UCSF

DNA microarray-based approaches to viral detection and discovery help overcome many limitations of the existing diagnostic methods. A panviral detection microarray has been developed in our laboratory and is comprised of oligonucleotides derived from ~1200 viral species representing all viral sequences present in the NCBI Nucleotide database as of Fall 2004. The array is capable of detecting viruses from all know viral families, including novel viruses through the use of oligonucleotides derived from the most conserved viral sequences. The platform was successfully used to discover a novel coronavirus in a viral culture sample derived from a patient with Severe Acute Respiratory Syndrome (SARS) during the 2003 outbreak. In addition, a novel retrovirus has been discovered in a subset of prostate tumors from patients with a mutation in the RNASEL gene. The platform has also been applied to clinical diagnostics for detecting viruses associated with acute respiratory infections in pediatric patients. The success of the platform has been linked to the development of new algorithms for microarray oligonucleotide selection, tools for microarray-based species identification, optimized techniques for viral nucleic acid extraction and amplification, and novel strategies for viral sequence recovery from analyzed samples.