scholarly journals Improvement of HIV-1 coreceptor tropism prediction by employing selected nucleotide positions of the env gene in a Bayesian network classifier

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.


2012 ◽  
Vol 15 (6(Suppl 4)) ◽  
Author(s):  
M Obermeier ◽  
R Ehret ◽  
T Berg ◽  
P Braun ◽  
K Korn ◽  
...  

Retrovirology ◽  
2011 ◽  
Vol 8 (Suppl 2) ◽  
pp. P70 ◽  
Author(s):  
Joke Snoek ◽  
Concepción Casado ◽  
Sara Colombo ◽  
Andri Rauch ◽  
Soledad García ◽  
...  

2018 ◽  
Vol 132 ◽  
pp. 1412-1421 ◽  
Author(s):  
Sushant Kumar Pandey ◽  
Ravi Bhushan Mishra ◽  
Anil Kumar Triphathi

2020 ◽  
Vol 9 (1) ◽  
pp. 88-94 ◽  
Author(s):  
Sudeep Tanwar ◽  
Jayneel Vora ◽  
Shriya Kaneriya ◽  
Sudhanshu Tyagi ◽  
Neeraj Kumar ◽  
...  

2020 ◽  
Vol 208 ◽  
pp. 106422 ◽  
Author(s):  
Yang Liu ◽  
Limin Wang ◽  
Musa Mammadov

2019 ◽  
Vol 12 (1) ◽  
pp. 105 ◽  
Author(s):  
Seyed Mohammad Bolouki ◽  
Hamid Reza Ramazi ◽  
Abbas Maghsoudi ◽  
Amin Beiranvand Pour ◽  
Ghahraman Sohrabi

Mapping hydrothermal alteration minerals using multispectral remote sensing satellite imagery provides vital information for the exploration of porphyry and epithermal ore mineralizations. The Ahar-Arasbaran region, NW Iran, contains a variety of porphyry, skarn and epithermal ore deposits. Gold mineralization occurs in the form of epithermal veins and veinlets, which is associated with hydrothermal alteration zones. Thus, the identification of hydrothermal alteration zones is one of the key indicators for targeting new prospective zones of epithermal gold mineralization in the Ahar-Arasbaran region. In this study, Landsat Enhanced Thematic Mapper+ (Landsat-7 ETM+), Landsat-8 and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) multispectral remote sensing datasets were processed to detect hydrothermal alteration zones associated with epithermal gold mineralization in the Ahar-Arasbaran region. Band ratio techniques and principal component analysis (PCA) were applied on Landsat-7 ETM+ and Landsat-8 data to map hydrothermal alteration zones. Advanced argillic, argillic-phyllic, propylitic and hydrous silica alteration zones were detected and discriminated by implementing band ratio, relative absorption band depth (RBD) and selective PCA to ASTER data. Subsequently, the Bayesian network classifier was used to synthesize the thematic layers of hydrothermal alteration zones. A mineral potential map was generated by the Bayesian network classifier, which shows several new prospective zones of epithermal gold mineralization in the Ahar-Arasbaran region. Besides, comprehensive field surveying and laboratory analysis were conducted to verify the remote sensing results and mineral potential map produced by the Bayesian network classifier. A good rate of agreement with field and laboratory data is achieved for remote sensing results and consequential mineral potential map. It is recommended that the Bayesian network classifier can be broadly used as a valuable model for fusing multi-sensor remote sensing results to generate mineral potential map for reconnaissance stages of epithermal gold exploration in the Ahar-Arasbaran region and other analogous metallogenic provinces around the world.


Sign in / Sign up

Export Citation Format

Share Document