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1. Highly Pathogenic Avian Influenza A(H5N8) Virus Spread by Short- and Long-Range Transmission, France, 2016–17

Author

Audrey Schmitz, François-Xavier Briand, Florian Kerbrat, Eric Niqueux, Yannick Blanchard, Marina Chatel, Béatrice Grasland, Chantal Allée, Véronique Béven, Katell Ogor, Axelle Scoizec, Carole Guillemoto, Sophie Le Bouquin, Martine Cherbonnel, Nicolas Eterradossi, Edouard Hirchaud, Pascale Massin, Cécile Guillou-Cloarec, Aurélie Le Prioux, Claire Martenot, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and Fonds de la Recherche pour l’Influenza Aviaire 2019 from the French Ministry of Agriculture

Subjects
Epidemiology, Range (biology), viruses, highly pathogenic, lcsh:Medicine, medicine.disease_cause, epizootic, Disease Outbreaks, law.invention, 0302 clinical medicine, law, Genotype, Pathogenic Avian Influenza A(H5N8) Virus Spread by Short- and Long-Range Transmission, France, 2016–17, MESH: Influenza A Virus, H5N8 Subtype, Influenza A Virus, H5N8 Subtype, 030212 general & internal medicine, MESH: Phylogeny, Phylogeny, Phylogenetic tree, transmission, Infectious Diseases, Transmission (mechanics), MESH: Birds, France, influenza, Microbiology (medical), Highly pathogenic, 030231 tropical medicine, Zoology, Animals, Wild, Biology, Virus, lcsh:Infectious and parasitic diseases, Birds, 03 medical and health sciences, MESH: Influenza in Birds, H5N8, genotypes, evolution, medicine, Animals, MESH: Animals, Wild, lcsh:RC109-216, highly pathogenic avian influenza, Epizootic, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, viral zoonoses, Research, geoclusters, lcsh:R, medicine.disease, Influenza A virus subtype H5N1, zoonoses, MESH: France, Influenza in Birds, avian influenza
Abstract

International audience; We detected 3 genotypes of highly pathogenic avian influenza A(H5N8) virus in France during winter 2016–17. Genotype A viruses caused dramatic economic losses in the domestic duck farm industry in southwestern France. Our phylogenetic analysis suggests that genotype A viruses formed 5 distinct geographic clusters in southwestern France. In some clusters, local secondary transmission might have been started by a single introduction. The intensity of the viral spread seems to correspond to the density of duck holdings in each production area. To avoid the introduction of disease into an unaffected area, it is crucial that authorities limit the movements of potentially infected birds.

Published
2021

2. Role of Backyard Flocks in Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N8) Clade 2.3.4.4, France, 2016–2017

Author

Audrey Schmitz, Luc Robertet, Eric Niqueux, Marie Souvestre, Claire Guinat, Nicolas Eterradossi, Guillaume Croville, Mathilde Paul, Anne Bronner, Jean-Luc Guérin, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Ploufragan - Plouzané, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Direction Générale de l'Alimentation (DGAL), This project was implemented through the Chaire de Biosécurité Aviaire, granted by the French Ministry of Agriculture (Direction Générale de l’Alimentation). The research leading to these results received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. PCOFUND-GA-2013-609102, through the PRESTIGE Programme coordinated by Campus France., European Project: 609102,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,PRESTIGE(2014), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
Epidemiology, [SDV]Life Sciences [q-bio], animal diseases, Biosecurity, lcsh:Medicine, HPAI, medicine.disease_cause, Disease Outbreaks, law.invention, 0302 clinical medicine, Seroepidemiologic Studies, law, Role of Backyard Flocks in Transmission Dynamics of Highly Pathogenic Avian Influenza A(H5N8) Clade 2.3.4.4, France, 2016–2017, Odds Ratio, risk factors, Influenza A Virus, H5N8 Subtype, 030212 general & internal medicine, Clade, Avian influenza virus, poultry, Dispatch, France, H5N8, backyard flocks, biosecurity, clade 2.3.4.4, highly pathogenic avian influenza, influenza, viruses, zoonoses, Infectious Diseases, Transmission (mechanics), Microbiology (medical), Farms, Highly pathogenic, 030231 tropical medicine, Enzyme-Linked Immunosorbent Assay, Biology, History, 21st Century, lcsh:Infectious and parasitic diseases, Birds, 03 medical and health sciences, medicine, Animals, lcsh:RC109-216, Poultry Diseases, lcsh:R, Virology, Influenza A virus subtype H5N1, Molecular Typing, Influenza in Birds, Flock
Abstract

