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Eco-Épidémiologie Du Virus Influenza D : Évaluation Du Spectre D’Hôtes Et Du Risque D’Émergence Justine Oliva

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Eco-Épidémiologie Du Virus Influenza D : Évaluation Du Spectre D’Hôtes Et Du Risque D’Émergence Justine Oliva Eco-épidémiologie du virus influenza D : évaluation du spectre d’hôtes et du risque d’émergence Justine Oliva To cite this version: Justine Oliva. Eco-épidémiologie du virus influenza D : évaluation du spectre d’hôtes et du risque d’émergence. Virologie. Université Paul Sabatier - Toulouse III, 2019. Français. NNT : 2019TOU30171. tel-02651515 HAL Id: tel-02651515 https://tel.archives-ouvertes.fr/tel-02651515 Submitted on 29 May 2020 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. THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par l'Université Toulouse 3 - Paul Sabatier Présentée et soutenue par Justine OLIVA Le 4 octobre 2019 Eco-épidémiologie de virus Influenza D : évaluation du spectre d'hôtes et du risque d'émergence Ecole doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Spécialité : Pathologie, Toxicologie, Génétique et Nutrition Unité de recherche : IHAP - Laboratoire Interactions Hôtes-Agents Pathogènes Thèse dirigée par Mariette DUCATEZ et Gilles MEYER Jury Mme Gaëlle SIMON, Rapporteure Mme Sophie LEPODER, Rapporteure Mme Sabine RIFFAULT, Examinatrice M. Daniel DUNIA, Examinateur Mme Mariette DUCATEZ, Co-directrice de thèse M. Gilles MEYER, Co-directeur de thèse Remerciements Mes premiers remerciements vont à mes encadrants de thèse, avec qui j’ai eu le plaisir de travailler durant ces trois années, et qui m’ont beaucoup apporté, Le Docteur Mariette Ducatez pour m’avoir offert l’opportunité de réaliser cette thèse. Merci pour ta disponibilité, tes connaissances et ton dynamisme. Merci aussi pour ta patience, pour avoir supporté mes « chouineries » quand les manips ne marchaient pas et de m’avoir remonté le moral. Le professeur Gilles Meyer pour avoir partagé ton temps précieux et m’avoir guidé dans ce projet, avec des conseils scientifiques et techniques toujours pertinents, surtout sur la partie « bovine », ainsi que tes petites piques qui m’ont toujours fait réagir. Je tiens ensuite à remercier les membres de mon Jury de thèse, le docteur Gaëlle Simon et le professeur Sophie Lepoder, qui ont accepté d’être les rapporteurs de ce manuscrit. Je remercie également le docteur Sabine Riffault d’avoir accepté d’examiner et de participer à ce jury de thèse, le docteur Daniel Dunia pour avoir accepté de présider ce jury ainsi que Mr Jean-Michel Mansuy. Je remercie également toute l’équipe de virologie, Le Professeur Jean-Luc Guérin, de m’avoir accueillie dans cette super équipe, pour ta sollicitude et les multiples surnoms dont tu m’as affublé. Je remercie bien sûr Jade, Amit, Maria et Sarah qui ont grandement participé à ce projet de thèse lors de leurs stages ou thèse vétérinaire. Merci aux différentes personnes de l’équipe avec qui j’ai passé de bons moments et qui m’ont aidé sur bien des aspects pendant cette thèse : Sylvie, Stéphane, Romain (merci pour tes plasmides), Brigitte, Kateri, Anne-Laure, Hadrien, Christelle et Cécile. Merci aussi à Guillaume et Kunta pour les parties de billard (ou ce qui s’en rapproche dans mon cas). Merci à Petit Guillaume pour les hérissons (c’est l’avenir !) et Josy pour m’avoir aidé dans mes manips. Merci aussi à Angélique pour ta gentillesse, ton aide et pour tout petit. Merci aux autres personnes, résidents ou non du 10.1 : Françoise et Benoit, Christian, Julie (La Reine des gâteaux), Mattias, Laure, Hélène... Je souhaite remercier Séverine et Diane, ainsi que Petit Lou et Sweet, pour le sang de cheval, qui m’a été fort utile pour réaliser toutes ces IHA. Un grand merci aussi à toutes les personnes du poulailler, les doctorants et les post-doc : Adrien, Thomas, Petite Charlotte, Jessica, Aurélie, Gabriel, Marie, Julien, Adam et Chloé pour tous les moments passés ensemble. À tous ceux qui sont en thèse, je vous dis bon courage, et pour ceux qui vont commencer : Fuyez, pauvres fous ! Merci Elias, pour ton aide sur la FluD (avant que tu ne passes du côté obscur des pox), ta bonne humeur matinale, tes « Déjà ? » et pour nos éternelles « disputes » de petits vieux. Merci tout spécialement à Charlotte pour tes encouragements, tes précieux conseils et ta bonne humeur. Merci aussi pour tes délicieux cookies qui n’ont pas leurs pareils. Un grand merci à Maxime et Pierre (mes Frodon et Sam) pour tous les bons moments passés ensemble (nos voyages épiques, les randos et tout le reste…). Merci à toi, Toutouille, forever your Lady Brienne. Merci surtout à Pollito d’avoir