medicine, Skin infection, medicine.disease_cause, MESH: Tetracycline, Polymerase Chain Reaction, 0302 clinical medicine, MESH: Streptococcal Infections, 030212 general & internal medicine, Fasciitis, ComputingMilieux_MISCELLANEOUS, MESH: Aged, MESH: Microbial Sensitivity Tests, 0303 health sciences, MESH: Middle Aged, drug users, homeless persons, 1. No poverty, Tetracycline Resistance, Immunosuppression, Middle Aged, Pharyngitis, 3. Good health, Anti-Bacterial Agents, Electrophoresis, Gel, Pulsed-Field, skin infections, MESH: Electrophoresis, Gel, Pulsed-Field, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, MESH: Young Adult, Cellulitis, Ill-Housed Persons, Female, France, medicine.symptom, MESH: Streptococcus pyogenes, Bacterial Outer Membrane Proteins, Microbiology (medical), Adult, Streptococcus pyogenes, letter, MESH: Carrier Proteins, Microbial Sensitivity Tests, Biology, lcsh:Infectious and parasitic diseases, Microbiology, 03 medical and health sciences, Young Adult, MESH: Anti-Bacterial Agents, Streptococcal Infections, medicine, Humans, lcsh:RC109-216, Epidemics, Letters to the Editor, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Epidemics, Aged, Antigens, Bacterial, MESH: Humans, Bacteria, 030306 microbiology, lcsh:R, MESH: Bacterial Outer Membrane Proteins, MESH: Homeless Persons, Toxic shock syndrome, MESH: Adult, MESH: Polymerase Chain Reaction, Tetracycline, medicine.disease, MESH: Male, MESH: France, emm typing, Bacteremia, Immunology, Carrier Proteins, MESH: Female, MESH: Antigens, Bacterial
Abstract: To the Editor: Streptococcus pyogenes, or group A streptococci (GAS), are human pathogens responsible for pharyngitis as well as skin and soft tissue infections. Invasive GAS diseases, including bacteremia, cellulitis, and necrotizing fasciitis, are life-threatening, especially when associated with toxic shock syndrome. Several risk factors for GAS infections are known, such as diabetes, immunosuppression, drug use, and skin lesions (1,2).
Published: 2011

45. Distinct Clones of Yersinia pestis Caused the Black Death

Author: Elisabeth Carniel, Derek Hurst, Raffaella Bianucci, Michel Signoli, Sacha Kacki, Marco Vermunt, Stephanie Haensch, Barbara Bramanti, Mark Achtman, Michael D. Schultz, Minoarisoa Rajerison, Darlene A. Weston, Besansky, Nora J., Institute for Anthropology, Johannes Gutenberg - Universität Mainz (JGU), Laboratory of Criminialistic sciences Department of anatomy Turin, University of Turin, UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centre d'Études Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Unité Peste - Plague Unit [Antananarivo, Madagascar], Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Department of Anatomy and Embryology Medical Faculty, Georg-August-University [Göttingen], Institut national de recherches archéologiques préventives (Inrap), Laboratoire d'anthropologie des populations du passé, Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Department of Monuments and Archaeology, Municipality of Bergen op Zoom, Barge's Anthropologica, Department of Anatomy and Embryology, Leiden University Medical Center (LUMC), Division of Archaeological Sciences, University of Bradford, Department of Human Evolution [Leipzig], Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Worcestershire Historic Environment and Archaeology Service, Worcestershire County Council, Department of Microbiology and Environmental Research Institute (Cork, Ireland), University College Cork (UCC), Yersinia, Institut Pasteur [Paris], This research was supported by grants from the Deutsche Forschungsgemeinschaft (DFG Br 2965/1-1 and Br 2965/1-2), the University of Mainz (FP1-2007) and the Science Foundation of Ireland (05/FE1/B882). The RDT analysis was supported by Compagnia di San Paolo (2007.0171), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Università degli studi di Torino = University of Turin (UNITO), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Georg-August-University = Georg-August-Universität Göttingen, Université Sciences et Technologies - Bordeaux 1 (UB)-Centre National de la Recherche Scientifique (CNRS), Universiteit Leiden-Universiteit Leiden, and Institut Pasteur [Paris] (IP)