International audience; Highly pathogenic avian influenza A(H5N8) clade 2.3.4.4 spread in France during 2016-2017. We assessed the biosecurity and avian influenza virus infection status of 70 backyard flocks near H5N8-infected commercial farms. One flock was seropositive for clade 2.3.4.4. Backyard flocks linked to commercial farms had elevated risk for H5 infection.

Published
2019

3. Sustained Low-Level Transmission of Zika and Chikungunya Viruses after Emergence in the Fiji Islands

Author

Jessica Vanhomwegen, Taina Naivalu, Teheipuaura Mariteragi-Helle, Colleen L. Lau, John Aaskov, Jean-Claude Manuguerra, Maite Aubry, Conall H. Watson, Van-Mai Cao-Lormeau, Anita Teissier, Stéphane Hué, Martin L. Hibberd, Ketan S. Christi, Adam J. Kucharski, Mike Kama, Tuterarii Paoaafaite, Didier Musso, Eric J. Nilles, Fiji Centre for Communicable Disease Control [Suva, Fidji], University of the South Pacific (USP), Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Fiji National University, Institut Pasteur [Paris] (IP), London School of Hygiene and Tropical Medicine (LSHTM), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Brigham & Women’s Hospital [Boston] (BWH), Harvard Medical School [Boston] (HMS), Harvard Humanitarian Initiative [Cambridge, Massachusetts], Queensland University of Technology [Brisbane] (QUT), Australian National University (ANU), Aix Marseille Université (AMU), This work was part of ISID-Pacific and R-ZERO Pacific programs funded by the French Ministry for Europe and Foreign Affairs (Pacific Fund nos. 06314-09/04/14, 12115-02/09/15, 03016-20/05/16, and 04917-19/07/17). The study also received support from the Embassy of France in the Republic of the Fiji Islands. The study was supported by the French Government’s 'Investissement d’Avenir' Program (Labex IBEID no. ANR-10-LABX-62-IBEID). C.L.L. was supported by an Australia National Health and Medical Research Council Fellowship (grant no. 1109035). A.J.K. was supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (grant no. 206250/Z/17/Z). The seroprevalence study was part of MSc research work by M.K. performed at the University of the South Pacific., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and Institut Pasteur [Paris]

Subjects
Male, MESH: Sequence Analysis, DNA, chikungunya, Epidemiology, viruses, vector-borne infections, lcsh:Medicine, MESH: Chikungunya Fever, medicine.disease_cause, phylogeny, law.invention, Dengue fever, Disease Outbreaks, 0302 clinical medicine, Viral Envelope Proteins, law, MESH: Risk Factors, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Risk Factors, Seroepidemiologic Studies, 030212 general & internal medicine, Chikungunya, MESH: Fiji, MESH: Disease Outbreaks, MESH: Phylogeny, Islands, mosquitoborne diseases, Phylogenetic tree, seroprevalence, Zika Virus Infection, Dispatch, virus diseases, 3. Good health, Infectious Diseases, Transmission (mechanics), arboviruses, Population Surveillance, surveillance, Female, Chikungunya virus, Microbiology (medical), MESH: Islands, 030231 tropical medicine, MESH: Zika Virus, Sustained Low-Level Transmission of Zika and Chikungunya Viruses after Emergence in the Fiji Islands, Biology, Virus, MESH: Population Surveillance, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, MESH: Zika Virus Infection, Zika, Phylogenetics, medicine, Seroprevalence, Fiji, Humans, lcsh:RC109-216, MESH: Humans, MESH: Seroepidemiologic Studies, lcsh:R, Outbreak, MESH: Chikungunya virus, Sequence Analysis, DNA, Zika Virus, medicine.disease, Virology, dengue, MESH: Male, Pacific, MESH: Viral Envelope Proteins, Chikungunya Fever, MESH: Female
Abstract

