The genomes of penaeid shrimps and other decapods harbor endogenous nimaviruses , relatives of the devastating pathogen white spot syndrome virus (WSSV). Endogenous nimaviruses exclusively insert into specific nucleotide motifs occurring in repetitive sequences, e.g., microsatellites and 28S rDNA, most likely by using virus-encoded DNA recombination enzymes, the integrase. This strongly suggests that endogenous nimaviruses are actively colonizing sequence "niches" within the host genome. Repeat-specific integration, which targets redundant parts of the host genome, can be seen as an adaptive tactic that minimizes the cost on the fitness of the host.
To investigate the prevalence and diversity of endogenous nimaviruses in publicly available crustacean genome data, we queried WSSV proteins against the NCBI whole-genome shotgun contigs (wgs ) database. Majanivirus genomes were identified from all penaeid genomes analyzed, demonstrating the prevalence of endogenous nimaviruses in Penaeidae . Nimaviral sequences were absent from Astacidea and Palaemonidae , suggesting that nimaviral colonization is subject to lineage-specific biases within Decapoda. Genomes of clopoviruses , a group of divergent nimavirus -like endogenous viruses, were identified from isopod genomes, indicating that Nimaviridae and its close relatives represent an important part of the crustacean virome.
Discovery of endogenous nimaviruses has redefined Nimaviridae as a diverse viral family with many representatives hiding in the host genome. The current ICTV Taxonomy designates WSSV as the only member of Nimaviridae . Given the abundance and diversity of endogenous nimavirus genomes in the sequence database, we envision that there will be a need to formalize a sequence-based taxonomy and description of nimaviruses, as has already been implemented for other viral families.