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1. One Health surveillance of West Nile and Usutu viruses

Author

Orianne Constant, Patricia Gil, Jonathan Barthelemy, Karine Bolloré, Vincent Foulongne, Caroline Desmetz, Agnès Leblond, Isabelle Desjardins, Sophie Pradier, Aurélien Joulié, Alain Sandoz, Rayane Amaral, Michel Boisseau, Ignace Rakotoarivony, Thierry Baldet, Albane Marie, Benoît Frances, Florence Reboul Salze, Bachirou Tinto, Philippe Van de Perre, Sara Salinas, Cécile Beck, Sylvie Lecollinet, Serafin Gutierrez, Yannick Simonin, Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier]-Université de Montpellier (UM), 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), Biocommunication en Cardio-Métabolique (BC2M), Université de Montpellier (UM), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), GREMERES ICE, Clinique Vétérinaire Jolimont, Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Laboratoire Chimie de l'environnement (LCE), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Entente interdépartementale pour la démoustication du littoral méditerranéen [Montpellier] (EID Méditerranée), EID-Méditerranée, This study was funded by the ANR (French National Research Agency, reference ANR-16-IDEX-0006), the KIM RIVE initiative, the Labex EpiGenMed 'Investissements d’avenir' programme (reference ANR- 10-LABX-12-01), and Montpellier University of Excellence (MUSE, ArboSud project). Moreover, SG was recipient of funding from the Direction Générale de l’Alimentation from the French Ministry of Agriculture and Food. Horse serosurveys were funded by the French Horse and Riding Institute, IFCE, and the EPERON fund (Encouragement aux ProjetsEquestres Régionaux Ou Nationaux) (OpIUM project)., ANR-16-IDEX-0006,MUSE,MUSE(2016), and ANR-10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010)

Subjects
Epidemiology, viruses, [SDV]Life Sciences [q-bio], L73 - Maladies des animaux, Flavivirus Infections, Virus des animaux, Birds, Dogs, Endémie, Seroepidemiologic Studies, Virology, Animals, Humans, Surveillance épidémiologique, Horses, One Health, Usutu virus, Transmission des maladies, seroprevalence, virus du Nil occidental, Flavivirus, Public Health, Environmental and Occupational Health, virus diseases, Morbidité, Cross-Sectional Studies, Culicidae, S50 - Santé humaine, France, One Health surveillance, West Nile virus, West Nile Fever, co-circulation
Abstract

Background West Nile virus (WNV) and Usutu virus (USUV), two closely related flaviviruses, mainly follow an enzootic cycle involving mosquitoes and birds, but also infect humans and other mammals. Since 2010, their epidemiological situation may have shifted from irregular epidemics to endemicity in several European regions; this requires confirmation, as it could have implications for risk assessment and surveillance strategies. Aim To explore the seroprevalence in animals and humans and potential endemicity of WNV and USUV in Southern France, given a long history of WNV outbreaks and the only severe human USUV case in France in this region. Methods We evaluated the prevalence of WNV and USUV in a repeated cross-sectional study by serological and molecular analyses of human, dog, horse, bird and mosquito samples in the Camargue area, including the city of Montpellier, between 2016 and 2020. Results We observed the active transmission of both viruses and higher USUV prevalence in humans, dogs, birds and mosquitoes, while WNV prevalence was higher in horses. In 500 human samples, 15 were positive for USUV and 6 for WNV. Genetic data showed that the same lineages, WNV lineage 1a and USUV lineage Africa 3, were found in mosquitoes in 2015, 2018 and 2020. Conclusion These findings support existing literature suggesting endemisation in the study region and contribute to a better understanding of USUV and WNV circulation in Southern France. Our study underlines the importance of a One Health approach for the surveillance of these viruses.

Published
2022

2. Identification of Umbre Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 French Patients with Hypogammaglobulinemia

Author

Franck Bielle, Sophie Demeret, David Brassat, Philippe Pérot, Susana Boluda, Fabrice Bonneville, Charles Duyckaerts, Anne Huard de Verneuil, Grégory L'Ambert, Bertrand Mathon, Marie Bernadette Delisle, Delphine Chrétien, Jan Hellert, Karine Bollore, Vincent Foulongne, Isabelle Plu, Karima Mokhtari, Muriel Coulpier, Claire Fieschi, Patricia Gil, Edouard de Sousa Cunha, Thérèse Couderc, Marc Eloit, Marion Malphettes, Marie Flamand, Serafin Gutierrez, Carole Tamietti, Thomas Bigot, Danielle Seilhean, Sarah Temmam, Découverte de pathogènes – Pathogen discovery, Institut Pasteur [Paris] (IP), Laboratoire de Neuropathologie Raymond Escourolle [CHU Pitié-Salpétriêre], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Etablissement français du don du sang [Montpellier], 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 Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), 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), Entente Interdépartementale pour la démoustication du littoral méditerranéen (EID), Virologie Structurale - Structural Virology, Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-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)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre national de référence des Agents Transmissibles Non Conventionnels, Institut de Veille Sanitaire (INVS), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Toulouse Neuro Imaging Center (ToNIC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre de Physiopathologie Toulouse Purpan (CPTP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Pôle Neurosciences [CHU Toulouse], Service d'Immunopathologie [Hôpital Saint-Louis, Paris], Université Paris Diderot - Paris 7 (UPD7)-Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Charles Foix [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre d'investigation clinique Neurosciences [CHU Pitié Salpêtrière] (CIC Neurosciences), Centre d'investigation clinique pluridisciplinaire [CHU Pitié Salpêtrière] (CIC-P 1421), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], École nationale vétérinaire - Alfort (ENVA), This work was supported by the Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant number ANR-10-LABX-62-IBEID)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Pérot, Philippe, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Pasteur [Paris], Laboratoire de Neuropathologie Raymond Escourolle, Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université des Antilles (UA)-Etablissement français du don du sang [Montpellier]-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Toulouse [Toulouse], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse], Pôle neurosciences [Hôpital de Purpan - Toulouse], Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), École nationale vétérinaire d'Alfort (ENVA), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), [SDV.MHEP.AHA] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Orthobunyavirus, Culex, viruses, [SDE.MCG]Environmental Sciences/Global Changes, Population, Arbovirus, Virus, Serology, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Agammaglobulinemia, Umbre virus, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Culex pipiens, medicine, [SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, Humans, education, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, education.field_of_study, metatranscriptomics, biology, business.industry, biology.organism_classification, medicine.disease, Virology, 3. Good health, Europe, [SDE.MCG] Environmental Sciences/Global Changes, 030104 developmental biology, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Encephalitis, next-generation sequencing, France, business, 030217 neurology & neurosurgery
Abstract

