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1. Structural insights of a highly potent pan-neutralizing SARS-CoV-2 human monoclonal antibody

Author: Lorena Donnici, Rino Rappuoli, Ian A. Wilson, Matteo Conti, Hugo Mouquet, Hejun Liu, Raffaele De Francesco, Claudia Sala, Ida Paciello, Gabriel Ozorowski, Timothée Bruel, Giulia Piccini, Cyril Planchais, Jonathan L. Torres, Olivier Schwartz, Jeffrey Copps, Piero Pileri, Noemi Manganaro, Elisa Pantano, Emanuele Montomoli, Delphine Planas, Andrew B. Ward, Emanuele Andreano, The Scripps Research Institute [La Jolla, San Diego], Fondazione Toscana Gabriele Monasterio, Istituto Nazionale Genetica Molecolare [Milano] (INGM), Immunologie humorale - Humoral Immunology, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Virus et Immunité - Virus and immunity (CNRS-UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Vaccine Research Institute [Créteil, France] (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Università degli Studi di Siena = University of Siena (UNISI), Università degli Studi di Milano = University of Milan (UNIMI), This work was funded by Toscana Life Sciences, through the European Research Council advanced Grant agreement number 787552 (vAMRes), the European Union’s Horizon 2020 research and innovation program under Grant agreement no. 653316, and the Italian Ministry of Health COVID-2020-12371817 project, under collaborative agreements with The Scripps Research Institute. Work in the O.S. lab is funded by Institut Pasteur, Urgence COVID-19 Fundraising Campaign of Institut Pasteur, ANRS, the Vaccine Research Institute (ANR-10-LABX-77), Labex IBEID (ANR-10-LABX-62-IBEID), ANR/FRM Flash Covid PROTEO-SARS-CoV-2, and IDISCOVR. This work was also funded by the Bill & Melinda Gates Foundation (OPP1170236/INV-004923)., We thank B. Anderson and H. Turner for microscope assistance, C. Bowman for computational assistance, and G.K. Hedestam and M. Corcoran for scientific discussion regarding human antibody germline genes. We thank Dr. Piet Maes from NRC UZ/KU Leuven (Leuven, Belgium) for kindly providing the Omicron live., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-20-COVI-0059,PROTEO-SARS-CoV-2,Protéomique du SARS-CoV-2(2020), and European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015)
Subjects: 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), medicine.drug_class, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], Cell, Antibody Affinity, cryoelectron microscopy, Alpha (ethology), Biology, Monoclonal antibody, Antibodies, Viral, variants of concern, MESH: Antibodies, Monoclonal, MESH: Antibodies, Neutralizing, MESH: Antibody Affinity, Neutralization Tests, medicine, Potency, Humans, MESH: COVID-19, MESH: SARS-CoV-2, MESH: Humans, Multidisciplinary, SARS-CoV-2, monoclonal therapy, MESH: Neutralization Tests, Antibodies, Monoclonal, COVID-19, neutralizing antibody, Virology, Antibodies, Neutralizing, medicine.anatomical_structure, Monoclonal, MESH: Antibodies, Viral
Abstract: As the coronavirus disease 2019 (COVID-19) pandemic continues, there is a strong need for highly potent monoclonal antibodies (mAbs) that are resistant against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants of concern (VoCs). Here, we evaluate the potency of a previously described mAb J08 against these variants using cell-based assays and delve into the molecular details of the binding interaction using cryo-EM. We show that mAb J08 has low nanomolar affinity against VoCs, binds high on the receptor binding domain (RBD) ridge and is therefore unaffected by most mutations, and can bind in the RBD-up and -down conformations. These findings further validate the phase II/III human clinical trial underway using mAb J08 as a monoclonal therapy.One Sentence SummaryPotent neutralizing monoclonal antibody J08 binds SARS-CoV-2 spike independent of known escape mutations.
Published: 2022

2. A case study to dissect immunity to SARS-CoV-2 in a neonate nonhuman primate model

Author: Claire-Maëlle Fovet, Camille Pimienta, Mathilde Galhaut, Francis Relouzat, Natalia Nunez, Mariangela Cavarelli, Quentin Sconosciuti, Nina Dhooge, Ilaria Marzinotto, Vito Lampasona, Monica Tolazzi, Gabriella Scarlatti, Raphaël Ho Tsong Fang, Thibaut Naninck, Nathalie Dereuddre-Bosquet, Jérôme Van Wassenhove, Anne-Sophie Gallouët, Pauline Maisonnasse, Roger Le Grand, Elisabeth Menu, Nabila Seddiki, Infectious Diseases Models for Innovative Therapies (IDMIT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Life and Soft, IRCCS Ospedale San Raffaele [Milan, Italy], Mucosal Immunity and Sexually Transmitted Infection Control (MISTIC), Institut Pasteur [Paris] (IP), The Fondation Bettencourt Schueller and the Region Ile-de-France contributed to the implementation of IDMIT’s facilities and imaging technologies. The NHP model of SARS-CoV-2 infection have been developed thanks to the support from REACTing, the Fondation pour la Recherche Medicale (FRM, AM-CoV-Path) The virus stock used in NHPs was obtained even through the EVAg platform (https://www.european-virus-archive.com/), funded by H2020 (653316). The work performed at IRCCS Ospedale San Raffaele (OSR) was funded by Program Project COVID-19 OSR-UniSR and Ministero della Salute (COVID-2020-12371617)., ANR-11-INBS-0008,IDMIT,Infrastructure nationale pour la modélisation des maladies infectieuses humaines(2011), ANR-10-EQPX-0002,FlowCyTech,Plateforme de phénotypage en Mass cytométrie pour l'analyse multiparamétrique de biomarqueurs complexes de l'efficacité de nouvelles stratégies thérapeutiques ou vaccinales(2010), European Project: 730964, H2020, RIA,H2020-INFRAIA-2016-1,TRANSVAC2(2017), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), MENU, Elisabeth, Infrastructures - Infrastructure nationale pour la modélisation des maladies infectieuses humaines - - IDMIT2011 - ANR-11-INBS-0008 - INBS - VALID, Equipements d'excellence - Plateforme de phénotypage en Mass cytométrie pour l'analyse multiparamétrique de biomarqueurs complexes de l'efficacité de nouvelles stratégies thérapeutiques ou vaccinales - - FlowCyTech2010 - ANR-10-EQPX-0002 - EQPX - VALID, European Vaccine Research and Development Infrastructure - TRANSVAC2 - - H2020, RIA2017-05-01 - 2022-04-30 - 730964 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: Primates, [SDV]Life Sciences [q-bio], Immunology, Pilot Projects, nonhuman primate, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, children, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, microbiota, Animals, Humans, Immunology and Allergy, Child, [SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity, innate immunity, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, type-I IFN, SARS-CoV-2, Infant, Newborn, COVID-19, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV] Life Sciences [q-bio], pediatric, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, [SDV.IMM.IA] Life Sciences [q-bio]/Immunology/Adaptive immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Cytokines, RNA, Viral, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, neonate
Abstract: International audience; Most children are less severely affected by coronavirus-induced disease 2019 (COVID-19) than adults, and thus more difficult to study progressively. Here, we provide a neonatal nonhuman primate (NHP) deep analysis of early immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in blood and mucosal tissues. In addition, we provide a comparison with SARS-CoV-2-infected adult NHP. Infection of the neonate resulted in a mild disease compared with adult NHPs that develop, in most cases, moderate lung lesions. In concomitance with the viral RNA load increase, we observed the development of an early innate response in the blood, as demonstrated by RNA sequencing, flow cytometry, and cytokine longitudinal data analyses. This response included the presence of an antiviral type-I IFN gene signature, a persistent and lasting NKT cell population, a balanced peripheral and mucosal IFN-γ/IL-10 cytokine response, and an increase in B cells that was accompanied with anti-SARS-CoV-2 antibody response. Viral kinetics and immune responses coincided with changes in the microbiota profile composition in the pharyngeal and rectal mucosae. In the mother, viral RNA loads were close to the quantification limit, despite the very close contact with SARS-CoV-2-exposed neonate. This pilot study demonstrates that neonatal NHPs are a relevant model for pediatric SARS-CoV-2 infection, permitting insights into the early steps of anti-SARS-CoV-2 immune responses in infants.
Published: 2022

3. Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection

Author: Isabelle Bally, Judith A. Burger, Rogier W. Sanders, M. Buisson, Wesley Gros, Pascal Poignard, Axelle Amen, Roger Le Grand, Daphna Fenel, Francis Relouzat, Guy Schoehn, Camille Bouillier, Vanessa Contreras, Nicole M. Thielens, Julien Lemaitre, Franck Fieschi, Guidenn Sulbaran, Sylvie van der Werf, Anne-Sophie Gallouet, Nathalie Dereuddre-Bosquet, Winfried Weissenhorn, Romain Marlin, Michel Thépaut, Thibaut Naninck, Delphine Guilligay, Sebastian Dergan Dylon, Marit J. van Gils, Pauline Maisonnasse, Meliawati Poniman, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Department of Medical Microbiology and Infection Prevention [Amsterdam], University of Amsterdam [Amsterdam] (UvA), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), This work acknowledges support by the European Union's Horizon 2020 research and innovation program under grant agreement no. 681032, H2020 EHVA (W.W.), the ANR, RA-Covid-19 (W.W. and R.l.G.), and the CNRS (W.W.). W.W. acknowledges access to the platforms of the Grenoble Instruct-ERIC center (IBS and ISBG, UMS 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), with support from FRISBI (ANR-10-INBS-05-02) and GRAL, a project of the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). The IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, CEA) and financial support from CEA, CNRS, and UGA. The Infectious Disease Models and Innovative Therapies (IDMIT) research infrastructure is supported by the Program Investissements d’Avenir, managed by the National Research Agency (ANR) under reference ANR-11-INBS-0008. The Fondation Bettencourt Schueller and the Region Ile-de-France contributed to the implementation of IDMIT’s facilities and imaging technologies. The NHP study received financial support from REACTing, the Fondation pour la Recherche Médicale (AM-CoV-Path), and the European Infrastructure TRANSVAC2 (730964). We acknowledge support from CoVIC, supported by the Bill and Melinda Gates Foundation. The virus stock was obtained through the EVAg platform (https://www.european-virus-archive.com/), funded by H2020 (653316)., ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-11-INBS-0008,IDMIT,Infrastructure nationale pour la modélisation des maladies infectieuses humaines(2011), European Project: 681032,H2020,H2020-PHC-2015-single-stage_RTD,EHVA(2016), European Project: 730964, H2020, RIA,H2020-INFRAIA-2016-1,TRANSVAC2(2017), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Thomas, Frank, Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, Infrastructures - Infrastructure nationale pour la modélisation des maladies infectieuses humaines - - IDMIT2011 - ANR-11-INBS-0008 - INBS - VALID, European HIV Vaccine Alliance (EHVA): a EU platform for the discovery and evaluation of novel prophylactic and therapeutic vaccine candidates - EHVA - - H20202016-01-01 - 2020-12-31 - 681032 - VALID, European Vaccine Research and Development Infrastructure - TRANSVAC2 - - H2020, RIA2017-05-01 - 2022-04-30 - 730964 - VALID, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, Medical Microbiology and Infection Prevention, AII - Infectious diseases, Graduate School, Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Epidémiologie et Physiopathologie des Virus Oncogènes / Oncogenic Virus Epidemiology and Pathophysiology (EPVO (UMR_3569 / U-Pasteur_3)), platforms of the Grenoble Instruct-ERIC center (IBS and ISBG, and UMS 3518 CNRS-CEA-UGA-EMBL)
Subjects: Male, [SDV]Life Sciences [q-bio], MESH: Spike Glycoprotein, Coronavirus, Antibodies, Viral, Neutralization, MESH: Antibodies, Neutralizing, MESH: Chlorocebus aethiops, Chlorocebus aethiops, MESH: COVID-19, antibodies, MESH: Animals, MESH: Treatment Outcome, MESH: Immunoglobulin G, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Vaccination, Antibody titer, formaldehyde cross-linking, protection, S glycoprotein, medicine.anatomical_structure, Treatment Outcome, MESH: COVID-19 Vaccines, MESH: HEK293 Cells, Spike Glycoprotein, Coronavirus, Antibody, MESH: Pandemics, COVID-19 Vaccines, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], macaques, T cell, MESH: Vero Cells, Biology, General Biochemistry, Genetics and Molecular Biology, Virus, Article, Immunity, medicine, Animals, Humans, MESH: SARS-CoV-2, Vaccines, Virus-Like Particle, MESH: Immunoglobulin A, MESH: Vaccines, Virus-Like Particle, Pandemics, Vero Cells, B cells, MESH: Humans, SARS-CoV-2, COVID-19, MESH: Vaccination, Th1 Cells, Virology, Antibodies, Neutralizing, immunity, MESH: Male, Immunoglobulin A, Disease Models, Animal, Macaca fascicularis, HEK293 Cells, Immunization, MESH: Macaca fascicularis, MESH: Th1 Cells, Immunoglobulin G, Liposomes, biology.protein, MESH: Liposomes, nanoparticles, MESH: Disease Models, Animal, MESH: Antibodies, Viral
Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused an ongoing global health crisis. Here, we present as a vaccine candidate synthetic SARS-CoV-2 spike (S) glycoprotein-coated lipid vesicles that resemble virus-like particles. Soluble S glycoprotein trimer stabilization by formaldehyde cross-linking introduces two major inter-protomer cross-links that keep all receptor-binding domains in the “down” conformation. Immunization of cynomolgus macaques with S coated onto lipid vesicles (S-LVs) induces high antibody titers with potent neutralizing activity against the vaccine strain, Alpha, Beta, and Gamma variants as well as T helper (Th)1 CD4+-biased T cell responses. Although anti-receptor-binding domain (RBD)-specific antibody responses are initially predominant, the third immunization boosts significant non-RBD antibody titers. Challenging vaccinated animals with SARS-CoV-2 shows a complete protection through sterilizing immunity, which correlates with the presence of nasopharyngeal anti-S immunoglobulin G (IgG) and IgA titers. Thus, the S-LV approach is an efficient and safe vaccine candidate based on a proven classical approach for further development and clinical testing., Graphical abstract, Sulbaran et al. find that formaldehyde cross-linked S lipid nanoparticles induce potent neutralizing antibody titers upon cynomolgus macaque vaccination. Notably, vaccinated animals develop sterilizing immunity as highlighted upon virus challenge. Thus, the study provides a path to induce sterilizing immunity correlating with mucosal immune responses, which are desired to prevent virus spreading.
Published: 2022

4. Antiviral efficacy of favipiravir against Zika and SARS-CoV-2 viruses in non-human primates

Author: Romain Marlin, Delphine Desjardins, Vanessa Contreras, Guillaume Lingas, Caroline Solas, Pierre Roques, Thibaut Naninck, Quentin Pascal, Sylvie Behillil, Pauline Maisonnasse, Julien Lemaitre, Nidhal Kahlaoui, Benoit Delache, Andrés Pizzorno, Antoine Nougairede, Camille Ludot, Olivier Terrier, Nathalie Dereuddre-Bosquet, Francis Relouzat, Catherine Chapon, Raphael Ho Tsong Fang, Sylvie van der Werf, Manuel Rosa Calatrava, Denis Malvy, Xavier de Lamballerie, Jeremie Guedj, Roger Le Grand, Infectious Diseases Models for Innovative Therapies (IDMIT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, 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, 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), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), 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), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Global Health in the Global South (GHiGS), Institut de Recherche pour le Développement (IRD)- Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Infectious Disease Modelsand Innovative Therapies (IDMIT) research infrastructure is supported bythe 'Programme Investissements d’Avenir', managed by the ANR underreference ANR-11-INBS-0008. The Fondation Bettencourt Schueller andthe Region Ile-de-France contributed to the implementation of IDMIT’sfacilities and imaging technologies. The NHP study received financialsupport from REACTing, the Fondation pour la Recherche Medicale(FRM, AM-CoV-Path), the 'Agence Nationale de Recherche sur le SIDA etles hépatites virales – Maladies infectieuses émergentes' (ANRS-MIE), theZIKAlliance project which received funding from the European Union’sHorizon 2020 Research and Innovation Programme under Grant Agree-ment N.734548, and the European Infrastructure TRANSVAC2 (730964)for implementation of in vivo imaging technologies an NHP immunoassays. The European Union IMI2 program CARE (101005077) supportsthe development of the models. The HAE study received financial sup-port from REACTing, the Fondation pour la Recherche Medicale (FRM, AM-CoV-Path) and the Région Auvergne-Rhône-Alpes. The virus stocksused in NHPs were obtained through the EVAg platform (https://www.european-virus-archive.com/), funded by H2020 (653316)., ANR-11-INBS-0008,IDMIT,Infrastructure nationale pour la modélisation des maladies infectieuses humaines(2011), European Project: 734548,ZIKAlliance(2016), European Project: 730964, H2020, RIA,H2020-INFRAIA-2016-1,TRANSVAC2(2017), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), 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), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Terrier, Olivier, Infrastructures - Infrastructure nationale pour la modélisation des maladies infectieuses humaines - - IDMIT2011 - ANR-11-INBS-0008 - INBS - VALID, A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID, European Vaccine Research and Development Infrastructure - TRANSVAC2 - - H2020, RIA2017-05-01 - 2022-04-30 - 730964 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Primates, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, SARS-CoV-2, Zika Virus Infection, General Physics and Astronomy, Zika Virus, General Chemistry, Amides, Antiviral Agents, General Biochemistry, Genetics and Molecular Biology, COVID-19 Drug Treatment, Macaca fascicularis, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Pyrazines, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Animals, Humans, Pandemics
Abstract: The COVID-19 pandemic has exemplified that rigorous evaluation in large animal models is key for translation from promising in vitro results to successful clinical implementation. Among the drugs that have been largely tested in clinical trials but failed so far to bring clear evidence of clinical efficacy is favipiravir, a nucleoside analogue with large spectrum activity against several RNA viruses in vitro and in small animal models. Here, we evaluate the antiviral activity of favipiravir against Zika or SARS-CoV-2 virus in cynomolgus macaques. In both models, high doses of favipiravir are initiated before infection and viral kinetics are evaluated during 7 to 15 days after infection. Favipiravir leads to a statistically significant reduction in plasma Zika viral load compared to untreated animals. However, favipiravir has no effects on SARS-CoV-2 viral kinetics, and 4 treated animals have to be euthanized due to rapid clinical deterioration, suggesting a potential role of favipiravir in disease worsening in SARS-CoV-2 infected animals. To summarize, favipiravir has an antiviral activity against Zika virus but not against SARS-CoV-2 infection in the cynomolgus macaque model. Our results support the clinical evaluation of favipiravir against Zika virus but they advocate against its use against SARS-CoV-2 infection.
Published: 2022

5. Development of a highly specific and sensitive VHH-based sandwich immunoassay for the detection of the SARS-CoV-2 nucleoprotein

Author: Gransagne, Marion, Aymé, Gabriel, Brier, Sébastien, Chauveau-Le Friec, Gaëlle, Meriaux, Véronique, Nowakowski, Mireille, Déjardin, François, Levallois, Sylvain, Dias de Melo, Guilherme, Donati, Flora, Prot, Matthieu, Brûlé, Sébastien, Raynal, Bertrand, Bellalou, Jacques, Goncalves, Pedro, Montagutelli, Xavier, Di Santo, James, Lazarini, Françoise, England, Patrick, Petres, Stéphane, Escriou, Nicolas, Lafaye, Pierre, Département de Santé Globale - Department Global Health, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Ingénierie des Anticorps (plate-forme) - Antibody Engineering (Platform), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Plateforme Technologique de RMN Biologique et HDX-MS - Biological NMR and HDX-MS Technological Platform, Plateforme technologique Production et purification de protéines recombinantes – Production and Purification of Recombinant Proteins Technological Platform (PPR), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Lyssavirus, épidémiologie et neuropathologie - Lyssavirus Epidemiology and Neuropathology, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses, Biophysique Moléculaire (plateforme) - Molecular Biophysics (platform), Immunité Innée - Innate Immunity, Génétique de la souris - Mouse Genetics, Perception et Mémoire / Perception and Memory, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), P. G. and J. P. D. received support from the ANR grant 'COVARIMM.'We want to thank Nicolas Wolff and Baptiste Colcombet-Cazenave for their technical help for the production of the different VHHs. The strain BetaCoV/France/IDF0372/2020 was supplied by the National Reference Centre for Respiratory Viruses hosted by Institut Pasteur (Paris, France) and headed by Pr. Sylvie van der Werf. The human sample from which strain BetaCoV/France/IDF0372/2020 was isolated was provided by Dr X. Lescure and Pr. Y. Yazdanpanah from the Bichat Hospital, Paris, France. Moreover, the strain BetaCoV/France/IDF0372/2020 was supplied through the European Virus Archive goes Global (Evag) platform, a project that has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No 653316. We are grateful to the National Reference Center for Respiratory Viruses for providing the variants of concern used in mouse experiments, to Sylvie van der Werf and Etienne Simon-Lorière for support and scientific advice, and to Grégory Jouvion for histological evaluation. We thank the Institut Pasteur Histology platform for histological slides preparation. Mouse experiments on variants of concern were supported by ANR grants HUMOCID (ANR-20-COVI-0028-01) and IBEID (ANR-10-LABX-62-IBEID) and by the EU Horizon 2020 RECOVER project (No. 101003589). The authors would like to thank the DIM 1HEALTH région Ile-de-France scheme for funding the Centrifection project that allowed to purchase the Optima ultracentrifuge. The CACSICE Equipex ANR-11-EQPX-0008 is acknowledged., ANR-20-COVI-0053,CoVarImm,Variation de la réponse immune systémique et muqueuse pendant l'infection par le SRAS-CoV-2 et la convalescence(2020), ANR-20-COVI-0028,HuMoCID,Développement de modèles murins de COVID-19(2020), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-11-EQPX-0008,CACSICE,Centre d'analyse de systèmes complexes dans les environnements complexes(2011), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut Pasteur [Paris], ENGLAND, Patrick, Variation de la réponse immune systémique et muqueuse pendant l'infection par le SRAS-CoV-2 et la convalescence - - CoVarImm2020 - ANR-20-COVI-0053 - COVID-19 - VALID, Développement de modèles murins de COVID-19 - - HuMoCID2020 - ANR-20-COVI-0028 - COVID-19 - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Equipements d'excellence - Centre d'analyse de systèmes complexes dans les environnements complexes - - CACSICE2011 - ANR-11-EQPX-0008 - EQPX - VALID, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR)
Subjects: viruses, diagnostic, Enzyme-Linked Immunosorbent Assay, single domain antibodies, Limit of Detection, Cricetinae, Animals, Humans, NTD, N Terminal Domain of the Nucleoprotein, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS, Research Articles, hydrogen‐deuterium exchange, nucleoprotein, antibody engineering, SARS-CoV-2, N, Nucleoprotein, CTD, C Terminal Domain of the Nucleoprotein, virus diseases, COVID-19, Covid19, Nucleocapsid Proteins, Single-Domain Antibodies, nanobodies, hydrogen-deuterium exchange, body regions, HDX-MS, Hydrogen Deuterium eXchange-Mass Spectrometry, immunochemistry, [SDV.IMM]Life Sciences [q-bio]/Immunology, Electrophoresis, Polyacrylamide Gel, phage display
Abstract: International audience; The current COVID-19 pandemic illustrates the importance of obtaining reliable methods for the rapid detection of SARS-CoV-2. A highly specific and sensitive diagnostic test able to differentiate the SARS-CoV-2 virus from common human coronaviruses is therefore needed. Coronavirus nucleoprotein (N) localizes to the cytoplasm and the nucleolus and is required for viral RNA synthesis. N is the most abundant coronavirus protein, so it is of utmost importance to develop specific antibodies for its detection. In this study, we developed a sandwich immunoassay to recognize the SARS-CoV-2 N protein. We immunized one alpaca with recombinant SARS-CoV-2 N and constructed a large single variable domain on heavy chain (VHH) antibody library. After phage display selection, seven VHHs recognizing the full N protein were identified by ELISA. These VHHs did not recognize the nucleoproteins of the four common human coronaviruses. Hydrogen Deuterium eXchange-Mass Spectrometry (HDX-MS) analysis also showed that these VHHs mainly targeted conformational epitopes in either the C-terminal or the N-terminal domains. All VHHs were able to recognize SARS-CoV-2 in infected cells or on infected hamster tissues. Moreover, the VHHs could detect the SARS variants B.1.17/alpha, B.1.351/beta, and P1/gamma. We propose that this sandwich immunoassay could be applied to specifically detect the SARS-CoV-2 N in human nasal swabs.
Published: 2022

