Viral discovery is made difficult by the frequent inability to replicate these agents in vitro and the limitations of traditional methods requiring antigenic/serological cross-reactivity or nucleic acid hybridization. We postulate, based on our recent study of viral capsid-protected nucleic acids in symptomatic humans, that new viruses, both commensal and pathogenic, can be readily identified using a metagenomic approach. Our successes finding both new as well as a diverse mix of previously known human viruses in unprocessed biological samples using a minimal amount of sequencing indicate that a rich yield of previously unknown viruses is present in human samples. We have assembled for this nucleic acid survey a collection of samples from extensively characterized patients showing a range of symptoms including hepatitis, encephalitis and pneumonia of unexplained etiology. Samples from heavily virus-exposed (IDUs, MSM) and susceptible subjects (AIDS patients) and from humans frequently exposed to non-human primates will be similarly analyzed. Using an unbiased viral DNA and RNA amplification method, together with both traditional shotgun library sequencing and high throughput pyrosequencing, we will conduct a metagenomic survey of the human virome. Virus-specific bioinformatics methods will be developed to facilitate the detection of phylogenetically close as well as distant relatives of known viral species. Initial viral sequence similarity matches will be followed by full viral genome sequencing and phylogenetic analysis. The prevalence of newly identified viruses will then be determined using real-time PCR on different populations including healthy blood donors, IDUs and patients with identical symptoms or exposure risks. This metagenomic survey of non-human nucleic acids in humans will therefore begin the task of determining the full range of viral diversity in humans.
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