scholarly journals Genotypic HIV-coreceptor tropism prediction with geno2pheno [coreceptor]: differences depending on HIV-1-subtype

2012 ◽  
Vol 15 (6(Suppl 4)) ◽  
Author(s):  
M Obermeier ◽  
R Ehret ◽  
T Berg ◽  
P Braun ◽  
K Korn ◽  
...  
2013 ◽  
Vol 68 (7) ◽  
pp. 1471-1485 ◽  
Author(s):  
Francisco Díez-Fuertes ◽  
Elena Delgado ◽  
Yolanda Vega ◽  
Aurora Fernández-García ◽  
María Teresa Cuevas ◽  
...  

2018 ◽  
Vol 16 (2) ◽  
pp. 113-120
Author(s):  
Amare Worku Kalu ◽  
Nigus Fikrie Telele ◽  
Shambhu G Aralaguppe ◽  
Solomon Gebre-Selassie ◽  
Daniel Fekade ◽  
...  

Objectives:Genotypic Tropism Testing (GTT) tools are generally developed based on HIV-1 subtype B (HIV-1B) and used for HIV-1C as well but with a large discordance of prediction between different methods. We used an established phenotypic assay for comparison with GTT methods and for the determination of in vitro maraviroc sensitivity of pure R5-tropic and dual-tropic HIV-1C.Methods:Plasma was obtained from 58 HIV-1C infected Ethiopians. Envgp120 was cloned into a luciferase tagged NL4-3 plasmid. Phenotypic tropism was determined by in house method and the V3 sequences were analysed by five GTT methods. In vitro maraviroc sensitivity of R5-tropic and dual-tropic isolates were compared in the TZMbl cell-line.Results:The phenotypes were classified as R5 in 92.4% and dual tropic (R5X4) in 7.6% of 79 clones. The concordance between phenotype and genotype ranged from 64.7% to 84.3% depending on the GTT method. Only 46.9% of the R5 phenotypes were predicted as R5 by all GTT tools while R5X4 phenotypes were predicted as X4 by four methods, but not by Raymond’s method. All six tested phenotypic R5 clones, as well as five of six of dual tropic clones, showed a dose response to maraviroc.Conclusion:There is a high discordance between GTT methods, which underestimates the presence of R5 and overestimates X4 strains compared to a phenotypic assay. Currently available GTT algorithms should be further improved for tropism prediction in HIV-1C. Maraviroc has an in vitro activity against most HIV-1C viruses and could be considered as an alternative regimen in individuals infected with CCR5-tropic HIV-1C viruses.


2011 ◽  
Vol 52 (7) ◽  
pp. 925-928 ◽  
Author(s):  
T. J. Wilkin ◽  
M. B. Goetz ◽  
R. Leduc ◽  
G. Skowron ◽  
Z. Su ◽  
...  

2014 ◽  
Vol 65 (4) ◽  
pp. 397-404 ◽  
Author(s):  
Soham Gupta ◽  
Ujjwal Neogi ◽  
Hiresave Srinivasa ◽  
Akhil C. Banerjea ◽  
Anita Shet
Keyword(s):  

2014 ◽  
Vol 30 (12) ◽  
pp. 1203-1212 ◽  
Author(s):  
Claudia Montagna ◽  
Elisa De Crignis ◽  
Isabella Bon ◽  
Maria Carla Re ◽  
Ivano Mezzaroma ◽  
...  

2010 ◽  
Vol 48 (11) ◽  
pp. 4135-4139 ◽  
Author(s):  
V. Sanchez ◽  
M. Masia ◽  
C. Robledano ◽  
S. Padilla ◽  
J. M. Ramos ◽  
...  

Intervirology ◽  
2015 ◽  
Vol 58 (3) ◽  
pp. 155-159 ◽  
Author(s):  
Matthieu Sechet ◽  
Catherine Roussel ◽  
Jean-Luc Schmit ◽  
Carlo Saroufim ◽  
Kamel Ghomari ◽  
...  

Objective: The aim of this study was to evaluate tropism prediction performances of three algorithms [geno2pheno false-positive rate 10% (G2P10), position-specific scoring matrix (PSSM) and a combination of the 11/25 and net charge rules] and to investigate the viral and host factors potentially involved in the X4 or R5 prediction in human immunodeficiency virus-1 (HIV-1) patients. Methods: Viral tropism was determined in 179 HIV-1-infected patients eligible for CCR5 antagonist therapy. HIV-1 RNA or DNA was extracted and amplified for env gp120 sequencing. In parallel, demographic, viral, immunological and clinical determinants were analyzed. Results: According to the G2P10 algorithm, 48 patients harbored X4 or X4R5 virus. The tropism prediction was concordant for 87.7 and 88.2% of samples when comparing G2P10 with PSSM or with a combination of the 11/25 and net charge rules, respectively. X4 prediction was significantly associated with more than 35 amino acids in the V3 domain (p < 0.0001) and loss of an N-linked glycosylation site (p < 0.0001). Of the factors studied, only the nadir CD4 T-cell count was significantly associated with X4 tropism (p = 0.01). Conclusion: We determined that the X4 virus detection is closely linked to the nadir CD4 T-cell count below 100 cells/mm3 that must be taken into account when considering a CCR5 antagonist therapy switch.


2006 ◽  
Vol 80 (10) ◽  
pp. 4909-4920 ◽  
Author(s):  
Mike Westby ◽  
Marilyn Lewis ◽  
Jeannette Whitcomb ◽  
Mike Youle ◽  
Anton L. Pozniak ◽  
...  

ABSTRACT Antagonists of the human immunodeficiency virus type 1 (HIV-1) coreceptor, CCR5, are being developed as the first anti-HIV agents acting on a host cell target. We monitored the coreceptor tropism of circulating virus, screened at baseline for coreceptor tropism, in 64 HIV-1-infected patients who received maraviroc (MVC, UK-427,857) as monotherapy for 10 days. Sixty-two patients harbored CCR5-tropic virus at baseline and had a posttreatment phenotype result. Circulating virus remained CCR5 tropic in 60/62 patients, 51 of whom experienced an HIV RNA reduction from baseline of >1 log10 copies/ml, indicating that CXCR4-using variants were not rapidly selected despite CCR5-specific drug pressure. In two patients, viral load declined during treatment and CXCR4-using virus was detected at day 11. No pretreatment factor predicted the emergence of CXCR4-tropic virus during maraviroc therapy in these two patients. Phylogenetic analysis of envelope (Env) clones from pre- and posttreatment time points indicated that the CXCR4-using variants probably emerged by outgrowth of a pretreatment CXCR4-using reservoir, rather than via coreceptor switch of a CCR5-tropic clone under selection pressure from maraviroc. Phylogenetic analysis was also performed on Env clones from a third patient harboring CXCR4-using virus prior to treatment. This patient was enrolled due to a sample labeling error. Although this patient experienced no overall reduction in viral load in response to treatment, the CCR5-tropic components of the circulating virus did appear to be suppressed while receiving maraviroc as monotherapy. Importantly, in all three patients, circulating virus reverted to predominantly CCR5 tropic following cessation of maraviroc.


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