6. Emerging preclinical evidence does not support broad use of hydroxychloroquine in COVID-19 patients

Author: Donald E. Ingber, H. Feldmann, Kyle Rosenke, César Muñoz-Fontela, Joana Rocha-Pereira, Pierre Stéphane Gsell, Matthew B. Frieman, Simon G. P. Funnell, Kai Dallmeier, Suzanne J.F. Kaptein, E. de Wit, Johan Neyts, Leen Delang, R. Le Grand, Pauline Maisonnasse, W. E. Dowling, G. A. Hamilton, C. M. Coleman, Public Health England [London], Coalition for Epidemic Preparedness Innovations [Washington, DC, États-Unis] (CEPI), Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Harvard University [Cambridge], Emulate, Inc. [Boston, MA, États-Unis], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), National Institute of Health [Hamilton, MT, États-Unis], Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, University of Maryland School of Medicine, University of Maryland System, University of Nottingham, UK (UON), D.E. Ingber acknowledges research funding from NIH NCATS UH3-HL-141797 and DARPA under Cooperative Agreements HR00111920008 and HR0011-20-2-0040. P. Maisonnass acknowledges financial support from REACTing, the National Research Agency (ANR-AM-CoV-Path), the European Union’s Horizon 2020 (H2020) research and innovation programme Fight-nCov (grant No. 101003555), the European Union IMI2 programme CARE (grant No. 101005077), the European Infrastructure TRANSVAC2 (grant No. 730964) and virus stock was obtained through the EVAg platform (https://www.european-virus-archive.com/) funded by H2020 (Grant No. 653316). The Inserm Infectious Disease Models and Innovative Therapies research infrastructure (IDMIT) is supported by the 'Programme Investissements d’Avenir' (PIA), managed by the ANR under reference ANR-11-INBS-0008, the Fondation Bettencourt Schueller, the Region Ile-de-France and the Domaine d’Intérêt Majeur (DIM, Paris, France) 'One Health'. H. Feldmann acknowledges that the Laboratory of Virology was funded by the NIAID Intramural Research Programme, ANR-11-INBS-0008,IDMIT,Infrastructure nationale pour la modélisation des maladies infectieuses humaines(2011), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Harvard University, Bodescot, Myriam, Infrastructures - Infrastructure nationale pour la modélisation des maladies infectieuses humaines - - IDMIT2011 - ANR-11-INBS-0008 - INBS - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, General Physics and Astronomy, 02 engineering and technology, Treatment failure, Mice, Cricetinae, Treatment Failure, lcsh:Science, Repurposing, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, 021001 nanoscience & nanotechnology, 3. Good health, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0210 nano-technology, Coronavirus Infections, medicine.drug, Hydroxychloroquine, Primates, medicine.medical_specialty, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Science, Population, Pneumonia, Viral, Antiviral Agents, Models, Biological, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Betacoronavirus, Animal disease models, medicine, Animals, Humans, Intensive care medicine, education, Pandemics, Extramural, business.industry, SARS-CoV-2, Comment, COVID-19, General Chemistry, COVID-19 Drug Treatment, Respiratory system models, 030104 developmental biology, Preclinical research, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, lcsh:Q, business
Abstract: There is an urgent need for drugs, therapies and vaccines to be available to protect the human population against COVID-19. One of the first approaches taken in the COVID-19 global response was to consider repurposing licensed drugs. This commentary highlights an extraordinary international collaborative effort of independent researchers who have recently all come to the same conclusion—that chloroquine or hydroxchloroquine are unlikely to provide clinical benefit against COVID-19. ispartof: NATURE COMMUNICATIONS vol:11 issue:1 ispartof: location:England status: published
Published: 2020

7. Targeting SARS-CoV-2 receptor-binding domain to cells expressing CD40 improves protection to infection in convalescent macaques

Author: Zhiqing Wang, Olivier Schwartz, Mathieu Surenaud, Mireille Centlivre, Gerard Zurawski, Julien Lemaitre, Léa Dupaty, Christine Lacabaratz, Yves Levy, Rodolphe Thiébaut, Sylvie van der Werf, Inga Szurgot, Romain Marlin, Véronique Godot, Severin Coleon, Aurélie Wiedemann, Giuseppe Pantaleo, Pauline Maisonnasse, Delphine Planas, Mélanie Prague, Catherine Chapon, Mario Gomez-Pacheco, Thibaut Naninck, Mathilde Galhaut, Anne-Sophie Gallouet, Jerome Ellis, Mariangela Cavarelli, Sandra Zurawski, Nidhal Kahlaoui, Roger Le Grand, Timothée Bruel, Francis Relouzat, Craig Fenwick, Nathalie Dereuddre-Bosquet, Sylvain Cardinaud, Raphael Ho Tsong Fang, Peter Liljeström, Vanessa Contreras, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Vaccine Research Institute (VRI), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Baylor Scott & White Charles A. Sammons Cancer Center [Dallas, TX, USA], Lausanne University Hospital, Université de Lausanne = University of Lausanne (UNIL), Karolinska Institutet [Stockholm], Virus et Immunité - Virus and immunity, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Institut Pasteur [Paris]-Université Paris Cité (UPCité), Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Statistics In System biology and Translational Medicine (SISTM), Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)- Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Bordeaux [Bordeaux], Hôpital Henri Mondor, Hôpital Albert Chenevier, The programme was funded by the Vaccine Research Institute via the ANR-10-LABX-77 grant. Studies in hu-mice model have been supported by ARN grant ANR-20-COV6-0004-01. The Infectious Disease Models and Innovative Therapies (IDMIT) research infrastructure is supported by the 'Programme Investissements d’Avenir', managed by the ANR under reference ANR-11-INBS-0008. The Fondation Bettencourt Schueller and the Region Ile-de-France contributed to the implementation of IDMIT’s facilities and imaging technologies. The NHP study received financial support from REACTing, the Fondation pour la Recherche Medicale (FRM, AM-CoV-Path) and the European Infrastructure TRANSVAC2 (730964) for implementation of in vivo imaging technologies an NHP immuno assays. The virus stock used in NHPs was obtained through the EVAg platform (https://www.european-virus-archive.com/), funded by H2020 (653316)., ANR-10-LABX-0077,VRI,Initiative for the creation of a Vaccine Research Institute(2010), ANR-20-COV6-0004,DC-CoVaC,Développement de vaccins anti-SARS-CoV-2(2020), ANR-11-INBS-0008,IDMIT,Infrastructure nationale pour la modélisation des maladies infectieuses humaines(2011), European Project: 730964, H2020, RIA,H2020-INFRAIA-2016-1,TRANSVAC2(2017), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), University of Lausanne (UNIL), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut Pasteur [Paris], Vaccine Research Institute [Créteil, France] (VRI), Virus et Immunité - Virus and immunity (CNRS-UMR3569), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), DARMIGNY, SANDRINE, Laboratoires d'excellence - Initiative for the creation of a Vaccine Research Institute - - VRI2010 - ANR-10-LABX-0077 - LABX - VALID, Développement de vaccins anti-SARS-CoV-2 - - DC-CoVaC2020 - ANR-20-COV6-0004 - COVID-19 - VALID, Infrastructures - Infrastructure nationale pour la modélisation des maladies infectieuses humaines - - IDMIT2011 - ANR-11-INBS-0008 - INBS - VALID, European Vaccine Research and Development Infrastructure - TRANSVAC2 - - H2020, RIA2017-05-01 - 2022-04-30 - 730964 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: T-Lymphocytes, medicine.medical_treatment, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Mice, 0302 clinical medicine, 030212 general & internal medicine, skin and connective tissue diseases, B-Lymphocytes, 0303 health sciences, Multidisciplinary, biology, Vaccination, 3. Good health, [SDV] Life Sciences [q-bio], Spike Glycoprotein, Coronavirus, Vaccines, Subunit, Antibody, Adjuvant, Protein vaccines, COVID-19 Vaccines, Science, Protein domain, Antigen-Presenting Cells, Virulence, Article, General Biochemistry, Genetics and Molecular Biology, Viral vector, 03 medical and health sciences, Protein Domains, medicine, Animals, Humans, CD40 Antigens, 030304 developmental biology, CD40, SARS-CoV-2, fungi, COVID-19, Convalescence, General Chemistry, Virology, body regions, Viral infection, Preclinical research, Reinfection, Mutation, Humanized mouse, biology.protein, Macaca
Abstract: Achieving sufficient worldwide vaccination coverage against SARS-CoV-2 will require additional approaches to currently approved viral vector and mRNA vaccines. Subunit vaccines may have distinct advantages when immunizing vulnerable individuals, children and pregnant women. Here, we present a new generation of subunit vaccines targeting viral antigens to CD40-expressing antigen-presenting cells. We demonstrate that targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to CD40 (αCD40.RBD) induces significant levels of specific T and B cells, with long-term memory phenotypes, in a humanized mouse model. Additionally, we demonstrate that a single dose of the αCD40.RBD vaccine, injected without adjuvant, is sufficient to boost a rapid increase in neutralizing antibodies in convalescent non-human primates (NHPs) exposed six months previously to SARS-CoV-2. Vaccine-elicited antibodies cross-neutralize different SARS-CoV-2 variants, including D614G, B1.1.7 and to a lesser extent B1.351. Such vaccination significantly improves protection against a new high-dose virulent challenge versus that in non-vaccinated convalescent animals., In this study, Marlin et al. provide insights into the potential use of subunit vaccines that induce a high level of protection against SARS-CoV-2 in animal models.
Published: 2021

8. COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models

Author: Maisonnasse, Pauline, Aldon, Yoann, Marc, Aurélien, Marlin, Romain, Dereuddre-Bosquet, Nathalie, Kuzmina, Natalia A., Freyn, Alec W., Snitselaar, Jonne L., Gonçalves, Antonio, Caniels, Tom G., Burger, Judith A., Poniman, Meliawati, Bontjer, Ilja, Chesnais, Virginie, Diry, Ségolène, Iershov, Anton, Ronk, Adam J., Jangra, Sonia, Rathnasinghe, Raveen, Brouwer, Philip J. M., Bijl, Tom P. L., van Schooten, Jelle, Brinkkemper, Mitch, Liu, Hejun, Yuan, Meng, Mire, Chad E., van Breemen, Mariëlle J., Contreras, Vanessa, Naninck, Thibaut, Lemaître, Julien, Kahlaoui, Nidhal, Relouzat, Francis, Chapon, Catherine, Ho Tsong Fang, Raphaël, McDanal, Charlene, Osei-Twum, Mary, St-Amant, Natalie, Gagnon, Luc, Montefiori, David C., Wilson, Ian A., Ginoux, Eric, de Bree, Godelieve J., García-Sastre, Adolfo, Schotsaert, Michael, Coughlan, Lynda, Bukreyev, Alexander, van der Werf, Sylvie, Guedj, Jérémie, Sanders, Rogier W., van Gils, Marit J., Le Grand, Roger, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Imperial College London, 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, University of Texas Medical Branch at Galveston, Icahn School of Medicine at Mount Sinai [New York] (MSSM), Department of Medical Microbiology and Infection Prevention [Amsterdam], University of Amsterdam [Amsterdam] (UvA), Amsterdam UMC - Amsterdam University Medical Center, Life and Soft, The Scripps Research Institute [La Jolla, San Diego], Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), This study was supported by the Netherlands Organization for Scientific Research (NWO) Vici grant (to R.W.S.), the Bill & Melinda Gates Foundation through the Collaboration for AIDS Vaccine Discovery (CAVD) grant INV-002022 (to R.W.S.), the Fondation Dormeur, Vaduz (to R.W.S. and to M.J.v.G.) and Health Holland PPS-allowance LSHM20040 (to M.J.v.G.). M.J.v.G. is a recipient of an AMC Fellowship, Amsterdam UMC and a COVID-19 grant of the Amsterdam Institute of Infection and Immunity, the Netherlands. R.W.S and M.J.v.G. are recipients of support from the University of Amsterdam Proof of Concept fund (contract no 200421) as managed by Innovation Exchange Amsterdam (IXA). The Infectious Disease Models and Innovative Therapies (IDMIT) research infrastructure is supported by the 'Programme Investissements d’Avenir', managed by the ANR under reference ANR-11-INBS-0008. The Fondation Bettencourt Schueller and the Region Ile-de-France contributed to the implementation of IDMIT’s facilities and imaging technologies. The NHP study received financial support from REACTing, the Fondation pour la Recherche Médicale (FRM, France, AM-CoV-Path) and the European Infrastructure TRANSVAC2 (730964). The virus stock used in NHPs was obtained through the EVAg platform (https://www.european-virus-archive.com/), funded by H2020 (653316). Work performed at Duke University was supported by the CoVPN grant (NIH AI46705) (to D.C.M.). The Ad5-hACE2 mouse work was supported in part by NIAID R21AI157606 (L.C.), and was partially supported by CRIP (Center for Research for Influenza Pathogenesis), an NIAID supported Center of Excellence for Influenza Research and Surveillance (CEIRS, contract # HHSN272201400008C) (A.G.S.), by supplements to NIAID grant U19AI135972 and DoD grant W81XWH-20-1-0270, by the Defense Advanced Research Projects Agency (HR0011-19-2-0020), and by the generous support of the JPB Foundation, the Open Philanthropy Project (research grant 2020-215611 (5384) and anonymous donors to A.G.S. Part of this study was supported by the Bill and Melinda Gates Foundation through grants OPP1170236 and INV-004923 (I.A.W.) and through the Global Health Vaccine Accelerator Platforms (GH-VAP) and the Coronavirus Immunotherapy Consortium (CoVIC) (Nexelis)., ANR-11-INBS-0008,IDMIT,Infrastructure nationale pour la modélisation des maladies infectieuses humaines(2011), ANR-20-COVI-0021,AM-Cov-Path,Pathogénèse de l'infection SARS-Cov-2 dans un modèle de primates non humains : un modèle pour les traitements et la prévention(2020), European Project: 730964, H2020, RIA,H2020-INFRAIA-2016-1,TRANSVAC2(2017), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Medical Microbiology and Infection Prevention, Graduate School, AII - Infectious diseases, Infectious diseases, APH - Aging & Later Life, and APH - Global Health
Subjects: Male, medicine.drug_class, Science, [SDV]Life Sciences [q-bio], Drug Evaluation, Preclinical, Mice, Transgenic, Monoclonal antibody, Antiviral Agents, Article, Mice, In vivo, medicine, Animals, Humans, Tissue Distribution, Respiratory system, Neutralizing antibody, Lung, Infectivity, Mesocricetus, biology, SARS-CoV-2, business.industry, Therapeutic effect, Antibodies, Monoclonal, COVID-19, Viral Load, Antibodies, Neutralizing, COVID-19 Drug Treatment, Disease Models, Animal, Macaca fascicularis, medicine.anatomical_structure, Preclinical research, Immunology, biology.protein, Infectious diseases, Female, Immunotherapy, Angiotensin-Converting Enzyme 2, business, Viral load
Abstract: Effective treatments against Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) are urgently needed. Monoclonal antibodies have shown promising results in patients. Here, we evaluate the in vivo prophylactic and therapeutic effect of COVA1-18, a neutralizing antibody highly potent against the B.1.1.7 isolate. In both prophylactic and therapeutic settings, SARS-CoV-2 remains undetectable in the lungs of treated hACE2 mice. Therapeutic treatment also causes a reduction in viral loads in the lungs of Syrian hamsters. When administered at 10 mg kg-1 one day prior to a high dose SARS-CoV-2 challenge in cynomolgus macaques, COVA1-18 shows very strong antiviral activity in the upper respiratory compartments. Using a mathematical model, we estimate that COVA1-18 reduces viral infectivity by more than 95% in these compartments, preventing lymphopenia and extensive lung lesions. Our findings demonstrate that COVA1-18 has a strong antiviral activity in three preclinical models and could be a valuable candidate for further clinical evaluation., Monoclonal antibodies show great promise in treating Covid-19 patients. Here, Maisonnasse, Aldon and colleagues report pre-clinical results for COVA1-18 and demonstrate that it reduces viral infectivity in three animal models with over 95% efficacy in macaques upper respiratory tract.
Published: 2021

9. A laboratory-based study to explore the use of honey-impregnated cards to detect chikungunya virus in mosquito saliva

Author: Fourniol, Lisa, Madec, Yoann, Mousson, Laurence, Vazeille, Marie, Failloux, Anna-Bella, Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), This study was supported by the European Union’s Horizon 2020 research and innovation program under EVAg grant agreement no. 653316 and the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°ANR-10-LABX-62-IBEID)., We thank Malika Hocine and Jocelyne Alexandre for helping in rearing mosquitoes., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)
Subjects: RNA viruses, Physiology, viruses, [SDV]Life Sciences [q-bio], Disease Vectors, Pathology and Laboratory Medicine, Mosquitoes, Medical Conditions, Filter Paper, Animal Products, Aedes, Medicine and Health Sciences, Chikungunya Virus, Reverse Transcriptase Polymerase Chain Reaction, Eukaryota, virus diseases, Agriculture, Honey, Body Fluids, Insects, Laboratory Equipment, Infectious Diseases, Blood, Medical Microbiology, Viral Pathogens, Viruses, Engineering and Technology, RNA, Viral, Medicine, Pathogens, Anatomy, Salivation, Research Article, Paper, Arthropoda, Alphaviruses, Science, education, Equipment, Aedes Aegypti, Microbiology, Specimen Handling, Togaviruses, parasitic diseases, Animals, Saliva, Microbial Pathogens, Nutrition, fungi, Organisms, Biology and Life Sciences, Invertebrates, Insect Vectors, Diet, Species Interactions, Food, Physiological Processes, Zoology, Entomology
Abstract: International audience; Mosquito control is implemented when arboviruses are detected in patients or in field-collected mosquitoes. However, mass screening of mosquitoes is usually laborious and expensive, requiring specialized expertise and equipment. Detection of virus in mosquito saliva using honey-impregnated filter papers seems to be a promising method as it is non-destructive and allows monitoring the viral excretion dynamics over time from the same mosquito. Here we test the use of filter papers to detect chikungunya virus in mosquito saliva in laboratory conditions, before proposing this method in large-scale mosquito surveillance programs. We found that 0.9 cm 2 cards impregnated with a 50% honey solution could replace the forced salivation technique as they offered a viral RNA detection until 7 days after oral infection of Aedes aegypti and Aedes albopictus mosquitoes with CHIKV.
Published: 2021

10. At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions

Author: Ceren Simsek, Alexander N. Lukashev, Ward Deboutte, Yaw Adu Sarkodie, Daan Jansen, Hermann Ulrich Everling, Kwe Claude Yinda, Tabea Binger, Florian Gloza-Rausch, Eric M. Leroy, Mathieu Bourgarel, Leen Beller, Victor M. Corman, Augustina Sylverken, Stoian Yordanov, Marc Van Ranst, Jan Felix Drexler, Samuel Oppong, Gael Darren Maganga, Jelle Matthijnssens, Peter Vallo, Christian Drosten, Antje Seebens-Hoyer, Andrea Rasche, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], German Center for Infection Research, Partnersite Munich (DZIF), University of Bonn, Sechenov First Moscow State Medical University, Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), Centre International de Recherches Médicales de Franceville (CIRMF), Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Noctalis, Centre for Bat Protection and Information, Forestry Board Directorate of Strandja Natural Park, Strandja Natural Park, Kwame Nkrumah University of Science and Technology [GHANA] (KNUST), Institute of Vertebrate Biology of the Czech Academy of Sciences (IVB / CAS), Czech Academy of Sciences [Prague] (CAS), 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]), 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), This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie agreement no. 721367 granted to J.F.D., J.M., and M.V.R. EU Horizon 2020 projects EVAg (grant agreement number 653316) and COMPARE (agreement number 643476) granted to C.D., and the Russian Science Foundation grant 19-15-00055 to A.N.L. also provided funding to the current study. H.U.E. had a personal scholarship from the BONFOR intramural program at the University of Bonn. German Federal Ministry of Education and Research (BMBF) (project code 01KIO16D), Deutsche Forschungsgemeinschaft (DFG DR 772-3/1), Deutsche Forschungsgemeinschaft within the Africa Infectious Diseases program gave grants to C.D. and Y.A.S. (DR 772/3-1) and to S.O. (KA1241/18-1) that were also among the funding contributions. A personal scholarship granted to A.R. from the German Academic Exchange Service (DAAD) supported field work in Costa Rica. D. J. was supported by the Fonds Wetenschappelijk Onderzoek (Research foundation Flanders) (1S78019N). L.B. was supported by the Fonds Wetenschappelijk Onderzoek (1S61618N). K.C.Y. was funded by the Interfaculty Council for Development Cooperation (IRO) from the KU Leuven. The computing power in this work was provided by the VSC (Flemish Supercomputer Centre), financed by the FWO and the Flemish government, department EWI., European Project: 777657,H2020-EU.1.3.3. - Stimulating innovation by means of cross-fertilisation of knowledge,777657,MSCA-RISE(2018), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 643476,H2020,H2020-PHC-2014-single-stage,COMPARE(2014), Universität Bonn = University of Bonn, Université des Sciences et Techniques de Masuku (USTM), and Kwame Nkrumah University of Science and Technology (KNUST)
Subjects: Rotavirus, Viral metagenomics, [SDV]Life Sciences [q-bio], viruses, Reassortment, medicine.disease_cause, L73 - Maladies des animaux, Genome, Zoonoses, Chiroptera, Genotype, Phylogeny, 0303 health sciences, Phylogenetic tree, Strain (biology), [SDV.BA]Life Sciences [q-bio]/Animal biology, Zoonosis, virus diseases, QR1-502, 3. Good health, S50 - Santé humaine, Middle East Respiratory Syndrome Coronavirus, Research Article, Diarrhea, zoonose, Middle East respiratory syndrome coronavirus, relation homme-faune, Genome, Viral, Ecological and Evolutionary Science, Biology, Microbiology, Rotavirus Infections, rotavirus genetic diversity, SA11, 03 medical and health sciences, Coronavirus 2 du syndrome respiratoire aigu sévère, Virology, medicine, Animals, Humans, Horses, Transmission des maladies, 030304 developmental biology, Genetic diversity, 030306 microbiology, SARS-CoV-2, COVID-19, Genetic Variation, zoonosis, medicine.disease, respiratory tract diseases, Evolutionary biology, bat rotavirus, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Metagenomics, Virus pathogène
Abstract: The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens., Bats host many viruses pathogenic to humans, and increasing evidence suggests that rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America, and Africa were PCR-positive for RVA, and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, which included evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite various levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.
Published: 2021

