454 Sequencing Helps Identify Herpes-like Viruses That May Contribute To Pandemic Decline Of Tropical Reefs

February 1, 2009 at 8:00 am Leave a comment


In an effort to determine the influence of viral pathogens in declining coral health, researchers at San Diego State University recently used metagenomic analysis with the Genome Sequencer System from 454 Life Sciences to sequence Porites compressa coral samples under varying environmental stressors. The purpose of the study, led by Dr. Forest Rohwer, was to replicate current ecological changes in tropical reef habitats such as reduced pH, elevated nutrients and increased temperatures to determine their effects on viral populations within the coral. The experiments found highly-abundant levels of a herpes-like viruses in stressed Porites compressa corals. Interestingly, the viral sequences were rarely detected in un-stressed, healthy samples.




Although corals are the main builders of tropical reef systems, little is known about their microbiology. As a result, studies on coral disease have been limited to bacteria and fungus that can be easily cultivated. The depth of coverage and absence of cloning steps make 454 Sequencing ideally suited for unbiased metagenomic surveys of highly diverse samples. In this study, the Genome Sequencer system enabled the identification of over 15,000 coral associated viral sequences and, among those, herpes viruses were the most common. “The sheer number of available sequences has allowed me to demonstrate that the similarities have broad and deep coverage across the a-herpesvirus genomes and are not due to bias in the database,” states lead author Rebecca Vega Thurber, Assistant Professor of Biology at Florida International University and former member of Forest Rohwer’s lab in San Diego. “Most importantly, these sequences have allowed us to use alternative measures to test and confirm the hypothesis that stress causes production of these herpes-like viruses.”




“Dr. Rohwer’s study of how climate change is impacting tropical coral reefs by inducing changes in the viral community of that ecosystem is extremely interesting and important research,” said Christopher McLeod, President and CEO of 454 Life Sciences. “We are excited to see that metagenomic analyses using long reads and high-throughput of our 454 Sequencing system are enabling discoveries in completely new fields of biology, such as coral virology, that were simply not possible only a few years ago.”




While further studies are needed to understand how these viruses affect coral physiology, it is clear that environmental stressors not only result in coral symbiont loss and bacterial and fungal diseases but also in increased herpes-like virus production that together may explain the devastating death of coral reefs as ocean temperatures rise and pollution increases.




454 Life Sciences, a center of excellence of Roche Applied Science, develops and commercializes the innovative 454 Sequencing system for ultra-high-throughput DNA sequencing. Specific applications include de novo sequencing and re-sequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of DNA regions of interest. The hallmarks of the 454 Sequencing system are its simple, unbiased sample preparation and long, highly accurate sequence reads, including paired-end reads. The technology of the 454 Sequencing system has enabled hundreds of peer-reviewed studies in diverse research fields, such as cancer and infectious disease research, drug discovery, marine biology, anthropology, paleontology and many more.



About Roche




Headquartered in Basel, Switzerland, Roche is one of the world’s leading research-focused healthcare groups in the fields of pharmaceuticals and diagnostics. As the world’s biggest biotech company and an innovator of products and services for the early detection, prevention, diagnosis and treatment of diseases, the Group contributes on a broad range of fronts to improving people’s health and quality of life. Roche is the world leader in in-vitro diagnostics and drugs for cancer and transplantation, and is a market leader in virology. It is also active in other major therapeutic areas such as autoimmune diseases, inflammatory and metabolic disorders and diseases of the central nervous system. In 2007 sales by the Pharmaceuticals Division totaled 36.8 billion Swiss francs, and the Diagnostics Division posted sales of 9.3 billion francs. Roche has R&D agreements and strategic alliances with numerous partners, including majority ownership interests in Genentech and Chugai, and invested over 8 billion Swiss francs in R&D in 2007. Worldwide, the Group employs about 80,000 people. Additional information is available on the Internet at http://www.roche.com.




The 454 GS FLX is sold for life science research use only. The 454 Genome Sequencer FLX is intended only for use in basic or applied laboratory research, and is not intended for use in human diagnostics. Roche Diagnostics does not condone any use of the 454 Genome Sequencer FLX other than basic or applied laboratory research, and Roche Diagnostics will not support any other use.




(1) Vega Thurber et al. Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. (2008) PNAS 105:18413-8.



Roche

[Via http://www.medicalnewstoday.com]

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