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

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

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish (US)
Article number7480
JournalScientific Reports
Volume7
Issue number1
DOIs
StatePublished - Dec 1 2017

Fingerprint

HIV
Incidence
Infection
Biomarkers
Genome
Genes
Meta-Analysis

ASJC Scopus subject areas

  • General

Cite this

The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards. / Park, Sung Yong; Love, Tanzy M.T.; Reynell, Lucy; Yu, Carl; Kang, Tina Manzhu; Anastos, Kathryn; Dehovitz, Jack; Liu, Chenglong; Kober, Kord M.; Cohen, Mardge; Mack, Wendy J.; Lee, Ha Youn.

In: Scientific Reports, Vol. 7, No. 1, 7480, 01.12.2017.

Research output: Contribution to journalArticle

Park, SY, Love, TMT, Reynell, L, Yu, C, Kang, TM, Anastos, K, Dehovitz, J, Liu, C, Kober, KM, Cohen, M, Mack, WJ & Lee, HY 2017, 'The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards', Scientific Reports, vol. 7, no. 1, 7480. https://doi.org/10.1038/s41598-017-07490-4
Park, Sung Yong ; Love, Tanzy M.T. ; Reynell, Lucy ; Yu, Carl ; Kang, Tina Manzhu ; Anastos, Kathryn ; Dehovitz, Jack ; Liu, Chenglong ; Kober, Kord M. ; Cohen, Mardge ; Mack, Wendy J. ; Lee, Ha Youn. / The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards. In: Scientific Reports. 2017 ; Vol. 7, No. 1.
@article{15087dff7383437593b7330fbed5fdd7,
title = "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 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.",
author = "Park, {Sung Yong} and Love, {Tanzy M.T.} and Lucy Reynell and Carl Yu and Kang, {Tina Manzhu} and Kathryn Anastos and Jack Dehovitz and Chenglong Liu and Kober, {Kord M.} and Mardge Cohen and Mack, {Wendy J.} and Lee, {Ha Youn}",
year = "2017",
month = "12",
day = "1",
doi = "10.1038/s41598-017-07490-4",
language = "English (US)",
volume = "7",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",

}

TY - JOUR

T1 - The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards

AU - Park, Sung Yong

AU - Love, Tanzy M.T.

AU - Reynell, Lucy

AU - Yu, Carl

AU - Kang, Tina Manzhu

AU - Anastos, Kathryn

AU - Dehovitz, Jack

AU - Liu, Chenglong

AU - Kober, Kord M.

AU - Cohen, Mardge

AU - Mack, Wendy J.

AU - Lee, Ha Youn

PY - 2017/12/1

Y1 - 2017/12/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85027286859&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85027286859&partnerID=8YFLogxK

U2 - 10.1038/s41598-017-07490-4

DO - 10.1038/s41598-017-07490-4

M3 - Article

C2 - 28785052

AN - SCOPUS:85027286859

VL - 7

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 7480

ER -