11. 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

12. Intranasal vaccination with a lentiviral vector protects against SARS-CoV-2 in preclinical animal models

Author: Hugo Mouquet, Benjamin Vesin, Houda Tabbal, Françoise Guinet, Jodie Lopez, Pierre Authié, Laurence Fiette, Marine Le Dudal, Catherine Blanc, François Anna, Maryline Bourgine, Nicolas Escriou, David Hardy, Fanny Moncoq, Kirill Nemirov, Fabien Nevo, Annette Martin, Pierre Charneau, Philippe Souque, Laleh Majlessi, Emeline Simon, Amandine Noirat, Min Wen Ku, Laboratoire commun Pasteur-TheraVectys, Institut Pasteur [Paris] (IP)-TheraVectys, Virologie Moléculaire et Vaccinologie / Molecular Virology and Vaccinology, Institut Pasteur [Paris] (IP), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Neuropathologie expérimentale / Experimental neuropathology, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Institut Mutualiste de Montsouris (IMM), Lymphocytes et Immunité - Lymphocytes and Immunity, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Immunologie humorale - Humoral Immunology, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d’innovation : vaccins – Innovation lab : vaccines, The authors are grateful to Prof. Sylvie van der Werf (National Reference Centre for Respiratory Viruses, Institut Pasteur, France) for providing the BetaCoV/France/IDF0372/2020 SARS-CoV-2 clinical isolate, supplied through the European Virus Archive Global (Evag), funded by the European Union’s Horizon 2020 program under grant agreement no. 653316. This work was also supported by grants from Institut Pasteur, TheraVectys, and Agence Nationale de la Recherche HuMoCID. M.W.K. is part of the Pasteur - Paris University PhD program and received funding from Institut Carnot Pasteur Microbes & Santé and the European Union’s Horizon 2020 program under Marie Sklodowska-Curie grant agreement no. 665807., ANR-20-COVI-0028,HuMoCID,Développement de modèles murins de COVID-19(2020), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 665807,H2020,H2020-MSCA-COFUND-2014,PASTEURDOC(2015), Institut Pasteur [Paris]-TheraVectys, Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut Pasteur [Paris]-Université de Paris (UP), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Hardy, David, Développement de modèles murins de COVID-19 - - HuMoCID2020 - ANR-20-COVI-0028 - COVID-19 - VALID, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Institut Pasteur International Docotal Program - PASTEURDOC - - H20202015-10-01 - 2020-10-01 - 665807 - VALID
Subjects: Male, [SDV]Life Sciences [q-bio], Respiratory System, lentiviral vectors, immunoglobulin A, Antibodies, Viral, Mice, Transduction (genetics), 0302 clinical medicine, Cricetinae, respiratory tracts, 0303 health sciences, Viral Load, 3. Good health, Vaccination, [SDV] Life Sciences [q-bio], medicine.anatomical_structure, in vivo Ad5 transduction, Models, Animal, Spike Glycoprotein, Coronavirus, Lentivirus, Female, COVID-19 Vaccines, Genetic Vectors, Immunization, Secondary, Biology, Microbiology, Article, Viral vector, 03 medical and health sciences, Immune system, [SDV.IMM.VAC] Life Sciences [q-bio]/Immunology/Vaccinology, Virology, boost-target, medicine, Animals, neutralizing antibodies, Immunity, Mucosal, Administration, Intranasal, 030304 developmental biology, SARS-CoV-2, lung inflammation, COVID-19, beta-coronavirus, Vaccine efficacy, biology.organism_classification, Antibodies, Neutralizing, intranasal vaccination, Immunology, mucosal immunity, Parasitology, Nasal administration, golden hamsters, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, 030217 neurology & neurosurgery, Respiratory tract
Abstract: To develop a vaccine candidate against COVID-19, we generated a Lentiviral Vector (LV), eliciting neutralizing antibodies against the Spike glycoprotein of SARS-CoV-2. Systemic vaccination by this vector in mice, in which the expression of the SARS-CoV-2 receptor hACE2 has been induced by transduction of respiratory tract cells by an adenoviral vector, confers only partial protection, despite high levels of serum neutralizing activity. However, eliciting an immune response in the respiratory tract through an intranasal boost results in > 3 log10 decrease in the lung viral loads and reduces local inflammation. Moreover, both integrative and non-integrative LV platforms display strong vaccine efficacy and inhibit lung deleterious injury in golden hamsters, which are naturally permissive to SARS-CoV-2 replication and closely mirror human COVID-19 physiopathology. Our results provide evidence of marked prophylactic effects of the LV-based vaccination against SARS-CoV-2 and designate intranasal immunization as a powerful approach against COVID-19., Graphical Abstract, Highlights A lentiviral vector encoding for Spike shows preclinical efficacy as a COVID-19 vaccine. Targeting the immune response to the upper respiratory tract provides critical protection. Intranasal vaccination induces protective mucosal immunity against SARS-CoV-2 in rodents. Lung anti-Spike IgA responses correlate with protection and reduced inflammation., Ku and colleagues present a lentiviral vaccination vector that encodes a full-length, membrane anchored form of SARS-CoV-2 Spike glycoprotein that induces neutralizing antibodies and T-cell responses. An intranasal boost strategy triggers a localized immune response in the upper respiratory tract that provides disease protection in mouse and hamster COVID-19 models.
Published: 2020

13. Different populations of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) from Central Africa are susceptible to Zika virus infection

Author: Aurelie P. Yougang, Theodel A. Wilson-Bahun, Marie Vazeille, Armel N. Tedjou, Basile Kamgang, Laurence Mousson, Anna-Bella Failloux, Charles S. Wondji, Centre for Research in Infectious Diseases [Yaoundé] (CRID), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), University of Yaoundé [Cameroun], University Marien Ngouabi of Brazzaville (umng), Liverpool School of Tropical Medicine (LSTM), This study was primarily supported by the Wellcome Trust Training Fellowship in Public Health and Tropical Medicine (204862/Z/16/Z) awarded to BK. It was partly supported by the European Union’s Horizon 2020 research and innovation program under ZIKAlliance grant agreement no. 734548, and the European Union's Horizon 2020 research and innovation program under grant agreement No 731060 (Infravec2, Research Infrastructures for the control of vector-borne diseases, European Project: 734548,ZIKAlliance(2016), European Project: 731060,INFRAVEC2(2017), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), and Institut Pasteur [Paris]
Subjects: RNA viruses, 0301 basic medicine, Physiology, Epidemiology, viruses, RC955-962, Geographic Mapping, Disease Vectors, Pathology and Laboratory Medicine, Mosquitoes, Zika virus, Geographical Locations, 0302 clinical medicine, Aedes, Arctic medicine. Tropical medicine, Medicine and Health Sciences, MESH: Animals, Cameroon, MESH: Geographic Mapping, biology, Zika Virus Infection, Eukaryota, virus diseases, MESH: Aedes, Body Fluids, 3. Good health, Insects, Flavivirus, Blood, Infectious Diseases, qx_510, Medical Microbiology, Viral Pathogens, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, qw_160, Female, MESH: Mosquito Vectors, Disease Susceptibility, Pathogens, Anatomy, Public aspects of medicine, RA1-1270, Research Article, Aedes albopictus, Arthropoda, 030231 tropical medicine, MESH: Disease Susceptibility, wa_395, MESH: Zika Virus, Mosquito Vectors, Aedes aegypti, Aedes Aegypti, Microbiology, 03 medical and health sciences, Flaviviridae, MESH: Zika Virus Infection, parasitic diseases, qx_525, Animals, Africa, Central, Saliva, Microbial Pathogens, Biology and life sciences, Flaviviruses, fungi, Organisms, Public Health, Environmental and Occupational Health, Outbreak, Zika Virus, biology.organism_classification, Invertebrates, Virology, Insect Vectors, MESH: Africa, Central, Species Interactions, 030104 developmental biology, Vector (epidemiology), People and Places, Africa, MESH: Female
Abstract: Zika virus (ZIKV) is a Flavivirus (Flaviviridae) transmitted to humans mainly by the bite of an infected Aedes mosquitoes. Aedes aegypti is the primary epidemic vector of ZIKV and Ae. albopictus, the secondary one. However, the epidemiological role of both Aedes species in Central Africa where Ae. albopictus was recently introduced is poorly characterized. Field-collected strains of Ae. aegypti and Ae. albopictus from different ecological settings in Central Africa were experimentally infected with a ZIKV strain isolated in West Africa. Mosquitoes were analysed at 14- and 21-days post-exposure. Both Ae. aegypti and Ae. albopictus were able to transmit ZIKV but with higher overall transmission efficiency for Ae. aegypti (57.9%) compared to Ae. albopictus (41.5%). In addition, disseminated infection and transmission rates for both Ae. aegypti and Ae. albopictus varied significantly according to the location where they were sampled from. We conclude that both Ae. aegypti and Ae. albopictus are able to transmit ZIKV and may intervene as active Zika vectors in Central Africa. These findings could contribute to a better understanding of the epidemiological transmission of ZIKV in Central Africa and develop suitable strategy to prevent major ZIKV outbreaks in this region., Author summary Zika virus (ZIKV), isolated for the first time in Uganda in 1947, is transmitted to human beings mainly by the bite of an infected mosquitoes belonging to the Aedes genus notably Ae. aegypti and Ae. albopictus. Both Aedes species are present in Central Africa, however their epidemiological role is poorly characterized. Here, we assessed the ability of Ae. aegypti and Ae. albopictus collected in different ecological settings in Central Africa to transmit a ZIKV strain isolated in West Africa. Analysis showed that both Ae. aegypti and Ae. albopictus are able to transmit ZIKV but with higher overall transmission efficiency for Ae. aegypti compared to Ae. albopictus. In addition, disseminated infection and transmission rates for both Aedes species varied significantly according to the sampling location. Overall, our result suggests that in Central Africa, Ae. aegypti is more competent to transmit ZIKV than Ae. albopictus although parameters such as the feeding behaviour, longevity and mosquito densities can modulate pathogens transmission in nature. These findings could contribute to a better understanding of the epidemiological transmission of ZIKV in Central Africa and develop suitable strategy to prevent major ZIKV outbreaks in this region.
Published: 2020

14. Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology

Author: Mhammed Touinssi, Xavier de Lamballerie, Laura Pezzi, Audrey Dubot-Pérès, Laurence Thirion, Iban Corcostegui, Rémi N. Charrel, 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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Laboratoire de Virologie [UNIV Corse-Inserm] (EA7310), Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Établissement Français du Sang Alpes-Méditerranée (EFS Alpes-Méditerranée), University of Florida [Gainesville] (UF), and European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015)
Subjects: 0301 basic medicine, Rift Valley fever phlebovirus, diagnosis, [SDV]Life Sciences [q-bio], 030106 microbiology, TaqMan, lcsh:QR1-502, lyophilization, virus, Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, Article, lcsh:Microbiology, epidemic, Single tube, Matrix (chemical analysis), 03 medical and health sciences, Freeze-drying, Virology, ComputingMilieux_MISCELLANEOUS, DNA Primers, Chromatography, Reverse Transcriptase Polymerase Chain Reaction, Chemistry, emerging, 3. Good health, Oligonucleotide primers, Freeze Drying, 030104 developmental biology, Infectious Diseases, Real-time polymerase chain reaction, PCR, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Diagnostic Techniques, Viruses, freeze-drying, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Ready to use, DNA Probes, pathogen
Abstract: Real-time molecular techniques have become the reference methods for direct diagnosis of pathogens. The reduction of steps is a key factor in order to decrease the risk of human errors resulting in invalid series and delayed results. We describe here a process of preparation of oligonucleotide primers and hydrolysis probe in a single tube at predefined optimized concentrations that are stabilized via lyophilization (Lyoph-P&amp, P). Lyoph-P&amp, P was compared versus the classic protocol using extemporaneously prepared liquid reagents using (i) sensitivity study, (ii) long-term stability at 4 &deg, C, and (iii) long-term stability at 37 &deg, C mimicking transportation without cold chain. Two previously published molecular assays were selected for this study. They target two emerging viruses that are listed on the blueprint of the WHO as to be considered for preparedness and response actions: chikungunya virus (CHIKV) and Rift Valley fever phlebovirus (RVFV). Results of our study demonstrate that (i) Lyoph-P&amp, P is stable for at least 4 days at 37 &deg, C supporting shipping without the need of cold chain, (ii) Lyoph-P&amp, P rehydrated solution is stable at +4 &deg, C for at least two weeks, (iii) sensitivity observed with Lyoph-P&amp, P is at least equal to, often better than, that observed with liquid formulation, (iv) validation of results observed with low-copy specimens is rendered easier by higher fluorescence level. In conclusion, Lyoph-P&amp, P holds several advantages over extemporaneously preparer liquid formulation that merit to be considered when a novel real-time molecular assay is implemented in a laboratory in charge of routine diagnostic activity.
Published: 2020

15. Development and Evaluation of a Duo Zaire ebolavirus Real-Time RT-PCR Assay Targeting Two Regions within the Genome

Author: Yannik Boehmann, Hervé Raoul, Rémi N. Charrel, Xavier de Lamballerie, Laurence Thirion, Iban Corcostegui, 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), Laboratoire P4 - Jean Mérieux, Centre Européen de Virologie/Immunologie-Institut National de la Santé et de la Recherche Médicale (INSERM), This project has received funding (i) from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 115843 (EbolaModRad), this Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA (www.imi.europa.eu), (ii) by the European 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, (iii) the European Union Horizon 2020 program, grant No. 666092 REACTION., European Project: 666092,H2020,H2020-Adhoc-2014-20,REACTION(2014), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), BUISINE, Soline, Evaluation of the efficacy and of the antiviral activity of T-705 (favipiravir) duringEbola virus infection in non-human primates humans - REACTION - - H20202014-11-01 - 2016-10-31 - 666092 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, Microbiology (medical), Zaire ebolavirus, In silico, 030106 microbiology, Filoviridae, Biology, medicine.disease_cause, Microbiology, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, filoviridae, diagnostics, medicine, viral hemorrhagic fever, ebola virus disease, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, response, Multiple sequence alignment, Ebola virus, GeneXpert MTB/RIF, emerging, Outbreak, biology.organism_classification, preparedness, 3. Good health, diagnostics, emerging, viral hemorrhagic fever, preparedness, response, 030104 developmental biology, Real-time polymerase chain reaction, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, hemorrhagic fever, viral
Abstract: Preparedness and response actions to mitigate Ebola virus disease (EVD) outbreaks rely on rapid diagnosis to be implemented locally to sort suspect patients attending health centers. Our aim was (i) to develop and evaluate an RT-qPCR assay combining primers and probes derived from two reference assays targeting different genomic regions, (ii) to study whether sensitivity and specificity of this dual-target assay were at least equal or better to the parental assays, (iii) to implement this dual-target assay onto the Cepheid GeneXpert open cartridge as a proof of principle for technological transfer aiming at bedsite testing locally. To do so, three home-made published RT-qPCR assays were selected to be compared with the RealStar&reg, Filovirus Screen RT-PCR kit 1.0 (Altona Diagnostics, Hamburg, Germany), a technique that was largely deployed during the 2014&ndash, 2015 West African EVD outbreak. Primers and probes sequences of the custom-made assays were analyzed in silico against a multiple sequence alignment, including &gt, 250 complete sequences corresponding to strains that have caused EVD epidemics in the past. Genomic RNA purified from the Mekambo strain of Zaire ebolavirus (EBOV) was used to study the sensitivity of the five methods. Based on these results, two in-house methods were selected and adapted to design the dual-target assay, which performances were compared to those of the parental assays using a synthetic RNA control. The dual-target assay showed better sensitivity and limit of detection (LoD95 at 0.4 copies/&micro, L) than the parental methods (1.7 and 2.2 copies/&micro, L). Ultimately, the dual-target assay was transferred onto the GeneXpert Flex-03 open cartridge, demonstrating a LoD95 at 0.75 copies/&micro, L. Together these results indicate that EBOV dual-target assay has the potential to be used during EVD outbreak in the laboratory having performed molecular testing during the recent outbreaks.
Published: 2019
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16. Meta-transcriptomic identification of hepatitis B virus in cerebrospinal fluid in patients with central nervous system disease

Author: Viengmon Davong, Mayfong Mayxay, Xavier de Lamballerie, Sayaphet Rattanavong, Kristian Alfsnes, Audrey Dubot-Pérès, Vegard Eldholm, Paul N. Newton, Edward C. Holmes, John H.-O. Pettersson, Géraldine Piorkowski, Manivanh Vongsouvath, Department of Medical Biochemistry and Microbiology [Uppsala, Sweden], Uppsala University, Public Health Agency of Sweden, The University of Sydney, Norwegian Institute of Public Health [Oslo] (NIPH), 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), Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, Institute of Research and Education Development [Vientiane, Lao People’s Democratic Republic], University of Health Sciences [Vientiane, Laos] (UHS), Nuffield Department of Clinical Medicine [Oxford], University of Oxford [Oxford], JHOP is funded by the Swedish research council FORMAS (grant no: 2015–710). ECH is funded by an ARC Australian Laureate Fellowship (FL170100022). JHOP, VE, XDL are members of the ZIKAlliance Programme of the European Union. This study was supported by the ZIKAlliance project under European Union Horizon 2020 programme (Grant Agreement no: 734548), the European Union's Horizon 2020 research and innovation programme EVAg under grant agreement N°653316, and Aix-Marseille University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The work in Laos was funded by the Wellcome Trust of UK, which also supports Paul Newton, and the Institute of Research for Development (IRD)., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 734548,ZIKAlliance(2016), University of Oxford, BUISINE, Soline, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID
Subjects: 0301 basic medicine, Microbiology (medical), Male, Infectious Medicine, Hepatitis B virus, Genotype, 030106 microbiology, Infektionsmedicin, Genome, Viral, medicine.disease_cause, Real-Time Polymerase Chain Reaction, Virus, Article, Central nervous system disease, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Cerebrospinal fluid, Central Nervous System Infections, Streptococcus pneumoniae, medicine, Humans, 030212 general & internal medicine, Meta-transcriptomics, Phylogeny, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, business.industry, Gene Expression Profiling, RNA sequencing, General Medicine, medicine.disease, Hepatitis B, 3. Good health, Anti-Bacterial Agents, Infectious Diseases, Treatment Outcome, Immunology, DNA, Viral, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Etiology, Encephalitis, business
Abstract: Determining the etiological basis of central nervous system (CNS) infections is inherently challenging, primarily due to the multi-etiological nature. Using RNA sequencing, we aimed to identify microbes present in cerebrospinal fluid (CSF) of two patients suffering CNS infection, previously diagnosed with Cryptococcus sp. and Streptococcus pneumoniae infection, respectively. After meta-transcriptomic analysis, and confirmation with real-time PCR, hepatitis B virus (HBV) was detected in the CSF of two patients diagnosed with CNS syndrome. Phylogenetic analysis of the partial HBV genomes from these patients showed that they belonged to genotypes B and C and clustered with other viruses of Asian origin. In countries with high levels of HBV endemicity, the virus is likely to be found in patients diagnosed with CNS infections, although whether it contributes to symptoms and pathology, or is simply a coincidental infection, is unknown and merits further investigation. (C) 2019 The Authors. Published by Elsevier Inc.
Published: 2019

17. Genetic and phenotypic characterization of recently discovered enterovirus D type 111

Author: Marie-Line Joffret, Maël Bessaud, Ionela Gouandjika-Vasilache, Marie-Claire Endegue-Zanga, Francis Delpeyroux, Richard Njouom, Arthur Mazitchi, Serge Alain Sadeuh-Mba, Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur (RIIP), Biologie des virus entériques (BVE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Institut Pasteur de Bangui, This project was supported by the Fondation Total (grant S-CM15010-05B), by an ACIP grant (ACIP 162-19) from Institut Pasteur Paris and by the European Virus Archive goes global project (EVAg, European Union's Horizon 2020 research and innovation programme, grant agreement No 653316). We are grateful for the financial support of the World Health Organization, The authors thank the staff of the Pasteur International Bioresources network (PIBnet), Plateforme de microbiologie mutualisée, Institut Pasteur, Paris. This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Bessaud, Maël, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, RNA viruses, Physiology, Epidemiology, RC955-962, Simian, medicine.disease_cause, Pathology and Laboratory Medicine, Genetic recombination, Biochemistry, Enteroviruses, Database and Informatics Methods, 0302 clinical medicine, Immune Physiology, Arctic medicine. Tropical medicine, Medicine and Health Sciences, Phylogeny, Genetics, Enterovirus D, Human, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Immune System Proteins, Strain (biology), Poliovirus, Genomics, 3. Good health, Infectious Diseases, Phenotype, Medical Microbiology, Viral Pathogens, Genetic Epidemiology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Biological Cultures, Pathogens, Public aspects of medicine, RA1-1270, Sequence Analysis, Research Article, Bioinformatics, 030231 tropical medicine, Immunology, Sequence Databases, Enterovirus D, Genome, Viral, Biology, Research and Analysis Methods, Microbiology, Antibodies, Cell Line, 03 medical and health sciences, Open Reading Frames, Sequence Motif Analysis, Virology, medicine, Enterovirus Infections, Humans, Microbial Pathogens, Comparative genomics, Public Health, Environmental and Occupational Health, Organisms, Outbreak, Biology and Life Sciences, Computational Biology, Proteins, Comparative Genomics, Cell Cultures, biology.organism_classification, Viral Replication, 030104 developmental biology, Biological Databases, Viral replication, Sequence Alignment
Abstract: Members of the species Enterovirus D (EV-D) remain poorly studied. The two first EV-D types (EV-D68 and EV-D70) have regularly caused outbreaks in humans since their discovery five decades ago but have been neglected until the recent occurrence of severe respiratory diseases due to EV-D68. The three other known EV-D types (EV-D94, EV-D111 and EV-D120) were discovered in the 2000s-2010s in Africa and have never been observed elsewhere. One strain of EV-D111 and all known EV-D120s were detected in stool samples of wild non-human primates, suggesting that these viruses could be zoonotic viruses. To date, EV-D111s are only known through partial genetic sequences of the few strains that have been identified so far. In an attempt to bring new pieces to the puzzle, we genetically characterized four EV-D111 strains (among the seven that have been reported until now). We observed that the EV-D111 strains from human samples and the unique simian EV-D111 strain were not phylogenetically distinct, thus suggesting a recent zoonotic transmission. We also discovered evidences of probable intertypic genetic recombination events between EV-D111s and EV-D94s. As recombination can only happen in co-infected cells, this suggests that EV-D94s and EV-D111s share common replication sites in the infected hosts. These sites could be located in the gut since the phenotypic analysis we performed showed that, contrary to EV-D68s and like EV-D94s, EV-D111s are resistant to acid pHs. We also found that EV-D111s induce strong cytopathic effects on L20B cells, a cell line routinely used to specifically detect polioviruses. An active circulation of EV-D111s among humans could then induce a high number of false-positive detection of polioviruses, which could be particularly problematic in Central Africa, where EV-D111 circulates and which is a key region for poliovirus eradication., Author summary Many examples of emergence of viruses that trigger severe diseases in humans are known. Emergence can be due to the sudden increase of the pathogenic power of a virus that had silently circulated into human populations for a long period; it can also be due to the cross-species transmission of a virus from its animal host to humans. The recent outbreaks of severe respiratory diseases due to enteroviruses D68 (EV-D68) brought to the light to potency of members of the species Enterovirus D (EV-D) to emerge as severe human pathogens. By many aspects, EV-Ds are still mysterious: their natural history and epidemiology are poorly studied and even their main hosts remain unknown. For decades, EV-Ds were believed to infect mainly humans but recent data about EV-Ds identified in sub-Saharan Africa support their zoonotic origin. In an attempt to increase our knowledge about EV-Ds, we undertook genetic and phenotypic characterization of four EV-D111 isolates, a virus type that was recently uncovered in humans and in non-human primates in Central Africa. Our results show that EV-D111s are probably enteric viruses and evolve by exchanging genetic sequences with EV-D94.
Published: 2019

