Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species
The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic seque...
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doaj-215a5be40816485a920c4ff8ba8abe172021-07-13T07:43:24ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-07-011210.3389/fmicb.2021.711377711377Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host SpeciesBenjamin Morga0Maude Jacquot1Camille Pelletier2Germain Chevignon3Lionel Dégremont4Antoine Biétry5Jean-François Pepin6Serge Heurtebise7Jean-Michel Escoubas8Tim P. Bean9Tim P. Bean10Umberto Rosani11Chang-Ming Bai12Tristan Renault13Jean-Baptiste Lamy14Ifremer, RBE-SGMM-LGPMM, La Tremblade, FranceIfremer, RBE-SGMM-LGPMM, La Tremblade, FranceIfremer, RBE-SGMM-LGPMM, La Tremblade, FranceIfremer, RBE-SGMM-LGPMM, La Tremblade, FranceIfremer, RBE-SGMM-LGPMM, La Tremblade, FranceIfremer, RBE-SGMM-LGPMM, La Tremblade, FranceIfremer, ODE-Littoral-Laboratoire Environnement Ressources des Pertuis Charentais (LER-PC), La Tremblade, FranceIfremer, RBE-SGMM-LGPMM, La Tremblade, FranceIHPE, CNRS, Ifremer, Université de Montpellier – Université de Perpignan Via Domitia, Montpellier, FranceThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United KingdomCentre for Environment, Fisheries and Aquaculture Science, Weymouth, United KingdomDepartment of Biology, University of Padua, Padua, ItalyYellow Sea Fisheries Research Institute, CAFS, Qingdao, ChinaIfremer, RBE, Nantes, FranceIfremer, RBE-SGMM-LGPMM, La Tremblade, FranceThe mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.https://www.frontiersin.org/articles/10.3389/fmicb.2021.711377/fullmarine virusOsHV-1diversityshellfish farmingmeasurably evolution |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Benjamin Morga Maude Jacquot Camille Pelletier Germain Chevignon Lionel Dégremont Antoine Biétry Jean-François Pepin Serge Heurtebise Jean-Michel Escoubas Tim P. Bean Tim P. Bean Umberto Rosani Chang-Ming Bai Tristan Renault Jean-Baptiste Lamy |
spellingShingle |
Benjamin Morga Maude Jacquot Camille Pelletier Germain Chevignon Lionel Dégremont Antoine Biétry Jean-François Pepin Serge Heurtebise Jean-Michel Escoubas Tim P. Bean Tim P. Bean Umberto Rosani Chang-Ming Bai Tristan Renault Jean-Baptiste Lamy Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species Frontiers in Microbiology marine virus OsHV-1 diversity shellfish farming measurably evolution |
author_facet |
Benjamin Morga Maude Jacquot Camille Pelletier Germain Chevignon Lionel Dégremont Antoine Biétry Jean-François Pepin Serge Heurtebise Jean-Michel Escoubas Tim P. Bean Tim P. Bean Umberto Rosani Chang-Ming Bai Tristan Renault Jean-Baptiste Lamy |
author_sort |
Benjamin Morga |
title |
Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species |
title_short |
Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species |
title_full |
Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species |
title_fullStr |
Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species |
title_full_unstemmed |
Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species |
title_sort |
genomic diversity of the ostreid herpesvirus type 1 across time and location and among host species |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2021-07-01 |
description |
The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses. |
topic |
marine virus OsHV-1 diversity shellfish farming measurably evolution |
url |
https://www.frontiersin.org/articles/10.3389/fmicb.2021.711377/full |
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