Background Human encephalitis represents a medical challenge from a diagnostic and therapeutic point of view. We investigated the cause of 2 fatal cases of encephalitis of unknown origin in immunocompromised patients. Methods Untargeted metatranscriptomics was applied on the brain tissue of 2 patients to search for pathogens (viruses, bacteria, fungi, or protozoans) without a prior hypothesis. Results Umbre arbovirus, an orthobunyavirus never previously identified in humans, was found in 2 patients. In situ hybridization and reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) showed that Umbre virus infected neurons and replicated at high titers. The virus was not detected in cerebrospinal fluid by RT-qPCR. Viral sequences related to Koongol virus, another orthobunyavirus close to Umbre virus, were found in Culex pipiens mosquitoes captured in the south of France where the patients had spent some time before the onset of symptoms, demonstrating the presence of the same clade of arboviruses in Europe and their potential public health impact. A serological survey conducted in the same area did not identify individuals positive for Umbre virus. The absence of seropositivity in the population may not reflect the actual risk of disease transmission in immunocompromised individuals. Conclusions Umbre arbovirus can cause encephalitis in immunocompromised humans and is present in Europe.

Published
2020

3. Identification of Eilat virus and prevalence of infection among Culex pipiens L. populations, Morocco, 2016

Author

Antoni Exbrayat, Ghita Chlyeh, Ouafaa Fassi Fihri, Etienne Loire, Thomas Balenghien, Patricia Gil, Hicham El Rhaffouli, Amal Bennouna, Serafin Gutierrez, Institut Agronomique et Vétérinaire Hassan II (IAV), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), FAR Military Health Service, Partenaires INRAE, European Project: 613996,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,VMERGE(2013), Institut Agronomique et Vétérinaire Hassan II (IAV Hassan II), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
Phylogénie, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], animal structures, viruses, Eilat virus, Zoology, Alphavirus, Genome, Viral, Biology, L73 - Maladies des animaux, Distance génétique, Virus, 03 medical and health sciences, Virology, Culex pipiens, parasitic diseases, Prevalence, Animals, 030304 developmental biology, 0303 health sciences, Larva, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Phylogenetic tree, Transmission (medicine), 030302 biochemistry & molecular biology, fungi, Sequence Analysis, DNA, biology.organism_classification, Insect Vectors, Culex, Morocco, Genetic distance, S50 - Santé humaine
Abstract

International audience; Eilat virus (EILV) is described as one of the few alphaviruses restricted to insects. We report the record of a nearly-complete sequence of an alphavirus genome showing 95% identity with EILV during a metagenomic analysis performed on 1488 unblood-fed females and 1076 larvae of the mosquito Culex pipiens captured in Rabat (Morocco). Genetic distance and phylogenetic analyses placed the EILV-Morocco as a variant of EILV. The observed infection rates in both larvae and adults suggested an active circulation of the virus in Rabat and its maintenance in the environment either through vertical transmission or through horizontal infection of larvae in breeding sites. This is the first report of EILV out of Israel and in Culex pipiens populations.

Published
2019

4. Human Usutu Virus Infection with Atypical Neurologic Presentation, Montpellier, France, 2016

Author

Isabelle Leparc-Goffart, Marie-France Martin, Patricia Gil, Yannick Simonin, Olivier Sillam, Serafin Gutierrez, Gilda Grard, Philippe Van de Perre, Orianne Constant, Sara Salinas, Marie Carles, Vincent Foulongne, Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Simonin, Yannick, Pathogénèse et contrôle des infections chroniques (PCCI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Thales Services, THALES, Laboratoire de Virologie, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Unité des Virus Emergents (UVE), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de Référence des Arbovirus [Marseille], Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA)-Unité d'Arbovirologie [Marseille], Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées-Service de Santé des Armées-Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées-Service de Santé des Armées, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Nîmes (CHU de Nîmes), and BUISINE, Soline

Subjects
0301 basic medicine, Male, Epidemiology, [SDV]Life Sciences [q-bio], lcsh:Medicine, flavivirus, Adrenal Cortex Hormones, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Bell's palsy, Blepharoptosis, Flavivirus Infections, Usutu virus, Phylogeny, idiopathic facial paralysis, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, atypical neurologic presentation, biology, Dispatch, 000 - Autres thèmes, Meningoencephalitis, Facial paralysis, 3. Good health, [SDV] Life Sciences [q-bio], Flavivirus, USUV, Infectious Diseases, Valacyclovir, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Viral, France, meningitis/encephalitis, Presentation (obstetrics), Encephalitis, Microbiology (medical), Human Usutu Virus Infection with Atypical Neurologic Presentation, Montpellier, France, 2016, Adult, 030106 microbiology, Facial Paralysis, Antiviral Agents, lcsh:Infectious and parasitic diseases, Montpellier, 03 medical and health sciences, medicine, Humans, lcsh:RC109-216, viruses, business.industry, lcsh:R, Bell’s palsy, human infections, medicine.disease, biology.organism_classification, Virology, 030104 developmental biology, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; Infection with Usutu virus (USUV) has been recently associated with neurologic disorders, such as encephalitis or meningoencephalitis, in humans. These findings indicate that USUV is a potential health threat. We report an acute human infection with USUV in France putatively associated with a clinical diagnosis of idiopathic facial paralysis.

Published
2018

5. Cleavage site of Newcastle disease virus determines viral fitness in persistent infection cells

Author

Patricia Gil, Renata Servan de Almeida, Emmanuel Albina, Haijin Liu, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), and Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0301 basic medicine, Proteases, animal structures, animal diseases, viruses, Population, Newcastle disease virus, Virulence, Viral quasispecies, Cleavage site, Biology, Superinfection exclusion, Persistent infection, L73 - Maladies des animaux, Microbiology, Newcastle disease, Poultry, Virus, Cell Line, 03 medical and health sciences, Animals, education, Poultry Diseases, RNA Cleavage, education.field_of_study, General Veterinary, [SDV.BA]Life Sciences [q-bio]/Animal biology, General Medicine, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Virology, Fusion protein, Quasispecies, 030104 developmental biology, Mutation, embryonic structures, Genetic Fitness, Chickens
Abstract