18. A New High-Throughput Tool to Screen Mosquito-Borne Viruses in Zika Virus Endemic/Epidemic Areas

Author: Yvon Perrin, Mawlouth Diallo, Frédéric Jourdain, Amandine Guidez, Xavier de Lamballerie, Marie Vazeille, Isabelle Dusfour, Anubis Vega-Rúa, Davy Jiolle, Johana Restrepo, Lena Yousfi, Géraldine Piorkowski, Fabrice Chandre, Alioune Gaye, Filipe Vieira Santos de Abreu, Sara Moutailler, Anna-Bella Failloux, Merril Wongsokarijo, Tessa M. Visser, Sandrine Chantilly, Constantianus J. M. Koenraadt, Diawo Diallo, Laurence Mousson, Christophe Paupy, Taissa Pereira dos Santos, Sébastien Boyer, Ricardo Lourenço de Oliveira, Arnaud Cannet, Veasna Duong, Elodie Devillers, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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 la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Arbovirus et Insectes Vecteurs, Institut Pasteur [Paris], Institut Pasteur de la Guadeloupe, Réseau International des Instituts Pasteur (RIIP), Centre national d'expertise des vecteurs, Montpellier (CNEV), 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]), Collectivité Territoriale de Guyane (CTG), Institut Pasteur de la Guyane, Fundação Oswaldo Cruz (FIOCRUZ), Wageningen University and Research Centre [Wageningen] (WUR), Public Health Central Laboratory of Suriname, Public health, Institut Pasteur de Dakar, Institut Pasteur du Cambodge, 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 work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under ZIKAlliance Grant Agreement no. 734548. The project also received funding from the 2014 PTR Anses-Institut Pasteur project (N° 511) for CHIPARBO, and the European Union’s Horizon 2020 Research and Innovation Programme under EVAg Grant Agreement no. 653316, and from an 'Investissement d’Avenir' ‘grant from the Agence Nationale de la Recherche (CEBA ANR-10-LABX-2501 grant) supporting the project TIGERAMAZON.. The French General Directorate of Health funded the work performed in Guadeloupe and French Guiana. The Programme Opérationnel FEDER-Guadeloupe-Conseil Régional 2014–2020 (grant 2015-FED-192) supported the researchers from Guadeloupe., We thank Christelle Delannay and the staff of the Regional Health Agency of Guadeloupe for their support during the sampling campaigns, ANR-10-LABX-25-01/10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Vector Control Group (MIVEGEC-VCG), Evolution des Systèmes Vectoriels (ESV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-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])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Wageningen University and Research [Wageningen] (WUR), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-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)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut Pasteur [Paris] (IP), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé
Subjects: Male, Endemic Diseases, mosquito-borne viruses, [SDV]Life Sciences [q-bio], viruses, lcsh:QR1-502, Pilot Projects, Disease Vectors, molecular epidemiology, lcsh:Microbiology, Zika virus, Human health, Pandemic, Laboratory of Entomology, Guadeloupe, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Suriname, biology, Zika Virus Infection, virus diseases, PE&RC, Senegal, French Guiana, 3. Good health, Epidemiological Monitoring, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, surveillance, RNA, Viral, Enzootic, Female, Cambodia, Brazil, Context (language use), Mosquito Vectors, Arbovirus Infections, Arbovirus, Article, 03 medical and health sciences, parasitic diseases, medicine, Animals, Humans, Epidemics, 030304 developmental biology, 030306 microbiology, fungi, Zika Virus, Mosquito-borne viruses, biology.organism_classification, medicine.disease, Laboratorium voor Entomologie, Virology, High-Throughput Screening Assays, Culicidae, Vector (epidemiology), microfluidic analysis, Arboviruses
Abstract: Mosquitoes are vectors of arboviruses affecting animal and human health. Arboviruses circulate primarily within an enzootic cycle and recurrent spillovers contribute to the emergence of human-adapted viruses able to initiate an urban cycle involving anthropophilic mosquitoes. The increasing volume of travel and trade offers multiple opportunities for arbovirus introduction in new regions. This scenario has been exemplified recently with the Zika pandemic. To incriminate a mosquito as vector of a pathogen, several criteria are required such as the detection of natural infections in mosquitoes. In this study, we used a high-throughput chip based on the BioMark&trade, Dynamic arrays system capable of detecting 64 arboviruses in a single experiment. A total of 17,958 mosquitoes collected in Zika-endemic/epidemic countries (Brazil, French Guiana, Guadeloupe, Suriname, Senegal, and Cambodia) were analyzed. Here we show that this new tool can detect endemic and epidemic viruses in different mosquito species in an epidemic context. Thus, this fast and low-cost method can be suggested as a novel epidemiological surveillance tool to identify circulating arboviruses.
Published: 2019

19. High specificity and sensitivity of Zika EDIII-based ELISA diagnosis highlighted by a large human reference panel

Author: Cyril Badaut, Véronique Chastres, Bernard Tenebray, Jessica Denis, Sébastien Briolant, Annabelle Garnier, Isabelle Leparc-Goffart, Patrick Gravier, Sarah Attoumani, Franck de Laval, Gilda Grard, Bruno Coutard, Unité de Biothérapies anti-Infectieuses et Immunité [Brétigny-sur-Orge], Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), 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, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), 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), Unité de Parasitologie et d’Entomologie, Département des Maladies Infectieuses-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), 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), Centre d'Epidémiologie et de Santé Public des Armées, 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), This work was partially supported by the European Union’s Horizon 2020 Research and Innovation Programme, under ZIKAlliance Grant Agreement no. 734548, as well as by the European Virus Archive goes global (EVAg) project, under Grant Agreement no. 653316, and partially funded by the Direction Générale de l’Armement and the Service de Santé des Armées, Biomedef PDH-2-NRBC-2-B2-205 and PDH-2-NRBC-2-B-2111, European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut de Recherche Biomédicale des Armées (IRBA), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département des Maladies Infectieuses-Institut de Recherche Biomédicale des Armées (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Unité de Parasitologie et d'Entomologie [Marseille], Département des Maladies Infectieuses [Marseille], Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA)-Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Centre d'épidémiologie et de santé publique des armées (CESPA), Unité Perception [Brétigny-sur-Orge], Département Neurosciences et Sciences Cognitives [Brétigny-sur-Orge], Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche Biomédicale des Armées (IRBA), This work was partially supported by the European Union’s Horizon 2020 Research and Innovation Programme, under ZIKAlliance Grant Agreement no. 734548, as well as by the European Virus Archive goes global (EVAg) project, under Grant Agreement no. 653316, and partially funded by the Direction Générale de l’Armement and the Service de Santé des Armées, Biomedef PDH-2-NRBC-2-B2-205 and PDH-2-NRBC-2-B-2111., coutard, bruno, A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, Serotype, RNA viruses, Male, Physiology, viruses, RC955-962, Dengue virus, medicine.disease_cause, Pathology and Laboratory Medicine, Antibodies, Viral, Cross-reactivity, Biochemistry, Zika virus, Serology, Dengue, Mice, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Immune Physiology, Arctic medicine. Tropical medicine, Medicine and Health Sciences, Enzyme-Linked Immunoassays, Child, Cross Reactivity, Aged, 80 and over, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Immune System Proteins, biology, Zika Virus Infection, virus diseases, Middle Aged, Recombinant Proteins, 3. Good health, Infectious Diseases, Medical Microbiology, Viral Pathogens, Child, Preschool, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Antibody, Pathogens, Public aspects of medicine, RA1-1270, Research Article, Adult, Adolescent, 030231 tropical medicine, Immunology, Enzyme-Linked Immunosorbent Assay, Research and Analysis Methods, Microbiology, Sensitivity and Specificity, Virus, Antibodies, 03 medical and health sciences, medicine, Animals, Humans, Immunoassays, Microbial Pathogens, Aged, Biology and life sciences, Flaviviruses, Public Health, Environmental and Occupational Health, Organisms, Proteins, Infant, Zika Virus, Dengue Virus, biology.organism_classification, Virology, 030104 developmental biology, Polyclonal antibodies, Immunoglobulin G, biology.protein, Immunologic Techniques, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Arboviruses
Abstract: Background Zika virus (ZIKV) and Dengue virus (DENV) are often co-endemic. The high protein-sequence homology of flaviviruses renders IgG induced by and directed against them highly cross-reactive against their antigen(s), as observed on a large set of sera, leading to poorly reliable sero-diagnosis. Methods We selected Domain III of the ZIKV Envelope (ZEDIII) sequence, which is virus specific. This recombinant domain was expressed and purified for the specific detection of ZEDIII-induced IgG by ELISA from ZIKV-RT-PCR-positive, ZIKV-IgM-positive, flavivirus-positive but ZIKV-negative, or flavivirus-negative sera. We also assessed the reactivity of ZEDIII-specific human antibodies against EDIII of DENV serotype 4 (D4EDIII) as a specific control. Sera from ZEDIII-immunized mice were also tested. Results Cross-reactivity of IgG from 5,600 sera against total inactivated DENV or ZIKV was high (71.0% [69.1; 72.2]), whereas the specificity and sensitivity calculated using a representative cohort (242 sera) reached 90% [84.0; 95.8] and 92% [84.5; 99.5], respectively, using a ZEDIII-based ELISA. Moreover, purified human IgG against D2EDIII or D4EDIII did not bind to ZEDIII and we observed no D4EDIII reactivity with ZIKV-induced mouse polyclonal IgGs. Conclusions We developed a ZEDIII-based ELISA that can discriminate between past or current DENV and ZIKV infections, allowing the detection of a serological scar from other flaviviruses. This could be used to confirm exposure of pregnant women or to follow the spread of an endemic disease., Author summary The serological detection of Zika virus (ZIKV) is a challenge, as ZIKV infection generally leads to an immune response with a high level of cross reactivity against related viruses, such as Dengue virus. Although seroneutralization assays are the gold-standard to address specificity, a rapid and cost-effective detection assay with good specificity and sensitivity could be used for first-line screening. We used a large cohort to define a set of human reference sera to validate an ELISA based on a recombinant ZIKV antigen. The assay showed 90% specificity and 92% sensitivity, providing a good basis for the development of diagnostic assays. Characterization of both DENV-EDIII-purified human and murine IgG induced by ZIKV infection or ZEDIII, respectively, confirmed the good specificity of the antigen.
Published: 2019

20. Antibody Response to Toscana Virus and Sandfly Fever Sicilian Virus in Cats Naturally Exposed to Phlebotomine Sand Fly Bites in Portugal

Author: Pereira, André, Ayhan, Nazli, Cristóvão, José Manuel, Vilhena, Hugo, Martins, Ângela, Cachola, Patrícia, Henriques, Joaquim, Coimbra, Mónica, Catarino, Ana, Lestinova, Tereza, Spitzova, Tatiana, Volf, Petr, Campino, Lenea, Charrel, Remi, Maia, Carla, Global Health and Tropical Medicine [Lisbonne, Portugal] (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), 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), Center for Investigation Vasco da Gama [Coimbra, Portugal] (Department of Veterinary Medicine), Vasco da Gama Universitary School [Coimbra, Portugal], University Veterinary Hospital [Coimbra, Portugal], Animal and Veterinary Research Centre - CECAV [Vila Real, Portugal], University of Trás-os-Montes and Alto Douro [Portugal] (UTAD), Hospital Veterinário da Arrábida [Azeitão, Portugal], Hospital Veterinário do Algarve [Faro, Portugal], Hospital Veterinário de Berna [Lisboa, Portugal], Clínica Veterinária Porto Seguro [Olhão, Portugal], VetCoa - Serviços Veterinários [Sabugal, Portugal], Department of Parasitology [Prague, Czech Republic] (Faculty of Science), Charles University [Prague] (CU), This work was partially supported by Bayer Animal Health, Germany and Global Health and Tropical Medicine Center (UID/Multi/04413/2013) and by the European Virus Archive goes Global (EVAg) project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 653316. AP and CM have the support of the Portuguese Ministry of Education and Science (via Fundação para a Ciência e a Tecnologia, I.P.), through a PhD grant (SFRH/BD/116516/2016) and an Investigator Starting Grant (IF/01302/2015), respectively. PV, TS and TL are supported by ERD funds, project CeRaViP (16_019/0000759) and UNCE 204072., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), BUISINE, Soline, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Bunyavirales, Phlebovirus, Toscana virus, saliva, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Communication, cat, Phenuiviridae, Phlebotomus perniciosus, arbovirus, lcsh:Biology (General), [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:QH301-705.5, Sandfly Fever Sicilian Virus
Abstract: Phlebotomine sand fly-borne pathogens such as Leishmania spp. and phleboviruses are emerging threats to humans and animals worldwide. The aim of this work was to evaluate the exposure of cats from Portugal to Toscana virus (TOSV) and Sandfly Fever Sicilian virus (SFSV) and assess the associated risk factors. The possible association between exposure to Phlebotomus perniciosus saliva with TOSV and SFSV was also investigated. Out of 369 cats tested, 18 (4.9%, n = 365) were seropositive for TOSV, and eight (2.2%, n = 367) were seropositive for SFSV. Multivariate logistic regression analysis showed that cats presenting clinical signs that were compatible with leishmaniosis and antibodies to TOSV had a significantly higher risk of being SFSV seropositive. The presence of antibodies to sand fly-borne viruses in cats indicate that these animals are frequently exposed to sand flies and transmitted pathogens. Data suggest that cats can be used to qualitatively monitor human exposure to TOSV and SFSV in endemic areas. The clinical impact of SFSV in cats’ health should be investigated. The identification of the sand fly species responsible for the circulation of TOSV and SFSV in nature and the evaluation of the vectorial competence of P. perniciosus to SFSV should also be addressed.
Published: 2019

21. Development and Evaluation of a Duo Chikungunya Virus Real-Time RT-PCR Assay Targeting Two Regions within the Genome

Author: Rémi N. Charrel, Laurence Thirion, Iban Corcostegui, Xavier de Lamballerie, Alessandra Falchi, Laura Pezzi, Audrey Dubot-Pérès, 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), Laboratoire de Virologie [UNIV Corse-Inserm] (EA7310), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pascal Paoli (UPP), Emerging Pathogens Institute [Gainesville, FL, USA], University of Florida [Gainesville] (UF), This research was partly funded by (i) the European Virus Archive (European Union Seventh Framework Programme under grant agreement no. 228292) (http://www.european-virus-archive.com/), (ii) the European Virus Archive goes Global (EVAg) project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 653316, (iii) Université de Corse Pasquale Paoli, Corte, France (UCPP), (iv) Emerging Viral Diseases-Expert Laboratory Network (EVD-LabNet). L.P. is a PhD student granted by UCPP and INSERM., European Project: 228292,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,EVA(2009), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), NOUGAIREDE, Antoine, European Virus Archive - EVA - - EC:FP7:INFRA2009-01-01 - 2014-12-31 - 228292 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, In silico, 030106 microbiology, lcsh:QR1-502, Alphavirus, Genome, Viral, Biology, medicine.disease_cause, Genome, Arbovirus, Virus, lcsh:Microbiology, Article, epidemic, Evolution, Molecular, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, medicine, Togaviridae, emergence, Humans, Chikungunya, arthropod-borne, Genetics, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, fever, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, outbreak, Reverse Transcriptase Polymerase Chain Reaction, Point mutation, virus diseases, medicine.disease, biology.organism_classification, tropical disease, 030104 developmental biology, Infectious Diseases, arbovirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Mutation, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Chikungunya Fever, Chikungunya virus
Abstract: Laurence Thirion and Laura Pezzi contributed equally.; International audience; Chikungunya virus (CHIKV) re-emerged as a globalized health threat fifteen years ago. There are dozens of RT-PCR assays published. An inventory of the latter was made, and after in silico analysis, two assays were selected for their ability to detect strains belonging to the five CHIKV genetic lineages. They were combined in order to provide a robust assay not affected by genetic point mutations and the resulting Duo CHIKV real-time RT-PCR assay was compared to the two parental single-plex tests against five strains belonging to the five genetic lineages. The Duo CHIKV assay performed equally, or better, in terms of sensitivity, specificity, linearity and signal intensity. Dual-target assays are better suited for viruses having the propensity to evolve into new variants via point mutations or major sequence deletions/insertions. Here, we demonstrated that combining two single systems into a dual-target assay did not impair sensitivity and specificity, and proved a potent diagnostic tool to face a potential emergence of CHIKV variants by newly evolving mutations.
Published: 2019

22. Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission

Author: Marion Tanguy, Jacques Barrat, Emilie M. Bonnaud, Florence Cliquet, Elodie Monchatre-Leroy, Laurent Dacheux, Edward C. Holmes, Hervé Bourhy, Cécile Troupin, Christiane Bouchier, Centre collaborateur de l'OMS - Rage / World Health Organization Collaboration Centres - Rabies (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), The University of Sydney, Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), This work was supported by European Union Seventh Framework Programme PREDEMICS (grant number 278433) and by the Agence Nationale de la Recherche (grant number BSV3-0019). The Genomics Platform is member of ªFrance Génomiqueº consortium (ANR10-INBS- 09-08). HB, LD and EB were supported by the European Virus Archive goes Global (EVAg) project that has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 653316. ECH is funded by an ARC Australian Laureate Fellowship (FL170100022)., We are grateful to Karine Reynaud from the Unit Biology of Development and Reproduction of the Ecole Nationale Vétérinaire d'Alfort for providing the dog embryos, and to Benoît Combe of the Entente de Lutte Interdépartementale contre les Zoonoses of Malzeville for his help in obtaining fox embryos. We also thank Laurence Ma and Magali Tichit from the Genomics Platform for technical assistance with NGS sequencing., ANR-12-BSV3-0019,Viva&host,Variabilité génétique au sein des populations de virus à ARN négatif non segmenté et adaptation à l'hôte(2012), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), and Institut Pasteur [Paris]
Subjects: Male, RNA viruses, Evolutionary Genetics, Cross-species transmission, Foxes, medicine.disease_cause, Pathology and Laboratory Medicine, Salivary Glands, MESH: Dogs, Medicine and Health Sciences, MESH: Animals, Dog Diseases, Biology (General), MESH: High-Throughput Nucleotide Sequencing, MESH: Evolution, Molecular, Genetics, Mammals, 0303 health sciences, Experimental evolution, Mutation, 030302 biochemistry & molecular biology, Microbial Genetics, High-Throughput Nucleotide Sequencing, Eukaryota, 3. Good health, MESH: Rabies virus, Medical Microbiology, Viral evolution, Viral Pathogens, Vertebrates, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Host adaptation, Pathogens, Anatomy, Research Article, Evolutionary Processes, MESH: Mutation, QH301-705.5, Rabies, MESH: Dog Diseases, Immunology, Biology, Microbiology, MESH: Host-Parasite Interactions, Virus, Viral Evolution, Cell Line, Host-Parasite Interactions, Evolution, Molecular, 03 medical and health sciences, Rabies Virus, Dogs, Exocrine Glands, MESH: Rabies, Evolutionary Adaptation, Virology, medicine, Animals, Molecular Biology, Microbial Pathogens, 030304 developmental biology, Evolutionary Biology, MESH: Foxes, Host (biology), Rabies virus, Organisms, Biology and Life Sciences, RC581-607, Organismal Evolution, MESH: Male, MESH: Cell Line, Amniotes, Microbial Evolution, Parasitology, Lyssavirus, Immunologic diseases. Allergy, Digestive System, MESH: Female
Abstract: The development of high-throughput genome sequencing enables accurate measurements of levels of sub-consensus intra-host virus genetic diversity and analysis of the role played by natural selection during cross-species transmission. We analysed the natural and experimental evolution of rabies virus (RABV), an important example of a virus that is able to make multiple host jumps. In particular, we (i) analyzed RABV evolution during experimental host switching with the goal of identifying possible genetic markers of host adaptation, (ii) compared the mutational changes observed during passage with those observed in natura, and (iii) determined whether the colonization of new hosts or tissues requires adaptive evolution in the virus. To address these aims, animal infection models (dog and fox) and primary cell culture models (embryo brain cells of dog and fox) were developed and viral variation was studied in detail through deep genome sequencing. Our analysis revealed a strong unidirectional host evolutionary effect, as dog-adapted rabies virus was able to replicate in fox and fox cells relatively easily, while dogs or neuronal dog cells were not easily susceptible to fox adapted-RABV. This suggests that dog RABV may be able to adapt to some hosts more easily than other host variants, or that when RABV switched from dogs to red foxes it lost its ability to adapt easily to other species. Although no difference in patterns of mutation variation between different host organs was observed, mutations were common following both in vitro and in vivo passage. However, only a small number of these mutations also appeared in natura, suggesting that adaptation during successful cross-species virus transmission is a complex, multifactorial evolutionary process., Author summary Understanding the mechanisms that underpin the cross-species transmission and host adaptation of rabies virus (RABV) remains an important part of the ongoing goal to reduce and eliminate rabies. We utilized next-generation sequencing to perform a deep comparative analysis of the genomic evolution of RABV subpopulations during host adaptation in culture and in animals, with the aim of determining the molecular mechanisms involved in the host-species or tissue adaptation of rabies virus. In particular, we aimed to determine whether experimental evolution can recapitulate evolution in nature. Our results suggest that a limited number of mutations that appeared following both in vitro and in vivo passage were observed in natura. This study also suggests that dog RABV may be able to adapt to some hosts more easily than other host variants.
Published: 2019

23. Nasal or throat sampling is adequate for the detection of the human respiratory syncytial virus in children with acute respiratory infections

Author: Nguyen, V, Russell, F, Dance, D, Vilivong, K, Phommachan, S, Syladeth, C, Lai, J, Lim, R, Morpeth, M, Mayxay, M, Newton, P, De Lamballerie, X, Dubot-Pérès, A, 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), Murdoch Children's Research Institute (MCRI), Department of Paediatrics [Melbourne], Melbourne Medical School [Melbourne], Faculty of Medicine, Dentistry and Health Sciences [Melbourne], University of Melbourne-University of Melbourne-Faculty of Medicine, Dentistry and Health Sciences [Melbourne], University of Melbourne-University of Melbourne, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, Nuffield Department of Clinical Medicine [Oxford], University of Oxford [Oxford], London School of Hygiene and Tropical Medicine (LSHTM), Institute of Research and Education Development [Vientiane, Lao People’s Democratic Republic], University of Health Sciences [Vientiane, Laos] (UHS), Murdoch Children’s Research Institute, European Union’s Horizon 2020 research and innovation programme EVAg, Grant/Award Number: 653316, Aix‐Marseille University, Bill & Melinda Gates Foundation, Grant/Award Number: OPP1115490, Wellcome Trust of Great Britain, Grant/Award Number: 089275/H/09/Z0, Institute of Research for Development, European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Oxford, BUISINE, Soline, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: Male, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, detection rate, nasal swab, Infant, Reproducibility of Results, throat swab, Respiratory Syncytial Virus Infections, Viral Load, Real-Time Polymerase Chain Reaction, nasopharyngeal swab, Laos, Child, Preschool, Respiratory Syncytial Virus, Human, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Pharynx, Female, Nasal Cavity, human respiratory syncytial virus, Research Articles, Research Article
Abstract: International audience; Human respiratory syncytial virus (HRSV) is one of the most important causes of acute respiratory infections (ARI) in young children. HRSV diagnosis is based on the detection of the virus in respiratory specimens. Nasopharyngeal swabbing is considered the preferred method of sampling, although there is limited evidence of the superiority of nasopharyngeal swabs (NPS) over the less invasive nasal (NS) and throat (TS) swabs for virus detection by real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). In the current study, we compared the three swabbing methods for the detection of HRSV by RT-qPCR in children hospitalized with ARI at Mahosot Hospital, Vientiane, Laos. In 2014, NS, NPS, and TS were collected from 288 children. All three samples were tested for HRSV by RT-qPCR; 141 patients were found positive for at least one sample. Almost perfect agreements (κ > 0.8) between the swabs, compared two by two, were observed. Detection rates for the three swabs (between 93% and 95%) were not significantly different, regardless of the clinical presentation. Our findings suggest that the uncomfortable and technically more demanding NPS method is not mandatory for HRSV detection by RT-qPCR.
Published: 2019