Subjects: Yersinia pestis, [SDV]Life Sciences [q-bio], Sequence Homology, Disease, MESH: Base Sequence, MESH: Genetic Markers, [SHS]Humanities and Social Sciences, Disease Outbreaks, Infectious Diseases/Bacterial Infections, MESH: Genotype, Genotype, Mass Screening, Biology (General), MESH: Disease Outbreaks, MESH: Phylogeny, Clade, Phylogeny, Genetics, 0303 health sciences, Microbiology/Microbial Evolution and Genomics, biology, Clones, Black Death, Bacterial, Genetics and Genomics/Microbial Evolution and Genomics, 3. Good health, Europe, Evolutionary Biology/Human Evolution, Infectious Diseases, Research Article, DNA, Bacterial, Genetic Markers, QH301-705.5, Molecular Sequence Data, Immunology, MESH: Yersinia pestis, Zoology, Molecular Biology/Molecular Evolution, Plague (disease), MESH: Plague, MESH: Sequence Homology, Nucleic Acid, Microbiology, NO, 03 medical and health sciences, Phylogenetics, Sequence Homology, Nucleic Acid, Virology, Humans, MESH: Mass Screening, Epidemics, Molecular Biology, MESH: Epidemics, Mass screening, 030304 developmental biology, Plague, Evolutionary Biology, MESH: Humans, MESH: Molecular Sequence Data, Nucleic Acid, Base Sequence, 030306 microbiology, Genetics and Genomics, DNA, RC581-607, biology.organism_classification, MESH: DNA, Bacterial, Etiology, Parasitology, MESH: Europe, Immunologic diseases. Allergy
Abstract: From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18th century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to conclusions that it must have been caused by other pathogens. It has also been disputed whether plague had the same etiology in northern and southern Europe. Here we identified DNA and protein signatures specific for Y. pestis in human skeletons from mass graves in northern, central and southern Europe that were associated archaeologically with the Black Death and subsequent resurgences. We confirm that Y. pestis caused the Black Death and later epidemics on the entire European continent over the course of four centuries. Furthermore, on the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route. These two clades are ancestral to modern isolates of Y. pestis biovars Orientalis and Medievalis. Our results clarify the etiology of the Black Death and provide a paradigm for a detailed historical reconstruction of the infection routes followed by this disease., Author Summary Several historical epidemic waves of plague have been attributed to Yersinia pestis, the etiologic agent of modern plague. The most famous of these was the second pandemic which was active in Europe from AD 1347 until 1750, and began with the ‘Black Death’. The most informative method to establish the etiological nature of these ancient infections should be the analysis of ancient DNA, but the results of this method have been controversial. Here, by combining ancient DNA analyses and protein-specific detection, we demonstrate unambiguously that Y. pestis caused the Black Death. Furthermore, we show that at least two variants of Y. pestis spread over Europe during the second pandemic. The analysis of up to 20 diagnostic markers reveals that the two variants evolved near the time that phylogenetic branches 1 and 2 separated and may no longer exist. Our results thus resolve a long-standing debate about the etiology of the Black Death and provide key information about the evolution of the plague bacillus and the spread of the disease during the Middle Ages.
