A novel nudivirus infecting the invasive demon shrimp Dikerogammarus haemobaphes (Amphipoda)

Thomas W. Allain,David Bass,Jamie Bojko,Donald C. Behringer,Grant D. Stentiford

doi:10.1038/s41598-020-71776-3

Abstract

The Nudiviridae are a family of large double-stranded DNA viruses that infects the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae).

Highlights

The family Nudiviridae comprises a group of non-occluded, double-stranded DNA viruses infecting arthropods
We use these data to provisionally name the virus as Dikerogammarus haemobaphes nudivirus (DhNV) and place the virus within a newly suggested genus Epsilonnudivirus of the family Nudiviridae
A protein signature match to the inhibitor of apoptosis repeat superfamily in DhNV_059 may indicate the presence of a homolog of the Iap nudivirus gene; BLASTp annotations did not yield any similarity results to the Iap gene found in other nudiviruses

Summary

Introduction

The family Nudiviridae comprises a group of non-occluded, double-stranded DNA (dsDNA) viruses infecting arthropods. Many of the amphipod hosts in which putative nudiviruses have been reported are non-native or invasive species present outside of their native ranges. Infection with this viral family may have potential for transboundary transmission when their hosts are present in their invasive range 7,10,11. We provide full genome characterisation of a nudivirus infecting the amphipod D. haemobaphes collected from outside of its native range. We use these data to provisionally name the virus as Dikerogammarus haemobaphes nudivirus (DhNV) and place the virus within a newly suggested genus Epsilonnudivirus of the family Nudiviridae

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Conclusion