International audience; Newcastle disease, caused by infection with virulent strains of Newcastle disease virus (NDV), poses a risk for the poultry industry. The virulence of NDV is mainly deterthined by the cleavage site of F protein. Lentogenic NDV can become velogenic after passages in SPF chicken brain and air sac based on some strains isolated from water birds, because the proportion of virulent-related strains gradually increases. In contrast, this proportion remains unchanged if NDV is passaged via 10-day-old SPF chicken embryos. This information suggests that environmental conditions rather than mutation affect NDV fitness in quasispecies. However, it is unknown how the environment selects virulent-related strains from a viral population. In this study, velogenic and lentogenic NDV marked by green or red fluorescence were used to establish persistent infection (PI) in BHK-21 cells. Monitoring viruses by different methods, we found that, without competition, persistently infected cells harbored lentogenic and velogenic NDV strains similarly in terms of viral release, viral spread and the period of persistent viral infection. In contrast, under competitive co-infection, velogenic NDV became dominant in quasispecies from the fifth passage of PI cells, which resulted in the progressive disappearance of the lentogenic NDV strain. This domination was concomitant with a short-term reduction in the superinfection exclusion and supernatant interference in PI cells resulting in a velogenic virus rebound. We concluded that virulent-related F protein cleavage site facilitates the spread and replication of NDV in conditions under which cells do not secret trypsin-like proteases and do not inhibit free virus infection, resulting in a gradual increase in virulent strains in quasispecies with the number of passages.

Published
2018

6. Can genotype mismatch really affect the level of protection conferred by Newcastle disease vaccines against heterologous virulent strains?

Author

Natàlia Majó, Miquel Nofrarías, Emmanuel Albina, Véronique Jestin, Patricia Gil, Renata Servan de Almeida, Haijin Liu, François-Xavier Briand, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Northwest A&F University, Universitat Autònoma de Barcelona (UAB), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), AxLR, SATT Languedoc Roussillon, Montpellier [16/300], China Scholarship Council (CSC) [201306300089], and European research Group EPIZONE

Subjects
0301 basic medicine, Genotype mismatch, Base Pair Mismatch, [SDV]Life Sciences [q-bio], Antibodies, Viral, L73 - Maladies des animaux, Cricetinae, Genotype, Specific-pathogen-free, Protection, biology, Vaccination, 3. Good health, Virus Shedding, Maladie de Newcastle, Infectious Diseases, S50 - Santé humaine, Molecular Medicine, Vaccin, Newcastle Disease, 030106 microbiology, Newcastle disease virus, Enzyme-Linked Immunosorbent Assay, Vaccines, Attenuated, Newcastle disease, Virus, Volaille, Cell Line, 03 medical and health sciences, Animals, Viral shedding, Poultry Diseases, Hemagglutination assay, General Veterinary, General Immunology and Microbiology, Public Health, Environmental and Occupational Health, Viral Vaccines, biology.organism_classification, Virology, 030104 developmental biology, Viral replication, Vaccine, Chickens
Abstract

International audience; Newcastle disease (ND), caused by virulent class II avian paramyxovirus 1 (Newcastle disease virus, NDV), occurs sporadically in poultry despite their having been immunized with commercial vaccines. These vaccines were all derived from NDV strains isolated around 70 years ago. Since then, class II NDV strains have evolved into 18 genotypes. Whether the vaccination failure results from genotype mismatches between the currently used vaccine strains and field-circulating velogenic strains or from an impaired immune response in the vaccination remains unclear. To test the first hypothesis, we performed a heterologous genotype II vaccine/genotype XI challenge in one-day old specific pathogen free (SPF) chicks and reproduced viral shedding. We then produced two attenuated strains of genotype II and XI by reverse genetics and used them to immunize two-week old SPF chickens that were subsequently challenged with velogenic strains of genotypes II, VII and XI. We found that both vaccines could induce antibodies with hemagglutination inhibition titers higher than 6.5 log(2). Vaccination also completely prevented disease, viral shedding in swabs, and blocked viral replication in tissues from different genotypes in contrast to unvaccinated chickens that died shortly after challenge. Taken together, our results support the hypothesis that, in immunocompetent poultry, genotype mismatch is not the main reason for vaccination failure.

Published
2018

7. Comparison of the efficiency of different newcastle disease virus reverse genetics systems

Author

Patricia Gil, Haijin Liu, Renata Servan de Almeida, Emmanuel Albina, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Chinese government (CSC) and is the beneficiary of scientific grants from the European research Group EPIZONE.

Subjects
0301 basic medicine, Newcastle Disease, viruses, [SDV]Life Sciences [q-bio], Genome, Viral, L73 - Maladies des animaux, Transfection, Genome, Newcastle disease, Virus, Cell Line, 03 medical and health sciences, reverse genetics, Plasmid, Virology, Animals, Gene, Genetics, biology, Virion, RNA, RNA virus, newcastle disease virus, biology.organism_classification, Reverse genetics, 030104 developmental biology, RNA, Viral, higher rescuing efficiency, Plasmids
Abstract

International audience; Rescue of negative-sense single-stranded RNA viruses ((-)ssRNA virus), generally requires-the handling of a large number of plasmids to provide the virus genome and essential components for gene expression and genome replication. This constraint probably renders reverse genetics of (-)ssRNA virus more complex and less efficient. Some authors have shown that the fewer the plasmids, the more efficient reverse genetics is for segmented RNA virus. However, it is not clear if the same applies for (-)ssRNA, such as Newcastle disease virus (NDV). To address this issue, six variants of NDV reverse genetic systems were established by cloning combinations of NP, P and L genes, mini-genome or full-genome in 4, 3, 2 and 1 plasmid. In terms of mini-genome and full-genome rescue, we showed that only the 2-plasmid system, assembling three support plasmids together, was able to improve the rescue efficiency over that of the conventional 4-plasmid system. These results may help establish and/or improve reverse genetics for other mononegaviruses.

