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Positions | Contact Info | Education and Training | Research | Publications | Lab Members |
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Contact Information: Download a curriculum vitae [pdf file]
Training/Appointments:
Research Program How many more human viral species remain to be identified? The recent discovery of highly prevalent human viruses indicates that this is a fertile field of research. As an example of the potential impact of viral discovery approximately half of all analyzed cases of encephalitis and gastroenteritis have no identified etiology. Identifying new disease causing viruses could reduce their negative impact by improving our understanding of their transmission, provide diagnostic tools, provide candidate immunogens, and targets for the development of anti-virals. We are therefore accelerating our search for new human and animal viruses. Our bioinformatics collaborators have now created a greatly enhanced web site using a computer cluster for added speed of DNA sequence analysis. The web site is now reporting results of sequence similarity searches in a more user friendly fashion as well as performing internal database searches to identify related non-human nucleic acids found in different individuals. We are using massively parallel pyrosequencing (www.454.com) at the Stanford Genome Technology Center. This novel technology lowers the cost of sequencing approximately 10 fold. We have identified a new and highly diverse species of picobirnavirus in samples provided by the Minnesota dept of health and have measured its prevalence in 180 patients and healthy controls. We have received from the CA dept of Health Services seven viral culture showing cytopathic effects supernatants in which the viruses could not be identified. Within a week viral sequences were rapidly identified in each of them. We have also identified several new viruses in stool samples from Pakistani children with acute flaccid paralysis. These viruses are both new species and genus within known viral families as well as viruses with previously unseen genomic organizations. A large fraction of sequences show no detectable linear sequence similarities to any sequence in the database. Viral fragments from yet un-sampled highly divergent viral families might be expected to share such a property and be particularly interesting to identify. With Dr Peter Simmonds at the University of Edinburgh we have initiated a novel form of DNA sequence analysis based on composition rather than translated sequence protein similarities. Several sequences with full open reading frame show nucleic acid characteristics associated with polyoma viruses and anelloviruses. We are now attending to confirm this novel method of new virus discovery by extending these initial sequences to determine if detectable viral characteristic can be identified. More potential viruses have been identified than are listed above in the form of small viral fragments with significant sequence matches to known viruses. These viral candidates with low viral loads will be further studied using a variety of sequence extension methods. Acquiring longer sequences will allow us to confirm/refute the detection of new viruses. We will continue our outreach to investigators with appropriate samples for viral discovery to propose collaborations. We encourage interested persons to contact us.
Publications Herring BL, Page-Shafer K, Tobler LH, Delwart EL. Frequent hepatitis C virus superinfection in injection drug users. The Journal of infectious diseases 2004;190(8):1396-403. 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. Bernardin F, Kong D, Peddada L, Baxter-Lowe LA, Delwart E. Human immunodeficiency virus mutations during the first month of infection are preferentially found in known cytotoxic T-lymphocyte epitopes. Journal of virology 2005;79(17):11523-8. Herring BL, Bernardin F, Caglioti S, Stramer S, Tobler L, Andrews W, Cheng L, Rampersad S, Cameron C, Saldanha J, Busch MP, Delwart E. Phylogenetic analysis of WNV in North American blood donors during the 2003-2004 epidemic seasons. Virology 2007;363(1):220-8. 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. F Bernardin,L Tobler,I Walsh,J Dunn Williams,MP Busch, and E Delwart. Clearance of Hepatitis C Virus RNA from the peripheral blood mononuclear cells of blood donors who spontaneously or therapeutically control their plasma viremia. Hepatology. 2007 ;47:1446-1452. Delwart EL. Viral metagenomics. Reviews in Medical Virology 2007;17(2):115-31. |
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Eric Delwart, Ph.D.