A New Family of DNA Viruses Causing Disease in Crustaceans from Diverse Aquatic Biomes

ABSTRACT Panulirus argus virus 1 (PaV1) is the only known virus infecting the Caribbean
spiny lobster (Panulirus argus) from the Caribbean Sea. Recently, related viruses,
Dikerogammarus haemobaphes virus 1 (DhV1) and Carcinus maenas virus 1
(CmV1), have been detected in the demon shrimp (Dikerogammarus haemobaphes)
and the European shore crab (Carcinus maenas), respectively, from sites in the
United Kingdom. The virion morphology of these crustacean viruses is similar to that
of iridoviruses. However, unlike iridoviruses and other nucleocytoplasmic large DNA
viruses (NCLDVs), these viruses complete their morphogenesis in the host cell nucleus
rather than in the cytoplasm. To date, these crustacean viruses have remained
unclassified due to a lack of genomic data. Using an Illumina MiSeq sequencer, we
sequenced the complete genomes of PaV1, CmV1, and DhV1. Comparative genome
analysis shows that these crustacean virus genomes encode the 10 hallmark proteins
previously described for the NCLDVs of eukaryotes, strongly suggesting that they are
members of this group. With a size range of 70 to 74 kb, these are the smallest
NCLDV genomes identified to date. Extensive gene loss, divergence of gene sequences,
and the accumulation of low-complexity sequences reflect the extreme
degradation of the genomes of these “minimal” NCLDVs rather than any direct relationship
with the NCLDV ancestor. Phylogenomic analysis supports the classification
of these crustacean viruses as a distinct family, “Mininucleoviridae,” within the pithoirido-
Marseille branch of the NCLDVs.
IMPORTANCE Recent genomic and metagenomic studies have led to a dramatic expansion
of the known diversity of nucleocytoplasmic large DNA viruses (NCLDVs) of
eukaryotes, which include giant viruses of protists and important pathogens of vertebrates,
such as poxviruses. However, the characterization of viruses from nonmodel
hosts still lags behind. We sequenced the complete genomes of three viruses
infecting crustaceans, the Caribbean spiny lobster, demon shrimp, and European
shore crab. These viruses have the smallest genomes among the known NCLDVs,
with losses of many core genes, some of which are shared with iridoviruses. The deterioration
of the transcription apparatus is compatible with microscopic and ultrastructural
observations indicating that these viruses replicate in the nucleus of infected
cells rather than in the cytoplasm. Phylogenomic analysis indicates that these
viruses are sufficiently distinct from all other NCLDVs to justify the creation of a separate
family, for which we propose the name “Mininucleoviridae” (i.e., small viruses
reproducing in the cell nucleus).