Published
2017

8. Vaccination with Trypanosoma rangeli reduces the infectiousness of dogs experimentally infected with Trypanosoma cruzi

Author

Irma Castro, Patricia Gil, Carine Truyens, Virginia Introini, Edgardo Moretti, and Beatriz Basso

Subjects
Chagas disease, Chagas’ disease, Protozoan Vaccines, Trypanosoma rangeli, Trypanosoma, Trypanosoma cruzi, Antibodies, Protozoan, Parasitemia, Article, Dogs, Triatoma infestans, parasitic diseases, medicine, Vaccination of dogs, Animals, Chagas Disease, Dog Diseases, Triatoma, Domestic reservoirs, General Veterinary, General Immunology and Microbiology, biology, Vaccination, Public Health, Environmental and Occupational Health, Feeding Behavior, medicine.disease, biology.organism_classification, Virology, Infectious Diseases, Immunology, Molecular Medicine, Trypanosomiasis
Abstract

The goal of this work was to test the efficacy of the vaccination with Trypanosoma rangeli in dogs. Mongrel dogs received three subcutaneous injections of fixed T. rangeli epimastigotes at 6-week intervals. Such immunisation induced antibodies against Trypanosoma cruzi. While both control and immunised dogs developed detectable parasitemia, this was lower and shorter in vaccinated animals. Interestingly, feeding of Triatoma infestans nymphs on vaccinated and chronically infected dogs led to a sharp reduction in the rate of bug infection. These results suggest that it might be possible to reduce the vectorial parasitemia through vaccination of dogs. As dogs are known to play a major role in the domestic cycle of T. cruzi, this might represent a strategy to reduce parasite transmission to humans.

Published
2007

9. Avian influenza in backyard poultry of the Mopti region, Mali

Author

Patricia Gil, Véronique Chevalier, Sophie Molia, Saliha Hammoumi, Emmanuel Albina, Abdallah Traoré, Stéphanie Lesceu, Renata Servan de Almeida, Inconnu, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)

Subjects
Male, Veterinary medicine, 040301 veterinary sciences, [SDV]Life Sciences [q-bio], Virus isolation, L73 - Maladies des animaux, Mali, medicine.disease_cause, Volaille, 0403 veterinary science, 03 medical and health sciences, Food Animals, medicine, Animals, Influenzavirus aviaire, Animal Husbandry, Galliformes, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, biology, 030306 microbiology, business.industry, virus diseases, 04 agricultural and veterinary sciences, Virology, Low pathogenic, Influenza A virus subtype H5N1, 3. Good health, Ducks, Influenza in Birds, Elisa test, biology.protein, Female, Animal Science and Zoology, Livestock, Cloaca, Antibody, business
Abstract

This study reports the first evidence of circulation of avian influenza viruses (AIV) in domestic poultry in Mali. In the Mopti region, where AIV have already been isolated in migratory water birds, we sampled 223 backyard domestic birds potentially in contact with wild birds and found that 3.6% had tracheal or cloacal swabs positive by real-time reverse transcription PCR (rRT-PCR) for type A influenza viruses (IVA) and that 13.7% had sera positive by commercial ELISA test detecting antibodies against IVA. None of the birds positive by rRT-PCR for IVA was positive by rRT-PCR for H5 and H7 subtypes, and none showed any clinical signs therefore indicating the circulation of low pathogenic avian influenza. Unfortunately, no virus isolation was possible. Further studies are needed to assess the temporal evolution of AIV circulation in the Mopti region and its possible correlation with the presence of wild birds.

Published
2009

10. Plasminogen controls inflammation and pathogenesis of influenza virus infections via fibrinolysis

Author

Stella E. Vogelzang-van Trierum, Vuong Ba Lê, Bruno Lina, Peter Carmeliet, Roger Lijnen, Fatima Berri, Michel Hanss, Eric Camerer, Guus F. Rimmelzwaan, Emmanuel Albina, Marie-Laure Foucault-Grunenwald, Dominique Martinez, Patricia Gil, Béatrice Riteau, Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (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), Dept Virol, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Hospices Civils de Lyon (HCL), Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Paris-Centre de Recherche Cardiovasculaire (PARCC - UMR-S U970), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), Université Catholique de Louvain = Catholic University of Louvain (UCL), Flanders Institute for Biotechnology, Département Santé Animale (DEPT SA), Institut National de la Recherche Agronomique (INRA), Agence Nationale de la Recherche (ANR), Long term Structural funding - Methusalem by the Flemish Government, INSERM avenir, 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), ProdInra, Migration, Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), and Virology

Subjects
Male, Pulmonology, medicine.medical_treatment, [SDV]Life Sciences [q-bio], 030204 cardiovascular system & hematology, medicine.disease_cause, L73 - Maladies des animaux, Virus Replication, Fibrinogène, Pathogenesis, Pathogénèse, Mice, 0302 clinical medicine, Influenza A Virus, H1N1 Subtype, Influenza A virus, Coagulation sanguine, Biology (General), Mice, Knockout, 0303 health sciences, Fibrinolysis, Hematology, 3. Good health, Host-Pathogen Interaction, [SDV] Life Sciences [q-bio], Cytokine, Expérimentation en laboratoire, Host-Pathogen Interactions, Medicine, Female, medicine.symptom, Infection, Fibrin Clot Lysis Time, Research Article, Souris, QH301-705.5, Immunology, Pneumonia, Viral, Inflammation, Immunopathology, Biology, Microbiology, Antiviral Agents, Virus, Immunomodulation, 03 medical and health sciences, Fibrinolytic Agents, Orthomyxoviridae Infections, Virology, Genetics, medicine, Animals, Influenzavirus aviaire, Molecular Biology, 030304 developmental biology, Fibrin, Influenza A Virus, H5N1 Subtype, Fibrinogen, Plasminogen, RC581-607, Influenza A virus subtype H5N1, Mice, Inbred C57BL, Poumon, Parasitology, Immunologic diseases. Allergy, Fibrinolytic agent
Abstract

Detrimental inflammation of the lungs is a hallmark of severe influenza virus infections. Endothelial cells are the source of cytokine amplification, although mechanisms underlying this process are unknown. Here, using combined pharmacological and gene-deletion approaches, we show that plasminogen controls lung inflammation and pathogenesis of infections with influenza A/PR/8/34, highly pathogenic H5N1 and 2009 pandemic H1N1 viruses. Reduction of virus replication was not responsible for the observed effect. However, pharmacological depletion of fibrinogen, the main target of plasminogen reversed disease resistance of plasminogen-deficient mice or mice treated with an inhibitor of plasminogen-mediated fibrinolysis. Therefore, plasminogen contributes to the deleterious inflammation of the lungs and local fibrin clot formation may be implicated in host defense against influenza virus infections. Our studies suggest that the hemostatic system might be explored for novel treatments against influenza., Author Summary Influenza viruses, including H5N1 bird influenza viruses continue to form a major threat for public health. Available antiviral drugs for the treatment of influenza are effective to a limited extent and the emergence of resistant viruses may further undermine their use. The symptoms associated with influenza are caused by replication of the virus in the respiratory tract and the host immune response. Here, we report that a molecule of the fibrinolytic system, plasminogen, contributes to inflammation caused by influenza. Inhibiting the action of plasminogen protected mice from severe influenza infections, including those caused by H5N1 and H1N1 pandemic 2009 viruses and may be a promising novel strategy to treat influenza.

