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Study of Chikungunya Virus Entry and Host Response to Infection Marie Cresson

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Study of chikungunya virus entry and host response to infection Marie Cresson To cite this version: Marie Cresson. Study of chikungunya virus entry and host response to infection. Virology. Uni- versité de Lyon; Institut Pasteur of Shanghai. Chinese Academy of Sciences, 2019. English. NNT : 2019LYSE1050. tel-03270900 HAL Id: tel-03270900 https://tel.archives-ouvertes.fr/tel-03270900 Submitted on 25 Jun 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. N°d’ordre NNT : 2019LYSE1050 THESE de DOCTORAT DE L’UNIVERSITE DE LYON opérée au sein de l’Université Claude Bernard Lyon 1 Ecole Doctorale N° 341 – E2M2 Evolution, Ecosystèmes, Microbiologie, Modélisation Spécialité de doctorat : Biologie Discipline : Virologie Soutenue publiquement le 15/04/2019, par : Marie Cresson Study of chikungunya virus entry and host response to infection Devant le jury composé de : Choumet Valérie - Chargée de recherche - Institut Pasteur Paris Rapporteure Meng Guangxun - Professeur - Institut Pasteur Shanghai Rapporteur Lozach Pierre-Yves - Chargé de recherche - CHU d'Heidelberg Rapporteur Kretz Carole - Professeure - Université Claude Bernard Lyon 1 Examinatrice Roques Pierre - Directeur de recherche - CEA Fontenay-aux-Roses Examinateur Maisse-Paradisi Carine - Chargée de recherche - INRA Directrice de thèse Lavillette Dimitri - Professeur - Institut Pasteur Shanghai Co-directeur de thèse 2 UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M. le Professeur Frédéric FLEURY Président du Conseil Académique M. le Professeur Hamda BEN HADID Vice-président du Conseil d’Administration M. le Professeur Didier REVEL Vice-président du Conseil Formation et Vie M. le Professeur Philippe CHEVALIER Universitaire M. Fabrice VALLÉE Vice-président de la Commission Recherche M. Alain HELLEU Directeur Général des Services COMPOSANTES SANTE Faculté de Médecine Lyon Est – Claude Bernard Directeur : M. le Professeur J. ETIENNE Faculté de Médecine et de Maïeutique Lyon Sud – Charles Directeur : Mme la Professeure C. BURILLON Mérieux Directeur : M. le Professeur D. BOURGEOIS Faculté d’Odontologie Directeur : Mme la Professeure C. Institut des Sciences Pharmaceutiques et Biologiques VINCIGUERRA Institut des Sciences et Techniques de la Réadaptation Directeur : M. le Professeur Y. MATILLON Département de formation et Centre de Recherche en Directeur : Mme la Professeure A-M. SCHOTT Biologie Humaine COMPOSANTES ET DEPARTEMENTS DE SCIENCES ET TECHNOLOGIE Faculté des Sciences et Technologies Directeur : M. F. DE MARCHI Département Biologie Directeur : M. le Professeur F. THEVENARD Département Chimie Biochimie Directeur : Mme C. FELIX Département GEP Directeur : M. Hassan HAMMOURI Département Informatique Directeur : M. le Professeur S. AKKOUCHE Département Mathématiques Directeur : M. le Professeur G. TOMANOV Département Mécanique Directeur : M. le Professeur H. BEN HADID Département Physique Directeur : M. le Professeur J-C PLENET UFR Sciences et Techniques des Activités Physiques et Directeur : M. Y.VANPOULLE Sportives Directeur : M. B. GUIDERDONI Observatoire des Sciences de l’Univers de Lyon Directeur : M. le Professeur E.PERRIN Polytech Lyon Directeur : M. G. PIGNAULT Ecole Supérieure de Chimie Physique Electronique Directeur : M. le Professeur C. VITON Institut Universitaire de Technologie de Lyon 1 Directeur : M. le Professeur A. MOUGNIOTTE Ecole Supérieure du Professorat et de l’Education Directeur : M. N. LEBOISNE Institut de Science Financière et d'Assurances 3 4 This work has been realized in the Viral Infections and Comparative Pathology (IVPC) joined research unit from INRA, Lyon 1 university and EPHE in Lyon (France) and the Pasteur Institute of Shanghai - Chinese Academy of Sciences in Shanghai (China). 5 Remerciements Aux membres du jury pour avoir évalué et jugé mon travail ainsi que pour leurs questions pertinentes et la discussion durant ma soutenance de thèse. À la Pr Carole Kretz d’avoir accepté de présider le jury. Aux Dr Valérie Choumet, Dr Pierre-Yves Lozach et Pr Guangxun Meng pour avoir lu en profondeur et fait une analyse critique et constructive de ce manuscrit. À la Pr Carole Kretz et au Dr Pierre Roques pour leurs questions et nos échanges lors de la soutenance. Aux Dr Branka Horvat, Dr Fabrice Vavre, Dr Nathalie Davoust, Pr Jin Zhong pour leurs conseils et leurs encouragements lors des comités de suivi de thèse. Cette thèse et mes voyages à Shanghai ont été possibles, entre autres, grâce à la bourse doctorale Calmette et Yersin du réseau international des instituts Pasteur, aux bourses doctorales du gouvernement chinois et à la bourse de mobilité Cai Yuanpei de Campus France. À Dimitri et à Carine pour m’avoir permis de réaliser cette thèse