viral genetic diversity what is its role in the interaction of the ostreid herpesvirus 1 virus and its host the oyster crassostrea gigas?

• Main Author: Delmotte, Jean
• Other Authors: Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Montpellier, Jean-Michel Escoubas
• Format: Doctoral or Postdoctoral Thesis
• Language: French
• Published: HAL CCSD 2021
• Subjects: Host pathogene interaction; Genetic diversity; Ostreid herpesvirus 1; Oyster; Viral diversity; Interactions hôte pathogène; Diversité génétique; Huître; [SDV.SA]Life Sciences [q-bio]/Agricultural sciences; Crassostrea gigas
• Online Access: https://theses.hal.science/tel-03343932; https://theses.hal.science/tel-03343932/document; https://theses.hal.science/tel-03343932/file/2021_DELMOTTE_archivage.pdf

The contemporary genetic diversity of viruses is the result of the continuous and dynamic interaction of past ecological and evolutionary processes with its host. For more than 30 years, mortality episodes have been impacting the oyster industry. These have complex etiologies but are often associated with a Herpesvirus: Ostreid Herpesvirus 1 (OsHV-1). Since 2008, unprecedented mortality events in Crassostra gigas species have been reported worldwide. The appearance of these excess mortalities coincides with the emergence of a new genotype of the virus: the OsHV-1 µVar. After several years of research to understand this pathosystem, it was recently demonstrated that a Herpesvirus: Ostreid herpesvirus 1 (OsHV-1) was the agent initiating pathogenesis and leading to host death. In parallel, the observation of other related variants of OsHV-1 virus have been associated with other mortality epidemics in other bivalve species. However, until recently, studies on the genetic diversity of the virus used a short fragment of the virus genome. There is therefore an urgent need to characterize this OsHV-1 genetic diversity at the whole genome level. This thesis manuscript provides us with the tools necessary for a complete characterization of the virus genome. We confirm that OsHV-1 viral populations are different according to their geographical location with potential genomic signatures between sites. Finally, thanks to the complete assembly of twenty-one genomes, we propose a scheme of virus dissemination through molecular epidemiology analysis using innovative bioinformatics tools. Our results suggest that the genetic diversity of the virus within the C. gigas species is relatively small. This observation seems to contrast with previous work suggesting a significant genetic diversity of the OsHV-1 virus. However, we show that it is necessary to better define the diversity within a particular species and within a given time frame in order to correctly interpret it. However, this diversity is not non-existent and we discuss ...