Published
2013

11. New avian paramyxoviruses type I strains identified in Africa provide new outcomes for phylogeny reconstruction and genotype classification

Author

Ould El Mamy Bezeid, Renata Servan de Almeida, Kassim Samake, Abdallah Traoré, Gilles Balança, Julien Cappelle, Saliha Hammoumi, Peter N. Thompson, Nicolas Gaidet, Sophie Molia, Patricia Gil, Véronique Jestin, Emmanuel Albina, François-Xavier Briand, Samia Guendouz, Dominique Martinez, Colette Grillet, Flavie Goutard, Marthin Dakouo, Olivier Fridolin Maminiaina, Hassen Chaka, Abbas Diarra, Véronique Chevalier, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal et gestion intégrée des risques (UPR AGIRs), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Central Vétérinaire [Bamako, Mali], Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Centre National d’Elevage et de Recherches Vétérinaires (CNERV), Animal Health, Fac Vet Sci, The University of Sydney, French Ministry of Foreign Affairs (MAE) [GRIPAVI 2006-26], and EU network of excellence [EPIZONE (016236)]

Subjects
Phylogénie, [SDV]Life Sciences [q-bio], lcsh:Medicine, Évolution, L73 - Maladies des animaux, Genome, Genotype, Avulavirus, lcsh:Science, Phylogeny, Genetics, 0303 health sciences, Multidisciplinary, Phylogenetic tree, Classification, Provenance, Paramyxoviridae, RNA, Viral, Génotype, Research Article, Séquence nucléotidique, Sequence analysis, Newcastle Disease, Genome, Viral, Biology, Newcastle disease, Volaille, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Animals, Surveillance épidémiologique, Poultry Diseases, 030304 developmental biology, Whole genome sequencing, 030306 microbiology, Avulavirus Infections, Virus maladie de newcastle, lcsh:R, Oiseau, Animal sauvage, biology.organism_classification, Virology, Enquête pathologique, Africa, lcsh:Q
Abstract

International audience; Newcastle disease (ND) is one of the most lethal diseases of poultry worldwide. It is caused by an avian paramyxovirus 1 that has high genomic diversity. In the framework of an international surveillance program launched in 2007, several thousand samples from domestic and wild birds in Africa were collected and analyzed. ND viruses (NDV) were detected and isolated in apparently healthy fowls and wild birds. However, two thirds of the isolates collected in this study were classified as virulent strains of NDV based on the molecular analysis of the fusion protein and experimental in vivo challenges with two representative isolates. Phylogenetic analysis based on the F and HN genes showed that isolates recovered from poultry in Mali and Ethiopia form new groups, herein proposed as genotypes XIV and sub-genotype VIf with reference to the new nomenclature described by Diel's group. In Madagascar, the circulation of NDV strains of genotype XI, originally reported elsewhere, is also confirmed. Full genome sequencing of five African isolates was generated and an extensive phylogeny reconstruction was carried out based on the nucleotide sequences. The evolutionary distances between groups and the specific amino acid signatures of each cluster allowed us to refine the genotype nomenclature.

Published
2013

12. Serological and molecular investigation of Newcastle disease in household chicken flocks and associated markets in Eastern Shewa zone, Ethiopia

Author

S.P.R. Bisschop, Flavie Goutard, Hassen Chaka, Renata Servan de Almeida, Patricia Gil, Peter N. Thompson, and Celia Abolnik

Subjects
Veterinary medicine, Poulet, L73 - Maladies des animaux, Antibodies, Viral, law.invention, Serology, Food Animals, Cloaca, law, Seroepidemiologic Studies, Analyse du risque, Immunologie, Dry season, Prevalence, Polymerase chain reaction, education.field_of_study, Enquête, biology, Reverse Transcriptase Polymerase Chain Reaction, Paramyxovirus aviaire, Maladie de Newcastle, Trachea, Test ELISA, PCR, Circuit de commercialisation, Seasons, Wet season, Exploitation agricole familiale, Newcastle Disease, E70 - Commerce, commercialisation et distribution, Population, Newcastle disease virus, Virulence, Enzyme-Linked Immunosorbent Assay, Real-Time Polymerase Chain Reaction, Newcastle disease, Animals, Surveillance épidémiologique, education, Transmission des maladies, Virus maladie de newcastle, Biologie moléculaire, biology.organism_classification, Virology, Cross-Sectional Studies, Animal Science and Zoology, Flock, Ethiopia, Chickens, Viral Fusion Proteins
Abstract

Cross-sectional survey for Newcastle disease (ND) were conducted in nonvaccinated household flocks of village chickens to assess serological and virological ND status in households and associated live bird markets. In total, 1,899 sera and 460 pools of cloacal and tracheal swabs were sampled and tested using a commercial enzyme-linked immunosorbent assay (ELISA) and real-time reverse transcriptase polymerase chain reaction (rRT-PCR), respectively. Additionally, paired cloacal and tracheal swabs from 1,269 individual chickens were collected from markets and tested using RT-PCR. The prevalence of households with at least one seropositive chicken was higher during the dry season (27.4 %) than during the wet season (17.4 %) (P = 0.003). Viral genome was detected in 14.2 % of households during the wet season using a fusion (F) gene assay and in 24.2 % of households during the dry season using a polymerase (L) gene assay that targets both class I and class II viruses. At the markets sampled, overall bird level prevalence was 4.9 % for period 1 (F gene assay), and 38.2 % and 27.6 % for periods 2 and 3, respectively (L gene assay). Partial sequencing of the F gene (239 bp) cleavage site indicated that the majority of the circulating strains exhibited motifs specific to virulent strains. Seroepidemiology coupled with molecular analysis can be a useful tool to assess the status of NDV infection. The village chicken population in Ethiopia is endemically infected with virulent NDV that pose a significant threat to emerging small- and medium-scale commercial poultry production.