24. Management of Central Nervous System Infections, Vientiane, Laos, 2003–2011

Author: Phonelavanh Phoumin, Amphonesavanh Sengduangphachanh, Rattanaphone Phetsouvanh, Mary-Anne Burns, Scott B. Craig, Valy Keoluangkot, Audrey Dubot-Pérès, Olay Lattana, Khonesavanh Luangxay, Prasith Phimmasone, Koukeo Phommasone, Sue J. Lee, Manivanh Vongsouvath, Kongkham Sisout, David A. B. Dance, Amphaivanh Seubsanith, Catrin E. Moore, Mayfong Mayxay, Khamsai Detleuxay, Vilada Chansamouth, Viengmon Davong, Sabine Dittrich, Xavier de Lamballerie, S. M. Tulsiani, Stuart D. Blacksell, Inpanh Phouangsouvanh, Sayaphet Rattanavong, Phonepasith Panyanivong, Paul N. Newton, Anisone Chanthongthip, Bountoy Sibounheuang, Manivone Simmalavong, Joy Sirisouk, Davanh Sengdatka, 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), Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, University of Health Sciences, Mahidol Oxford Tropical Medicine Research Unit (MORU), Wellcome Trust-Mahidol University [Bangkok]-University of Oxford [Oxford], Nuffield Department of Clinical Medicine [Oxford], University of Oxford [Oxford], Mahosot Hospital, Queensland Health Forensic and Scientific Services, London School of Hygiene and Tropical Medicine (LSHTM), This work was supported by the Wellcome Trust of Great Britain, the Institute of Research for Development, AixMarseille University, and the European Union’s Horizon 2020 research and innovation program European Virus Archive global (grant agreement no. 653316)., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Graduate School, AII - Infectious diseases, APH - Global Health, APH - Methodology, University of Oxford-Mahidol University [Bangkok]-Wellcome Trust, University of Oxford, BUISINE, Soline, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: Infectious Encephalitis, Male, Orientia tsutsugamushi, Epidemiology, encephalitis, Antibiotics, Cryptococcus, lcsh:Medicine, antibiotics, 0302 clinical medicine, 030212 general & internal medicine, Prospective Studies, Rickettsia, Child, bacteria, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Leptospira, Cross Infection, biology, diabetes, Mortality rate, Health Policy, meningitis, 3. Good health, Infectious Diseases, Laos, Child, Preschool, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Ceftriaxone, Female, meningitis/encephalitis, Meningitis, Encephalitis, medicine.drug, Microbiology (medical), Adult, medicine.medical_specialty, patient care management, Asia, Adolescent, medicine.drug_class, viral infections, 030231 tropical medicine, central nervous system infections, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Young Adult, Internal medicine, WHO meningitis, medicine, Humans, lcsh:RC109-216, viruses, antimicrobial medicines, business.industry, Research, lcsh:R, Infant, WHO encephalitis, Japanese encephalitis, medicine.disease, biology.organism_classification, mortality, Japanese encephalitis virus, bacterial infections, Lao, business
Abstract: International audience; During 2003-2011, we recruited 1,065 patients of all ages admitted to Mahosot Hospital (Vientiane, Laos) with suspected central nervous system (CNS) infection. Etiologies were laboratory confirmed for 42.3% of patients, who mostly had infections with emerging pathogens: viruses in 16.2% (mainly Japanese encephalitis virus [8.8%]); bacteria in 16.4% (including Orientia tsutsugamushi [2.9%], Leptospira spp. [2.3%], and Rickettsia spp. [2.3%]); and Cryptococcus spp. fungi in 6.6%. We observed no significant differences in distribution of clinical encephalitis and meningitis by bacterial or viral etiology. However, patients with bacterial CNS infection were more likely to have a history of diabetes than others. Death (26.3%) was associated with low Glasgow Coma Scale score, and the mortality rate was higher for patients with bacterial than viral infections. No clinical or laboratory variables could guide antibiotic selection. We conclude that high-dependency units and first-line treatment with ceftriaxone and doxycycline for suspected CNS infections could improve patient survival in Laos.
Published: 2019

25. The Unfolded Protein Response: A Key Player in Zika Virus-Associated Congenital Microcephaly

Author: Christian Alfano, Ivan Gladwyn-Ng, Thérèse Couderc, Marc Lecuit, Laurent Nguyen, Université de Liège, Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Descartes - Paris 5 (UPD5), This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under ZIKAlliance Grant Agreement N° 734548 (to LN and ML) and by the European Virus Archives goes Global (EVAg) project under grant agreement N° 653316. ML was also funded by Institut Pasteur, INSERM, and LabEx IBEID. LN was funded by F.R.S.-F.N.R.S., the Fonds Léon Fredericq, the Fondation Médicale Reine Elisabeth, the Fondation Simone et Pierre Clerdent, the Belgian Science Policy (IAP-VII network P7/20), the ARC (ARC11/16-01), the EU H2020 ZIKAlliance (#734548), the ERANET Neuron STEM-MCD, and NeuroTalk. LN and IG-N are, respectively senior research associate and postdoctoral fellows from F.R.S- F.N.R.S., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), DIAKITE, andrée, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, Microcephaly, [SDV]Life Sciences [q-bio], Mini Review, Arbovirus, Virus, Zika virus, Dengue fever, lcsh:RC321-571, 03 medical and health sciences, Flaviviridae, Cellular and Molecular Neuroscience, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, cortical progenitors, microcephaly, lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Neurogenesis, unfolded protein response, medicine.disease, biology.organism_classification, Virology, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Unfolded protein response, cerebral cortex, ER stress, 030217 neurology & neurosurgery, Neuroscience
Abstract: International audience; Zika virus (ZIKV) is a mosquito-borne virus that belongs to the Flaviviridae family, together with dengue, yellow fever, and West Nile viruses. In the wake of its emergence in the French Polynesia and in the Americas, ZIKV has been shown to cause congenital microcephaly. It is the first arbovirus which has been proven to be teratogenic and sexually transmissible. Confronted with this major public health challenge, the scientific and medical communities teamed up to precisely characterize the clinical features of congenital ZIKV syndrome and its underlying pathophysiological mechanisms. This review focuses on the critical impact of the unfolded protein response (UPR) on ZIKV-associated congenital microcephaly. ZIKV infection of cortical neuron progenitors leads to high endoplasmic reticulum (ER) stress. This results in both the stalling of indirect neurogenesis, and UPR-dependent neuronal apoptotic death, and leads to cortical microcephaly. In line with these results, the administration of molecules inhibiting UPR prevents ZIKV-induced cortical microcephaly. The discovery of the link between ZIKV infection and UPR activation has a broader relevance, since this pathway plays a crucial role in many distinct cellular processes and its induction by ZIKV may account for several reported ZIKV-associated defects.
Published: 2019

26. Low Zika Virus Seroprevalence in Vientiane, Laos, 2003–2015

Author: Pastorino, B, Sengvilaipaseuth, O, Chanthongthip, A, Vongsouvath, M, Souksakhone, C, Mayxay, M, Thirion, L, Newton, P, De Lamballerie, X, Dubot-Pérès, A, 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), Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, National Blood Transfusion Centre [Vientiane, Laos] (Lao Red Cross), Institute of Research and Education Development [Vientiane, Lao People’s Democratic Republic], University of Health Sciences [Vientiane, Laos] (UHS), Nuffield Department of Clinical Medicine [Oxford], University of Oxford, This study was funded by the Wellcome Trust of Great Britain, the Institute of Research for Development, and Aix Marseille University, by the European Union’s Horizon 2020 Research and Innovation Programme EVAg under grant agreement No. 653316 and by the European Union`s Horizon 2020 Research and Innovation Programme under ZIKAlliance grant agreement No. 734548., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 734548,ZIKAlliance(2016), University of Oxford [Oxford], BUISINE, Soline, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID
Subjects: [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Adult, Male, Adolescent, Zika Virus Infection, Articles, Middle Aged, Young Adult, Laos, Seroepidemiologic Studies, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Female, Sex Ratio, Aged
Abstract: International audience; Zika virus (ZIKV) has been presumed to be endemic in Southeast Asia (SEA), with a low rate of human infections. Although the first ZIKV evidence was obtained in the 1950s through serosurveys, the first laboratory-confirmed case was only detected in 2010 in Cambodia. The epidemiology of ZIKV in SEA remains uncertain because of the scarcity of available data. From 2016, subsequent to the large outbreaks in the Pacific and Latin America, several Asian countries started reporting increasing numbers of confirmed ZIKV patients, but no global epidemiological assessment is available to date. Here, with the aim of providing information on ZIKV circulation and population immunity, we conducted a seroprevalence study among blood donors in Vientiane, Laos. Sera from 359 asymptomatic consenting adult donors in 2003-2004 and 687 in 2015 were screened for anti-ZIKV IgG using NS1 ELISA assay (Euroimmun, Luebeck, Germany). Positive and equivocal samples were confirmed for anti-ZIKV-neutralizing antibodies by virus neutralization tests. Our findings suggest that ZIKV has been circulating in Vientiane over at least the last decade. Zika virus seroprevalence observed in the studied blood donors was low, 4.5% in 2003-2004 with an increase in 2015 to 9.9% (P = 0.002), possibly reflecting the increase of ZIKV incident cases reported over this period. We did not observe any significant difference in seroprevalence according to gender. With a low herd immunity in the Vientiane population, ZIKV represents a risk for future large-scale outbreaks. Implementation of a nationwide ZIKV surveillance network and epidemiological studies throughout the country is needed.
Published: 2019
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27. Optimization of a fragment linking hit toward Dengue and Zika virus NS5 methyltransferases inhibitors

Author: Jessica Hernandez, Etienne Decroly, Karine Barral, Gilles Querat, Bruno Coutard, Philippe Roche, Laurent Hoffer, Xavier Morelli, Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), 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), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the European program H2020 under the ZIKAlliance project (grant agreement 734548), the EVAg Research Infrastructure (grant agreement 653316) and by the French research agency ANR (VMTaseIn, grant ANR-ST14-ASTR-0026, and FragVir, grant ANR-13-JS07-0006-01)., ANR-14-ASTR-0026,VMTaseIn,Identification d'inhibiteurs de méthyltransférases de virus: une nouvelle stratégégie antivirale(2014), ANR-13-JS07-0006,FragVir,Développement d'inhibiteurs de la réplication de Flavivirus par une stratégie de « Fragment-Based Drug Discovery » ciblant l'activité méthyltransférase(2013), European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Strasbourg, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), ANR-13-JS07-0006,FragVir,Développement d'inhibiteurs de la réplication de Flavivirus par une stratégie de ' Fragment-Based Drug Discovery ' ciblant l'activité méthyltransférase(2013), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), BUISINE, Soline, Accompagnement spécifique des travaux de recherches et d’innovation défense - Identification d'inhibiteurs de méthyltransférases de virus: une nouvelle stratégégie antivirale - - VMTaseIn2014 - ANR-14-ASTR-0026 - ASTRID - VALID, Jeunes Chercheuses et Jeunes Chercheurs - Développement d'inhibiteurs de la réplication de Flavivirus par une stratégie de ' Fragment-Based Drug Discovery ' ciblant l'activité méthyltransférase - - FragVir2013 - ANR-13-JS07-0006 - JC - VALID, A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: Models, Molecular, Methyltransferase, viruses, Fragment growing, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, medicine.disease_cause, Crystallography, X-Ray, 01 natural sciences, Flavivirus NS5 methyltransferase inhibitors, Dengue fever, Zika virus, Drug Discovery, Flavivirus Infections, Enzyme Inhibitors, ComputingMilieux_MISCELLANEOUS, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, biology, Molecular Structure, Chemistry, virus diseases, General Medicine, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, 3. Good health, Flavivirus, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Structure-based drug design, RNA capping, Viral protein, Microbial Sensitivity Tests, Antiviral Agents, 03 medical and health sciences, Structure-Activity Relationship, Dengue and Zika viruses, medicine, [CHIM]Chemical Sciences, 030304 developmental biology, Pharmacology, Dose-Response Relationship, Drug, 010405 organic chemistry, Organic Chemistry, Methyltransferases, Zika Virus, Dengue Virus, medicine.disease, biology.organism_classification, Virology, 0104 chemical sciences, Docking (molecular)
Abstract: International audience; Structure-based drug design Dengue and Zika viruses Flavivirus NS5 methyltransferase inhibitors a b s t r a c t No antiviral drugs to treat or prevent life-threatening flavivirus infections such as those caused by mosquito-borne Dengue (DENV) and more recently Zika (ZIKV) viruses are yet available. We aim to develop, through a structure-based drug design approach, novel inhibitors targeting the NS5 AdoMet-dependent mRNA methyltransferase (MTase), a viral protein involved in the RNA capping process essential for flaviviruses replication. Herein, we describe the optimization of a hit (5) identified using fragment-based and structure-guided linking techniques, which binds to a proximal site of the AdoMet binding pocket. X-ray crystallographic structures and computational docking were used to guide our optimization process and lead to compounds 30 and 33 (DENV IC 50 ¼ 26 mM and 23 mM; ZIKV IC 50 ¼ 28 mM and 19 mM, respectively), two representatives of novel non-nucleoside inhibitors of flavi-virus MTases.
Published: 2019

28. Co‐circulation and characterization of novel African arboviruses (genus Ephemerovirus ) in cattle, Mayotte island, Indian Ocean, 2017

Author: Dacheux, Laurent, Dommergues, Laure, Chouanibou, Youssouffi, Domeon, Lionel, Schuler, Christian, Bonas, Simon, Luo, Dongsheng, Maufrais, Corinne, Cêtre-Sossah, Catherine, Cardinale, Eric, Bourhy, Hervé, Métras, Raphaëlle, Lyssavirus, épidémiologie et neuropathologie - Lyssavirus Epidemiology and Neuropathology, Institut Pasteur [Paris] (IP), Coopérative des Éleveurs Mahorais, Partenaires INRAE, Clinique Vétérinaire de Doméon/Schuler, Wuhan Institute of Virology [Wuhan, China], Chinese Academy of Sciences [Wuhan Branch], University of Chinese Academy of Sciences [Beijing] (UCAS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), DP One health Indian Ocean, European Virus Archive goes Global (EVAg) [653316], European Union's Horizon 2020 Research and Innovation Programme, Sir Henry Wellcome Fellowship [101581/Z/13/Z], European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Ephemeral Fever, Bétail, Short Communication, Short Communications, Mayotte, next‐generation sequencing, Cattle Diseases, Genome, Viral, L73 - Maladies des animaux, MESH: Sequence Analysis, DNA / veterinary, Comoros, MESH: Population Surveillance, ephemerovirus, Animals, MESH: Animals, Surveillance épidémiologique, MESH: Ephemerovirus / genetics, MESH: Phylogeny, MESH: Cattle Diseases / epidemiology, MESH: Cattle Diseases / virology, Phylogeny, [SDV.BA]Life Sciences [q-bio]/Animal biology, L01 - Élevage - Considérations générales, Sequence Analysis, DNA, MESH: Ephemerovirus / classification, arboviruses [EN], MESH: Cattle, MESH: Comoros / epidemiology, arbovirus, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Population Surveillance, Africa, Cattle, next-generation sequencing, MESH: Ephemeral Fever / epidemiology, L20 - Écologie animale, MESH: Genome, Viral, rhabdovirus, MESH: Ephemeral Fever / virology
Abstract: International audience; Mayotte is an island located in the Mozambique Channel, between Mozambique and Madagascar, in the South Western Indian Ocean region. A severe syndrome of unknown aetiology has been observed seasonally since 2009 in cattle (locally named "cattle flu"), associated with anorexia, nasal discharge, hyperthermia and lameness. We sampled blood from a panel of those severely affected animals at the onset of disease signs and analysed these samples by next-generation sequencing. We first identified the presence of ephemeral bovine fever viruses (BEFV), an arbovirus belonging to the genus Ephemerovirus within the family Rhabdoviridae, thus representing the first published sequences of BEFV viruses of African origin. In addition, we also discovered and genetically characterized a potential new species within the genus Ephemerovirus, called Mavingoni virus (MVGV) from one diseased animal. Finally, both MVGV and BEFV have been identified in cattle from the same herd, evidencing a co-circulation of different ephemeroviruses on the island. The clinical, epidemiological and virological information strongly suggests that these viruses represent the etiological agents of the observed "cattle flu" within this region. This study highlights the importance of the strengthening and harmonizing arboviral surveillance in Mayotte and its neighbouring areas, including Africa mainland, given the importance of the diffusion of infectious diseases (such as BEFV) mediated by animal and human movements in the South Western Indian Ocean area.
Published: 2019

29. Modulation of Measles Virus NTAIL Interactions through Fuzziness and Sequence Features of Disordered Binding Sites

Author: Francesca Troilo, Sonia Longhi, Stefano Gianni, Christophe Bignon, Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Biochemical Sciences 'Rossi Fanelli', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), The studies herein reviewed were carried out with the financial support of the CNRS, of the Direction Générale de l’Armement (DGA), and of the Agence Nationale de la Recherche, specific programs 'Physico-Chimie du Vivant', ANR-08-PCVI-0020-01, and 'ASTRID', ANR-11-ASTR-003-01 to S.L. They were also partly supported by the European program H2020 under the EVAg Research Infrastructure (grant agreement Nb. 653316 to C.B.), and by the Italian Ministero dell’Istruzione dell’Università e della Ricerca (Progetto di Interesse ‘Invecchiamento’ to S.G.) and by Sapienza University of Rome (C26A155S48 to S.G). F.T. is a recipient of a Ph.D. fellowship from the Italo-French University., S.L. wishes to thank former members of her lab who contributed to these studies: D. Blocquel (The Scripps Institute, La Jolla, CA, USA), A. Gruet (Memorial Sloan Kettering Cancer Center, New York, USA) and M. Dosnon. The authors also thank D. Gerlier (CIRI, INSERM U758, Lyon, FR), R. Das (Dept. of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, USA) and M. Fuxreiter (Hungarian Academy of Sciences, Momentum Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary)., ANR-08-PCVI-0020,AFF-IDP,Determinants of specificity and affinity in partner recognition by intrinsically disordered proteins(2008), ANR-11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' [Rome], ANR-11-INBS-0003/11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011), and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome]
Subjects: 0301 basic medicine, Viral protein, lcsh:QR1-502, IDP, medicine.disease_cause, Biochemistry, lcsh:Microbiology, Measles virus, 03 medical and health sciences, protein complementation assays, medicine, Binding site, Molecular Biology, Protein secondary structure, Mutation, 030102 biochemistry & molecular biology, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, folding, binding, experiments, biology.organism_classification, fuzzy interactions, split-GFP reassembly, kinetics, Nucleoprotein, Folding (chemistry), [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, Phosphoprotein, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Biophysics
Abstract: International audience; In this paper we review our recent findings on the different interaction mechanisms of the C-terminal domain of the nucleoprotein (N) of measles virus (MeV) NTAIL, a model viral intrinsically disordered protein (IDP), with two of its known binding partners, i.e., the C-terminal X domain of the phosphoprotein of MeV XD (a globular viral protein) and the heat-shock protein 70 hsp70 (a globular cellular protein). The NTAIL binds both XD and hsp70 via a molecular recognition element (MoRE) that is flanked by two fuzzy regions. The long (85 residues) N-terminal fuzzy region is a natural dampener of the interaction with both XD and hsp70. In the case of binding to XD, the N-terminal fuzzy appendage of NTAIL reduces the rate of α-helical folding of the MoRE. The dampening effect of the fuzzy appendage on XD and hsp70 binding depends on the length and fuzziness of the N-terminal region. Despite this similarity, NTAIL binding to XD and hsp70 appears to rely on completely different requirements. Almost any mutation within the MoRE decreases XD binding, whereas many of them increase the binding to hsp70. In addition, XD binding is very sensitive to the α-helical state of the MoRE, whereas hsp70 is not. Thus, contrary to hsp70, XD binding appears to be strictly dependent on the wild-type primary and secondary structure of the MoRE.
Published: 2019

30. Emergent Sand Fly–Borne Phleboviruses in the Balkan Region

Author: Rémi N. Charrel, Nazli Ayhan, 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), University of Florida [Gainesville] (UF), This work was supported in part by the European Virus Archive Goes Global (EVAg) project, which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 653316., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), BUISINE, Soline, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, Microbiology (medical), Emergent Sand Fly–Borne Phleboviruses in the Balkan Region, Balkan region, Epidemiology, lcsh:Medicine, Mediterranean Basin, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Balkan peninsula, sandfly fever Naples virus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Balkan virus, lcsh:RC109-216, viruses, Sandfly Fever Sicilian Virus, phlebovirus, sandfly fever Sicilian virus, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Toscana virus, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Ecology, Historical Review, lcsh:R, biology.organism_classification, Adria virus, 3. Good health, Sandfly, 030104 developmental biology, Infectious Diseases, Geography, Phlebovirus, Phlebotomus, Sandfly fever Naples virus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, sand fly
Abstract: International audience; Sand fly–borne phleboviruses are associated with febrile diseases and nervous system infections in the Mediterranean basin. Sandfly fever was first reported in the Balkan Peninsula at the end of the 19th century. Since then, accumulating data show that the Balkan Peninsula, as a transboundary region between Asia and Europe, plays a major role in the emergence of vectorborne diseases in Europe. To provide an inclusive approach, we collected published data on phleboviruses in the Balkan countries and used them to evaluate the impact of these pathogens from virologic, epidemiologic, and public health perspectives. Recent findings show a high diversity of phleboviruses belonging to 3 species or serocomplexes circulating heavily in the Balkans. Focusing on undisputable human pathogens, we found direct and indirect laboratory documentation for Toscana virus, Sandfly fever Sicilian virus, and Adria virus. These data demonstrate that the Balkans are a hotspot for phleboviruses transmitted by sand flies.
Published: 2018

