HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure

Authors: Beheydt G, Bruzzone B, Camacho RJ, De Luca A, Deforche K, Grossman Z, Imbrechts S, Incardona F, Libin P, Pironti A, Rhee SY, Ruiz L, Sangeda RZ, Shafer RW, Sönnerborg A, Theys K, Torti C, Van de Vijver DA, Van Laethem K, Van Wijngaerden E, Vandamme AM, Vercauteren J, Zazzi M
Journal: Infection Genetics and Evolution
Link: http://www.ncbi.nlm.nih.gov/pubmed/23523594

We previously modeled the in vivo evolution of human immunodeficiency virus-1 (HIV-1) under drug selective pressure from cross-sectional viral sequences. These fitness landscapes (FLs) were made by using first a Bayesian network (BN) to map epistatic substitutions, followed by scaling the fitness landscape based on an HIV evolution simulator trying to evolve the sequences from treatment naïve patients into sequences from patients failing treatment.
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Predicted residual activity of rilpivirine in HIV-1 infected patients failing therapy including NNRTIs efavirenz or nevirapine

Authors: Camacho RJ, Gomes P, Portuguese HIVRSG, Rhee SY, Theys K, Vandamme AM
Publication Year: 2015
Journal: Clinical Microbiology and Infection
Link: http://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(15)00299-2/fulltext%20

Rilpivirine is a second-generation nonnucleoside reverse-transcriptase inhibitor (NNRTI) currently indicated for first-line therapy, but its clinical benefit for HIV-1 infected patients failing first-generation NNRTIs is largely undefined. This study quantified the extent of genotypic rilpivirine resistance in viral isolates from 1212 patients upon failure of efavirenz- or nevirapine-containing antiretroviral treatment, of whom more than respectively […]
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Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

Authors: Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bertagnolio S, Bessong PO, Blanco JL, Boucher CA, Brooks JI, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, de Wit TR, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Hamers RL, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Ioannidis JPA, Jordan MR, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Lemey P, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rhee SY, Rolland M, Shafer RW, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Taylor J, Tee KK, Truong HM, Van de Vijver DA, Vandamme AM, Varghese V, Vidal N, Yang C, Yang R, Yebra G
Publication Year: 2015
Journal: Plos Medicine
Link: http://www.ncbi.nlm.nih.gov/pubmed/25849352

BACKGROUND: Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for […]
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HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure

Predicted residual activity of rilpivirine in HIV-1 infected patients failing therapy including NNRTIs efavirenz or nevirapine

Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

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