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PLoS One. 2016 Aug 23;11(8):e0160649. doi: 10.1371/journal.pone.0160649. eCollection 2016.

Analysis of Viral Diversity in Relation to the Recency of HIV-1C Infection in Botswana.

Author information

Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa.
Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana.
Wellcome Trust Africa Centre for Health and Population Studies, Dorris Duke Medical Research Centre, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
National Health Laboratory Services (NHLS), Tygerberg Coastal, South Africa.
Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.
Research Department of Infection, University College London, London, United Kingdom.
College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.



Cross-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.


The 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%.


The 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.


PwD can accurately determine HIV infection recency. A secondary PwD screening reduces misclassification and increases the accuracy of serologic-based assays.

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