Dotto-Maurel, A. | bioRxiv Science

bioRxiv2025

Dynamic of the transcriptomic landscape of OsHV-1 replication in haemocytes of Pacific oyster

Since the 1990s, the Pacific oyster (Magallana gigas) has experienced repeated mortality events associated with Ostreid herpesvirus 1 (OsHV-1). Although the virus has been genomically characterised, its replication cycle and its interactions with the oyster immune system are still not well understood. In particular, little is known about the dynamics of OsHV-1 gene expression and the immune responses of haemocytes from oysters with varying susceptibility to the virus. While some studies have focused on the expression of specific viral and host genes on whole oysters, none have provided a comprehensive analysis of genomes-wide expression across multiple post-infection time points in haemocytes. The lack of oyster cell lines makes studying virus-host interactions in vitro challenging. However, haemocytes, the key immune cells circulating in hemolymph, can be maintained in vitro in the short term and represent a relevant model for analyzing infection dynamics. In this study, haemocytes from two M. gigas families, one highly susceptible and one less susceptible to OsHV-1, were infected in vitro. We tracked the viral and host transcriptomes over a 24-hour period post-infection using high-throughput dual transcriptomics. Our results provide a detailed overview of the OsHV-1 transcriptomic landscape in haemocytes from high and low susceptible M. gigas over time. In addition, WGCNA analysis of host genes expression provided insights into the haemocytes response to infection, and highlighted family-specific immune responses. This comprehensive transcriptomic study is the first to describe virus-host interactions across multiple stages of infection in haemocytes from Pacific oysters showing contrasted survival when exposed to OsHV-1. IMPORTANCEThis study provides valuable insights into the interaction between M. gigas and OsHV-1 by analyzing viral expression and host immune response at the cellular level. By focusing on haemocytes, the key immune cells in Pacific oysters, the results reveal a link between host genotype and viral transcriptomic activity, providing new perspectives on molecular basis of natural susceptibility levels to OsHV-1 infection depending of the genetic background. Overall, our findings deepen the understanding of OsHV-1 gene expression dynamics and antiviral defense mechanisms in key species cultivated worldwide.

bioinformatics↗

bioRxiv2024

Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization from Magallana gigas infected tissues

2Since the 1990s, the Pacific oyster Magallana gigas has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence of multiple genomic isomers, short-read sequencing using Illumina method struggles to accurately assemble tandem and repeat regions and to identify and characterize large structural variations in the OsHV-1 genome. Third-generation sequencing technologies, as long-read real-time nanopore sequencing from Oxford Nanopore Technologies (ONT), offer new possibilities for OsHV-1 whole genome analysis. Identification of the best method for extraction of high molecular weight (HMW) DNA and development of accurate bioinformatic pipelines for its characterization are now required. To this end, we evaluated and compared six HWM methods and one conventional DNA extraction kit for their ability to extract OsHV-1 DNA from M. gigas- infected tissues. We then evaluated the ability of ONT sequencing to produce an accurate OsHV-1 genome from both whole genome and "adaptive sampling" (AS) sequencing approaches. Finally, we evaluated the efficiency of bioinformatics tools for de novo assembly and consensus calling to generate accurate OsHV-1 genomes. The HMW DNA extraction kit coupled with ONT sequencing and dedicated bioinformatics tools allowed us to produce accurate OsHV-1 genomes compared to those assembled using Illumina technology. The AS approach allowed up to 60% enrichment for viral data, and the long reads generated by ONT allowed the characterization of OsHV-1 isomers. Together with its portability, this sequencing shows great promise as a diagnostic tool for the characterization of unculturable aquatic viruses directly from host tissues. 3 ImportanceMany aquatic viruses threaten commercially valuable species and cause significant economic losses during outbreaks. To improve our understanding of the origin, transmission patterns and spread of these viruses, additional genomic data are essential. However, genomic characterization of unculturable large DNA viruses is a major challenge. In the present study, we have successfully evaluated the ability of ONT sequencing and adaptive sequencing (AS) to sequence and assemble the complete OsHV-1 genome. Our results show that it is now possible to sequence the whole genome of large DNA viruses directly from infected host tissue, without the need for prior in vitro propagation or prior laboratory steps for virus enrichment.

genomics↗