Metatranscriptomics unmasks Mollusca virome with a remarkable presence of rhabdovirus in cephalopods

Abstract

IntroductionMollusks play a significant role in marine ecosystems and have economic value for aquaculture. Sometimes, unexpected and unexplained mortalities among mollusks have been described. The role of potential pathogens such as viruses remains unknown due to the lack of molluscan cell cultures, which is one of the major drawbacks to determining the viral role in such mortalities. Several oceanographic studies have suggested a high abundance of viruses in the oceans. Virus identification and understanding of viral interaction with organisms in marine ecosystems are in their infancy. Metatranscriptomics could become a useful tool to identify viruses using a shotgun approach and the growing number of viral genomes and sequences deposited in public databases.MethodsIn this work, several bioinformatics approaches were set up to screen Mollusca RNA sequences to find and confirm viral traces in their transcriptomes. This meta-analysis included an extensive search of SRA datasets belonging to mollusks available in the NCBI database, selecting a total of 55 SRA datasets that were further analyzed searching for viral sequences.ResultsTwenty-two bivalves, 19 cephalopods and 16 gastropods from 16 geographical origins and 17 different tissues were considered. The domain search approach was the most productive method to find viral sequences. This virus search showed that Cephalopoda samples (Idiosepius notoides and Amphioctopus fangsiao) exhibited the highest number of virus identifications. Some of the detected viral sequences were similar or identical to others previously identified. However, 33 putative new viruses were identified and analyzed phylogenetically when the RdRp domain was available. Specifically, Cephalopoda samples showed a considerable number of viruses belonging to the Rhabdoviridae family.

Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla

“…True viral presence of both families among the samples seems likely, although the abundance of potyviruses was probably overestimated. Interestingly, Betaflexiviridae -like sequences were also identified in different transcriptomes of marine mollusk samples by a recent study ( 97 ).…”

Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla

“…True viral presence of both families among the samples seems likely, although the abundance of potyviruses was probably overestimated. Interestingly, Betaflexiviridae-like sequences were also identified in different transcriptomes of marine mollusk samples by a recent study (Rey-Campos et al, 2023). Unlike the clustering observed for viral families, the separation of phyla into clusters was less obvious.…”

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

“…Furthermore, Di Gaspero et al (2022) evaluated the sensitivity and specificity of high-throughput RNA-seq in plants for classifying infected and uninfected samples of Vitis vinifera [ 40 ]. Similarly, in aquatic organisms, RNA-seq meta-transcriptomic studies have been used to reveal the presence of viruses, bacteria, and host–pathogen interactions, respectively [ 41 , 42 ]. Ample work using RNA-seq for active chicken poultry farm surveillance has been recently reviewed by Afonso (2023) with the detection of most viral and bacterial species in respiratory, cloacal, and tissue samples [ 43 ].…”