The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards

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...

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Autores principales:	Sung Yong Park, Tanzy M. T. Love, Lucy Reynell, Carl Yu, Tina Manzhu Kang, Kathryn Anastos, Jack DeHovitz, Chenglong Liu, Kord M. Kober, Mardge Cohen, Wendy J. Mack, Ha Youn Lee
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/03fa9c58903d40c9bfd7e86326df169b
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spelling	oai:doaj.org-article:03fa9c58903d40c9bfd7e86326df169b2021-12-02T12:31:53ZThe HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards10.1038/s41598-017-07490-42045-2322https://doaj.org/article/03fa9c58903d40c9bfd7e86326df169b2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07490-4https://doaj.org/toc/2045-2322Abstract 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.Sung Yong ParkTanzy M. T. LoveLucy ReynellCarl YuTina Manzhu KangKathryn AnastosJack DeHovitzChenglong LiuKord M. KoberMardge CohenWendy J. MackHa Youn LeeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sung Yong Park Tanzy M. T. Love Lucy Reynell Carl Yu Tina Manzhu Kang Kathryn Anastos Jack DeHovitz Chenglong Liu Kord M. Kober Mardge Cohen Wendy J. Mack Ha Youn Lee The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards
description	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.
format	article
author	Sung Yong Park Tanzy M. T. Love Lucy Reynell Carl Yu Tina Manzhu Kang Kathryn Anastos Jack DeHovitz Chenglong Liu Kord M. Kober Mardge Cohen Wendy J. Mack Ha Youn Lee
author_facet	Sung Yong Park Tanzy M. T. Love Lucy Reynell Carl Yu Tina Manzhu Kang Kathryn Anastos Jack DeHovitz Chenglong Liu Kord M. Kober Mardge Cohen Wendy J. Mack Ha Youn Lee
author_sort	Sung Yong Park
title	The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards
title_short	The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards
title_full	The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards
title_fullStr	The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards
title_full_unstemmed	The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards
title_sort	hiv genomic incidence assay meets false recency rate and mean duration of recency infection performance standards
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/03fa9c58903d40c9bfd7e86326df169b
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The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards

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