Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species

Abstract

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.

Genetic diversity and connectivity of the Ostreid herpesvirus 1 populations in France: a first attempt to phylogeographic inference for a marine mollusc disease

“…Our findings also showed that OsHV-1 µVar populations are much more diverse than previously thought. This is congruent with results from Delmotte et al showing that OsHV-1 µVar from the Bay of Brest and Thau Lagoon constitute two distinct viral populations (Delmotte et al, 2020) as well as with the recent relatively high estimate of OsHV-1 evolutionary rate (Morga et al, 2021). We therefore argue it is now necessary to combine common approaches relying on the generation and the analysis of consensus genomes to intra host diversity characterization in order to accurately study the epidemiology of DNA viruses (Renner and Szpara, 2018).…”

Understanding the Dynamic of POMS Infection and the Role of Microbiota Composition in the Survival of Pacific Oysters, Crassostrea gigas

“…With the recent advances in genomic sequencing efforts, considerable genotypic variations within the OsHV-1 species have been established. These variations are associated with different host species as well as temporal and geographical factors ( 59 – 61 ), supporting the possible emergence of specific variants in New Zealand. The current results indicate that genomic sequence comparison of strains between New Zealand, Australia, Europe, and the United States may indeed be a fruitful area for future research.…”

“…With the recent advances in genomic sequencing efforts, considerable genotypic variations within the OsHV-1 species have been established. These variations are associated with different host species as well as temporal and geographical factors [89][90][91], supporting the possible emergence of speci c variants in NZ.…”

Understanding the dynamic of POMS infection and the role of microbiota composition in the survival of Pacific oysters, Crassostrea gigas.

“…With the recent advances in genomic sequencing efforts, considerable genotypic variations within the OsHV-1 species have been established. These variations are associated with different host species as well as temporal and geographical factors (59)(60)(61), supporting the possible emergence of specific variants in New Zealand. The current results indicate that genomic sequence comparison of strains between New Zealand, Australia, Europe, and the United States may indeed be a fruitful area for future research.…”