Published: 2010

46. Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential

Author: Kenneth A. Stapleford, Sreyrath Lay, Veasna Duong, Isabelle Bonne, Camilo Arias-Goeta, Christine Schmitt, Hervé Blanc, Anna-Bella Failloux, Stéphanie Beaucourt, Kathryn Rozen-Gagnon, Lark L. Coffey, Turkan Haliloglu, Ofer Isakov, Noam Shomron, Marco Vignuzzi, Antonio V. Bordería, Philippe Buchy, Nir Ben-Tal, Populations virales et Pathogenèse - Viral Populations and Pathogenesis, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of California [Davis] (UC Davis), University of California (UC), Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Sackler Faculty of Medicine, Tel Aviv University (TAU), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Boǧaziçi üniversitesi = Boğaziçi University [Istanbul], Microscopie ultrastructurale - Ultrapole (CITECH), This work was supported by the European Research Council (ERC Starting Grant No. 242719), by the Bill and Melinda Gates Foundation Grand Challenges Exploration Initiative, the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant ANR-10-LABX-62-IBEID), and the Israel-France High Council for Science and Technology Research 'Complexity in Biology' program. Salary for L.L.C. and K.A.S. was provided by the Region of Ile-de-France DIM program on Infectious, Parasitic or Nosocomial Emerging Diseases and the Philippe Foundation. Salary for A.V.B. was supported by the French National grant ANR-09-JCJC-0118-1. Salary for C.A.-G. was supported by the French Ministry of Superior Education and Research. N.B.-T. and T.H. were supported by NATO traveling grant CBP.MD.CLG 984340., We are grateful to Ngan Chantha, Huy Rekol, and the team of the National Malaria Centre in Cambodia for providing clinical specimens. We thank Christophe Paupy (IRD), Louis Lambrechts, and Paul Reiter (IP) for providing some mosquito strains., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-09-JCJC-0118,QuasispeciesVax(2009), European Project: 242719,EC:FP7:ERC,ERC-2009-StG,RNAVIRUSPOPDIVNVAX(2009), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of California, Tel Aviv University [Tel Aviv], Institut Pasteur [Paris], and Boğaziçi University [Istanbul]
Subjects: Cancer Research, Mutation rate, viruses, MESH: Chikungunya Fever, medicine.disease_cause, Virus Replication, Aedes, MESH: Arboviruses, MESH: Animals, MESH: Genetic Variation, Chikungunya, Epidemic strain, Genetics, Mammals, Transmission (medicine), virus diseases, MESH: Aedes, Viral Load, Biological Evolution, 3. Good health, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Host-Pathogen Interactions, MESH: Arbovirus Infections, Female, MESH: Viral Load, Cambodia, Chikungunya virus, MESH: Biological Evolution, MESH: Insect Vectors, Biology, Arbovirus Infections, Microbiology, Arbovirus, MESH: Mammals, Virus, Article, MESH: Mice, Inbred C57BL, Immunology and Microbiology(all), Virology, parasitic diseases, medicine, Animals, Humans, MESH: Saliva, Epidemics, Saliva, Molecular Biology, MESH: Epidemics, MESH: Humans, MESH: Cambodia, MESH: Host-Pathogen Interactions, MESH: Virus Replication, fungi, RNA, Genetic Variation, MESH: Chikungunya virus, medicine.disease, Insect Vectors, Mice, Inbred C57BL, Disease Models, Animal, Population bottleneck, Culicidae, Chikungunya Fever, Parasitology, MESH: Disease Models, Animal, MESH: Culicidae, MESH: Female, Arboviruses
Abstract: Comment in: "Toward an activist agenda for monitoring virus emergence."https://doi.org/10.1016/j.chom.2014.05.014; International audience; The high replication and mutation rates of RNA viruses can result in the emergence of new epidemic variants. Thus, the ability to follow host-specific evolutionary trajectories of viruses is essential to predict and prevent epidemics. By studying the spatial and temporal evolution of chikungunya virus during natural transmission between mosquitoes and mammals, we have identified viral evolutionary intermediates prior to emergence. Analysis of virus populations at anatomical barriers revealed that the mosquito midgut and salivary gland pose population bottlenecks. By focusing on virus subpopulations in the saliva of multiple mosquito strains, we recapit-ulated the emergence of a recent epidemic strain of chikungunya and identified E1 glycoprotein mutations with potential to emerge in the future. These mutations confer fitness advantages in mosquito and mammalian hosts by altering virion stability and fusogenic activity. Thus, virus evolutionary tra-jectories can be predicted and studied in the short term before new variants displace currently circulating strains.
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