A method for high-throughput screening of known pathogenic viruses along with identification of "new" disease-associated viruses

The spectrum of pathogenic viruses of importance in human disease, agriculture and biology is not only large and diverse, but continually evolving. The identification or isolation of viral pathogens, in correlation with the presence of specific disease phenotypes, is of paramount importance both to diagnosis of disease and the subsequent management or treatment of viral infection. The limitations of current viral detection methods, such as PCR and immunoassays, led to the development of a novel microarray system for specific detection of viruses. The technology offered here for licensing provides a method for high- throughput screening of known pathogenic viruses along with identification of "new" disease-associated viruses. The novel method is based on a viral microarray containing 10,000 immobilized DNA oligonucleotide features, representing all known mammalian and avian pathogenic viruses (approximately 600). Software was also developed to analyze the viral microarray results. The oligonucleotide features in this system are 60-mer long and distributed across both conserved and non-conserved regions of known viral sequences. This design serves the dual purpose of: (1) facilitating validation via redundant signals associated with each represented virus and (2) allowing for the discovery of new viruses, which arise due to recombination. In addition, positive and negative controls against human and mouse housekeeping genes are included along with software for analysis of virus microarray results. Further advantages of the viral microarray include: (a) the use of sample inputs as little as 10ng of either total DNA or RNA extracted from virus infected cells, representing as few as 20 viral particles; (b) detection of viruses of both DNA and RNA classes; (c) a capacity for high-throughput screening of various sample types including serum, saliva and biopsy tissues; and (d) analysis of a large number of samples in parallel on identical arrays. The detection of viral DNA is unique to this technology, as other available technologies only detect viral genomic RNA or viral mRNA transcripts. Additionally, the viral chip was found to be highly specific and sensitive for detecting different viral genomic sequences in cell lines and multiple viral constructs co-infection in cultured cells. Applications: - Detection and identification of viruses that cause disease - Efficient discovery of new pathogenic viruses - Diagnosis of human and animal disease outbreaks - Identification of viral agents used in bioterrorism. Development Status: - The pre-clinical performance of the viral microarray was evaluated by application of four virally positive infected cell lines (JSC-1-harboring EBV and KSHV, BCBL-1 harboring KSHV, HeLa- harboring HPV18, Cem X 174 harboring SIV). - Clinical performance was tested and validated through analysis of total RNA from cold (swab), Japanese Encephalitis, Dengue, Ebola and West Nile virus samples.

U.S. Provisional Application No 60/797,334 filed 02 May 2006 (HHS Reference No. E-206-2006/0-US-01) Inventors: Cassio S. Baptista (NCI), Xiaolin Wu (NCI), David J. Munroe (NCI)

Licensees sought: Available for non-exclusive or exclusive licensing. Collaborative Research Opportunity: The NCI-Laboratory of Molecular Technology is seeking statements of capability or interest from parties interested in collaborative research to further develop, evaluate, or commercialize this oligo microarray for identification and detection of all known mammalian and avian pathogenic viruses. Please contact Betty Tong, Ph.D. at 301- 594-4263 or tongb@mail.nih.gov for more information.