Published
2012

13. Genetic data from avian influenza and avian paramyxoviruses generated by the European network of excellence (EPIZONE) between 2006 and 2011 - Review and recommendations for surveillance

Author

Maria Serena Beato, Mikael Berg, Ghislaine Le Gall-Reculé, Giovanni Cattoli, Siamak Zohari, Elke Starick, Renata Servan de Almeida, Thierry van den Berg, Ilaria Barbieri, Guus Koch, Giorgi Metreveli, Alireza Heidari, Isabella Monne, Ian H. Brown, William G. Dundon, Alice Fusaro, Poul Henrik Jørgensen, Katarzyna Domańska-Blicharz, Muhammad Munir, Véronique Jestin, Ana Moreno Martin, Karl Ståhl, Saliha Hammoumi, Zenon Minta, Elisabeth W. Aldous, François-Xavier Briand, Steven Van Borm, Patricia Gil, Emmanuel Albina, Krzysztof Śmietanka, and Ilaria Capua

Subjects
Knowledge management, Avian paramyxovirus, northern europe, subtype h5n1, L73 - Maladies des animaux, medicine.disease_cause, Data sequences, Wageningen Environmental Research, Avulavirus, biology, complete genome sequence, Contrôle de maladies, General Medicine, Paramyxovirus aviaire, Virology & Molecular Biology, Maladie de Newcastle, Épidémiologie, Europe, Influenza A virus, Population Surveillance, Séquence nucléotidique, Newcastle Disease, Context (language use), h5n1 viruses, Microbiology, Birds, a viruses, medicine, Animals, Humans, Network of excellence, Influenzavirus aviaire, wild birds, great-britain, General Veterinary, business.industry, Avulavirus Infections, phylogenetic analysis, Genetic data, L70 - Sciences et hygiène vétérinaires - Considérations générales, Sequence Analysis, DNA, biology.organism_classification, Virology, Influenza A virus subtype H5N1, Virologie & Moleculaire Biologie, Influenza in Birds, domestic ducks, newcastle-disease-virus, business
Abstract

Since 2006, the members of the molecular epidemiological working group of the European "EPIZONE" network of excellence have been generating sequence data on avian influenza and avian paramyxoviruses from both European and African sources in an attempt to more fully understand the circulation and impact of these viruses. This review presents a timely update on the epidemiological situation of these viruses based on sequence data generated during the lifetime of this project in addition to data produced by other groups during the same period. Based on this information and putting it all into a European context, recommendations for continued surveillance of these important viruses within Europe are presented.

Published
2012

14. Quantitative one-step real-time RT-PCR for the fast detection of the four genotypes of PPRV

Author

Geneviève Libeau, Djénéba Keita, Jovita Fernández-Pinero, Emmanuel Albina, Olivier Kwiatek, Patricia Gil, Miguel Angel Jimenez Clavero, Inconnu, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], L73 - Maladies des animaux, 0403 veterinary science, chemistry.chemical_compound, Peste des petits ruminants, Diagnosis, Taq Polymerase, Mononegavirales, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Proficiency panel, Reverse Transcriptase Polymerase Chain Reaction, Goats, Peste des petits ruminants virus, 04 agricultural and veterinary sciences, Nucleocapsid Proteins, Viral Load, Reverse transcription polymerase chain reaction, Real-time polymerase chain reaction, PCR, Génotype, Camelus, Paramyxoviridae, 040301 veterinary sciences, Sheep Diseases, Biology, Sensitivity and Specificity, Virus, Peste-des-petits-ruminants virus, Virus peste petits ruminants, Diagnosis, Differential, 03 medical and health sciences, Virology, Peste-des-Petits-Ruminants, TaqMan, Animals, 030304 developmental biology, Goat Diseases, Sheep, Nucleoprotein gene, biology.organism_classification, Molecular biology, Nucleoprotein, Real-time RT-PCR, chemistry, Morbillivirus, U30 - Méthodes de recherche, Taq polymerase
Abstract

A one-step real-time Taqman® RT-PCR assay (RRT-PCR) for peste des petits ruminants virus (PPRV) was developed to detect the four lineages of PPRV by targeting the nucleoprotein (N) gene of the virus. This new assay was compared to a conventional RT-PCR on reference strains and field materials. Quantitation was performed against a standard based on a synthetic transcript of the NPPR gene for which a minimum of 32 copies per reaction were detected with a corresponding Ct value of 39. Depending on the lineage involved, the detection limit of RRT-PCR was decreased by one to three log copies relative to the conventional method. The lower stringency occurred with lineage III because of minor nucleotide mismatches within the probe region. The assay did not detect phylogenetically or symptomatically related viruses of ruminants (such as rinderpest, bluetongue, and bovine viral diarrhea viruses). However, it was capable of detecting 20% more positive field samples with low viral RNA loads compared to the conventional PCR method. When compared on a proficiency panel to the method developed by Bao et al. (2008), the sensitivity of the in-house assay was slightly improved on lineage II. It proved significantly faster to perform and hence better adapted for monitoring large numbers of at risk or diseased animals. © 2010 Elsevier B.V.

Published
2010

15. Africa, a reservoir of new virulent strains of Newcastle disease virus?

Author

Sophie Molia, Abbas Diarra, Colette Grillet, Patricia Gil, Véronique Chevalier, M. Koko, Emmanuel Albina, Harentsoaniaina Rasamoelina Andriamanivo, Renata Servan de Almeida, Dominique Martinez, Abdallah Traoré, Saliha Hammoumi, Olivier Fridolin Maminiaina, Kassim Samake, Inconnu, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)

Subjects
Disease reservoir, Poulet, [SDV]Life Sciences [q-bio], Newcastle disease virus, Virulence, Biology, L73 - Maladies des animaux, Newcastle disease, Virus, Volaille, Microbiology, 03 medical and health sciences, Phylogenetics, Genotype, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Disease Reservoirs, 0303 health sciences, General Veterinary, General Immunology and Microbiology, 030306 microbiology, Virus maladie de newcastle, Vaccination, Public Health, Environmental and Occupational Health, Viral Vaccines, biology.organism_classification, Virology, Paramyxovirus aviaire, Maladie de Newcastle, Infectious Diseases, Africa, Molecular Medicine
Abstract

International audience

Published
2009

16. Sequence analysis of the large (L) polymerase gene and trailer of the peste des petits ruminants virus vaccine strain Nigeria 75/1: Expression and use of the L protein in reverse genetics