International audience; Zika and chikungunya viruses were first detected in Fiji in 2015. Examining surveillance and phylogenetic and serologic data, we found evidence of low-level transmission of Zika and chikungunya viruses during 2013-2017, in contrast to the major outbreaks caused by closely related virus strains in other Pacific Island countries.

Published
2019

4. Emergence of Neisseria meningitidis Serogroup W, Central African Republic, 2015–2016

Author

Jean-Robert Mbecko, Eva Hong, Muhamed-Kheir Taha, Thierry Frank, Jean-Pierre Lombart, Pierre-Alain Rubbo, Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Centre National de Référence des Méningocoques et Haemophilus influenzae - National Reference Center Meningococci and Haemophilus influenzae (CNR), Institut Pasteur [Paris] (IP), This work was supported by the French Ministry of Foreign Affairs and Institut Pasteur, Bangui, Central African Republic, and Paris, France., and Institut Pasteur [Paris]

Subjects
0301 basic medicine, Microbiology (medical), Male, sub-Saharan Africa, Adolescent, Epidemiology, 030106 microbiology, lcsh:Medicine, Biology, Meningitis, Meningococcal, Neisseria meningitidis, medicine.disease_cause, Serogroup, epidemics, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 0302 clinical medicine, Meningitis/encephalitis, medicine, Humans, lcsh:RC109-216, 030212 general & internal medicine, serogroup W, Child, Emergence of Neisseria meningitidis Serogroup W, Central African Republic, 2015–2016, bacteria, Sequence (medicine), Disease surveillance, Neisseria meningitidis serogroup, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], lcsh:R, Dispatch, meningococci, Infant, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virology, 3. Good health, Bacterial Typing Techniques, Central African Republic, Infectious Diseases, Child, Preschool, surveillance, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Female, meningitis/encephalitis, Meningitis, Multilocus Sequence Typing
Abstract

International audience; We analyzed data from the 2015 and 2016 meningitis epidemic seasons in Central African Republic as part of the national disease surveillance. Of 80 tested specimens, 66 belonged to meningococcal serogroup W. Further analysis found that 97.7% of 44 isolates belonged to the hyperinvasive clonal complex sequence type 11.

Published
2018

5. Reemergence of Chikungunya Virus in Cambodia

Author

Denis R. St. Laurent, Veasna Duong, Anne-Claire Andries, Bunheng Hok, Philippe Buchy, Nima Asgari-Jirhandeh, Meng Chuor Char, Maria Concepcion Roces, Sovann Ly, Rekol Huy, Chantha Ngan, Beat Richner, Arnaud Tarantola, Touch Sok, Steve Bjorge, Vincent Deubel, Sivuth Ong, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP), Ministry of Health [Phnom Penh], Jayavarman VII Hospital, World Health Organization [Phnom Penh] (WHO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Preah Vihear Provincial Health Department, Key Laboratory of Molecular Virology & Immunology (LMVI), Institut Pasteur de Shanghai, Académie des Sciences de Chine - Chinese Academy of Sciences (IPS-CAS), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), and This work was supported by French Ministry of Research. The serosurveillance studies and outbreak response were funded by a World Health Organization grant to the Ministry of Health and Institut Pasteur in Cambodia in 2011. The World Health Organization acknowledges the Korea International Cooperation Agency and the World Bank for their generous support for these activities.

