Metagenomic identification of a nodavirus and a circular ssDNA virus in semi-purified viral nucleic acids from the hepatopancreas of healthy Farfantepenaeus duorarum shrimp

Fisheries and aquaculture are impacted sporadically by newly emerged viral diseases. In most cases, searches for a causative pathogen only occur after a serious disease has emerged. As random shotgun sequencing (metagenomics) offers opportunities to identify novel viruses preemptively, the method wa...

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Bibliographic Details
Published in:Diseases of aquatic organisms 2013-09, Vol.105 (3), p.237-242
Main Authors: Ng, Terry Fei, Alavandi, Shankar, Varsani, Arvind, Burghart, Scott, Breitbart, Mya
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Animals
DNA, Circular - genetics
DNA, Circular - isolation & purification
DNA, Viral - genetics
DNA, Viral - isolation & purification
Farfantepenaeus duorarum
Genomics - methods
Hepatopancreas - virology
Litopenaeus vannamei
Macrobrachium rosenbergii
Marine
Molecular Sequence Data
Nodaviridae - isolation & purification
Nodavirus
Nodaviruses
Penaeidae
Penaeidae - virology
Phylogeny
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Summary:Fisheries and aquaculture are impacted sporadically by newly emerged viral diseases. In most cases, searches for a causative pathogen only occur after a serious disease has emerged. As random shotgun sequencing (metagenomics) offers opportunities to identify novel viruses preemptively, the method was tested on nucleic acids extracted from the hepatopancreas of 12 healthy northern pink shrimp Farfantepenaeus duorarum captured from the Gulf of Mexico. Among the sequences, a nodavirus (Farfantepenaeus duorarum nodavirus, FdNV) and a virus with similarities to circoviruses and cycloviruses that possess circular single-stranded DNA (ssDNA) genomes, were identified. The FdNV genome sequence was most closely related phylogenetically to nodaviruses causing white tail disease in Macrobrachium rosenbergii and muscle necrosis disease in Litopenaeus vannamei. While the circular ssDNA virus represents the third to be detected in association with a marine invertebrate, transmission trials are needed to confirm its infectivity for F. duorarum. This study highlights the potential for using metagenomic approaches in fisheries and aquaculture industries to identify new potential pathogens in asymptomatic marine invertebrates, uncharacterized pathogens causing a new disease, or multiple pathogens associated with disease syndromes.
ISSN:0177-5103
1616-1580
DOI:10.3354/dao02628