31. The European Virus Archive goes global: A growing resource for research

Author: P. Lieutaud, M. Eropkin, X. de Lamballerie, Jan Felix Drexler, Z. Hu, Boris Klempa, Daniel D. Pinschewer, Hervé Raoul, Chantal Reusken, Thomas Klimkait, Andreas Nitsche, M. Bardsley, Antonino DiCaro, Jean-Louis Romette, Rémi N. Charrel, F. Pradel, Zverev Vv, Anthony R. Fooks, Ali Mirazimi, Giuseppe Ippolito, Sven Reiche, Thomas C. Mettenleiter, Stephan Günther, C. Sabeta, Marion Koopmans, Michael C. Carroll, Janusz T. Paweska, Ernest A. Gould, Hervé Bourhy, C. Prat, Tatjana Avsic-Zupanc, S. Mac Cullough, Alexander E. Gorbalenya, Maria Rosaria Capobianchi, Bruno Coutard, Christian Drosten, Carrie Batten, 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), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Animal and Plant Health Agency [Weybridge] (APHA), Department of Health-Special Pathogens Laboratory, Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, Bernhard Nocht Institute for Tropical Medicine, National Reference Center for tropical Infectious Diseases, Slovak Academy of Science [Bratislava] (SAS), University of Basel (Unibas), Institute of Microbiology and Immunology, Lubljana, Slovenia, Istituto Nazionale di Malattie Infettive 'Lazzaro Spallanzani' (INMI), Robert Koch Institute [Berlin] (RKI), Erasmus University Medical Center [Rotterdam] (Erasmus MC), Leiden University Medical Center (LUMC), Laboratoire P4 - Jean Mérieux, Centre Européen de Virologie/Immunologie-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris], Friedrich-Loeffler-Institut (FLI), The Pirbright Institute, Onderstepoort Veterinary Institute (ARC - OVI), National Institute for Communicable Diseases (NICD), Research Institute of Influenza, St. Petersburg, Russia, Mechnikov Scientific Research Institute for Vaccines and Sera, Moscow, Russia, Wuhan Institute of Virology, Australian Animal Health Laboratory (AAHL), Health and Biosecurity CSIRO, Geelong, Australia (AAHL, CSIRO), Folkhalsomyndigheten, Stockholm, Sweden, Fondation Mérieux, This publication was supported by the European Virus Archive global (EVAg) project that has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 653316., We wish to thank the following scientists for their expertise and contributions during the successful establishment and development of the EVAg: C. Barontia, L. McElhinneyc, D. Marstonc, L. Thornec, R. Hewsond, T. Bleickere, T. Riegerf, M. Korvai, N. Knapi, S. Meschij, P. Jansen van Vurenl, B. Phahladiral, C. Carbonellen, S. Carpenterq, A. Nikonovau, F. Dengv, N. Romanenkova1, S. Becker2, M. Saijo3, G. Gao Fu4, A. Lukashev5, E. Koray6 1 St Petersburg Pasteur Institute, St Petersburg, Russia 2 Institut für Virologie (UMR-DE), Marburg, Germany 3 National Institute of Infectious Diseases (NIID), Tokyo, Japan 4 China CDC, Beijing, China 5 Chumakov institute of Poliomyelitis and viral Encephalitides (IPVE), Moscow, Russia, 6 Hacettepe University, Faculty of Medicine (HU), Ankara, Turkey, European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), National Institute for Communicable Diseases [Johannesburg] (NICD), Universiteit Leiden, Institut Pasteur [Paris] (IP), and Virology
Subjects: 0301 basic medicine, Quality Control, medicine.medical_specialty, Economic growth, Resource (biology), Biomedical Research, Virus archive, EU infrastructure, Article, 03 medical and health sciences, Virology, Management Service Organizations, Yellow Fever, medicine, Humans, ddc:610, China, Virus collection, Biological Specimen Banks, Pharmacology, Archives, Information Dissemination, Zika Virus Infection, Public health, Biobank, 3. Good health, Europe, 030104 developmental biology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Middle East Respiratory Syndrome Coronavirus, Health Resources, Business, Public Health, Safety, 610 Medizin und Gesundheit
Abstract: The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. Within three years, it developed from a consortium of nine European laboratories to encompass associated partners in Africa, Russia, China, Turkey, Germany and Italy. In 2014, the H2020 Research and Innovation Framework Programme (INFRAS projects) provided support for the transformation of the EVA from a European to a global organization (EVAg). The EVAg now operates as a non-profit consortium, with 26 partners and 20 associated partners from 21 EU and non-EU countries. In this paper, we outline the structure, management and goals of the EVAg, to bring to the attention of researchers the wealth of products it can provide and to illustrate how end-users can gain access to these resources. Organisations or individuals who would like to be considered as contributors are invited to contact the EVAg coordinator, Jean-Louis Romette, at jean-louis.romette@univmed.fr., Highlights • The EVAg was created as an international organization aiming to provide a gold standard resource to the scientific community. • The EVAg operates as a non-profit consortium of 26 partners and 20 associated partners from EU and non-EU countries. • Members and associated members retain ownership of the viruses that they disseminate via the EVAg infrastructure. • The EVAg approach to quality management is directed by the project's own quality standard, based upon OECD guidelines. • The ultimate objective is to make the EVAg a permanent archive that can provide access to viruses and reagents globally.
Published: 2018

32. First Identification and Genomic Characterization of a Porcine Sapelovirus from Corsica, France, 2017

Author: Piorkowski, Géraldine, Capai, Lisandru, Falchi, Alessandra, Casabianca, François, Maestrini, Oscar, Gallian, Pierre, Barthélémy, Karine, Py, Odile, Charrel, Rémi, De Lamballerie, Xavier, 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), EA Bioscope Corse Méditerranée : Dynamique des infections virales en milieu insulaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pascal Paoli (UPP), Epidémiologie des maladies infectieuses et modélisation (ESIM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de recherche Développement de l'Elevage (LRDE), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherches sur le Développement de l’Elevage (UR 045), Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Université Grenoble Alpes - UFR Pharmacie (UGA UFRP), Université Grenoble Alpes (UGA), Hôpital de la Timone [CHU - APHM] (TIMONE), Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Recherches sur le Développement de l'Elevage (LRDE), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Corsica territorial collectivity, and European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015)
Subjects: fluids and secretions, genetic structures, animal diseases, [SDV]Life Sciences [q-bio], Genome Sequences
Abstract: We report the isolation and genomic characterization of a Sapelovirus A strain, or porcine sapelovirus (PSV), from a diarrheic Corsican piglet in France. It shares 87% nucleotide identity with a 2014 German isolate.
Published: 2018

33. Comparison of chikungunya viruses generated using infectious clone or the Infectious Subgenomic Amplicons (ISA) method in Aedes mosquitoes

Author: Anna-Bella Failloux, Antoine Nougairède, Anubis Vega-Rúa, Xavier de Lamballerie, Souand Mohamed Ali, Jean-Sélim Driouich, 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), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris], This work was supported by the French 'Agence Nationale de la Recherche' under grant agreement no. ANR-14-CE14-0001 (RNA Vacci-Code) and by the European Union's Horizon 2020 Research and Innovation Programme under grants agreements no. 653316 (European Virus Archive goes global project: https://www.european-virus-archive.com/)., ANR-14-CE14-0001,RNA Vacci-Code,Ré-encodage génomique à large échelle des virus ARN pour la production de candidats vaccins atténués(2014), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, RNA viruses, Viral Diseases, viruses, lcsh:Medicine, Disease Vectors, medicine.disease_cause, Pathology and Laboratory Medicine, Mosquitoes, Aedes, Chlorocebus aethiops, Medicine and Health Sciences, Chikungunya, lcsh:Science, Subgenomic mRNA, Multidisciplinary, Chikungunya Virus, Microbial Genetics, Eukaryota, Biological Evolution, 3. Good health, Insects, Infectious Diseases, Medical Microbiology, Viral Pathogens, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viruses, RNA, Viral, Female, Pathogens, Research Article, Neglected Tropical Diseases, Aedes albopictus, Substitution Mutation, Arthropoda, Alphaviruses, Aedes aegypti, Genome, Viral, Biology, Aedes Aegypti, Research and Analysis Methods, Microbiology, Virus, Togaviruses, 03 medical and health sciences, medicine, Genetics, Animals, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, Vero Cells, Evolutionary Biology, Population Biology, lcsh:R, Organisms, Biology and Life Sciences, Chikungunya Infection, Genetic Variation, biology.organism_classification, Tropical Diseases, Virology, Invertebrates, Reverse genetics, Insect Vectors, Species Interactions, 030104 developmental biology, Vector (epidemiology), Mutation, lcsh:Q, Population Genetics, Cloning
Abstract: International audience; Reverse genetics systems provide the opportunity to manipulate viral genomes and have been widely used to study RNA viruses and to develop new antiviral compounds and vaccine strategies. The recently described method called ISA (Infectious Subgenomic Amplicons) gives the possibility to rescue RNA viruses in days. We demonstrated in cell culture that the use of the ISA method led to a higher genetic diversity of viral populations than that observed using infectious clone technology. However, no replicative fitness difference was observed. In the present study, we used the chikungunya virus as a model to compare in Aedes aegypti and Aedes albopictus mosquitoes the genotypic and phenotypic characteristics of viruses produced either from an infectious clone or using the ISA method. We confirmed the results found in cellulo corroborating that the use of the ISA method was associated with higher genetic diversity of viral populations in mosquitoes but did not affect the vector competence validating its use for in vivo experiments.
Published: 2018

34. Zika virus epidemiology in Bolivia : A seroprevalence study in volunteer blood donors

Author: Xavier de Lamballerie, Thomas Jaenisch, Paola Mariela Saba Villarroel, Stéphane Priet, Laetitia Ninove, Boris Pastorino, Pierre Gallian, Elif Nurtop, Isabelle Leparc-Goffart, Jan Felix Drexler, Yelin Roca, 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), Centro Nacional de Enfermedades Tropicales [Santa Cruz de la Sierra, Bolivia] (CENETROP), Institute of Virology [Berlin, Germany] (Charité), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], German Centre for Infection Research [Berlin, Germany] (DZIF - Charité), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Section Clinical Tropical Medicine [Heidelberg], Department of Infectious Diseases [Heidelberg, Germany], Heidelberg University Hospital [Heidelberg]-Heidelberg University Hospital [Heidelberg], Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), German Centre for Infection Research (DZIF), Etablissement Français du Sang [La Plaine Saint-Denis] (EFS), European Union’s Horizon 2020 research and innovation programmes ZIKAlliance and EVAg under grant agreements No 734548 and 653316, Dubois Frid, Caroline, A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: RNA viruses, Male, Volunteers, 0301 basic medicine, [SDV]Life Sciences [q-bio], Disease Vectors, Dengue virus, Pathology and Laboratory Medicine, medicine.disease_cause, Mosquitoes, Geographical locations, Zika virus, Dengue fever, Dengue, 0302 clinical medicine, Aedes aegypti, Aedes, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Epidemiology, Medicine and Health Sciences, Mass Screening, Enzyme-linked immunoassays, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Zika Virus Infection, lcsh:Public aspects of medicine, Eukaryota, Middle Aged, 3. Good health, Insects, [SDV] Life Sciences [q-bio], Infectious Diseases, Geography, Medical Microbiology, Viral Pathogens, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Pathogens, Chikungunya virus, Research Article, Adult, medicine.medical_specialty, Bolivia, lcsh:Arctic medicine. Tropical medicine, Arthropoda, Adolescent, lcsh:RC955-962, Alphaviruses, Immunology, 030231 tropical medicine, Mosquito Vectors, Research and Analysis Methods, Blood donors, Microbiology, Virus, Togaviruses, Young Adult, 03 medical and health sciences, Environmental health, parasitic diseases, medicine, Animals, Humans, Seroprevalence, Immunoassays, Microbial Pathogens, Biology and life sciences, Flaviviruses, Organisms, Public Health, Environmental and Occupational Health, Immunity, lcsh:RA1-1270, South America, biology.organism_classification, medicine.disease, Invertebrates, Insect Vectors, Health Care, Species Interactions, 030104 developmental biology, Immunologic Techniques, Chikungunya Fever, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, People and places
Abstract: Background Zika virus (ZIKV), was widely reported in Latin America and has been associated with neuropathologies, as microcephaly, but only few seroprevalence studies have been published to date. Our objective was to determine the seroprevalence amongst Bolivian blood donors and estimate the future potential circulation of the virus. Methodology A ZIKV seroprevalence study was conducted between December 2016 and April 2017 in 814 asymptomatic Bolivian volunteer blood donors residing in various eco-environments corresponding to contrasting entomological activities. It was based on detection of IgG to ZIKV using NS1 ELISA screening, followed by a seroneutralisation test in case of positive or equivocal ELISA result. Conclusions/Significance Analysis revealed that ZIKV circulation occurred in tropical areas (Beni: 39%; Santa Cruz de la Sierra: 21.5%) but not in highlands (~0% in Cochabamba, La Paz, Tarija). It was modulated by Aedes aegypti activity and the virus spread was not limited by previous immunity to dengue. Cases were geo-localised in a wide range of urban areas in Santa Cruz and Trinidad. No differences in seroprevalence related to gender or age-groups could be identified. It is concluded that ZIKV has been intensely circulating in the Beni region and has still a significant potential for propagating in the area of Santa Cruz., Author summary Zika virus (ZIKV) is a virus of African origin, transmitted by Aedes mosquitoes, and related to dengue and yellow fever virus. It was originally believed to be responsible for a mild febrile illness in Africa and South-east Asia. However, in recent years, ZIKV has been responsible for outbreaks in the Pacific Islands before massively spreading in Latin America and the Caribbean. On this occasion, ZIKV has unexpectedly been associated with non-vector transmission (i.e., sexual and mother-to-foetus transmission) and with severe complications such as foetal abnormalities (e.g. microcephaly) and Guillain-Barré syndromes. Little is known about the actual proportion of the populations infected by ZIKV in Latin America. Here, we report a seroprevalence data in this region, after studying 814 asymptomatic Bolivian volunteer blood donors residing in various eco-environments corresponding to contrasting entomological activities. We conclude that ZIKV has been circulating in Bolivian tropical areas but not in highlands, and that the epidemic has not been limited by previous immunity against dengue. Specific attention should be paid to the region of Santa Cruz, where the seroprevalence is still limited, but the density of Aedes aegypti populations makes plausible further spreading of the disease.
Published: 2018

35. Antiviral efficacy of favipiravir against Ebola virus: A translational study in cynomolgus macaques

Author: Guedj, Jérémie, Piorkowski, Géraldine, Jacquot, Frédéric, Madelain, Vincent, Nguyen, Thi Huyen Tram, Rodallec, Anne, Gunther, Stephan, Carbonnelle, Caroline, Mentré, France, Raoul, Hervé, de Lamballerie, Xavier, Bodescot, Myriam, Evaluation of the efficacy and of the antiviral activity of T-705 (favipiravir) duringEbola virus infection in non-human primates humans - REACTION - - H20202014-11-01 - 2016-10-31 - 666092 - VALID, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), Laboratoire P4 Jean Mérieux-Inserm [Lyon] (Unité de service 3), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Européen de Recherche en Virologie et Immunologie [Lyon] (Tour Inserm CERVI), Simulation & Modelling : Adaptive Response for Therapeutics in Cancer (SMARTc unit), Centre de Recherches en Oncologie biologique et Oncopharmacologie (CRO2), Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Aix Marseille Université (AMU), Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreements No 666092 (Reaction!), No 653316 (EVAg) and No 115843 (EbolaMoDRAD). It was also supported by the St. Luke's International University (Tokyo, Japan) in the framework of the Research Program on Emerging and Re-emerging Infectious Diseases of the Japan Agency for Medical Research and Development (AMED) and the multidisciplinary 'Reacting' consortium coordinated by INSERM (French National Institute of Health and Medical Research) on behalf of all partners of AVIESAN (French National Alliance for Life Sciences and Health)., European Project: 666092,H2020,H2020-Adhoc-2014-20,REACTION(2014), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC), and Aix Marseille Université (AMU)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: RNA viruses, Time Factors, Physiology, Monkeys, Pathology and Laboratory Medicine, Translational Research, Biomedical, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine and Health Sciences, Mammals, Viral Genomics, Antimicrobials, Pharmaceutics, Eukaryota, Drugs, Genomics, Viral Load, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, Antivirals, Ebolavirus, Body Fluids, [SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences, Blood, Medical Microbiology, Filoviruses, Viral Pathogens, Pyrazines, Vertebrates, Viruses, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, Female, Pathogens, Anatomy, Ebola Virus, Macaque, Research Article, Primates, Microbial Genomics, Genome, Viral, Microbiology, Antiviral Agents, Blood Plasma, Drug Therapy, Virology, Microbial Control, Old World monkeys, Genetics, Animals, Humans, Pharmacokinetics, Microbial Pathogens, Pharmacology, Dose-Response Relationship, Drug, Hemorrhagic Fever Viruses, Organisms, Biology and Life Sciences, Hemorrhagic Fever, Ebola, Amides, Macaca fascicularis, Mutagenesis, Amniotes, RNA, Viral Transmission and Infection
Abstract: Background Despite repeated outbreaks, in particular the devastating 2014–2016 epidemic, there is no effective treatment validated for patients with Ebola virus disease (EVD). Among the drug candidates is the broad-spectrum polymerase inhibitor favipiravir, which showed a good tolerance profile in patients with EVD (JIKI trial) but did not demonstrate a strong antiviral efficacy. In order to gain new insights into the antiviral efficacy of favipiravir and improve preparedness and public health management of future outbreaks, we assess the efficacy achieved by ascending doses of favipiravir in Ebola-virus-infected nonhuman primates (NHPs). Methods and findings A total of 26 animals (Macaca fascicularis) were challenged intramuscularly at day 0 with 1,000 focus-forming units of Ebola virus Gabon 2001 strain and followed for 21 days (study termination). This included 13 animals left untreated and 13 treated with doses of 100, 150, and 180 mg/kg (N = 3, 5, and 5, respectively) favipiravir administered intravenously twice a day for 14 days, starting 2 days before infection. All animals left untreated or treated with 100 mg/kg died within 10 days post-infection, while animals receiving 150 and 180 mg/kg had extended survival (P < 0.001 and 0.001, respectively, compared to untreated animals), leading to a survival rate of 40% (2/5) and 60% (3/5), respectively, at day 21. Favipiravir inhibited viral replication (molecular and infectious viral loads) in a drug-concentration-dependent manner (P values < 0.001), and genomic deep sequencing analyses showed an increase in virus mutagenesis over time. These results allowed us to identify that plasma trough favipiravir concentrations greater than 70–80 μg/ml were associated with reduced viral loads, lower virus infectivity, and extended survival. These levels are higher than those found in the JIKI trial, where patients had median trough drug concentrations equal to 46 and 26 μg/ml at day 2 and day 4 post-treatment, respectively, and suggest that the dosing regimen in the JIKI trial was suboptimal. The environment of a biosafety level 4 laboratory introduces a number of limitations, in particular the difficulty of conducting blind studies and performing detailed pharmacological assessments. Further, the extrapolation of the results to patients with EVD is limited by the fact that the model is fully lethal and that treatment initiation in patients with EVD is most often initiated several days after infection, when symptoms and high levels of viral replication are already present. Conclusions Our results suggest that favipiravir may be an effective antiviral drug against Ebola virus that relies on RNA chain termination and possibly error catastrophe. These results, together with previous data collected on tolerance and pharmacokinetics in both NHPs and humans, support a potential role for high doses of favipiravir for future human interventions., Author summary Why was this study done? In spite of repeated outbreaks, including the devastating 2014–2016 West Africa epidemic, there are no approved antiviral therapeutics against Ebola virus (EBOV). In 2014, the European consortium Reaction! was established to assess the anti-EBOV efficacy of favipiravir, a broad-spectrum RNA virus polymerase inhibitor approved for treatment of influenza in Japan. The consortium implemented the JIKI clinical trial, which showed that the drug was well tolerated but did not achieve a high antiviral efficacy. We here further aimed to determine whether the antiviral efficacy of favipiravir could be improved with higher doses, using a model of EBOV infection in nonhuman primates. What did the researchers do and find? Ascending doses of favipiravir were administered to cynomolgus macaques intravenously twice a day for 14 days, starting 2 days before infection with EBOV. Favipiravir inhibited EBOV viral production in a concentration-dependent manner, and doses of 150 and 180 mg/kg led to a survival rate of approximately 50%, allowing us to identify target drug concentrations. In addition, EBOV genomic deep sequencing showed an increase in virus mutagenesis over time with favipiravir treatment. What do these findings mean? Our results suggest that favipiravir may be an effective antiviral drug against EBOV that relies on RNA chain termination and possibly error catastrophe. These results, together with previous data collected on tolerance and pharmacokinetics in both nonhuman primates and humans, support a potential role for high doses of favipiravir for future human interventions.
Published: 2018

36. Combination of ELISA screening and seroneutralisation tests to expedite Zika virus seroprevalence studies

Author: Christophe N. Peyrefitte, Audrey Dubot-Pérès, Paola Mariela Saba Villarroel, Xavier de Lamballerie, Laetitia Ninove, Yelin Roca, Stéphane Priet, Elif Nurtop, Gilda Grard, Bouba Gake, Pierre Gallian, Jan Felix Drexler, Boris Pastorino, 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), Centro Nacional de Enfermedades Tropicales [Santa Cruz de la Sierra, Bolivia] (CENETROP), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur (RIIP), Institut de Recherche pour le Développement (IRD), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, This work was partially supported by the European Union’s Horizon 2020 Research and Innovation Programme under ZIKAlliance Grant Agreement no. 734548 and the European Virus Archive EVAg, European Union- Horizon 2020 programme under grant agreement no. 653316., European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Dubois Frid, Caroline, A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, viruses, Antibodies, Viral, Zika virus, Dengue fever, MESH: Antibodies, Neutralizing, Cytopathogenic Effect, Viral, Seroepidemiologic Studies, MESH: Martinique, Combination strategy, Mass Screening, Cytopathic effect, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Immunoglobulin G, education.field_of_study, Microscopy, biology, Zika Virus Infection, MESH: Neutralization Tests, MESH: Enzyme-Linked Immunosorbent Assay, 3. Good health, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Microscopy, Population, Virus Neutralization, Enzyme-Linked Immunosorbent Assay, MESH: Zika Virus, Sensitivity and Specificity, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, MESH: Zika Virus Infection, Neutralization Tests, Virology, medicine, Seroprevalence, Humans, lcsh:RC109-216, Martinique, Serologic Tests, MESH: Mass Screening, education, Igg elisa, Seroepidemiology, MESH: Seroepidemiologic Studies, MESH: Humans, MESH: Serologic Tests, Correction, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, medicine.disease, MESH: Cytopathogenic Effect, Viral, Antibodies, Neutralizing, MESH: Sensitivity and Specificity, 030104 developmental biology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Immunoglobulin G, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Virus neutralization test, MESH: Antibodies, Viral
Abstract: International audience; Here we propose a strategy allowing implementing efficient and practicable large-scale seroepidemiological studies for Zika Virus (ZIKV). It combines screening by a commercial NS1 protein-based Zika IgG ELISA, and confirmation by a cytopathic effect-based virus neutralization test (CPE-based VNT). In post-epidemic samples from Martinique Island blood donors (a population with a dengue seroprevalence above 90%), this strategy allowed reaching specificity and sensitivity values over 98%. The CPE-based VNT consists of recording CPE directly under the optical microscope, which is easy to identify with ZIKV strain H/PF/2013 at day 5 pi. Overall, considered that CPE-based VNT is cost effective and widely automatable, the NS1 protein-based Zika IgG ELISA+CPE-based VNT combination strategy represents a convenient tool to expedite ZIKV seroprevalence studies.
Published: 2018

