TY - JOUR T1 - Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France JF - bioRxiv DO - 10.1101/2021.04.30.442107 SP - 2021.04.30.442107 AU - Jean Delmotte AU - Camille Pelletier AU - Benjamin Morga AU - Richard Galinier AU - Bruno Petton AU - Jean-Baptiste Lamy AU - Oliver Kaltz AU - Jean-Christophe Avarre AU - Caroline Montagnani AU - Jean-Michel Escoubas Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/04/30/2021.04.30.442107.abstract N2 - 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-Oléron 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.Importance Phylogeography is a field of research that attempts to reconstruct the relationships between individual genotypes within a species and then correlate these genealogical relationships with their geographic origin. This field of research has become an essential step in the understanding of pandemics, in particular to determine the origin, spread and evolution of a pathogen as currently illustrated in studies on viral pandemics. However, because phylogeographic analyses are based on genome variation, stable genomes yield less information than labile genomes. Accordingly, viruses with double-stranded DNA (dsDNA) genomes generally have lower nucleotide diversity than RNA viruses. In this study, by combining the use of both major and minor variants with phylogeographic analyses of the oyster herpesvirus OsHV-1, we highlight genealogical relationships that have not been depicted in phylogenetic trees based on consensus viral genomes only. These data offer a plausible scenario reflecting the origin and spread of OsHV-1 populations between oyster-farming sites.Competing Interest StatementThe authors have declared no competing interest. ER -