On-site, high-fidelity target sequencing and absolute quantitation for HIV-1 surveillance

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PROJECT SUMMARY / ABSTRACT UNAIDS has set ambitious 90/90/90 targets toward ending the HIV/AIDS epidemic: that by 2020, 90% of people living with HIV will know their HIV status; 90% of those diagnosed will be on sustained antiretroviral treatment; and 90% of those on treatment will have achieved viral suppression. Reaching these goals will require precise and efficient testing, patient care, and prevention interventions for key populations, particularly in resource-limited settings. The genetic diversity of microbial pathogens – not just HIV-1 but any number of pathogens for which antimicrobial drugs are being developed/employed – remains a major challenge for those endeavoring to control them. Drug-resistance surveillance and the genotyping of microbial pathogens have long been plagued by limited read lengths and erroneous sequencing. The proposed project will develop an innovative sequencing and quantitation platform technology that can sensitively detect and accurately delineate HIV-1 variants in patients through barcode-mediated, whole-genome sequencing using the so-called “third-generation” Nanopore sequencing technology (Aims 1 and 2). Taking advantage of the pocket-size mobility of the MinION Nanopore sequencer and other portable biotechnology devices that have recently became available, we will further develop this technology for on-site and real-time surveillance and drug- resistance diagnosis of emerging viruses even in resource-limited settings (Aim 3). Successful completion of this study will produce a low-cost, ultra-high-accuracy sequencing and quantitation technology with broad applicability to problems in diverse areas of science and medicine, from de novo genome assembly to point-of- care drug-resistance genotyping. HIV-1 offers an excellent testbed for this technology due to the high degree intra-patient genetic diversity and the need for on-site and genome-wide genotyping.