Eric Delwart, Ph.D.
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How many more human viruses remain to be identified? The recent discoveries of highly prevalent human viruses indicate that this is a fertile field of research. As an example of the potential impact of viral discovery, 10-50% of cases of encephalitis, gastroenteritis, and hepatitis have no identified etiology. Identifying new viral pathogens can reduce their impact by improving our understanding of their mode of transmission, providing diagnostic tools, candidate immunogens, and targets for anti-virals.
We are using massively parallel pyrosequencing to sequence randomly amplified RNA and DNA from partially purified viral particles in clinical samples (i.e. viral metagenomics).
Our bioinformatics collaborators at Stanford are using cloud computing to speed DNA sequence similarity searches to identify new viruses. A user-friendly web site facilitates data visualization.
As of mid-2009 we have identified in human samples numerous new picornaviruses, astroviruses, anneloviruses, parvoviruses, circoviruses and a new papillomavirus. In animal samples we identified novel picornaviruses and reoviruses (see PubMed link below). Current studies include expanding our search for new viruses, determining their sero-prevalence in various human populations, and testing their association with different clinical symptoms.
Identifying new viral families showing no sequence similarity to currently known viruses would greatly expand our understanding of viral evolution. A large fraction of sequences generated from biological samples show no detectable linear sequence similarities to any sequence in Genbank. We are interested in new bioinformatics methods to identify such highly divergent viral families.
We are also continuing our outreach to other investigators with appropriate samples for viral discovery. Persons with such biological samples and post-docs interested in training in the field of viral metagenomics should contact us directly.
Delwart EL. Viral metagenomics. Reviews in Medical Virology 2007;17(2):115-31.
Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E. New DNA viruses identified in patients with acute viral infection syndrome. Journal of virology 2005;79(13):8230-6.
Kapoor A, Slikas E, Simmonds P, Chieochansin T, Naeem A, Shaukat S, Alam MM, Sharif S, Angez M, Zaidi S, Delwart E. 2009. A Newly Identified Bocavirus Species in Human Stool. Journal of Infectious Diseases 199:196-200.
Kapoor A, Victoria J, Simmonds P, Slikas E, Chieochansin T, Naeem A, Shaukat S, Sharif S, Alam MM, Angez M, Wang C, Shafer RW, Zaidi S, Delwart E. A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proceedings of the National Academy of Sciences USA 105:20482-7.
Kapoor A., Victoria J., Simmonds P., Wang C., Shafer R.W.,Nims R., Nielsen O., E. Delwart. A highly divergent picornavirus in a marine mammal. Journal of Virology 2008. 82:311-320.
Victoria JG, Kapoor A, Dupuis K, Schnurr DP, Delwart EL. 2008. Rapid identification of known and new RNA viruses from animal tissues. PLoS Pathog 4:e1000163.
Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, Wang C, Naeem A, Zaidi S, Delwart E. 2009. Metagenomic analysis of viruses in the stool of children with acute flaccid paralysis. Journal of Virology.