Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France
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 gen...
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ftoskarbordeaux:oai:oskar-bordeaux.fr:20.500.12278/31852 2023-05-15T17:54:20+02:00 Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France DELMOTTE, Jean PELLETIER, Camille MORGA, Benjamin GALINIER, Richard PETTON, Bruno LAMY, Jean-Baptiste KALTZ, Oliver AVARRE, Jean-Christophe MONTAGNANI, Caroline ESCOUBAS, Jean-Michel 2021-04-30 https://oskar-bordeaux.fr/handle/20.500.12278/31852 https://doi.org/10.1101/2021.04.30.442107 en eng https://oskar-bordeaux.fr/handle/20.500.12278/31852 doi:10.1101/2021.04.30.442107 Herpesvirus OsHV-1 cupped oyster phylogeography non-redundant genomes genetic diversity viral spread minor variant Sciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie Sciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE] Sciences du Vivant [q-bio]/Biodiversité Document de travail - Pré-publication 2021 ftoskarbordeaux https://doi.org/10.1101/2021.04.30.442107 2021-05-11T22:30:28Z 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. Other/Unknown Material Pacific oyster OSKAR Bordeaux (Open Science Knowledge ARchive) Pacific |
institution |
Open Polar |
collection |
OSKAR Bordeaux (Open Science Knowledge ARchive) |
op_collection_id |
ftoskarbordeaux |
language |
English |
topic |
Herpesvirus OsHV-1 cupped oyster phylogeography non-redundant genomes genetic diversity viral spread minor variant Sciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie Sciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE] Sciences du Vivant [q-bio]/Biodiversité |
spellingShingle |
Herpesvirus OsHV-1 cupped oyster phylogeography non-redundant genomes genetic diversity viral spread minor variant Sciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie Sciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE] Sciences du Vivant [q-bio]/Biodiversité DELMOTTE, Jean PELLETIER, Camille MORGA, Benjamin GALINIER, Richard PETTON, Bruno LAMY, Jean-Baptiste KALTZ, Oliver AVARRE, Jean-Christophe MONTAGNANI, Caroline ESCOUBAS, Jean-Michel Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France |
topic_facet |
Herpesvirus OsHV-1 cupped oyster phylogeography non-redundant genomes genetic diversity viral spread minor variant Sciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie Sciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE] Sciences du Vivant [q-bio]/Biodiversité |
description |
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. |
format |
Other/Unknown Material |
author |
DELMOTTE, Jean PELLETIER, Camille MORGA, Benjamin GALINIER, Richard PETTON, Bruno LAMY, Jean-Baptiste KALTZ, Oliver AVARRE, Jean-Christophe MONTAGNANI, Caroline ESCOUBAS, Jean-Michel |
author_facet |
DELMOTTE, Jean PELLETIER, Camille MORGA, Benjamin GALINIER, Richard PETTON, Bruno LAMY, Jean-Baptiste KALTZ, Oliver AVARRE, Jean-Christophe MONTAGNANI, Caroline ESCOUBAS, Jean-Michel |
author_sort |
DELMOTTE, Jean |
title |
Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France |
title_short |
Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France |
title_full |
Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France |
title_fullStr |
Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France |
title_full_unstemmed |
Phylogeography of infectious disease: genetic diversity and connectivity of the Ostreid herpesvirus 1 population in France |
title_sort |
phylogeography of infectious disease: genetic diversity and connectivity of the ostreid herpesvirus 1 population in france |
publishDate |
2021 |
url |
https://oskar-bordeaux.fr/handle/20.500.12278/31852 https://doi.org/10.1101/2021.04.30.442107 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Pacific oyster |
genre_facet |
Pacific oyster |
op_relation |
https://oskar-bordeaux.fr/handle/20.500.12278/31852 doi:10.1101/2021.04.30.442107 |
op_doi |
https://doi.org/10.1101/2021.04.30.442107 |
_version_ |
1766162084903518208 |