37. Stress-induced unfolded protein response contributes to Zika virus–associated microcephaly

Author: Nicolas Thelen, Christian Alfano, Pierre Vanderhaeghen, Thérèse Couderc, Maryse Bonnière, Michelle America, Giovanni Morelli, Ikuo K. Suzuki, Catherine Creppe, Bettina Bessières, Lluís Cordón-Barris, Laurent Nguyen, Marc Lecuit, Marie Flamand, Marc Thiry, Férechté Encha-Razavi, Ivan Gladwyn-Ng, GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R) [Liège], Université de Liège-C.H.U. Sart Tilman [Liège], Biologie des Infections - Biology of Infection, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], BIOMED [Hasselt], Hasselt University (UHasselt), Département d’Histologie-Embryologie-Cytogénétique, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université libre de Bruxelles (ULB), Virologie Structurale, Institut Pasteur [Paris], Walloon Excellence in Life sciences and BIOtechnology [Liège] (WELBIO), Université Paris Descartes - Paris 5 (UPD5), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), The authors are thankful for technical help from the GIGA-Imaging Platform of ULg, M. Leruez-Ville for human sample collection, P.V. Drion, E.D. Valentin and C. Grignet for the flaviviral facility, C. d’Alessandro, M. Sambon and M. Lavina for technical assistance, E. Simon-Loriere for sharing ZIKV quantification protocol, and E. Peyre for graphical assistance. L.N., I.G.-N. and C.C. receive financial support from F.R.S.-F.N.R.S. This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under ZIKAlliance Grant Agreement N° 734548 (to L.N. and M.L.) and by the European Virus Archives goes Global (EVAg) project under grant agreement N° 653316. M.L. is also funded by Institut Pasteur, Inserm and LabEx IBEID. L.N. and P.V. are funded by F.R.S.-F.N.R.S., the Fonds Léon Fredericq, the Fondation Médicale Reine Elisabeth, the Fondation Simone et Pierre Clerdent and the Belgian Science Policy (IAP-VII network P7/20). L.N. is funded by ARC (ARC11/16-01) and the ERANET Neuron STEM-MCD, P.V. is funded by the WELBIO Program of the Walloon Region, the AXA Research Fund, the Fondation ULB, ERANET Neuron Microkin, ERANET E-rare Euromicro and ERC-2013 ERC-2013-AG-340020., European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Hasselt University, Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Libre de Bruxelles [Bruxelles] (ULB), Welbio, and Free University of Brussels (BELGIUM)
Subjects: Gene Expression Regulation, Viral, 0301 basic medicine, Microcephaly, Mice, Transgenic, Nerve Tissue Proteins, Biology, Mice, Neuroblastoma, 03 medical and health sciences, Fetus, Cell Line, Tumor, medicine, Animals, Humans, Progenitor cell, Protein Unfolding, Activating Transcription Factor 3, Zika Virus Infection, General Neuroscience, Endoplasmic reticulum, Neurogenesis, Brain, Interferon-alpha, Zika Virus, Embryo, Mammalian, Endoplasmic Reticulum Stress, medicine.disease, Embryonic stem cell, Neural stem cell, 3. Good health, Cell biology, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, medicine.anatomical_structure, Cerebral cortex, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Unfolded protein response, Neuroscience
Abstract: Accumulating evidence support a causal link between Zika virus (ZIKV) infection during gestation and congenital microcephaly. However, the mechanism of ZIKV-associated microcephaly remains unclear. We combined analyses of ZIKV-infected human fetuses, cultured human neural stem cells and mouse embryos to understand how ZIKV induces microcephaly. We show that ZIKV triggers endoplasmic reticulum stress and unfolded protein response in the cerebral cortex of infected postmortem human fetuses as well as in cultured human neural stem cells. After intracerebral and intraplacental inoculation of ZIKV in mouse embryos, we show that it triggers endoplasmic reticulum stress in embryonic brains in vivo. This perturbs a physiological unfolded protein response within cortical progenitors that controls neurogenesis. Thus, ZIKV-infected progenitors generate fewer projection neurons that eventually settle in the cerebral cortex, whereupon sustained endoplasmic reticulum stress leads to apoptosis. Furthermore, we demonstrate that administration of pharmacological inhibitors of unfolded protein response counteracts these pathophysiological mechanisms and prevents microcephaly in ZIKV-infected mouse embryos. Such defects are specific to ZIKV, as they are not observed upon intraplacental injection of other related flaviviruses in mice. The authors are thankful for technical help from the GIGA-Imaging Platform of ULg; M. Leruez-Ville for human sample collection; P.V. Drion, E.D. Valentin and C. Grignet for the flaviviral facility; C. d'Alessandro, M. Sambon and M. Lavina for technical assistance; E. Simon-Loriere for sharing ZIKV quantification protocol; and E. Peyre for graphical assistance. L.N., I.G.-N. and C. C. receive financial support from F.R.S.-F.N.R.S. This work was supported by the European Union's Horizon 2020 Research and Innovation Programme under ZIKAlliance Grant Agreement No 734548 (to L.N. and M.L.) and by the European Virus Archives goes Global (EVAg) project under grant agreement No 653316. M.L. is also funded by Institut Pasteur, Inserm and LabEx IBEID. L.N. and P.V. are funded by F.R.S.-F.N.R.S., the Fonds Leon Fredericq, the Fondation Medicale Reine Elisabeth, the Fondation Simone et Pierre Clerdent and the Belgian Science Policy (IAP-VII network P7/20). L.N. is funded by ARC (ARC11/16-01) and the ERANET Neuron STEM-MCD; P.V. is funded by the WELBIO Program of the Walloon Region, the AXA Research Fund, the Fondation ULB, ERANET Neuron Microkin, ERANET E-rare Euromicro and ERC-2013 ERC-2013-AG-340020.
Published: 2018

38. Detection of Japanese Encephalitis Virus RNA in human throat samples in Laos : a pilot study

Author: Malee Seephonelee, Paul N. Newton, Audrey Dubot-Pérès, Tehmina Bharucha, Marc Lecuit, Onanong Sengvilaipaseuth, Xavier de Lamballerie, Malavanh Vongsouvath, Jean-David Pommier, Géraldine Piorkowski, Manivanh Vongsouvath, Sayaphet Rattanavong, Christopher Gorman, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, University College of London [London] (UCL), 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), Biologie des Infections - Biology of Infection, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Unité de Virologie / Virology Unit [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), University of Oxford, The SEAe project was supported by Total Foundation, Horizon 2020 research and innovation programme EVAg under grant agreement N° 653316, the Institute of Research for Development (IRD), Aix-Marseille University and the Wellcome Trust of Great Britain. The research was implemented in collaboration with ComAcross project (www.onehealthsea.org/comacross) thanks to the financial support of the European Union (EuropeAid, INNOVATE contract 315-047), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Bousquet, nathalie, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and University of Oxford [Oxford]
Subjects: Male, viruses, Pilot Projects, Antibodies, Viral, Serology, 0302 clinical medicine, 030212 general & internal medicine, Child, Encephalitis Virus, Japanese, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, education.field_of_study, Multidisciplinary, Middle Aged, 3. Good health, Vaccination, medicine.anatomical_structure, Molecular Diagnostic Techniques, Laos, Child, Preschool, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, Viral, Medicine, Female, Encephalitis, Adult, Adolescent, Science, 030231 tropical medicine, Population, Enzyme-Linked Immunosorbent Assay, Real-Time Polymerase Chain Reaction, Virus, Article, 03 medical and health sciences, Young Adult, Throat, medicine, Humans, Serologic Tests, education, Encephalitis, Japanese, Retrospective Studies, Molecular epidemiology, business.industry, Japanese encephalitis, medicine.disease, Virology, Immunoglobulin M, Pharynx, business
Abstract: International audience; Japanese encephalitis virus (JEV) is the most commonly identified cause of acute encephalitis syndrome (AES) in Asia. The WHO recommended test is anti-JEV IgM-antibody-capture-enzyme-linked-immunosorbent-assay (JEV MAC-ELISA). However, data suggest this has low positive predictive value, with false positives related to other Flavivirus infections and vaccination. JEV RT-PCR in cerebrospinal fluid (CSF) and/or serum is highly specific, but is rarely positive; 0–25% of patients that fulfil the WHO definition of JE (clinical Acute Encephalitis Syndrome (AES) and JEV MAC-ELISA positive). Testing other body fluids by JEV RT-qPCR may improve the diagnosis. As a pilot study thirty patients admitted to Mahosot Hospital 2014–2017, recruited to the SouthEast -Asia-Encephalitis study, were tested by JEV MAC-ELISA and two JEV real-time RT-PCR (RT-qPCR) assays (NS2A and NS3). Eleven (36.7%) were JEV MAC-ELISA positive. Available CSF and serum samples of these patients were JEV RT-qPCR negative but 2 (7%) had JEV RNA detected in their throat swabs. JEV RNA was confirmed by re-testing, and sequencing of RT-qPCR products. As the first apparent report of JEV RNA detection in human throat samples, the provides new perspectives on human JEV infection, potentially informing improving JEV detection. We suggest that testing patients' throat swabs for JEV RNA is performed, in combination with molecular and serological CSF and serum investigations, on a larger scale to investigate the epidemiology of the presence of JEV in human throats. Throat swabs are an easy and non-invasive tool that could be rolled out to a wider population to improve knowledge of JEV molecular epidemiology. Evidence continues to implicate Japanese encephalitis virus (JEV) as a major cause of encephalitis in Asia, with recent evidence of possible autochthonous transmission in Africa 1–3. Among the key factors in its persistent role as a public health problem are the limitations of existing diagnostic tests, our understanding of its epidemiology and inadequate implementation of vaccination programmes. The conventional mainstay of JEV encephalitis diagnosis is serology, with serum and cerebrospinal fluid (CSF) anti-JEV IgM antibody capture enzyme-linked immunosorbent assays (JEV MAC-ELISA) recommended by the World Health Organization (WHO) 4. However, there are concerns about the accuracy of JEV MAC-ELISA for diagnosing JEV. Low positive predictive value of JEV MAC-ELISA has been reported 5 , and there are recognised difficulties with false positives related to vaccination and in areas where other Flavivirus infections are endemic 6,7. Diagnosis of JEV by Reverse-Transcription (RT)-PCR is highly specific, and enables improved understanding of the molecular epidemiology of JEV 8. However, JEV RT-PCR testing of CSF and serum samples has low sensitivity , rarely positive in patients at presentation (0–25% that fulfil the WHO definition of Acute Encephalitis
Published: 2018

39. Cocirculation of Two Lineages of Toscana Virus in Croatia

Author: Nazli Ayhan, Bulent Alten, Vladimir Ivovic, Franjo Martinkovic, Ozge E. Kasap, Yusuf Ozbel, Xavier de Lamballerie, Remi N. Charrel, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Hacettepe University = Hacettepe Üniversitesi, Faculty of Mathematics, Natural Sciences and Information Technologies [Koper] (FAMNIT), University of Primorska, Department for Parasitology and Parasitic Diseases with Clinic [Zagreb, Croatia] (Faculty of Veterinary Medicine), University of Zagreb, Ege university, This work was supported by funds received from (i) VectorNet, a European network for sharing data on the geographic distribution of arthropod vectors, transmitting human and animal disease agents (Contract OC/EFSA/AHAW/2013/02-FWC1) funded by the European Food Safety Authority (EFSA) and the European Centre for Disease Prevention and Control (ECDC) (http://ecdc.europa.eu/en/healthtopics/vectors/VectorNet/Pages/VectorNet.aspx), (ii) the European Virus Archive goes Global (EVAg) project in the European Union’s Horizon 2020 research and innovation program under grant agreement No 653316 (http://global.european-virus-archive.com/). NA is a PhD student supported by a grant from Fondation Mediterranee Infection., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Ege Üniversitesi, Biyoloji, BUISINE, Soline, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: 0301 basic medicine, 030231 tropical medicine, Biology, Arbovirus, 03 medical and health sciences, 0302 clinical medicine, Data Report, medicine, phlebovirus, toscana virus, sandfly fever, Sandfly Fever Naples Virus, arbovirus, phlebovirus, ComputingMilieux_MISCELLANEOUS, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Toscana virus, lcsh:Public aspects of medicine, Public Health, Environmental and Occupational Health, lcsh:RA1-1270, Sandfly Fever Naples Virus, medicine.disease, biology.organism_classification, Virology, 3. Good health, 030104 developmental biology, arbovirus, Phlebovirus, Sandfly fever Naples virus, sandfly fever, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Public Health
Abstract: WOS: 000417780800001, PubMed ID: 29312917, VectorNet - European Food Safety Authority (EFSA) [OC/EFSA/AHAW/2013/02-FWC1]; European Centre for Disease Prevention and Control (ECDC); European UnionEuropean Union (EU) [653316]; Fondation Mediterranee Infection, This work was supported by funds received from (i) VectorNet, a European network for sharing data on the geographic distribution of arthropod vectors, transmitting human and animal disease agents (Contract OC/EFSA/AHAW/2013/02-FWC1) funded by the European Food Safety Authority (EFSA) and the European Centre for Disease Prevention and Control (ECDC) (http://ecdc.europa.eu/en/healthtopics/vectors/VectorNet/Pages/VectorNet.aspx), (ii) the European Virus Archive goes Global (EVAg) project in the European Union's Horizon 2020 research and innovation program under grant agreement No 653316 (http://global.european-virus-archive.com/). NA is a PhD student supported by a grant from Fondation Mediterranee Infection. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Published: 2017

40. Characterization of antibody response in neuroinvasive infection caused by Toscana virus

Author: Giada Rossini, Rémi N. Charrel, Vittorio Sambri, Silvia Morini, P. Cenni, Caterina Vocale, Nazli Ayhan, M. P. Landini, Anna Pierro, Paolo Gaibani, Stefania Varani, Michele Bartoletti, Antonio Mastroianni, F. Prati, Luigi Raumer, S. Schivazappa, Russell E. Lewis, S. Ficarelli, CRREM Laboratory [Bologna, Italy] (Unit of Microbiology), University hospital - Policlinico S.Orsola-Malpighi [Bologna, Italy], Unit of Microbiology [Pievesestina, Italy] (The Romagna Hub Laboratory), The Romagna Hub Laboratory [Pievesestina, Italy], Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Medical and Surgical Science [Bologna, Italy] (Infectious Disease Unit), University of Bologna/Università di Bologna, Infectious Disease Unit [Forlì, Italy], G.B. Morgagni-Pierantoni Hospital [Forlì, Italy], Infectious Disease Division [Reggio Emilia, Italy], Reggio Emilia Hospital [Italy], Emergency Department [Imola, Italy], Imola Hospital S. Maria della Scaletta [Imola, Italy], Department of Experimental, Diagnostic and Specialty Medicine [Bologna, Italy] (DIMES), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), This work was supported by the University of Bologna (RFO2013e2015 to SV, MPL) and by the Emilia-Romagna Region (Lab P3 funds). This work was also supported in part by the European Virus Archive goes Global (EVAg) project that has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 653316 (to RNC), the EDENext FP7- n261504 EU project (to RNC) and this paper is catalogued by the EDENext Steering Committee (http://www.edenext.eu) as EDENext467. The work of RNC was done under the frame of EurNegVec COST Action TD1303., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), University of Bologna, BUISINE, Soline, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, Biology and control of vector-borne infections in Europe - EDENEXT - - EC:FP7:HEALTH2011-01-01 - 2015-06-30 - 261504 - VALID, Pierro, A., Ficarelli, S., Ayhan, N., Morini, S., Raumer, L., Bartoletti, M., Mastroianni, A., Prati, F., Schivazappa, S., Cenni, P., Vocale, C., Rossini, G., Gaibani, P., Sambri, V., Landini, M.P., Lewis, R.E., Charrel, R.N., and Varani, S.
Subjects: Adult, Male, 0301 basic medicine, Microbiology (medical), Patients' follow-up, IgG avidity test, 030231 tropical medicine, 030106 microbiology, Antibodies, Viral, Bunyaviridae Infections, Antibody production, Neutralizing antibodies, Immunoglobulin G, Neutralization, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Neutralizing antibodie, medicine, Humans, Avidity, Toscana virus infection, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology, Toscana virus, Meningoencephalitis, Sandfly fever Naples virus, General Medicine, Middle Aged, medicine.disease, biology.organism_classification, Antibodies, Neutralizing, Meningitis, Viral, Virology, 3. Good health, Infectious Diseases, Immunoglobulin M, Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, Female, Antibody, Meningitis
Abstract: Among sandfly-borne pathogens, Toscana virus (TOSV) is a prominent cause of summer meningitis in Mediterranean Europe. Here, we assessed the kinetics of anti-TOSV antibodies over time in 41 patients diagnosed with TOSV-meningitis or meningoencephalitis in North-eastern Italy. Objectives: Among sandfly-borne pathogens, Toscana virus (TOSV) is a prominent cause of summer meningitis in Mediterranean Europe. Here, we assessed the kinetics of anti-TOSV antibodies over time in 41 patients diagnosed with TOSV meningitis or meningoencephalitis in northeastern Italy. Methods: Acute and follow-up serum samples were collected up to 20 months after diagnosis of TOSV infection and tested for the presence of specific antibody using immunoenzymatic and indirect immunofluorescence assays. In addition, maturation of anti-TOSV IgG over time was evaluated as well as production of neutralizing antibodies. Results: Specific IgM and IgG response was present at diagnosis in 100% of patients; TOSV-specific IgM and IgG were detected in patients' sera up to 6 and 20 months after diagnosis, respectively. The avidity index (AI) increased over the first month after infection in 100% of patients and most cases exceeded 60% by Day 30 post infection. The AI subsequently plateaued then declined at 20 months after diagnosis. Finally, neutralization assay to TOSV was performed in 217 sera collected from 41 patients; 69.6% of tested samples resulted in reactive and moderate levels of neutralizing antibodies observed during all phases of infection despite high titres of total anti-TOSV IgG. Conclusions: Specific antibody response develops rapidly and is long-lasting for neuroinvasive TOSV infection. Serodiagnosis of neuroinvasive TOSV requires simultaneous detection of specific IgM and IgG. Moderate levels of neutralizing antibodies were maintained over the study period, while the protective role of antibodies lacking neutralizing activity is unclear and requires further evaluation.
Published: 2017

41. New reverse genetics and transfection methods to rescue arboviruses in mosquito cells

Author: Raphaëlle Klitting, Xavier de Lamballerie, Antoine Nougairède, Stéphane Priet, Anna-Bella Failloux, Fabien Aubry, Thérèse Atieh, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), This work was supported by the French 'Agence Nationale de la Recherche' (grant agreement no. ANR-14-CE14–0001), by the Zikalliance project (European Union – Horizon 2020 programme under grant agreement no. 734548), the European Virus Archive goes global project (EVAg, European Union – Horizon 2020 programme under grant agreement no. 653316, IMI grant agreement no. 115760), with the assistance and financial support of IMI and the European Commission, and in-kind contributions from EFPIA partners., ANR-14-CE14-0001,RNA Vacci-Code,Ré-encodage génomique à large échelle des virus ARN pour la production de candidats vaccins atténués(2014), European Project: 734548,ZIKAlliance(2016), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), DEMESLAY GOUGAM, MARIE, Appel à projets générique - Ré-encodage génomique à large échelle des virus ARN pour la production de candidats vaccins atténués - - RNA Vacci-Code2014 - ANR-14-CE14-0001 - Appel à projets générique - VALID, A global alliance for Zika virus control and prevention - ZIKAlliance - 2016-10-01 - 2019-09-30 - 734548 - VALID, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, viruses, 030106 microbiology, lcsh:Medicine, Alphavirus, Arbovirus Infections, medicine.disease_cause, Transfection, Virus Replication, Article, 03 medical and health sciences, RNA Virus Infections, medicine, Animals, Humans, RNA Viruses, Chikungunya, lcsh:Science, Subgenomic mRNA, Genetics, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Multidisciplinary, biology, lcsh:R, Yellow fever, fungi, virus diseases, Japanese encephalitis, medicine.disease, biology.organism_classification, Virology, Reverse genetics, Reverse Genetics, 3. Good health, Flavivirus, 030104 developmental biology, Culicidae, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, lcsh:Q, Arboviruses
Abstract: International audience; Reverse genetics is a critical tool to decrypt the biological properties of arboviruses. However, whilst reverse genetics methods have been usually applied to vertebrate cells, their use in insect cells remains uncommon due to the conjunction of laborious molecular biology techniques and of specific difficulties surrounding the transfection of such cells. To leverage reverse genetics studies in both vertebrate and mosquito cells, we designed an improved DNA transfection protocol for insect cells and then demonstrated that the simple and flexible ISA (Infectious Subgenomic Amplicons) reverse-genetics method can be efficiently applied to both mammalian and mosquito cells to generate in days recombinant infectious positive-stranded RNA viruses belonging to genera Flavivirus (Japanese encephalitis, Yellow fever, West Nile and Zika viruses) and Alphavirus (Chikungunya virus). This method represents an effective option to potentially overcome technological issues related to the study of arboviruses. Arboviruses (Arthropod-borne viruses) constitute a large group of viruses carried and spread by blood feeding arthropods, especially mosquitoes, ticks and sandflies. They can be transmitted to a variety of vertebrates and are responsible for significant morbidity and mortality amongst humans and farmed animals globally. Arboviral diseases in humans range from mild febrile illness to severe encephalitis or haemorrhagic fever 1. Iterative outbreaks worldwide over the past decades have highlighted the emergence or re-emergence potential of arboviruses, which are thus considered to be significant public and animal health threats 1–3. Most arboviruses of public health importance are single-stranded RNA viruses belonging to the families Flavi-, Toga-, or Bunyaviridae. Research focusing on arboviruses knew dramatic progress thanks to the use of reverse genetics systems allowing the study of virus life cycles, understanding the effect of specific mutations on viral replication or pathogen-esis, and designing new vaccine strategies 4,5. However, these reverse genetics systems focused to date almost exclusively on mammalian cells. Since arboviruses life cycle involves replication in both invertebrate vectors and vertebrate hosts, a simple and universal reverse genetics method allowing producing recombinant arboviruses in both vertebrate and arthropod cells would obviously facilitate the study of arbovirus biological properties, of their genomic evolution or cell interactions and restrictions. This awaited knowledge could provide in the future the key elements needed to predict outbreaks and to find efficient therapy. Unfortunately, although most reverse genetics systems proved to be efficient to recover arboviruses from vertebrate cell lines (for reviews see 4,5), very few studies have reported such systems for arthropod cells and especially for cells from Aedes mosquitoes , one of the most important arbovirus vectors globally 6. Indeed, reverse genetics systems designed for positive-sense single-stranded RNA viruses in Aedes mosquito cells are typically based to date on the lipofection or electroporation of synthetic capped RNA transcripts generated by in vitro transcription from SP6-7–9 or T7 promoter-driven 10–16 full-length viral cDNA constructs. A second system only used marginally and based on the direct transfection of a T7 promoter-driven infectious clone in an Aedes mosquito cell line stably expressing the T7 RNA polymerase was established to produce a minireplicon of the Bunyamwera negative-strand RNA virus 17. Nevertheless, these reverse genetics systems suffer from two main limitations. First, the construction of full-length viral cDNA clones remains difficult and time consuming. To circumvent this issue, we recently developed a novel bacterium-free method of reverse genetics called ISA (Infectious Subgenomic Amplicons) 18. The
Published: 2017

42. High Rates of Neutralizing Antibodies to Toscana and Sandfly Fever Sicilian Viruses in Livestock, Kosovo

Author: Kurtesh Sherifi, Rémi N. Charrel, Kristaq Berxholi, Arber Taraku, Nazli Ayhan, Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), University of Prishtina, Agricultural University of Tirana, This work was supported in part by the European Virus Archive Goes Global project, which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 653316, the EDENext FP7-no. 261504 European Union project and this paper is catalogued by the EDENext Steering Committee as EDENext469 (http://www.edenext.eu). The work of N.A. and R.N.C. was conducted under the frame of EurNegVec COST Action TD1303. N.A. is supported by the Fondation Mediterranee Infection., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), BUISINE, Soline, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Biology and control of vector-borne infections in Europe - EDENEXT - - EC:FP7:HEALTH2011-01-01 - 2015-06-30 - 261504 - VALID
Subjects: 0301 basic medicine, Phlebovirus, Epidemiology, Kosovo, vector-borne infections, lcsh:Medicine, Mediterranean, Antibodies, Viral, 0302 clinical medicine, Phlebotomus Fever, Sandfly Fever Sicilian Virus, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Toscana virus, biology, Incidence, Dispatch, 3. Good health, Infectious Diseases, Epidemiological Monitoring, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Bunyaviridae, Microbiology (medical), Livestock, 030231 tropical medicine, Arbovirus, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Balkan, medicine, Animals, Humans, lcsh:RC109-216, viruses, sandfly fever Sicilian virus, Sheep, lcsh:R, Sandfly fever Naples virus, biology.organism_classification, medicine.disease, Antibodies, Neutralizing, Virology, Insect Vectors, Sandfly, 030104 developmental biology, arbovirus, High Rates of Neutralizing Antibodies to Toscana and Sandfly Fever Sicilian Viruses in Livestock, Kosovo, Cattle, Psychodidae, sand flies
Abstract: Kurtesh Sherifi and Rémi N. Charrel contributed equally to this article; International audience; Toscana and sandfly fever Sicilian viruses (TOSV and SFSV, respectively), both transmitted by sand flies, are prominent human pathogens in the Old World. Of 1,086 serum samples collected from cattle and sheep during 2013 in various regions of Kosovo (Balkan Peninsula), 4.7% and 53.4% had neutralizing antibodies against TOSV and SFSV, respectively.
Published: 2017

