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.
Highlights
HIV incidence is a primary metric for epidemic surveillance and prevention efficacy assessment
false recency rate (FRR) and mean duration of recent infection (MDRI) were measured using this cohort in which infection duration was well-characterized using documented HIV negative and positive dates, Fiebig stage, or specimen collection interval
The goal of this study was to assess the genomic incidence assay’s FRR and MDRI with a globally representative population to examine the application of this assay in a cross-sectional survey
Summary
HIV incidence is a primary metric for epidemic surveillance and prevention efficacy assessment. We tested the assay by newly sequencing 744 envelope genes from 59 specimens of 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. HIV incidence, the number of individuals newly-infected within a given time (1~2 years), is a key measure of the epidemic’s rise and decline[1] It serves as a direct metric of HIV intervention and prevention trial efficacy, providing timely feedback for intervention programs and guiding resource allocation and government responses[2,3,4]. Cross-sectional population sampling via a single blood draw has been considered to be the ideal platform to determine HIV incidence
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