Subjects
Microbiology (medical), Adult, Male, Adolescent, Epidemiology, viruses, lcsh:Medicine, Biology, medicine.disease_cause, Antibodies, Viral, East Central and South African genotype, Communicable Diseases, Emerging, Virus, Disease Outbreaks, lcsh:Infectious and parasitic diseases, Viral Proteins, Young Adult, Phylogenetics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genotype, parasitic diseases, medicine, Humans, Public Health Surveillance, lcsh:RC109-216, Chikungunya, Alphavirus infection, Child, genome, Phylogeny, Phylogenetic tree, Alphavirus Infections, lcsh:R, Dispatch, virus diseases, Middle Aged, medicine.disease, Virology, Southeast Asia, Infectious Diseases, Immunoglobulin M, Child, Preschool, RNA, Viral, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Cambodia, Chikungunya virus
Abstract

International audience; Chikungunya virus (CHIKV), probably Asian genotype, was first detected in Cambodia in 1961. Despite no evidence of acute or recent CHIKV infections since 2000, real-time reverse transcription PCR of serum collected in 2011 detected CHIKV, East Central South African genotype. Spatiotemporal patterns and phylogenetic clustering indicate that the virus probably originated in Thailand.

Published
2012

6. Molecular Epidemiology of Clade 1 Influenza A Viruses (H5N1), Southern Indochina Peninsula, 2004–2007

Author

Peiris, J S Malik, Buchy, Philippe, Fourment, Mathieu, Mardy, Sek, Sorn, San, Holl, Davun, Ly, Sowath, Vong, Sirenda, Enouf, Vincent, Peiris, J.S. Malik, Van Der Werf, Silvie, Centre de recherche Université de Hong-Kong-Pasteur, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur du Cambodge, Ministry of Agriculture, Forestry and Fisheries [Cambodia], Génétique moléculaire des virus à ARN, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This study was supported by the French Ministry of Health, the French Agency for Development and the US Department of Human Health Services., Buchy P, Fourment M, Mardy S, Sorn S, Holl D, Ly S, Vong S, Enouf V, Peiris JS, van der Werf S., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Time Factors, Epidemiology, viruses, animal diseases, lcsh:Medicine, medicine.disease_cause, Disease Outbreaks, Influenza A Virus, Influenza A virus, MESH: Animals, MESH: Disease Outbreaks, Clade, Molecular Epidemiology, 0303 health sciences, MESH: Influenza, Human, poultry, Dispatch, transmission, virus diseases, H5N1, Thailand, Infectious Diseases, Vietnam, MESH: Birds, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, H5N1 Subtype, influenza, Cambodia, Human, Microbiology (medical), medicine.medical_specialty, MESH: Influenza A Virus, H5N1 Subtype, Wild, Animals, Wild, Biology, Microbiology, Virus, lcsh:Infectious and parasitic diseases, Birds, 03 medical and health sciences, MESH: Influenza in Birds, Molecular genetics, Influenza, Human, parasitic diseases, medicine, MESH: Molecular Epidemiology, Animals, Humans, MESH: Animals, Wild, lcsh:RC109-216, wild birds, 030304 developmental biology, MESH: Humans, Influenza A Virus, H5N1 Subtype, Molecular epidemiology, 030306 microbiology, MESH: Cambodia, MESH: Time Factors, lcsh:R, Influenza a, Virology, Influenza A virus subtype H5N1, Influenza in Birds, Indochina peninsula
Abstract

International audience; To determine the origin of influenza A virus (H5N1) epizootics in Cambodia, we used maximum-likelihood and Bayesian methods to analyze the genetic sequences of subtype H5N1 strains from Cambodia and neighboring areas. Poultry movements, rather than repeated reintroduction of subtype H5N1 viruses by wild birds, appear to explain virus circulation and perpetuation.

Published
2009

7. Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France

Author

Jérôme Mariette, Guillaume Croville, Mariette F. Ducatez, Marie Noëlle Lucas, Leni Corrand, Jérôme Lluch, Christophe Klopp, Cécile Donnadieu, Jean-Luc Guérin, Maxence Delverdier, Etienne Liais, James S. Guy, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire de Toulouse (ENVT), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), French Ministry of Agriculture, Region Midi-Pyrenees, and French Comite Interprofessionnel de la Pintade

