Healthy and moribund Zhikong scallops (

Viral assemblages of scallops are still relatively unknown. Here, metagenomic analysis was used to study virus communities in the gut of scallops to establish the first scallop virome data set (SVD); this contains 7,447 viral operational taxonomic units. Protein-sharing networks and phylogenetic analyses demonstrated the high diversity and novelty of the SVD, which is very different from viromes from other habitats. Potentially pathogenic viruses are prevalent in the gut of scallops. In particular, the novel smacoviruses were identified, indicating that scallops may be a potential hotspot for this viral group. Inference of virus-host associations found extensive interactions between viruses and major prokaryotic lineages. Intriguingly, moribund scallops showed a higher diversity of auxiliary metabolic genes (AMGs) related to amino acid metabolism and cofactor and vitamin genes, while healthy scallops had fewer AMGs, with those present focusing on secondary metabolite biosynthesis and carbohydrate metabolism. These findings provide the first landscape of scallop gut viruses based on metagenomes and highlight the potential roles of diverse and unique gut viruses for the health of filter-feeding bivalves. IMPORTANCE: This study uses metagenome sequencing to establish the first scallop virome database. The study reveals previously unknown diversity of scallop-associated viruses and provides insights into links between disease status and viral diversity and genome content. The study will interest many aquatic virologists and could have important implications in managing marine resources.