Author

Patricia Gil, Martha Yami, Geneviève Libeau, Adama Diallo, Emmanuel Albina, Cécile Minet, B. Egzabhier, F. Tangy, Michel Brémont, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), National Veterinary Institute [Debre Zeit, Ethiopia] (NVI), Génomique Virale et Vaccination, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Animal Production Unit, International Atomic Energy Agency [Vienna] (IAEA), National Veterinary Institute, Unité de virologie et immunologie moléculaires, IAEA, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Untranslated region, Cancer Research, Genes, Viral, MESH: Amino Acid Sequence, L73 - Maladies des animaux, Peste des petits ruminants, Chlorocebus aethiops, MESH: Sequence Analysis, RNA, MESH: Animals, Viral, MESH: Phylogeny, Polymerase, Phylogeny, Genetics, MESH: Genes, Viral, 0303 health sciences, Genome, Multiple sequence alignment, DNA-Directed RNA Polymerases, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, MESH: RNA, Viral, Paramyxoviridae, RNA, Viral, Petits ruminants, MESH: Genome, Viral, Sequence Analysis, Sequence analysis, Ruminant, Vaccin, Molecular Sequence Data, MESH: Sequence Alignment, MESH: Vero Cells, Sequence alignment, Genome, Viral, Biology, Cercopithecus aethiops, Peste-des-petits-ruminants virus, Virus peste petits ruminants, 03 medical and health sciences, Viral Proteins, Virology, MESH: Peste-des-Petits-Ruminants, Peste-des-Petits-Ruminants, Animals, Amino Acid Sequence, Polymerase Gene, Gene, Vero Cells, 030304 developmental biology, MESH: Molecular Sequence Data, MESH: Peste-des-petits-ruminants virus, 030306 microbiology, Sequence Analysis, RNA, MESH: Viral Proteins, MESH: Cercopithecus aethiops, Reverse genetics, MESH: DNA-Directed RNA Polymerases, Genes, Morbillivirus, Enzyme, biology.protein, RNA, Sequence Alignment
Abstract

International audience; The large (L) polymerase gene and the 5'-terminal UTR of the genome of peste des petits ruminants virus (PPRV), vaccine strain Nigeria 75/1, were cloned and sequenced. The L protein was also expressed in eukaryotic cells and its polymerase activity was quantitatively measured in a PPR reverse genetics assay using a reporter minigenome. Comparative sequence analysis of this functional L gene with corresponding genes of other morbilliviruses showed a degree of conservation exceeding 70%. The multiple sequence alignment and the phylogenetic study of L gene discriminated the morbilliviruses in 6 clusters, which are more closely related to Tupaia and Henipaviruses than to other paramyxoviruses. Important protein domains and functional motifs of the L polymerase of the PPRV Nigeria 75/1 vaccine were also identified by using different bioinformatics tools.

Published
2009

17. Long-term storage at tropical temperature of dried-blood filter papers for detection and genotyping of RNA and DNA viruses by direct PCR

Author

Luis J. Romero, Linda K. Dixon, Geneviève Libeau, Emmanuel Albina, François Roger, Olivier Kwiatek, Patricia Gil, S. Prome, Marisa Arias, Vincent Michaud, M.-F. Le Potier, and Emmanuel Couacy-Hymann

Subjects
Génétique moléculaire, Phylogénie, Hot Temperature, Time Factors, Paramyxoviridae, Genotype, L73 - Maladies des animaux, Filter paper, Polymerase Chain Reaction, Sensitivity and Specificity, Virus, law.invention, Peste-des-petits-ruminants virus, law, Virology, Peste des petits ruminants, Peste-des-Petits-Ruminants, Animals, L50 - Physiologie et biochimie animales, Mononegavirales, African Swine Fever, Genotyping, Polymerase chain reaction, Phylogeny, Blood Specimen Collection, Tropical Climate, biology, Genetic analysis, DNA virus, RNA virus, biology.organism_classification, African Swine Fever Virus, PCR, Peste porcine africaine, Africa, Sample collection
Abstract

In tropical countries the diagnosis of viral infections of humans or animals is often hampered by the lack of suitable clinical material and the necessity to maintain a cold chain for sample preservation up to the laboratory. This study describes the use of filter papers for rapid sample collection, and the molecular detection and genotyping of viruses when stored over long periods at elevated temperatures. Infected blood was collected on filter papers, dried and stored at different temperatures (22, 32 and 37 °C) for various periods (up to 9 months). Two animal viruses, African swine fever, a large double-stranded DNA virus and Peste des Petits Ruminants, a negative single-stranded RNA virus, were used to validate the method. Filter papers with dried blood containing virus or control plasmid DNA were cut in small 5 mm2 pieces and added directly to the PCR tube for conventional PCR. Nucleic acid from both viruses could still be detected after 3 months at 32 °C. Moreover, the DNA virus could be detected at least 9 months after conservation at 37 °C. PCR products obtained from the filter papers were sequenced and phylogenetic analysis carried out. The results were consistent with published sequences, demonstrating that this method can be used for virus genotyping. © 2007 Elsevier B.V. All rights reserved.

Published
2006

18. Newcastle Disease Virus in Madagascar: Identification of an Original Genotype Possibly Deriving from a Died Out Ancestor of Genotype IV

Author

Renata Servan de Almeida, Jean-Joseph Rajaonarison, François-Xavier Briand, Emmanuel Albina, René Rakotondravao, M. Koko, Véronique Jestin, Patricia Gil, Harentsoaniaina Rasamoelina Andriamanivo, Renaud Lancelot, Véronique Chevalier, Djénéba Keita, Dominique Martinez, Abel Andriantsimahavandy, and Olivier Fridolin Maminiaina

Subjects
Models, Molecular, Identification, Phylogénie, lcsh:Medicine, Chick Embryo, L73 - Maladies des animaux, Poultry, Genotype, lcsh:Science, Phylogeny, Virology/Vaccines, Genetics, Multidisciplinary, biology, Vaccination, Virology/Diagnosis, Paramyxovirus aviaire, Maladie de Newcastle, Enzootic, Génotype, Research Article, zoonose, Séquence nucléotidique, Sequence analysis, Newcastle Disease, Pouvoir pathogène, Molecular Sequence Data, Newcastle disease virus, Genome, Viral, Newcastle disease, Virology/Emerging Viral Diseases, Virus, Viral Proteins, Species Specificity, Phylogenetics, Sequence Homology, Nucleic Acid, Madagascar, Animals, Gene, Base Sequence, Virus maladie de newcastle, lcsh:R, Biologie moléculaire, Outbreak, Sequence Analysis, DNA, biology.organism_classification, Virology, lcsh:Q, Protein Multimerization
Abstract

In Madagascar, Newcastle disease (ND) has become enzootic after the first documented epizootics in 1946, with recurrent annual outbreaks causing mortality up to 40%. Four ND viruses recently isolated in Madagascar were genotypically and pathotypically characterised. By phylogenetic inference based on the F and HN genes, and also full-genome sequence analyses, the NDV Malagasy isolates form a cluster distant enough to constitute a new genotype hereby proposed as genotype XI. This new genotype is presumably deriving from an ancestor close to genotype IV introduced in the island probably more than 50 years ago. Our data show also that all the previously described neutralising epitopes are conserved between Malagasy and vaccine strains. However, the potential implication in vaccination failures of specific amino acid substitutions predominantly found on surface-exposed epitopes of F and HN proteins is discussed.