entre Lyon et Shanghai qui a été très riche d’enseignements aussi bien d’un point de vue scientifique qu’humain. Ces 4 années ont été remplies d’apprentissages, de belles rencontres et de découvertes. Merci à toi, Carine, pour ta présence, ton accompagnement et tout ce que tu as partagé et m’as appris durant ces 4 années. Merci Dimitri de m’avoir permis de partager cette expérience chinoise à Shanghai en m’embarquant dans ce projet. J’ai eu la chance de vivre une expérience incroyable, en parallèle de mon apprentissage scientifique, en découvrant un pays, une culture et une autre manière de travailler. Merci de m’avoir soutenu dans mes démarches et d’avoir partagé tes connaissances avec moi. Aux Alphagirls, Carine, Lucie, Céline, Catherine et Aurélie pour leur bonne humeur, nos discussions scientifiques ou non et les heures passées dans les labos. À Lucie, je ne vais pas pouvoir écrire en détails tout ce pour quoi je te remercie, cela prendrait des pages… Merci pour avoir partagé ta bonne humeur, ta science et ta folie avec moi tous les jours durant ces années. Merci d’avoir été présente pour discuter de nos questions et doutes sur nos expériences et nos projets. Merci d’avoir été présente pour partager les craquages de fin de journée, les milliers conneries et les apéros. Merci d’avoir partagé des discussions sur nos futurs, sur la vie et surtout sur la nourriture (avec une préférence pour la nourriture chinoise quand même). Ta gentillesse et ton altruisme ont déteint sur moi, du moins je l’espère car je pense être devenue une meilleure personne en partageant ces moments avec toi. À Céline pour m’avoir aidé dans mes expériences, d’avoir compris ce que je voulais faire à chaque fois et d’avoir partagé ta bonne humeur. À Catherine, pour ta joie et ta bonne humeur au quotidien, ne change rien ! À Aurélie, pour avoir su si vite t’intégrer dans notre équipe, pour ta soif d’apprendre et de comprendre la biologie et la virologie et ta bonne humeur. Merci à vous 4, Carine, Céline, Catherine et Aurélie, pour nous avoir suivi Lucie et moi en Chine pour rencontrer l’équipe à Shanghai et découvrir notre environnement de vie et de travail. Évidemment, Céline ne va pas sans, Maitre Daouda, dit Kathy, merci à toi pour les belles rigolades, chansonnettes et bonne humeur dans le bureau. Merci pour nos discussions et tes conseils précieux pour les manips. À Maryline pour ta gentillesse, ton écoute, nos discussions et ta culture générale people inégalable. Tu es la grande sœur au laboratoire toujours prête à donner des conseils. À Wil pour ces heures passées à discuter en culture cellulaire, pour ton soutien et pour ton aide. Je n’arriverai pas à écrire des remerciements aussi longs que les tiens ni à faire des jeux de mots aussi nuls drôles, mais je tenais à te remercier pour m’avoir remotivé les jours de doutes, pour avoir partagé ta passion pour la recherche, ton savoir scientifique et ta paraformaldéhyde. À Marie-Pierre, Maxime, Barbara V, Fabienne, Barbara G, qui se sont occupés du laboratoire P3 durant mes années au laboratoire et qui m’ont permis de me former à la manipulation des pathogènes, d’y passer quelques centaines d’heures à chanter à tue-tête et d’apprendre à dompter un autoclave. Et un ENORME merci à tous les gens du l’IVPC que je n’ai pas cité pour leur bonne humeur, leur aide, leur écoute. Dans le désordre, Fabienne, Marie-Pierre, Alexandra, Saw-See, Barbara G, Angélique, Sylvie, Sophie, Christine, Fred, Maxime, Barbara V, Caroline, Jean-Michel, Marlène, François, Margot, Justine, Margaux, Claire, Etienne, Clémentine, Julien, Nader… À toute la bande de chercheurs/ingénieurs -en biérologie- de Lyon, dans le désordre, Maryline, Nicolas B, Lucie, Wilhelm, Marie, Stéphane, Lucile, Claire, Nicolas D, Marlène… Merci pour tous ces bons moments passés ensemble. À toute l’équipe de Shanghai pour leur accueil et leur aide. À Émilie, Luyan, Li, Wuning et tous les autres pour m’avoir accompagné durant mes premiers pas à Shanghai, expliqué des centaines de choses et assisté dans mes démarches administratives. À Lucie, Antoine, Clara, Blanche, Simon et toutes les personnes que j’ai eu l’occasion de rencontrer et de partager des moments à Shanghai. Merci aux gens rencontrés dans le cadre de l’institut Pasteur avec qui j’ai l’occasion de partager de très bons moments et des discussions intéressantes. Merci à Antoine et Lucie de m’avoir fait découvrir tellement de terrasses, restaurants, bars, brunch... Merci à Lucie pour nos discussions scientifiques à toute heure, dans un canapé, en terrasse, au labo ou en scooter. Merci à Lucie et Clara pour leur immense talent de Zapateuse. Aux différentes personnes de l’IGFL que j’ai eu le plaisir de côtoyer pendant ma thèse. En particulier, merci à Frédéric Flamant pour son aide pour l’analyse de mon screening, pour les mille et unes questions que j’avais sur le criblage et CRISPR.
