Arruda, LB;
de Araujo, ML;
Martinez, ML;
Gonsalez, CR;
da Silva Duarte, AJ;
Coakley, E;
Lie, Y;
(2014)
DETERMINATION OF VIRAL TROPISM BY GENOTYPING AND PHENOTYPING ASSAYS IN BRAZILIAN HIV-1-INFECTED PATIENTS.
REVISTA DO INSTITUTO DE MEDICINA TROPICAL DE SAO PAULO
, 56
(4)
pp. 287-290.
10.1590/S0036-46652014000400003.
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Abstract
The clinical application of CCR5 antagonists involves first determining the coreceptor usage by the infecting viral strain. Bioinformatics programs that predict coreceptor usage could provide an alternative method to screen candidates for treatment with CCR5 antagonists, particularly in countries with limited financial resources. Thus, the present study aims to identify the best approach using bioinformatics tools for determining HIV-1 coreceptor usage in clinical practice. Proviral DNA sequences and Trofile results from 99 HIV-1-infected subjects under clinical monitoring were analyzed in this study. Based on the Trofile results, the viral variants present were 81.1% R5, 21.4% R5X4 and 1.8% X4. Determination of tropism using a Geno2pheno[coreceptor] analysis with a false positive rate of 10% gave the most suitable performance in this sampling: the R5 and X4 strains were found at frequencies of 78.5% and 28.4%, respectively, and there was 78.6% concordance between the phenotypic and genotypic results. Further studies are needed to clarify how genetic diversity amongst virus strains affects bioinformatics-driven approaches for determining tropism. Although this strategy could be useful for screening patients in developing countries, some limitations remain that restrict the wider application of coreceptor usage tests in clinical practice.
| Type: | Article |
|---|---|
| Title: | DETERMINATION OF VIRAL TROPISM BY GENOTYPING AND PHENOTYPING ASSAYS IN BRAZILIAN HIV-1-INFECTED PATIENTS |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1590/S0036-46652014000400003 |
| Publisher version: | https://doi.org/10.1590/S0036-46652014000400003 |
| Language: | English |
| Additional information: | This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc/4.0/deed.en |
| Keywords: | Science & Technology, Life Sciences & Biomedicine, Tropical Medicine, HIV-1, Tropism, Brazil, V3 loop, HIV CORECEPTOR USAGE, CCR5 ANTAGONISTS, PREDICTION, ALGORITHMS, MANAGEMENT, MARAVIROC, SEQUENCES, VARIANTS, PLASMA, TOOLS |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10072744 |
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