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Abstract
HIV incidence is a primary metric for epidemic surveillance and prevention efficacy assessment. HIV incidence assay performance is evaluated via false recency rate (FRR) and mean duration of recent infection (MDRI). We conducted a meta-analysis of 438 incident and 305 chronic specimens’ HIV envelope genes from a diverse global cohort. The genome similarity index (GSI) accurately characterized infection stage across diverse host and viral factors. All except one chronic specimen had GSIs below 0.67, yielding a FRR of 0.33 [0-0.98] %. We modeled the incidence assay biomarker dynamics with a logistic link function assuming individual variabilities in a Beta distribution. The GSI probability density function peaked close to 1 in early infection and 0 around two years post infection, yielding MDRI of 420 [361, 467] days. We tested the assay by newly sequencing 744 envelope genes from 59 specimens of 21 subjects who followed from HIV negative status. Both standardized residuals and Anderson-Darling tests showed that the test dataset was statistically consistent with the model biomarker dynamics. This is the first reported incidence assay meeting the optimal FRR and MDRI performance standards. Signatures of HIV gene diversification can allow precise cross-sectional surveillance with a desirable temporal range of incidence detection.
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1 Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
2 Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
3 Department of Medicine, and Epidemiology & Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, United States
4 Department of Medicine, SUNY Downstate Medical Center, Brooklyn, NY, United States
5 Department of Medicine, Georgetown University, Washington, DC, United States
6 Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, United States
7 Department of Medicine, Stroger Hospital, Chicago, IL, United States
8 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States