ArticlePloS one2016
Analysis of Viral Diversity in Relation to the Recency of HIV-1C Infection in Botswana.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Use of HIV Recency Assays for HIV Incidence Estimation and Other Surveillance Use Cases: Systematic Review.JMIR public health and surveillance · 2022Pooled it
- Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.PLoS pathogens · 2020Trial
- Cross-sectional estimates revealed high HIV incidence in Botswana rural communities in the era of successful ART scale-up in 2013-2015.PloS one · 2018Trial
- HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.BMC bioinformatics · 2025Article
- Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.PLoS pathogens · 2024Article
- Using viral sequence diversity to estimate time of HIV infection in infants.PLoS pathogens · 2023Article
- Development of a multiassay algorithm (MAA) to identify recent HIV infection in newly diagnosed individuals in Indonesia.iScience · 2023Article
- Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana.The Journal of infectious diseases · 2022Article
- Next-generation sequencing of HIV-1 single genome amplicons.Biomolecular detection and quantification · 2019Article
- HIITE: HIV-1 incidence and infection time estimator.Bioinformatics (Oxford, England) · 2018Article
- Estimating time of HIV-1 infection from next-generation sequence diversity.PLoS computational biology · 2017Article
- Short Communication: Comparison of Maxim and Sedia Limiting Antigen Assay Performance for Measuring HIV Incidence.AIDS research and human retroviruses · 2017Article
- Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundCross-sectional, biomarker methods to determine HIV infection recency present a promising and cost-effective alternative to the repeated testing of uninfected individuals. We evaluate a viral-based assay that uses a measure of pairwise distances (PwD) to identify HIV infection recency, and compare its performance with two serologic incidence assays, BED and LAg. In addition, we assess whether combination BED plus PwD or LAg plus PwD screening can improve predictive accuracy by reducing the likelihood of a false-recent result.
methodsThe data comes from 854 time-points and 42 participants enrolled in a primary HIV-1C infection study in Botswana. Time points after treatment initiation or with evidence of multiplicity of infection were excluded from the final analysis. PwD was calculated from quasispecies generated using single genome amplification and sequencing. We evaluated the ability of PwD to correctly classify HIV infection recency within <130, <180 and <360 days post-seroconversion using Receiver Operator Characteristics (ROC) methods. Following a secondary PwD screening, we quantified the reduction in the relative false-recency rate (rFRR) of the BED and LAg assays while maintaining a sensitivity of either 75, 80, 85 or 90%.
resultsThe final analytic sample consisted of 758 time-points from 40 participants. The PwD assay was more accurate in classifying infection recency for the 130 and 180-day cut-offs when compared with the recommended LAg and BED thresholds. A higher AUC statistic confirmed the superior predictive performance of the PwD assay for the three cut-offs. When used for combination screening, the PwD assay reduced the rFRR of the LAg assay by 52% and the BED assay by 57.8% while maintaining a 90% sensitivity for the 130 and 180-day cut-offs respectively.
conclusionPwD can accurately determine HIV infection recency. A secondary PwD screening reduces misclassification and increases the accuracy of serologic-based assays.
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