Analysis of viral diversity in relation to the recency of HIV-1C infection in Botswana

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dc.contributor.authorMoyo, Sikhulileen_ZA
dc.contributor.authorVandormael, Alainen_ZA
dc.contributor.authorWilkinson, Eduanen_ZA
dc.contributor.authorEngelbrecht, Susanen_ZA
dc.contributor.authorGaseitsiwe, Simanien_ZA
dc.contributor.authorKotokwe, Kenanao P.en_ZA
dc.contributor.authorMusonda, Rosemaryen_ZA
dc.contributor.authorTanser, Franken_ZA
dc.contributor.authorEssex, Maxen_ZA
dc.contributor.authorNovitsk, Vladimiren_ZA
dc.contributor.authorDe Oliveira, Tulioen_ZA
dc.date.accessioned2017-10-10T08:23:14Z
dc.date.available2017-10-10T08:23:14Z
dc.date.issued2016
dc.descriptionCITATION: Moyo, S., et al. 2016. Analysis of viral diversity in relation to the recency of HIV-1C infection in Botswana. PLoS ONE, 11(8):e0160649, doi:10.1371/journal.pone.0160649.en_ZA
dc.descriptionThe original publication is available at http://journals.plos.org/plosoneen_ZA
dc.description.abstractBackground: 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. Methods: 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%. Results: 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. Conclusion: PwD can accurately determine HIV infection recency. A secondary PwD screening reduces misclassification and increases the accuracy of serologic-based assays.en_ZA
dc.description.urihttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160649en_ZA
dc.description.versionPublisher's versionen_ZA
dc.format.extent18 pages : illustrations (chiefly colour)en_ZA
dc.identifier.citationMoyo, S., et al. 2016. Analysis of viral diversity in relation to the recency of HIV-1C infection in Botswana. PLoS ONE, 11(8):e0160649, doi:10.1371/journal.pone.0160649en_ZA
dc.identifier.issn1932-6203 (online)
dc.identifier.otherdoi:10.1371/journal.pone.0160649
dc.identifier.urihttp://hdl.handle.net/10019.1/102303
dc.language.isoen_ZAen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectHIV infections - Subtypesen_ZA
dc.subjectHIV infections -- Botwsanaen_ZA
dc.subjectViral based assayen_ZA
dc.titleAnalysis of viral diversity in relation to the recency of HIV-1C infection in Botswanaen_ZA
dc.typeArticleen_ZA
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