Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France

• Main Authors: Delmotte, Jean, Pelletier, Camille, Morga, Benjamin, Galinier, Richard, Petton, Bruno, Lamy, Jean-Baptiste, Kaltz, Oliver, Avarre, Jean-Christophe, Montagnani, Caroline, Escoubas, Jean-Michel
• 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), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS), The present study was supported by the EU project VIVALDI (H2020 program, no. 678589) led by Ifremer; the CNRS and the University of Montpellier and the University of Perpignan Via Domitia. JD was supported by grant from the University of Montpellier. This work also benefitted from support from the “Laboratoire d’excellence” (LabEx) CeMEB, through the exploratory research project HaploFit and the use of the “environmental genomics” facility (http://www.labex-cemeb.org/fr/genomique-environnementale-1). This work was also supported by the Ifremer Scientific Board, through the HemoVir project. This study is set within the framework of the “Laboratoires d’Excellences (LABEX)” TULIP (ANR-10-LABX-41)., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016)
• Format: Report
• Language: English
• Published: HAL CCSD 2021
• Subjects: Herpesvirus; OsHV-1; cupped oyster; phylogeography; non-redundant genomes; genetic diversity; viral spread; minor variant; [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; [SDV.BID]Life Sciences [q-bio]/Biodiversity; Pacific; Pacific oyster
• Online Access: https://hal.science/hal-03217723; https://hal.science/hal-03217723/document; https://hal.science/hal-03217723/file/Delmotte-2021-BioRxiv-Phylogeography.pdf; https://doi.org/10.1101/2021.04.30.442107

The genetic diversity of viral populations is a key to understanding ther phylogeographic and dissemination history of viruses, but studying the diversity of whole genomes from natural populations remains a challenge. Molecular ecology approaches are commonly used for RNA viruses harboring small genomes, but have only rarely been applied to DNA viruses with large genomes. Here, we used the Pacific oyster mortality syndrome (POMS, a disease that affects oyster farms around the world) as a model to study the genetic diversity of its causative agent, the Ostreid herpesvirus 1 (OsHV-1) in the three main French oyster-farming areas. Using ultra-deep sequencing on individual moribund oysters and new bioinformatics methodology, we de novo assembled 21 OsHV-1 genomes. Combining whole-genome comparisons with phylogenetic analysis and quantification of major and minor variants, we assessed the connectivity of OsHV-1 viral populations between the three oyster-farming areas. Our results suggest that the Marennes-Oleron Bay represents the main source of OsHV-1 diversity, from where the virus has dispersed to other farming areas, a scenario consistent with current practices of oyster transfers in France. Here, we demonstrate that molecular ecology approaches can be applied to large-genome viruses to determine the extent of their genetic diversity and better understand the spread of viral populations in natural environments.