Prediction of coreceptor usage by five bioinformatics tools in a large Ethiopian HIV-1 subtype C cohort

• DOI: 10.1371/journal.pone.0182384
• Publication Date: 2017-08-25T17:39:30Z
• Authors: Amare Worku Kalu; Nigus Fikrie Telele; Solomon Gebreselasie; Daniel Fekade; Samir Abdurahman; Gaetano Marrone; Anders Sönnerborg
• Keywords: Concordance; Tissue tropism; Maraviroc

Genotypic tropism testing (GTT) has been developed largely on HIV-1 subtype B. Although a few reports have analysed the utility of GTT in other subtypes, more studies using C (HIV-1C) are needed, considering huge contribution HIV-1C to global epidemic.Plasma was obtained from 420 treatment-naïve infected Ethiopians recruited 2009-2011. The V3 region sequenced and coreceptor usage predicted by five tools: Geno2Pheno clinical-and clonal-models, PhenoSeq-C, C-PSSM Raymond's algorithm. impact baseline antiretroviral treatment (ART) outcome evaluated.Of 352 patients with successful sequences, proportion R5 virus varied between methods 12.5% (78.1%-90.6%). However, only 58.2% predictions were concordant 1.7% be X4-tropic across methods. Compared pairwise, highest concordance clonal (86.4%). In bivariate intention treat (ITT) analysis, achieved success frequently than X4 at month six as clinical (77.8% vs 58.7%, P = 0.004) 12 (61.9% 46.6%, 0.038). multivariable analysis adjusted for age, gender, CD4 viral load, showed an (P 0.04, OR 2.47, 95% CI 1.06-5.79).Each bioinformatics models comparable frequency but there large discordance Baseline had first line ART ITT based prediction which thus possibly could used predicting Ethiopians.