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The genetic diversity of viral populations is a key driver of the spatial and temporal diffusion of viruses; yet, studying the diversity of whole genomes from natural populations still remains a challenge. Phylodynamic approaches are commonly used for RNA viruses harboring small genomes but have only rarely been applied to DNA viruses with larger genomes. Here, we used the Pacific oyster mortality syndrome (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 an innovative combination of bioinformatics tools, we de novo assembled twenty-one OsHV-1 new genomes. Combining quantification of major and minor genetic variations, phylogenetic analysis, and ancestral state reconstruction of discrete traits approaches, 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. We demonstrate that phylodynamic approaches can be applied to aquatic DNA viruses to determine how epidemiological, immunological, and evolutionary processes act and potentially interact to shape their diversity patterns. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The intertidal zone is characterized by a sharp vertical gradient of environmental stress, which structures species distribution and their interactions. Few studies, however, have examined the influence of tidal height on host–pathogen interactions. Here, we investigated how the tidal height influence outbreak of the Ostreid herpesvirus type 1 (OsHV-1) affecting the Pacific oyster. A volunteer network composed of 20 oyster growers monitored the survival of 28 batches of oysters during an epizootic event in Southern Brittany, France. Oysters were spat from wild collection or hatchery production. The sampling sites were spread over a 150-km2 area with a tidal height ranging from 0.98 to 2.90 m. Concomitantly, we followed survival of oyster spats in relation with OsHV-1 DNA detection at two sites and conducted risk analysis. We found that tidal height was associated with a lower risk of mortality. This effect was higher for hatchery than for wild oysters probably reflecting differences in health status. Our study opens perspectives for mitigation strategies based on tidal height and emphasizes the value of volunteer science in marine epidemiological studies. [ABSTRACT FROM AUTHOR]

Abstract Due to massive mortality of Crassostrea gigas spat in France since 2008, a "plan de sauvegarde" was set up from 2011 to 2014 (hereafter referred to as PS1 to PS4), in order to reduce the shortage of spat. This plan involved the participation of commercial hatcheries, the French Research Institute for Exploitation of the Sea (Ifremer), and the Direction des Pêches Maritimes et de l'Aquaculture (DPMA) of the French Ministry of Agriculture. It was based on selecting diploid lines of C. gigas for their higher resistance to the oyster herpesvirus OsHV-1 (2nR group), and one of these lines was subsequently tetraploidized (4nR group). Both the 2nR and 4nR groups were produced by Ifremer, and then transferred to commercial hatcheries that produced the selected triploids (3nR groups). We report here the mortality rates of the 3nR group for each of the four "plan de sauvegarde" campaigns and compare these with the mortalities of the classic production of commercial hatcheries (both 2n and 3n), benchmarks of selected (2nR group) and unselected (2n-control group) oysters produced by Ifremer, and wild-caught spat, representing a total of 104 diploid and triploids batches. For PS1, the 3nR group had a mean mortality of 67% and did not show any advantage over the 2n- and 3n-commercial groups, suggesting a lack of genetic progress in the 2nR and 4nR groups. For PS2, OsHV-1 resistance was increased in both the 2nR and 4nR groups and, consequently, the 3nR group exhibited a mean mortality of 52%, which was significantly lower than the mortality of the 2n- (87%) and 3n-(76%) commercial groups in 2012. Unfortunately, the mortality of the 3nR group reached 62% and 71% in PS3 and PS4, respectively, although it was expected to be lower than that in PS2. OsHV-1 DNA was quantified in the live oysters at deployment (1356 oysters) and at the endpoint (1171 oysters), as well as in moribund oysters sampled during peak mortality (539 oysters). The results strongly supported the involvement of this pathogen during the main mortality outbreak in May/June. Meanwhile, Vibrio aestuarianus was also suspected to cause unexpected mortality of PS3 oysters in August and September, and it was detected in moribund PS4 oysters during both the mortality events, in May and July. Despite genetic improvement for OsHV-1 resistance, this translated into variable commercial genetic gain. This could be explained by the limited genetic backgrounds of the 2nR and 4nR groups, the reemergence of V. aestuarianus in France since 2012, the changing levels of genetic improvement in both the 3nR group and the commercial groups, as well as the limited broodstock genetic variation where small numbers of males were used. Results on growth and yield are discussed. Highlights • Four "plan de sauvegarde" campains (PS) were set up to reduce the spat shortage in France from 2011 to 2014. • Selection criterion was only based on the resistance to the infection by OsHV-1. • The mortality of 5 groups were compared for each PS representing a total of 104 diploid and triploids batches. • The 3nR group only had a significant decrease of mortality over the 2n and 3n commercial groups in 2012. • The failure of the "plan de sauvegarde" in 2013 and in 2014 could be explained by the role of V. aestuarianus. [ABSTRACT FROM AUTHOR]

