| Summary: | Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (<i>Crangon crangon</i>) and the European shore crab (<i>Carcinus maenas</i>). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family <i>Nudiviridae</i> but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (<i>tk</i>) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family <i>Nudiviridae</i> into four genera (<i>Alphanudivirus</i> to <i>Deltanudivirus),</i> as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family <i>Nudiviridae</i>, each subdivided into several genera.
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