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    UNIVERSIDADE DE SÃO PAULO PROGRAMA INTERUNIDADES DE PÓS-GRADUAÇÃO EM BIOINFORMÁTICA Construção e Aplicação de HMMs de Perfil para a Detecção e Classificação de Vírus Miriã Nunes Guimarães SÃO PAULO 2019 Construção e Aplicação de HMMs de Perfil para a Detecção e Classificação de Vírus Miriã Nunes Guimarães Dissertação apresentada à Universidade de São Paulo, como parte das exigências do Programa de Pós-Graduação Interunidades em Bioinformática, para obtenção do título de Mestre em Ciências. Área de Concentração: Bioinformática Orientador: Prof. Dr. Arthur Gruber SÃO PAULO 2019 “Na vida, não existe nada a temer, mas a entender.” Marie Curie Agradecimentos Ao Professor Arthur Gruber pela oportunidade desde o início como estagiária no laboratório, pela orientação neste período de aprendizado no mestrado e por fornecer um ambiente de trabalho favorável. À aluna de doutorado Liliane Santana Oliveira que aguentou todas as minhas amolações diárias no laboratório pelo Hangouts, por dúvidas que eram erros meus em comandos de execução, pela paciência, pela amizade, pela companhia nos bandejões da faculdade com cardápio glutenfree que nem sempre eram tão bons assim. À aluna de mestrado Irina Yuri Kawashima que estava comigo no laboratório diariamente, pelas várias discussões sobre o mundo dos vírus e de conhecimentos da bioinformática, pelas ferramentas para facilitar o andamento do projeto, por todas guloseimas glutenfree que seria impossível eu não agradecer pois tenho ciência que não vou encontrar outra amiga masterchef assim. À Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) pelo financiamento durante estes 24 meses de mestrado. Aos meus pais pelo carinho e preocupação comigo durante estes 24 anos, pelo incentivo aos estudos e pelo apoio para eu me manter a uma distância de quase 400km de pura saudade.
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    1 Lujo Viral Hemorrhagic Fever: Considering Diagnostic Capacity and 2 Preparedness in the Wake of Recent Ebola and Zika Virus Outbreaks 3 4 Dr Edgar Simulundu1,, Prof Aaron S Mweene1, Dr Katendi Changula1, Dr Mwaka 5 Monze2, Dr Elizabeth Chizema3, Dr Peter Mwaba3, Prof Ayato Takada1,4,5, Prof 6 Guiseppe Ippolito6, Dr Francis Kasolo7, Prof Alimuddin Zumla8,9, Dr Matthew Bates 7 8,9,10* 8 9 1 Department of Disease Control, School of Veterinary Medicine, University of Zambia, 10 Lusaka, Zambia 11 2 University Teaching Hospital & National Virology Reference Laboratory, Lusaka, Zambia 12 3 Ministry of Health, Republic of Zambia 13 4 Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis 14 Control, Sapporo, Japan 15 5 Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, 16 Japan 17 6 Lazzaro Spallanzani National Institute for Infectious Diseases, IRCCS, Rome, Italy 18 7 World Health Organization, WHO Africa, Brazzaville, Republic of Congo 19 8 Department of Infection, Division of Infection and Immunity, University College London, 20 U.K 21 9 University of Zambia – University College London Research & Training Programme 22 (www.unza-uclms.org), University Teaching Hospital, Lusaka, Zambia 23 10 HerpeZ (www.herpez.org), University Teaching Hospital, Lusaka, Zambia 24 25 *Corresponding author: Dr. Matthew Bates 26 Address: UNZA-UCLMS Research & Training Programme, University Teaching Hospital, 27 Lusaka, Zambia, RW1X 1 28 Email: [email protected]; Phone: +260974044708 29 30 2 31 Abstract 32 Lujo virus is a novel old world arenavirus identified in Southern Africa in 2008 as the 33 cause of a viral hemorrhagic fever (VHF) characterized by nosocomial transmission 34 with a high case fatality rate of 80% (4/5 cases).