Subjects
Epidemiology, viruses, coronavirus, lcsh:Medicine, Disease, medicine.disease_cause, 0403 veterinary science, Genotype, Avian coronavirus, Galliformes, Phylogeny, Coronavirus, Bird Diseases, Animal biology, 0303 health sciences, Gammacoronavirus, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Microbiology and Parasitology, Dispatch, 04 agricultural and veterinary sciences, Microbiologie et Parasitologie, 3. Good health, Santé publique et épidémiologie, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Spike Glycoprotein, Coronavirus, Coronavirus Infections, france, zoonose, Microbiology (medical), avian coronavirus, animal structures, 040301 veterinary sciences, Molecular Sequence Data, Genome, Viral, virus, lcsh:Infectious and parasitic diseases, Enteritis, 03 medical and health sciences, Biologie animale, medicine, Animals, lcsh:RC109-216, 030304 developmental biology, Essays, métagénomique, metagenomics, Guinea fowl, fulminating disease, lcsh:R, guinea fowl, next-generation sequencing, zoonoses, medicine.disease, biology.organism_classification, Virology, Molecular Typing, séquençage nouvelle génération, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract

International audience; For decades, French guinea fowl have been affected by fulminating enteritis of unclear origin. By using metagenomics, we identified a novel avian gammacoronavirus associated with this disease that is distantly related to turkey coronaviruses. Fatal respiratory diseases in humans have recently been caused by coronaviruses of animal origin.

Published
2014
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8. Dengue spatial and temporal patterns, French Guiana, 2001

Author

P. Rabarison, Franck Remy, Jacques Gardon, Jacques Morvan, Annelise Tran, Philippe Dussart, Laurent Polidori, Xavier Deparis, Institut de Recherche pour le Développement (IRD [Guyane]), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], and This study was carried out within a wider research program on remote sensing and epidemiology, funded by the European Commission (FEDER funds), the French Ministry of Research (RNTS Network funds), and the Regional Council of French Guiana.

Subjects
Geographic information system, Time Factors, Epidemiology, SYSTEME D'INFORMATION GEOGRAPHIQUE, lcsh:Medicine, MESH: Dengue, L73 - Maladies des animaux, Dengue fever, Disease Outbreaks, Dengue, Aedes aegypti, 0302 clinical medicine, VARIATION TEMPORELLE, Système d'information géographique, Dengue transmission, dengue fever, 030212 general & internal medicine, MESH: Disease Outbreaks, biology, Geographic Information System, Virus, 3. Good health, French Guiana, Épidémiologie, Vecteur de maladie, Infectious Diseases, Geography, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MOUSTIQUE, VIRUS, Spatio temporal clustering, Cartography, Microbiology (medical), DENGUE, TECHNIQUE RT PCR, 030231 tropical medicine, Epidemic, lcsh:Infectious and parasitic diseases, Fièvre, 03 medical and health sciences, SURVEILLANCE, MESH: French Guiana, medicine, Humans, lcsh:RC109-216, Epidemiologic Factors, MESH: Geographic Information Systems, Spatial analysis, SEROLOGIE, MESH: Humans, business.industry, Technique immunologique, Research, lcsh:R, VECTEUR, MESH: Time Factors, Outbreak, Distribution spatiale, PREVENTION SANITAIRE, biology.organism_classification, medicine.disease, control strategy, VARIATION SPATIALE, Geographic Information Systems, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, space-time analysis, Virose
Abstract

International audience; To study a 2001 dengue fever outbreak in Iracoubo, French Guiana, we recorded the location of all patients' homes and the date when symptoms were first observed. A geographic information system (GIS) was used to integrate the patient-related information. The Knox test, a classic space-time analysis technique, was used to detect spatiotemporal clustering. Analysis of the relative-risk (RR) variations when space and time distances vary, highlighted the maximum space and time extent of a dengue transmission focus. The results show that heterogeneity in the RR variations in space and time corresponds to known entomologic and epidemiologic factors, such as the mosquito feeding cycle and host-seeking behavior. This finding demonstrates the relevance and potential of the use of GIS and spatial statistics for elaborating a dengue fever surveillance strategy.

Published
2004

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