Background: Massive mortalities have been observed in France since 2008 on spat and juvenile Pacific oysters, Crassostrea gigas. A herpes virus called OsHV-1, easily detectable by PCR, has been implicated in the mortalities as demonstrated by the results of numerous field studies linking mortality with OsHV-1 prevalence. Moreover, experimental infections using viral particles have documented the pathogenicity of OsHV-1 but the physiological responses of host to pathogen are not well known. Results: The aim of this study was to understand mechanisms brought into play against the virus during infection in the field. A microarray assay has been developed for a major part of the oyster genome and used for studying the host transcriptome across mortality on field. Spat with and without detectable OsHV-1 infection presenting or not mortality respectively were compared by microarray during mortality episodes. In this study, a number of genes are regulated in the response to pathogen infection on field and seems to argue to an implication of the virus in the observed mortality. The result allowed establishment of a hypothetic scheme of the host cell's infection by, and response to, the pathogen. Conclusions: This response shows a "sensu stricto" innate immunity through genic regulation of the virus OsHV-1 life cycle, but also others biological processes resulting to complex interactions between host and pathogens in general. [ABSTRACT FROM AUTHOR]

Of all environmental factors, seawater temperature plays a decisive role in triggering marine diseases. Like fever in vertebrates, high seawater temperature could modulate the host response to pathogens in ectothermic animals. In France, massive mortality of Pacific oysters, Crassostrea gigas , caused by the ostreid herpesvirus 1 (OsHV-1) is markedly reduced when temperatures exceed 24°C in the field. In the present study we assess how high temperature influences the host response to the pathogen by comparing transcriptomes (RNA sequencing) during the course of experimental infection at 21°C (reference) and 29°C. We show that high temperature induced host physiological processes that are unfavorable to the viral infection. Temperature influenced the expression of transcripts related to the immune process and increased the transcription of genes related to the apoptotic process, synaptic signaling and protein processes at 29°C. Concomitantly, the expression of genes associated with catabolism, metabolite transport, macromolecule synthesis and cell growth remained low from the first stage of infection at 29°C. Moreover, viral entry into the host might have been limited at 29°C by changes in extracellular matrix composition and protein abundance. Overall, these results provide new insights into how environmental factors modulate host-pathogen interactions., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists Ltd.)

The acute course of disease in young oysters infected by OsHV-1 and the rapid tissue degradation often preclude histological examination of specimens collected during outbreaks in field. Herein, live spat originated from two geographical areas were sampled just at the onset of a mortality event that occurred in Normandy (France) in June 2016. The lesions, associated with high OsHV-1 DNA quantities, were characterized by severe and diffuse haemocytosis mainly involving blast-like cells, myocyte degeneration and large, irregularly shaped degenerate eosinophilic cells in the connective tissue. The herpesvirus was identified by negative staining TEM and real-time PCR. Sequencing of the C region and ORFs 42/43 confirmed that the variants met the definition of OsHV-1 μVar. We sequenced 30 other ORFs in twenty OsHV-1-positive individuals and compared them to the μVar specimens isolated between 2009 and 2011. The ORFs encoding putative membrane proteins showed the highest number of variations. Seven different genotypes were identified, confirming the presence of relevant genetic diversity. Phylogenetic analysis provided evidence for a well-separated μVar new group, with an evolutionary divergence estimated at 0.0013 from the other μVar variants. The geographical distribution of these newly described variants and their effective virulence should be investigated in future., (© 2018 John Wiley & Sons Ltd.)