Genomic Miniarrays for HIV-1 Subtyping

DESCRIPTION (provided by applicant): HIV/AIDS is an unprecedented viral pandemic with 42 million people infected worldwide and killing more than 3 million people per year. The high mutation rate of this virus has led to the evolution of multiple circulating genotypes, which confer variable disease outcomes, transmission rates, resistance to therapy, and responses to different vaccines. Worldwide efforts at vaccine development and trial evaluations depend on accurate information about which patient HIV-1 subtypes and circulating recombinant forms are present in the targeted populations. Current tests based on short sequencing, the heteroduplex mobility assay and realtime PCR are relatively expensive, can only detect a few targets, and are prone to error and misleading assessments. The PI has devised a novel miniarray and genomic probe set system for comprehensive SARS detection on a microarray platform. This new system can detect and distinguish the major genes of any viral species and provides a simplified profile of the genome structure. This grant Will adapt and extend this new technology to more accurate discrimination of HIV-1 subtypes by employing capture probe sets on the miniarray that parallel or duplicate essentially all the major gene targets which are presently employed in the above mentioned short-sequencing, HMA and real-time PCR assays. The proposed HIV-1 miniarrays will be populated with about 20 large and small probe sets for each of four reference subtypes, A1, B, C and D, with most targets in the conserved gag and the variable env gene regions. This system should therefore allow more exact and comprehensive subtype discrimination with a simple to use, inexpensive protocol, and with multiplex processing of patient samples. The proposed HIV-1 miniarrays will contain high specificity oligo-probes to selected consensus regions and larger target region probes that will be fault tolerant and will pick up new mutations and recombinant variations. The novel miniarrays and procedures are patent pending.