été à mon complice de LOTR, je n’ai plus qu’une chose à te dire : « Adieu mon brave Pollito, mon œuvre est désormais achevée. C’est ici, sur les rives du Touch que prend fin de notre communauté. Je ne vous dirais pas de ne pas pleurer, car toutes les larmes ne sont pas un mal ». Je souhaite également remercier mes amis, pour leurs encouragements et leurs conseils, de m’avoir écouté dans les meilleurs comme dans les pires moments. Merci de m’avoir permis de m’évader quand j’en ai eu besoin, même en étant (très) loin de Toulouse. Merci pour les discussions « poneys », les karaokés et les « défis dessins » qui m’ont toujours apporté une grande joie. Enfin, je remercie ma mère grâce à qui j’ai pu faire ces si longues études. Merci aussi au reste de ma famille, mon frère et ma sœur, mes grands-mères, Mama, Sylvain, mon pti poutchy et tous les autres pour leur soutien. Merci à Mister Tabernacle, pour son soutien et ses punchlines d’encouragements. Enfin, je remercie aussi ceux qui ne sont plus là, Pacha et Papy Raymond, qui même s’ils n’ont pas suivi le déroulement de cette thèse, ont toujours été dans mes pensées. Tables des matières TABLES DES MATIERES ..................................................................................................................................... 3 LISTE DES FIGURES ........................................................................................................................................... 5 LISTE DES TABLEAUX ........................................................................................................................................ 5 LISTE DES ABREVIATIONS ................................................................................................................................. 1 AVANT-PROPOS ............................................................................................................................................... 6 I. INTRODUCTION ....................................................................................................................................... 1 A. DECOUVERTE ET TAXONOMIE DES VIRUS INFLUENZA .............................................................................................. 1 1. Découverte des virus influenza A, B et C .............................................................................................. 1 2. Découverte du virus influenza D ........................................................................................................... 3 B. STRUCTURE DES VIRUS INFLUENZA ..................................................................................................................... 5 1. Eléments de structure des virus influenza A, B et C .............................................................................. 5 2. Eléments de structure du virus influenza D ........................................................................................ 20 C. ÉVOLUTION DES VIRUS INFLUENZA ................................................................................................................... 30 1. Dérive génétique et réassortiment ..................................................................................................... 30 2. Diversité génétique des IAV, IBC et ICV. ............................................................................................. 33 3. Diversité génétique d’IDV ................................................................................................................... 34 D. SPECTRE D’HOTES DES VIRUS INFLUENZA ........................................................................................................... 38 1. Hôtes des virus influenza A, B et C ..................................................................................................... 38 2. Hôtes du virus influenza D .................................................................................................................. 42 E. CIRCULATION GEOGRAPHIQUE DES VIRUS INFLUENZA .......................................................................................... 48 1. Circulation des virus influenza A, B et C ............................................................................................. 48 2. Circulation du virus influenza D .......................................................................................................... 48 F. PATHOGENICITE ET TRANSMISSION DES VIRUS INFLUENZA ..................................................................................... 52 1. Pathogénicité et transmission des virus influenza A, B et C ..............................................................
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