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Les Résultats 2020 En Génomique Des Virus Aviaires

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Les Résultats 2020 En Génomique Des Virus Aviaires Centre de Recherche en Infectiologie Porcine et Avicole Swine and Poultry Infectious Diseases research Center Les résultats 2020 de génomique des virus aviaires au Québec Carl A. Gagnon, DMV, PhD, Professeur titulaire, Laboratoire de diagnostic moléculaire (LDM), Réovirus (haut) et poxvirus (bas) aviaires. Image de C. Provost. Service de virologie, de sérologie aviaire et de de microscopie électronique, FMV. UdeM. séquençage à haut débit vétérinaire (LSHDV) Faculté de médecine vétérinaire (FMV), Poste: 8681 Courriel: [email protected] Séquençage du génome entier des pathogènes aviaires http://servicedediagnostic.com/personnel-et- laboratoires/service-de-sequencage/ Tableau 1 – Liste des pathogènes aviaires identifiés au Québec en 2020 par méthode moléculaire au Service de diagnostic Catégorie de Nom Abréviation Maladie pathogènes Bactéries Genre Espèce Chlamydophila spp a C. psittaci Chlamydiose aviairec Escherichia coli E. coli Colibacillose Mycobacterium spp b M. avium Tuberculose aviaire Mycoplasma gallisepticum M. gallisepticum (ou MG) Maladie respiratoire chronique Mycoplasma synoviae M. synoviae (ou MS) Synovite infectieuse Parasite Genre Espèce Histomonas meleagridis H meleagridis Histomonose (peut avoir différents noms selon le syndrome observé) Pathogènes Virus Genre (Espèce) Atadenovirus (Duck atadenovirus A; DAdV-1 Syndrome de la chute de pontec anciennement Duck adenovirus-1) identifiés par PCR Aviadenovirus (Fowl aviadenovirus A to FAdV Hépatite à corps d'inclusion E; anciennement Fowl adenovirus A to E) Avibirnavirus (Infectious bursal disease IBDV Maladie de la Bursite infectieuse (ou maladie de en 2020 virus) Gumboro) Avipoxvirus (Fowl and Canarypox virus) Avian pox Variole aviaire Flavivirus (West Nil Virus ou Virus du WNV ou VNO Fièvre du Nil occidentalc Nil occidental) , 2021. , Gammacoronavirus (Avian coronavirus) IBV Bronchite infectieuse aviaire (inclus un syndrome important: fausses pondeuses) Gyrovirus (Chicken anemia virus) CAV Anémie infectieuse du poulet Itovirus (Gallid alphaherpesvirus 1) ILTV ou GaHV-1 Laryngotrachéite infectieuse aviairec veterinarius Mardivirus (Gallid alphaherpesvirus 2) MDV ou GaHV-2 Maladie de Marek Orthobornavirus (Psittacine bornavirus) PaBV Maladie de dilatation du proventricule Orthoreovirus (Avian orthoreovirus) ARV Divers syndromes; ex. Arthrite virale Tremovirus (Tremovirus A); nom AEV Encéphalomyélite aviairec commun: Avian encephalomyelitis virus) GagnonLe al. et Nomenclature des virus qui seront discutés lors de la présentation Genre (Espèce) Abréviation Maladie Atadenovirus (Duck atadenovirus A; DAdV-1 Syndrome de la chute de pontea anciennement Duck adenovirus-1) Aviadenovirus (Fowl aviadenovirus A to FAdV Hépatite à corps d'inclusion E; anciennement Fowl adenovirus A to E) Avibirnavirus (Infectious bursal disease IBDV Maladie de la Bursite infectieuse (ou virus) maladie de Gumboro) Gammacoronavirus (Avian coronavirus) IBV Bronchite infectieuse aviaire (inclus un syndrome important: fausses pondeuses) Itovirus (Gallid alphaherpesvirus 1) ILTV ou GaHV-1 Laryngotrachéite infectieuse aviairea Orthoreovirus (Avian orthoreovirus) ARV Divers syndromes; ex. Arthrite virale aMaladies à notification immédiate. positifs en Nombre de cas 2020 PCR 2 2 1 1 2 2 * 200 Ferme/Basse-cour Exotique/Faune │ s Ferme/Basse-cour Exotique/Faune f 9 9 i 3 3 t 150 1 1 i 1 1 s 2 2 o 1 1 p s a 100 c e d 1 1 0 0 6 6 6 6 e 2 2 r 5 5 3 3 b 4 50 4 m 5 5 3 3 0 0 2 2 o 2 2 2 2 N 7 7 5 5 4 5 4 3 3 3 3 3 3 1 1 1 1 1 1 0 ) s x p p 1 e p V V V V V V V V V i O m - V o p a p p d T d i E B B A u D R D i N V s p I s s M r v L c a A A B A C i I d V M I t s g o a n F D P l m A i p u a n a i r u e h y i e e D i l v r h s v s p i e e A c l s . o l t u e d m c a M , 2021. , veterinarius Gagnon et al. Le Le al. et Gagnon o p y . a g r s b . ( H m e o a M H l V c h y B I C M Proportion des cas séquencés en 2020 à la demande des vétérinaires 220 22.6% 200 Séquencés 180 Non séquencés s a 160 c 8.6% e 140 d 6.6% e 120 r b m 50 o N 40 30 100% 0% 20 10 N.B.: Certains séquençages 0 (non-inclus) d’ARV et V V V V V d T R D B d’ILTV ont été fait dans I L A A B I I F le cadre de programmes de Pathogènes recherche. Aucun comparatif n’est possible avec la banque de données génomiques Québécoise de l’ORF5 du virus SRRP En date du 31 mars 2021: La banque de données génomiques de souches québécoises du VSRRP possède 5430 séquences! Rappel: Plusieurs vétérinaires du secteur aviaire ont signé un accord de partage des séquences Jusqu’à présent, un total de 13 vétérinaires ont signé cet accord. La majorité des signatures ont été obtenues en 2017. Quelques vétérinaires, dont certains soumettent une quantité non-négligeable de demandes d’analyses, n’ont pas signé l’accord. Est-ce toujours important pour les vétérinaires du secteur avicole? Accord de partage des séquences du secteur aviaire (en résumé) Dans le cadre de cette entente et après avoir effectué le séquençage et la comparaison, le SD transmettra au vétérinaire qui en a fait la demande, les informations suivantes : a) le nom du vétérinaire qui a fourni le Spécimen, b) l’identifiant du Spécimen attribué par le SD, c) le pourcentage d’homologie pour le micro-organisme testé avec les séquences de la BS-Aviaire, d) les noms des vétérinaires qui ont soumis des spécimens avec des séquences homologues ainsi que leurs numéros d’identifiant. Accord de partage des séquences du secteur aviaire Vous pouvez télécharger une copie de l’accord à l’adresse suivante: https://readycloud.netgear.com/client/browselink.html#t=02e3qv8 acbmrou9sfnnp83h70lu/Accord_S%C3%A9quences_Aviaires Si vous avez oubliez votre adhésion à cette accord, vous pouvez m’envoyer un courriel pour que je vous informe de votre participation (ou non) à cet accord. Atadenovirus (Duck atadenovirus A; anciennement Duck adenovirus-1; DAdV-1) Adénovirus de canard Généralement asymptomatique chez les oiseaux aquatiques qui sont considérés être les réservoirs de ce virus Agent étiologique du syndrome de la chute de