Published
2010

19. Evidence of Infection by H5N2 Highly Pathogenic Avian Influenza Viruses in Healthy Wild Waterfowl

Author

Pierfrancesco Micheloni, Saliha Hammoumi, Juan Lubroth, John Y. Takekawa, Giovanni Cattoli, François Monicat, Julien Cappelle, Joseph Domenech, John H. Mshelbwala, Scott H. Newman, Nicolas Gaidet, Tony M. Joannis, Isabella Monne, Patricia Gil, Tim Dodman, Ward Hagemeijer, Shiiwuua Manu, Ilaria Capua, Ulf Ottosson, Alice Fusaro, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Animal production and health division, Food and Agriculture Organization, Wetlands International, Partenaires INRAE, Western Ecological Research Center, National Veterinary Research Institute, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), AP Leventis Ornithological Research Institute, Istituto Nazionale per la Fauna Selvatica, Ottenby Bird Observatory, and Department of Forestry

Subjects
Phylogénie, [SDV]Life Sciences [q-bio], viruses, L73 - Maladies des animaux, medicine.disease_cause, Oiseau aquatique, Grippe aviaire, Genotype, Waterfowl, Influenza A virus, Biology (General), Phylogeny, 0303 health sciences, Ecology, Phylogenetic tree, biology, virus diseases, 3. Good health, Ducks, Infection, Influenza A Virus, H5N2 Subtype, Research Article, QH301-705.5, Télédétection, Pouvoir pathogène, Molecular Sequence Data, Immunology, Nigeria, Microbiology, Virus, Birds, 03 medical and health sciences, Phylogenetics, Virology, Infectious Diseases/Viral Infections, Genetics, medicine, Animals, Surveillance épidémiologique, Influenzavirus aviaire, Molecular Biology, Transmission des maladies, 030304 developmental biology, Génome, Base Sequence, 030306 microbiology, Migration animale, Biologie moléculaire, Outbreak, Genetics and Genomics, RC581-607, Animal sauvage, biology.organism_classification, Influenza A virus subtype H5N1, Influenza in Birds, Parasitology, Immunologic diseases. Allergy
Abstract

The potential existence of a wild bird reservoir for highly pathogenic avian influenza (HPAI) has been recently questioned by the spread and the persisting circulation of H5N1 HPAI viruses, responsible for concurrent outbreaks in migratory and domestic birds over Asia, Europe, and Africa. During a large-scale surveillance programme over Eastern Europe, the Middle East, and Africa, we detected avian influenza viruses of H5N2 subtype with a highly pathogenic (HP) viral genotype in healthy birds of two wild waterfowl species sampled in Nigeria. We monitored the survival and regional movements of one of the infected birds through satellite telemetry, providing a rare evidence of a non-lethal natural infection by an HP viral genotype in wild birds. Phylogenetic analysis of the H5N2 viruses revealed close genetic relationships with H5 viruses of low pathogenicity circulating in Eurasian wild and domestic ducks. In addition, genetic analysis did not reveal known gallinaceous poultry adaptive mutations, suggesting that the emergence of HP strains could have taken place in either wild or domestic ducks or in non-gallinaceous species. The presence of coexisting but genetically distinguishable avian influenza viruses with an HP viral genotype in two cohabiting species of wild waterfowl, with evidence of non-lethal infection at least in one species and without evidence of prior extensive circulation of the virus in domestic poultry, suggest that some strains with a potential high pathogenicity for poultry could be maintained in a community of wild waterfowl., Author Summary Until recently, the highly pathogenic avian influenza (HPAI) viruses responsible for high mortality in some domestic poultry were considered not to have a wild bird reservoir, but to emerge in domestic poultry populations from low pathogenic viruses perpetuated in wild waterbirds. The rapid spread of H5N1 HPAI virus in 2005–2006, with concurrent outbreaks reported in both domestic and wild birds over Asia, Europe, and Africa, has raised concerns about the potential role of migratory birds in the epidemiology of the HPAI infection. Wild birds were sampled in Africa and tested by molecular and virological methods in an attempt to trace the circulation of HPAI viruses. In addition, some of these wild birds were equipped with satellite transmitters to track their local and migratory movements in relation to the potential spread of avian diseases. Avian influenza viruses (H5N2) were detected in wild waterfowl in Nigeria, and were subsequently characterized as highly pathogenic by molecular sequencing (HPAI viral genotype). Movements of one infected bird tracked by satellite telemetry revealed that it survived infection by an HP viral genotype. This result constitutes a rare finding of infection by an AIV with an HPAI viral genotype in healthy wild birds.

Published
2008

20. Two-Plasmid system to increase the rescue efficiency of #Paramyxoviruses# by reverse genetics: the example of rescuing newcastle disease Virus

Author

Cécile Minet, Renata Servan de Almeida, Haijin Liu, Patricia Gil, Emmanuel Albina, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), supported by a scholarship from the Chinese government (CSC) and is the beneficiary of scientific grants from the European research Group EPIZONE, and Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0301 basic medicine, animal structures, [SDV]Life Sciences [q-bio], viruses, Genetic Vectors, Newcastle disease virus, Virulence, 2-plasmid system, Transfection, L73 - Maladies des animaux, Newcastle disease, Genome, Virus, Cell Line, 03 medical and health sciences, reverse genetics, Plasmid, paramyxovirus, Cricetinae, Virology, Animals, improved, Polymerase, Genetics, biology, biology.organism_classification, Reverse genetics, 030104 developmental biology, biology.protein, Plasmids
Abstract

Within paramyxoviruses, conventional reverse genetics require the transfection of a minimum of four plasmids: three to reconstruct the viral polymerase complex that replicates and expresses the virus genome delivered by a fourth plasmid. The successful transfection of four or more plasmids of different sizes into one cell and the subsequent generation of at least one viable and replicable viral particle is a rare event, which explains the low rescue efficiency, especially of low virulent viruses with reduced replication efficiency in cell lines. In this study, we report on an improved reverse genetics system developed for an avian paramyxovirus, Newcastle Disease Virus (NDV), in which the number of plasmids was reduced from four to two. Compared to the conventional method, the 2-plasmid system enables earlier and increased production of rescued viruses and, in addition, makes it possible to rescue viruses that it was not possible to rescue using the 4-plasmid system.

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