43. Practical Guidelines for Studies on Sandfly-Borne Phleboviruses: Part I: Important Points to Consider Ante Field Work

Author: Rémi N. Charrel, Fátima Amaro, Bulent Alten, Koray Ergünay, Hartwig P. Huemer, Nazli Ayhan, Gernot Walder, Sara Moutailler, Jorian Prudhomme, Amal Baklouti, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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]), Instituto Nacional de Saùde Dr Ricardo Jorge [Portugal] (INSA), Hacettepe University = Hacettepe Üniversitesi, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Innsbruck Medical University [Austria] (IMU), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Innsbruck Medical University = Medizinische Universität Innsbruck (IMU), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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 la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)
Subjects: Phlebovirus, 0301 basic medicine, Veterinary medicine, MESH: Phlebovirus, Bunyaviridae, 030231 tropical medicine, arbovirus(es), MESH: Insect Vectors, Biology, Microbiology, Data type, Field (computer science), 03 medical and health sciences, 0302 clinical medicine, sand fly (flies), MESH: Psychodidae, Virology, Animals, MESH: Phylogeny, Phylogeny, vector-borne, Infecções Sistémicas e Zoonoses, Toscana virus, Laboratory methods, Guideline, biology.organism_classification, Insect Vectors, Sandfly, 030104 developmental biology, Infectious Diseases, Work (electrical), Risk analysis (engineering), Research Design, Vector-borne, Sand fly, Arbovirus(es), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Psychodidae, Field studies, Animal Distribution, field studies
Abstract: The purpose of this review is to provide practical information to help researchers intending to perform "from field to laboratory" studies on phleboviruses transmitted by sandflies. This guideline addresses the different steps to be considered starting from the field collection of sandflies to the laboratory techniques aiming at the detection, isolation, and characterization of sandfly-borne phleboviruses. In this guideline article, we address the impact of various types of data for an optimal organization of the field work intending to collect wildlife sandflies for subsequent virology studies. Analysis of different data sets should result in the geographic positioning of the trapping stations. The overall planning, the equipment and tools needed, the manpower to be deployed, and the logistics to be anticipated and set up should be organized according to the objectives of the field study for optimal efficiency. This work was done under the frame of EurNegVec COST Action TD1303. This work was supported, in part, by (1) the European 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 and by (2) the EDENext FP7- n 261504 EU project; this article is cataloged by the EDENext Steering Committee as EDENext453 (www.edenext.eu). info:eu-repo/semantics/publishedVersion
Published: 2017

44. Epidemiology of Chikungunya Virus Outbreaks in Guadeloupe and Martinique, 2014: An Observational Study in Volunteer Blood Donors

Author: Isabelle Leparc-Goffart, Rachid Djoudi, Xavier de Lamballerie, Rémi N. Charrel, Pierre Gallian, Pascale Richard, Françoise Maire, Jacques Chiaroni, Pierre Tiberghien, Olivier Flusin, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Etablissement Français du Sang [La Plaine Saint-Denis] (EFS), Université des Antilles et de la Guyane - UFR des sciences médicales (UAG UFR SM), Université des Antilles et de la Guyane (UAG), Etablissement français du sang [Fort-de-France, Martinique] (EFS Martinique), French National Reference Centre for Arboviruses, Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: ENIVD, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), IRBA Armed Forces Biomedical Research Institute, Dubois Frid, Caroline, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, European Centre for Disease Prevention and Control - ENIVD - INCOMING, and Institut de Recherche Biomédicale des Armées (IRBA)
Subjects: 0301 basic medicine, Male, Volunteers, RNA viruses, Viral Diseases, Physiology, Attack rate, medicine.disease_cause, Antibodies, Viral, Pathology and Laboratory Medicine, Vascular Medicine, Geographical locations, 0302 clinical medicine, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine and Health Sciences, Medicine, Chikungunya, Prospective Studies, Guadeloupe, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Islands, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Incidence (epidemiology), lcsh:Public aspects of medicine, Hematology, Middle Aged, 3. Good health, Body Fluids, Blood, Infectious Diseases, Medical Microbiology, Viral Pathogens, Viruses, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Chikungunya infection, Pathogens, Anatomy, Martinique, Chikungunya virus, Research Article, Neglected Tropical Diseases, Adult, lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, Alphaviruses, 030231 tropical medicine, Population, Context (language use), Blood donors, Microbiology, Togaviruses, 03 medical and health sciences, Young Adult, Seroprevalence, Humans, Viremia, Blood Donation, education, Microbial Pathogens, Aged, Retrospective Studies, Caribbean, Biology and life sciences, business.industry, Public Health, Environmental and Occupational Health, Organisms, Outbreak, lcsh:RA1-1270, Tropical Diseases, Virology, Health Care, 030104 developmental biology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, North America, Chikungunya Fever, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Blood groups, People and places, business
Abstract: Background During Dec-2013, a chikungunya virus (CHIKV) outbreak was first detected in the French-West Indies. Subsequently, the virus dispersed to other Caribbean islands, continental America and many islands in the Pacific Ocean. Previous estimates of the attack rate were based on declaration of clinically suspected cases. Methods/Principal findings Individual testing for CHIKV RNA of all (n = 16,386) blood donations between Feb-24th 2014 and Jan-31st 2015 identified 0·36% and 0·42% of positives in Guadeloupe and Martinique, respectively. The incidence curves faithfully correlated with those of suspected clinical cases in the general population of Guadeloupe (abrupt epidemic peak), but not in Martinique (flatter epidemic growth). No significant relationship was identified between CHIKV RNA detection and age-classes or blood groups. Prospective (Feb-2014 to Jan-2015; n = 9,506) and retrospective (Aug-2013 to Feb-2014; n = 6,559) seroepidemiological surveys in blood donors identified a final seroprevalence of 48·1% in Guadeloupe and 41·9% in Martinique. Retrospective survey also suggested the absence or limited "silent" CHIKV circulation before the outbreak. Parameters associated with increased seroprevalence were: Gender (M>F), KEL-1, [RH+1/KEL-1], [A/RH+1] and [A/RH+1/KEL-1] blood groups in Martiniquan donors. A simulation model based on observed incidence and actual seroprevalence values predicted 2·5 and 2·3 days of asymptomatic viraemia in Martiniquan and Guadeloupian blood donors respectively. Conclusions/Significance This study, implemented promptly with relatively limited logistical requirements during CHIKV emergence in the Caribbean, provided unique information regarding retrospective and prospective epidemiology, infection risk factors and natural history of the disease. In the stressful context of emerging infectious disease outbreaks, blood donor-based studies can serve as robust and cost-effective first-line tools for public health surveys., Author Summary Chikungunya virus (CHIKV) is an emerging mosquito-borne arbovirus responsible of a large outbreak since December 2013 in the Americas from French islands in the Caribbean. Documentation of the epidemic was based on the survey of clinically suspected cases, providing limited information on the incidence of the disease overtime and the herd immunity of the general population at the end of the outbreak. Our study improved blood donors specimen collection and data obtained from the Nucleic Acid Testing (NAT) screening implemented during the outbreak in order to prevent CHIKV transmission by blood products. After an 11 month follow up, we determine for Martinique and Guadeloupe islands the CHIKV-RNA positive rate: 0.42% and 0.36% respectively and the final IgG seroprevalence: 41.2% and 48.1%. Using a simulation model, we estimate the CHIKV duration of asymptomatic viremia to be between 2.3 and 2.5 days. Our findings will help in the comprehension of the natural history of infection and provide helpful data for prevention of Transfusion transmitted infections. Our study provides evidence that monitoring of Chikungunya infection based on NAT screening of voluntary blood donors can be implemented rapidly and provides real-time epidemiological information. This should be of specific relevance to the case of epidemics caused by viral infections with high numbers of asymptomatic forms such as observed with the currently emerging Zika virus.
Published: 2017

45. G+C content differs in conserved and variable amino acid residues of flaviviruses and other evolutionary groups

Author: Klitting, Raphaëlle, Gould, Ernest Andrew, de Lamballerie, Xavier, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), ANR-14-CE14-0001,RNA Vacci-Code,Ré-encodage génomique à large échelle des virus ARN pour la production de candidats vaccins atténués(2014), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Klitting, Raphaëlle, Appel à projets générique - Ré-encodage génomique à large échelle des virus ARN pour la production de candidats vaccins atténués - - RNA Vacci-Code2014 - ANR-14-CE14-0001 - Appel à projets générique - VALID, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)
Subjects: Microbiology (medical), Base Composition, GC content, Evolution, viruses, Flavivirus, Microbiology, G+C content, Evolution, Molecular, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Genetics, Amino Acid Sequence, Amino Acids, Molecular Biology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Ecology, Evolution, Behavior and Systematics, Phylogeny
Abstract: International audience; Flaviviruses are small RNA viruses that exhibit genetic and ecological diversity and a wide range of G+C content (GC%). We discovered that, amongst flaviviruses, the GC% of nucleotides encoding conserved amino acid (AA) residues was consistently higher than that of nucleotides encoding variable AAs. This intriguing phenomenon was also identified for a wide range of other viruses, and some non-viral evolutionary groups. Here, we analyse the possible mechanisms underlying this imbalanced nucleotide content (in particular the role of the specific G content and the AA composition in flaviviral genomes) and discuss its evolutionary implications. Our findings suggest that one of the most simple characteristics of the genetic code (i.e., the G or G+C content of codons) is linked with the evolutionary behavior of the corresponding encoded AAs.
Published: 2016

46. How Did Zika Virus Emerge in the Pacific Islands and Latin America?

Author: Xavier de Lamballerie, Didier Musso, Rémi N. Charrel, Stephen J. Seligman, Michael W. Gaunt, Andrew K. I. Falconar, John H.-O. Pettersson, Vegard Eldholm, Antoine Nougairède, Åke Lundkvist, Ernest A. Gould, Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health [Oslo] (NIPH), Department of Medical Biochemistry and Microbiology, Uppsala University, St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Departmento de Medicina, Universidad del Norte, Barranquilla, London School of Hygiene and Tropical Medicine (LSHTM), 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 Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Hôpital Nord [CHU - APHM], European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), 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)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), COMBE, Isabelle, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Preparedness, Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidisciplinary Approaches - PREDEMICS - - EC:FP7:HEALTH2011-11-01 - 2016-10-31 - 278433 - VALID
Subjects: 0301 basic medicine, Microcephaly, Latin Americans, Guillain-Barre Syndrome, Pacific Islands, Genome, Microbiology, Microbiology in the medical area, Zika virus, 03 medical and health sciences, Aedes, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Mikrobiologi inom det medicinska området, medicine, Animals, Humans, zika virus, Epidemics, Genetics, [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, biology, Phylogenetic tree, Zika Virus Infection, Opinion/Hypothesis, 16. Peace & justice, biology.organism_classification, medicine.disease, Reverse genetics, QR1-502, 3. Good health, Flavivirus, 030104 developmental biology, Vector (epidemiology), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Americas
Abstract: The unexpected emergence of Zika virus (ZIKV) in the Pacific Islands and Latin America and its association with congenital Zika virus syndrome (CZVS) (which includes microcephaly) and Guillain-Barré syndrome (GBS) have stimulated wide-ranging research. High densities of susceptible Aedes spp., immunologically naive human populations, global population growth with increased urbanization, and escalation of global transportation of humans and commercial goods carrying vectors and ZIKV undoubtedly enhanced the emergence of ZIKV. However, flavivirus mutations accumulate with time, increasing the likelihood that genetic viral differences are determinants of change in viral phenotype. Based on comparative ZIKV complete genome phylogenetic analyses and temporal estimates, we identify amino acid substitutions that may be associated with increased viral epidemicity, CZVS, and GBS. Reverse genetics, vector competence, and seroepidemiological studies will test our hypothesis that these amino acid substitutions are determinants of epidemic and neurotropic ZIKV emergence.
Published: 2016

47. Utilisation of ISA Reverse Genetics and Large-Scale Random Codon Re-Encoding to Produce Attenuated Strains of Tick-Borne Encephalitis Virus within Days

Author: Lauriane, de Fabritus, Antoine, Nougairède, Fabien, Aubry, Ernest A, Gould, Xavier, de Lamballerie, Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), ANR-14-CE14-0001,RNA Vacci-Code,Ré-encodage génomique à large échelle des virus ARN pour la production de candidats vaccins atténués(2014), European Project: 278433,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,PREDEMICS(2011), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: RNA viruses, Physiology, viruses, lcsh:Medicine, Viral Nonstructural Proteins, Antibodies, Viral, Pathology and Laboratory Medicine, Mouse models, Biochemistry, Dengue virus, Mice, Cricetinae, Immune Physiology, Medicine and Health Sciences, Enzyme-linked immunoassays, lcsh:Science, Immune System Proteins, Serine Endopeptidases, Animal Models, Medical Microbiology, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Pathogens, Encephalitis, Tick-Borne, RNA Helicases, Research Article, Immunology, Vaccines, Attenuated, Research and Analysis Methods, Microbiology, Antibodies, Cell Line, Encephalitis Viruses, Tick-Borne, Open Reading Frames, Model Organisms, Extraction techniques, Animals, Humans, Codon, Immunoassays, Molecular Biology Techniques, Microbial Pathogens, Molecular Biology, Biology and life sciences, Flaviviruses, lcsh:R, Organisms, Viral pathogens, Proteins, Viral Vaccines, Antibodies, Neutralizing, Survival Analysis, Reverse Genetics, RNA extraction, Mice, Inbred C57BL, Japanese encephalitis virus, Mutation, Immunologic Techniques, lcsh:Q, Tick-borne encephalitis virus, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, Cloning
Abstract: International audience; Large-scale codon re-encoding is a new method of attenuating RNA viruses. However, the use of infectious clones to generate attenuated viruses has inherent technical problems. We previously developed a bacterium-free reverse genetics protocol, designated ISA, and now combined it with large-scale random codon-re-encoding method to produce attenuated tick-borne encephalitis virus (TBEV), a pathogenic flavivirus which causes febrile illness and encephalitis in humans. We produced wild-type (WT) and two re-encoded TBEVs, containing 273 or 273+284 synonymous mutations in the NS5 and NS5+NS3 coding regions respectively. Both re-encoded viruses were attenuated when compared with WT virus using a laboratory mouse model and the relative level of attenuation increased with the degree of re-encoding. Moreover, all infected animals produced neutralizing antibodies. This novel, rapid and efficient approach to engineering attenuated viruses could potentially expedite the development of safe and effective new-generation live attenuated vaccines.
Published: 2016

48. Seroprevalence of Toscana virus in dogs from Corsica, France

Author: Rémi N. Charrel, Jean-Lou Marié, Sébastien Grech-Angelini, Bernard Davoust, Mustapha Dahmani, Sulaf Alwassouf, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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), Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Recherches sur le Développement de l'Elevage (LRDE), Institut National de la Recherche Agronomique (INRA), Direction Régionale du Service de Santé des Armées (DRSSA - Toulon), European Virus Archive goes Global (EVAg) project - European Union's Horizon research and innovation programme [653316], AMIDEX project - 'Investissements d'Avenir' French Government programme [ANR-11-IDEX-0001-02], ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Unité de recherche Développement de l'Elevage (LRDE), ANR-11-IDEX-0001-02/11-IDEX-0001,AMIDEX,AMIDEX(2011), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Dahmani, Mustapha, COMBE, Isabelle, INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Biology and control of vector-borne infections in Europe - EDENEXT - - EC:FP7:HEALTH2011-01-01 - 2015-06-30 - 261504 - VALID
Subjects: 0301 basic medicine, Male, 030231 tropical medicine, 030106 microbiology, Short Report, Corsica, Bunyaviridae Infections, Antibodies, Viral, Arbovirus, 03 medical and health sciences, 0302 clinical medicine, Dogs, Seroepidemiologic Studies, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Dog, Seroprevalence, Animals, Humans, Meningitis, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Islands, Toscana virus, biology, Geography, Aseptic meningitis, Sandfly fever Naples virus, medicine.disease, biology.organism_classification, Virology, 3. Good health, France, Sand fly, Phlebotomus, Infectious Diseases, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Sentinel Species, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Parasitology, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Bunyaviridae, Encephalitis
Abstract: Background: Toscana virus (TOSV) is an arbovirus belonging to the Bunyaviridae, a family of negative-stranded, enveloped RNA viruses. The virus can be transmitted to humans through the bite of an infected female sand fly of the genus Phlebotomus. Infections are usually asymptomatic but the virus is known to cause aseptic meningitis and/or meningo-encephalitis in the Mediterranean countries. Dogs are good sentinels for detection of viral circulation and are more easily accessible than wild animals.Findings: In 2013 and 2014, we collected sera from 231 adult dogs living in 26 counties in two departments in Corsica, a French island in the Mediterranean. The virus microneutralization-based seroprevalence assay revealed a seropositivity of 3.9 % dogs on the eastern coast of Corsica.Conclusions: Our study confirms the circulation of TOSV in Corsica. Accordingly, in geographical areas where dogs possess TOSV neutralizing antibodies, direct and indirect TOSV diagnosis should be implemented in patients presenting with febrile illnesses and central nervous system infections such as meningitis and encephalitis.
Published: 2016

49. Development of an improved RT-qPCR Assay for detection of Japanese encephalitis virus (JEV) RNA including a systematic review and comprehensive comparison with published methods

Author: Paul N. Newton, Viengmon Davong, Géraldine Piorkowski, Manivanh Vongsouvath, Onanong Sengvilaipaseuth, Phonepasith Panyanouvong, Audrey Dubot-Pérès, Malavanh Vongsouvath, Jeremy A. Garson, Tehmina Bharucha, Xavier de Lamballerie, Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, Departments of Infectious Diseases and Microbiology [London, UK], Royal Free Hospital [London, UK], Division of Infection and Immunity [London, UK], University College of London [London] (UCL), 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), National Transfusion Microbiology Laboratories [London, UK], NHS Blood and Transplant [London, UK], Centre for Tropical Medicine and Global Health [Oxford, UK], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford [Oxford]-University of Oxford [Oxford], London School of Hygiene and Tropical Medicine (LSHTM), This study was supported by the Wellcome Trust of Great Britain, IRD to PNN and by the European Union’s Horizon 2020 research and innovation programme EVAg under grant agreement N˚ 653316 to XdL., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), University of Oxford-University of Oxford, BUISINE, Soline, and European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID
Subjects: RNA viruses, Central Nervous System, 0301 basic medicine, Serial dilution, viruses, lcsh:Medicine, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Nervous System, Biochemistry, Database and Informatics Methods, 0302 clinical medicine, Genotype, lcsh:Science, Pathology and laboratory medicine, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Encephalitis Virus, Japanese, Multidisciplinary, Reverse Transcriptase Polymerase Chain Reaction, Physics, Medical microbiology, Research Assessment, 3. Good health, Nucleic acids, GenBank, Physical Sciences, Viruses, Nucleic acid thermodynamics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA annealing, Pathogens, Anatomy, West Nile virus, Sequence Analysis, Encephalitis, Research Article, Optimization, Asia, Systematic Reviews, Bioinformatics, In silico, Annealing (genetics), 030231 tropical medicine, Biophysics, Biology, Research and Analysis Methods, Real-Time Polymerase Chain Reaction, Microbiology, Virus, 03 medical and health sciences, medicine, Humans, Molecular Biology Techniques, Encephalitis, Japanese, Molecular Biology, Medicine and health sciences, Flaviviruses, lcsh:R, Organisms, Viral pathogens, Biology and Life Sciences, RNA, Reverse Transcriptase-Polymerase Chain Reaction, Japanese encephalitis, medicine.disease, Virology, Microbial pathogens, 030104 developmental biology, lcsh:Q, Sequence Alignment, Mathematics
Abstract: Background Japanese encephalitis virus (JEV) is a major cause of encephalitis in Asia, and the commonest cause of mosquito-borne encephalitis worldwide. Detection of JEV RNA remains challenging due to the characteristic brief and low viraemia, with 0–25% of patients positive, and the mainstay of diagnosis remains detection of anti-JEV IgM antibody. Methods We performed a systematic review of published RT-PCR protocols, and evaluated them in silico and in vitro alongside new primers and probes designed using a multiple genome alignment of all JEV strains >9,000nt from GenBank, downloaded from the NCBI website (November 2016). The new assays included pan-genotype and genotype specific assays targeting genotypes 1 and 3. Results Ten RT-qPCR assays were compared, a pre-existing in-house assay, three published assays and six newly designed assays, using serial RNA dilutions. We selected three assays, one published and two novel assays, with the lowest limit of detection (LOD) for further optimisation and validation. One of the novel assays, detecting NS2A, showed the best results, with LOD approximately 4 copies/ reaction, and no cross-reaction on testing closely related viruses in the JEV serocomplex, West Nile Virus and St. Louis Virus. The optimised assays were validated in consecutive patients with central nervous system infections admitted to hospitals in Laos, testing paired CSF and serum samples. Conclusions We succeeded in developing a JEV specific RT-qPCR assay with at least 1 log10 improved sensitivity as compared to existing assays. Further evaluation is required, field-testing the assay in a larger group of patients.
Published: 2018

50. InSiDDe: A Server for Designing Artificial Disordered Proteins

Author: Sonia Longhi, Stefano Gianni, Antoine Schramm, Philippe Lieutaud, Christophe Bignon, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Biochemical Sciences 'Rossi Fanelli', Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), This work was carried out with the partial support from the following agencies: European program H2020 under the EVAg Research Infrastructure (grant agreement 653316) (CB), CNRS (CB, SL), Italian Ministero dell’Istruzione dell’Università e della Ricerca (Progetto di Interesse 'Invecchiamento' to S.G.) and Sapienza University of Rome (C26A155S48 and B52F16003410005 to S.G). It was also supported by the CNRS., We wish to thank Zsuzsanna Dosztanyi (Eötvös Loránd University, Budapest, Hungary) for granting us access to IUPred in local mode, Helena Berglund (Protein Science Facility, Karolinska Institutet, Sweden) for kindly providing us with the pTH24 derivative encoding the TEV protease, and Arie Geerlof (EMBL) for providing the pETG-20A plasmid. We also thank Vincent Bayle (AFMB lab) for technical help in deploying InSiDDe on the AFMB server. AS is supported by a PhD fellowship from the French Ministry of National Education, Research and Technology., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' [Rome]
Subjects: folding, Models, Molecular, 0301 basic medicine, Protein Folding, binding, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Computer science, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Gene Expression, Protein Engineering, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, 01 natural sciences, lcsh:Chemistry, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, NTAIL, Artificial protein, Cloning, Molecular, lcsh:QH301-705.5, Spectroscopy, artificial protein, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Sequence, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], experiments, General Medicine, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Computer Science Applications, XD, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], intrinsically disordered proteins, IUPred, recombinant protein, Python3, paramyxovirus, E. coli, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Recombinant Fusion Proteins, In silico, Genetic Vectors, Computational biology, 010402 general chemistry, Intrinsically disordered proteins, Article, Catalysis, Inorganic Chemistry, Set (abstract data type), 03 medical and health sciences, Molecular recognition, Escherichia coli, Amino Acid Sequence, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Physical and Theoretical Chemistry, Molecular Biology, Organic Chemistry, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Fusion protein, 0104 chemical sciences, 030104 developmental biology, lcsh:Biology (General), lcsh:QD1-999, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Software
Abstract: International audience; InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0.55 to 0.95 with 0.05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0.6 designed by InSiDDe could be recombinantly expressed in E. coli at high levels without degradation when fused to a natural molecular recognition element (MoRE). In addition, the artificial fusion protein exhibited the expected behavior in terms of binding modulation of the specific partner recognized by the MoRE. To the best of our knowledge, InSiDDe is the first publicly available software for the design of intrinsically disordered protein (IDP) sequences. InSiDDE is publicly available online.
Published: 2017

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