HIV Incidence and Drug Resistance Surveillance using Microdrop HIV Sequencing

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The movement of 90-90-90: Treatment for All aims to end the AIDS epidemic by 2030; however, there were still 1.7 million new HIV infections in 2019 worldwide, emphasizing the need to improve current systems of HIV epidemic monitoring and targeted preventions and interventions. As a renewal application of the parent R01 project (AI095066), this proposal builds upon our pioneering accomplishments of inventing microdrop HIV sequencing for high-resolution and low-cost simultaneous HIV incidence and drug resistance surveillance. Our single blood draw assay approach, HIDA (HIV Incidence and Drug Resistance Assay), responds to the growing need to precisely determine HIV incidence and identify drug resistance mutations, including minority variants and cross-class drug resistance mutations linked in a single genome. Our major innovation is to amplify HIV full- length envelope and pol gene sequences within micro-droplets and this compartmental amplification alongside with long-read high-throughput sequencing allows us to extract incidence and drug resistance signatures in a highly precise manner. The central goal of this application is to deliver an end-to-end platform for real-time HIV incidence and drug resistance cross-sectional surveillance. In Aim 1, we propose to conduct a cross-sectional surveillance by accessing 2,658 HIV positive plasma specimens from the Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS), in partnership with Nigeria CDC. By producing massive HIV full-length envelope and pol gene sequences, we will report Nigeria’s regional HIV incidence profiles and 93 WHO surveillance drug resistance mutation prevalence at the population and individual levels. Aim 2 of this application is devoted to devise a low- cost, open-source laboratory automation platform. Recent advances in do-it-yourself automation platforms will facilitate the deployment of HIDA’s microdrop HIV sequencing into low- and middle- income countries for their perpetual HIV surveillance. This standardized, high-throughput automation platform is ideal for performing cross- sectional surveys in resource-limited settings. Aim 3 will integrate HIDA with a cloud-based platform that fully automates incidence and drug resistance surveillance algorithms as a software-as-a-service. The standardization of high-throughput sequencing data analysis is a central requirement for routine surveillance. HIDA’s software- as-a-service will output standardized, high-quality surveillance outcomes directly to users, circumventing the need for investigators to invest in high-cost hardware to perform their own time-consuming analyses. This cloud platform will report both population-level and individual-level incidence and drug resistance profiles in a given geographic region. HIDA via microdrop HIV sequencing will promote global real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool for incidence and drug resistance.