Abstract

The emergence of viral pathogens is a serious threat to aquaculture worldwide. New viral infections, introduced either from the wild or through international trade, can devastate an aquaculture industry. However, our response to viral pathogens has been largely reactive--a new pathogen is usually not discovered until it has already reached epidemic proportions. Currently, diagnosing novel viral infections is difficult due to limitations of virus discovery methods. PCR, immunological assays, and pan-viral microarrays are only useful in identifying viruses with high levels of similarity to known viruses. Viral metagenomics, which involves viral particle purification and shotgun sequencing, has proven to be useful for describing novel viruses, including those with limited homology to previously described viral families. Viral metagenomics has previously been used to investigate viral pathogens associated with mortality events in marine animals, but this method can also be utilized to investigate the viral community in wild populations before signs of disease are observed. Proactive characterization of viral pathogens from aquaculture species before epidemics occur will have tremendous advantages, benefitting both disease monitoring efforts and aquaculture management.

This study investigates viruses in two important groups of marine invertebrates: shrimps and copepods. Shrimps, together with mollusks and other crustaceans, accounted for 17 percent of the total value of internationally-traded fishery products in 2006; while copepods are the most abundant zooplankton group in the oceans, supporting the fisheries food chain. As previous studies have focused on detecting individual viruses associated with disease outbreaks in an aquaculture setting, little is known about the viral communities naturally present in these marine invertebrates. We performed viral metagenomics on whole copepods (Labidocera) collected from Tampa Bay, Florida, and on hepatopancreas, heart and hemolymph from wild shrimp (Farfantepenaeus duorarum) collected from Tarpon Springs, Florida. Metagenomic sequencing of DNA and RNA viruses purified from these invertebrates led to the discovery of a novel shrimp circovirus, a novel copepod circovirus, and two novel shrimp nodaviruses. The two novel circoviruses had single-stranded DNA genomes of 1700-2000 nucleotides, and shared less than 50% amino acid identity to any known viruses in the Genbank database. All previously described circoviruses infect birds or pigs, making these shrimp and copepod circoviruses the first circoviruses described in invertebrates. The two marine invertebrate circoviruses represented a phylogenetic clade distinct from the known avian and porcine circoviruses, expanding our knowledge on the diversity and evolution of the Circoviridae.Two novel nodaviruses were identified in the shrimp, which shared less than 60% amino acid identity to known shrimp nodaviruses and likely represent a novel virus genus. Future research needs to examine the prevalence and ecological impact of these viruses; however, this study has clearly demonstrated the potential of viral metagenomics to characterize novel viruses in aquaculture species and/or marine invertebrates before any sign of disease is observed. This research has implications for preventing disease in aquaculture, as well as for understanding viral diversity of natural populations of marine invertebrates.

Acknowledgements

This project was funded by grants to MB from the Alfred P. Sloan Foundation (BR-4772) and the National Science Foundation (MCB-0701984). TFFN was supported by the Gulf Oceanographic Charitable Trust Fellowship and the Elsie and William Knight, Jr. Endowed Fellowship.

Contact Information: Terry Fei Fan Ng, College of Marine Science, University of South Florida, 140 Seventh Avenue South, St. Petersburg, FL 33701, USA. Tel: (727) 553-3930. Email: fng@mail.usf.edu