Biology subjects

Jacquot, M.

Publications and source records attributed to Jacquot, M..

8 recordsLinked to original sources

bioRxiv2026

Global diversity and dispersal routes of the Ostreid herpesvirus type 1 infecting Magallana gigas

The order Herpesvirales comprises double-stranded DNA viruses characterized by substantial genomic plasticity, including recombination, structural variation, gene gain and loss, and lineage turnover. These processes can obscure phylogenetic relationships and complicate the reconstruction of viral evolutionary histories. Within this order, Ostreid herpesvirus 1 (OsHV-1) is a major pathogen of the Pacific oyster Magallana gigas and is responsible for recurrent mortality events affecting global aquaculture. Early molecular investigations based on partial genomic regions identified several viral lineages, including the "var" and "{micro}Var" lineages, but provided limited resolution for genome-wide evolutionary inference. The subsequent availability of complete genomes revealed extensive structural variation, such as insertions, deletions, and genomic rearrangements, highlighting the high genomic plasticity of OsHV-1. Although phylogenomic analyses have estimated evolutionary rates compatible with other large double-stranded DNA viruses, current inferences remain based on geographically restricted datasets, leaving the global evolutionary dynamics of OsHV-1 within its principal host insufficiently resolved. Here, we present 275 newly sequenced OsHV-1 genomes collected from infected M. gigas oysters between 1994 and 2022 across major oyster-producing regions worldwide. Using de novo genome assembly combined with comparative genomics, population genetic analyses, and time-scaled phylogenetic reconstruction, we investigate global genomic diversity and the spatio-temporal dynamics of viral diversification. Our results reveal long-standing viral diversity in East Asia, the emergence of structurally distinct Pacific and microvariants lineages, and ongoing diversification shaped by recombination, structural genome plasticity, and anthropogenic oyster movements. By integrating three decades of whole-genome data, this study provides a phylogenomic framework for understanding the diversity, evolution, and dispersal of OsHV-1 in modern aquaculture systems.

evolutionary biology↗

bioRxiv2025

Comparative performance of novel viral landscape phylogeography approaches

The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.

evolutionary biology↗

bioRxiv2025

Experimentally mimicking 30 years of Magallana gigas infections with the OsHV-1 virus reveals evolution through positive selection

Ostreid herpesvirus 1 (OsHV-1) poses a significant threat to the global oyster farming industry, causing substantial economic losses due to mortality outbreaks. While OsHV-1 primarily affects the Pacific oyster Magallana gigas, it has also been associated with mortality events in various other host species. Despite progress in understanding OsHV-1 epidemiology, important knowledge gaps remain regarding its evolutionary mechanisms and adaptation to host genetic backgrounds. This study uses experimental evolution and extensive genomic analysis to investigate the dynamics of OsHV-1 evolution in response to oyster host genetic variation. Our results show that genetic mutations, particularly transitions and transversions, play a key role in shaping viral populations, contributing to a trend toward genetic homogenization. Notably, stronger positive selection signals were observed in viral genomes isolated from oyster populations with higher susceptibility, suggesting adaptation of viral genotypes to specific host genetic backgrounds. These findings shed light on the complex evolutionary dynamics of OsHV-1 and its interactions with oyster hosts. Understanding how this virus adapts to host genetic diversity is crucial for developing strategies to mitigate its impact on the oyster farming industry and provides valuable insights into the broader mechanisms of viral evolution in response to host variation.

evolutionary biology↗

bioRxiv2023

Genetic differentiation and host specialization among OsHV-1 infecting two oyster species in France

AbstractCross-species transmission is a major driver of disease emergence in humans and animals. The Ostreavirus ostreidmalaco1 (OsHV-1) is mainly associated with mortality in the Pacific oyster Magallana gigas, but has also been found in other mollusks, including the European flat oyster Ostrea edulis. This raises questions about OsHV-1 host specificity. This study explored the genetic differentiation of OsHV-1 in M. gigas and O. edulis and the underlying mechanisms. Using high-throughput sequencing, 40 OsHV-1 genomes were obtained from both O. edulis and M. gigas and were analyzed to assess viral diversity, lineage isolation, and cross-species transmission. Comparative genomics, population genetics, phylogenetic and phylodynamic methods revealed that host species significantly influence viral genetic structure. The data suggest that OsHV-1 was introduced in Europe with M. gigas, followed by a cross-species transmission event and divergence into two distinct lineages. Selection signals were identified in genomic regions involved in key viral functions, including host binding, DNA replication, and membrane-associated proteins, indicating possible adaptation to different hosts. Future research should investigate coevolution between OsHV-1 and a broader range of host species using phylogenetic approaches to better understand host-virus dynamics.

evolutionary biology↗

bioRxiv2022

Seasonality of host-seeking Ixodes ricinus nymph abundance in relation to climate