ponte chez la poule Peut provoquer jusqu’à une diminution de 40% de la production d’œufs avec des anomalies de la coquille. Maladie à déclaration immédiate Un cas de virus identifié en 2020 chez le canard. DAdV-1 Canard (lors de signes cliniques qui sont rares) Problèmes respiratoires chez les jeunes oiseaux 2 à 7% de mortalité Chenier et al., Can Vet J. 2019. Fowl aviadenovirus 4 strain HLJDAd15 (KX538980) Fowl adenovirus C (NC_015323) 100 Fowl adenovirus A (NC_001720) Turkey adenovirus 5 isolate 1277BT (NC_022613) 100 Turkey adenovirus 1 (NC_014564) 100 Pigeon adenovirus 1 strain IDA4 (NC_024474) 100 Fowl adenovirus 5 strain 340 (NC_021221) Turkey adenovirus 4 isolate TNI1 (NC_022612) 100 99 Fowl adenovirus D (NC_000899) 100 100 Fowl adenovirus 6 strain CR119 (NC_038332) Fowl adenovirus E (NC_014969) Goose adenovirus 4 (NC_017979) 9.7 Arbre phylogénique 100 Duck adenovirus 2 strain GR (NC_024486) 100 nucléotidique basé Duck adenovirus 3 isolate ZJJH07 (MH777397) 100 Duck adenovirus 3 isolate AHAQ13 (MH777396) 10 sur le génome Duck adenovirus 2 strain CH-GD-12-2014 (KR135164) 100 9.6 Duck adenovirus 3 isolate FJGT01 (MH777395) entier du DAdV-1 98 Duck adenovirus 3 isolate GDMM10 (MH777398) Psittacine adenovirus 3 isolate HKU/Parrot19 (NC_025962) 100 Duck adenovirus 1 strain FMV-19-2234581 2019 100 Duck adenovirus 1 strain FMV-20-2234581 2020 80 Duck adenovirus 1 isolate D11-JW-017 (KJ452171) 78 Duck adenovirus 1 isolate D11-JW-012 (KJ452170) 100 DAdV-1 Duck adenovirus 1 isolate FJ12025 (KF286430) 98 Duck adenovirus A (NC_001813) 56 Duck adenovirus 1 isolate C10-GY-001 (KJ452173) 0.7 Duck adenovirus 1 isolate D11-JW-032 (KJ452172) Les souches DAdV-1 du Québec semblent être distinctes des Duck adenovirus 1 strain FMV-19-2234581 (MN310513) autres souches rapportées au niveau mondial. Québec Duck adenovirus 1 strain FMV-20-2440252 Duck adenovirus 1 isolate D11-JW-017 (KJ452171) 100 Duck adenovirus 1 isolate D11-JW-012 (KJ452170) 100 Duck adenovirus 1 isolate FJ12025 (KF286430) Chine, Irlande, 66 Corée du sud Duck adenovirus A (NC_001813) 21 Duck adenovirus 1 isolate C10-GY-001 (KJ452173) 20 Duck adenovirus 1 isolate D11-JW-032 (KJ452172) 0.003 Adénovirus aviaire (Fowl aviadenovirus – FAdV) Virus à ADN double brin, non-enveloppé (donc très résistant dans l’environnement) 5 espèces: A à E 12 sérotypes (1 à 12) Certains sérotypes sont associés à la maladie de l’hépatite à corps d’inclusion Tiré de: Virus Taxonomy, Classification and Nomenclature of Viruses, Ninth Report of the International Committee on Taxonomy of Viruses (ICTV). 2012. Possède le plus long génome parmi tous les Adénovirus Longueur du génome en nucléotides Nombre total de cas de FAdV séquencés par année 50 s é c n 40 e u q é s 30 s a c e 20 d e r b m 10 o N 0 2015 2016 2017 2018 2019 2020 Année Demandes de séquençage de FAdV (distribution par vétérinaire) Vet 1 30 Vet 2 s é Vet 3 c 2019: n Vet 4 e n=4 u 16.7% Vet 5 q é Moy±SD = 5.3 ± 3.3 20 Vet 6 s s Vet 7 a c Vet 8 e d 28.6% 2020: Vet 9 e r 10 n=9 b Moy±SD = 3.3 ± 2.7 m 33.3% o N 42.9% 0 2019 2020 .
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