There is growing concern about climate change and its impact on human health. Specifically, global warming could increase the probability of emerging infectious diseases, notably because of changes in the geographical and seasonal distributions of disease vectors such as mosquitoes and ticks. For example, the range of Ixodes ricinus, the most common and widespread tick species in Europe, is currently expanding northward and at higher altitudes. However, little is known about the seasonal variation in tick abundance in different climates. Seasonality of I. ricinus is often based on expert opinions while field surveys are usually limited in time. Our objective was to describe seasonal variations in I. ricinus abundance under different climates. To this end, a seven-year longitudinal study, with monthly collections of I. ricinus host-seeking nymphs, was carried out in France, in six locations corresponding to different climates. Tick data were log-transformed and grouped between years so as to obtain seasonal variations for a typical year. Daily average temperature was measured during the study period. Seasonal patterns of nymph abundance were established for the six different locations using linear harmonic regression. Model parameters were estimated separately for each location. Seasonal patterns appeared different depending on the climate considered. Western temperate sites showed an early spring peak, a summer minimum and a moderate autumn and winter abundance. More continental sites showed a later peak in spring, and a minimum in winter. The peak occurred in summer for the mountainous site, with an absence of ticks in winter. In all cases except the mountainous site, the timing of the spring peak could be related to the sum of degree days since the beginning of the year. Winter abundance was positively correlated to the corresponding temperature. Our results highlight clear patterns in the different sites corresponding to different climates, which allow further forecast of tick seasonality under changing climate conditions.

ecology↗

bioRxiv2022

Emergence and clonal expansion in Europe of Vibrio aestuarianus lineages pathogenic for oysters

Crassostrea gigas oysters represent a significant global food source, with 4.7 million tons harvested per year. In 2001, the bacterium V. aesturianus francensis emerged as a pathogen that causes adult oyster mortality in France and Ireland. Its impact on oyster aquaculture has increased in Europe since its reemergence in 2012. To better understand the evolutionary mechanisms leading to the emergence and persistence over time of this pathogen, we conducted a survey of mollusk diseases through national reference laboratories (NRLs) across Europe. We analyzed 54 new genomes of V. aestuarianus (Va) isolated from multiple environmental compartments since 2001, in areas with and without bivalve mortalities. We used a combination of comparative genomics and population genetics approaches to show that Va francensis lineages have undergone clonal expansion in Europe, likely after a recent selective bottleneck. Low mutation and recombination rates may have selected particular virulent genotypes. Furthermore, we identified a specific cus-cop-containing island conferring copper resistance to Va francensis whose acquisition may have favored the emergence of pathogenic lineages adapted to oysters.

microbiology↗

bioRxiv2019

Evolutionary stasis of an RNA virus indicates arbovirus re-emergence triggered by accidental release

The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. Bluetongue virus serotype 8 (BTV-8), an insect-borne virus of ruminants, emerged in livestock in Northern Europe in 2006, spreading to most European countries by 2009 and causing losses of billions of Euros. Though the outbreak was successfully controlled through vaccination by early 2010, puzzlingly a closely-related BTV-8 strain re-emerged in France in 2015, triggering a second outbreak that is still ongoing. The origin of this virus and the mechanisms underlying its re-emergence are unknown. Here, we performed phylogenetic analyses of 164 whole BTV-8 genomes sampled throughout the two outbreaks. We demonstrate consistent clock-like virus evolution during both epizootics but found negligible evolutionary change between them. We estimate that the ancestor of the second outbreak dates from the height of the first outbreak in 2008. This implies that the virus had not been replicating for multiple years prior to its re-emergence in 2015. Given the absence of any known natural mechanism that could explain BTV-8 persistence over this period without replication, we conclude that the second outbreak was most likely initiated by accidental exposure of livestock to frozen material contaminated with virus from approximately 2008. Our work highlights new targets for pathogen surveillance programmes in livestock and illustrates the power of genomic epidemiology to identify pathways of infectious disease emergence.

evolutionary biology↗

bioRxiv2018

Chronic infections can shape epidemic exposure: Pathogen co-occurrence networks in the Serengeti lions

Pathogens are embedded in a complex network of microparasites that can collectively or individually alter disease dynamics and outcomes. Chronic pathogens, for example, can either facilitate or compete with subsequent pathogens thereby exacerbating morbidity and mortality. Pathogen interactions are ubiquitous in nature, but poorly understood, particularly in wild populations. We report here on ten years of serological and molecular data in African lions, leveraging comprehensive demographic and behavioral data to utilize pathogen networks to test if chronic infections shape infection by acute pathogens. We combine network and community ecology approaches to assess broad network structure and characterize associations between pathogens across spatial and temporal scales. We found significant non-random structure in the lion-pathogen co-occurrence network and identified potential facilitative and competitive interactions between acute and chronic pathogens. Our results provide a novel insight for untangling the complex associations underlying pathogen co-occurrence networks.

ecology↗