scholarly journals The next generation: etravirine in the treatment of HIV-1 infection in adults refractory to other antiretrovirals

2010 ◽  
pp. 91 ◽  
Author(s):  
Michelle Liedtke ◽  
Rathbun
Keyword(s):  
Next Generation ◽  
Hiv 1

scholarly journals Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes

2012 ◽  
Vol 50 (12) ◽  
pp. 3838-3844 ◽  
Author(s):  
A. Gall ◽  
B. Ferns ◽  
C. Morris ◽  
S. Watson ◽  
M. Cotten ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals In Vitro Evaluation of Bis-3-Chloropiperidines as RNA Modulators Targeting TAR and TAR-Protein Interaction

2022 ◽  
Vol 23 (2) ◽  
pp. 582
Author(s):  
Alice Sosic ◽  
Giulia Olivato ◽  
Caterina Carraro ◽  
Richard Göttlich ◽  
Dan Fabris ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Chaperone Activity ◽  
Next Generation ◽  
In Vitro Evaluation ◽  
Loop Domain ◽  
Activation Response ◽  
Analytical Approaches ◽  
Bulge Loop ◽  
Hiv 1

After a long limbo, RNA has gained its credibility as a druggable target, fully earning its deserved role in the next generation of pharmaceutical R&D. We have recently probed the trans-activation response (TAR) element, an RNA stem–bulge–loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabilizing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analytical approaches for the study of multicomponent RNA-based interactions.

scholarly journals HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences

2017 ◽  
Vol 33 (11) ◽  
pp. 1083-1098 ◽  
Author(s):  
Oliver Ratmann ◽  
Chris Wymant ◽  
Caroline Colijn ◽  
Siva Danaviah ◽  
Max Essex ◽  
...  
Keyword(s):  
Sub Saharan Africa ◽  
Full Genome ◽  
Next Generation ◽  
Sub Saharan ◽  
Hiv 1

Routine drug resistance testing in HIV-1 proviral DNA, using an automated next- generation sequencing assay

2019 ◽  
Vol 121 ◽  
pp. 104207 ◽  
Author(s):  
Enagnon Kazali Alidjinou ◽  
Pauline Coulon ◽  
Christophe Hallaert ◽  
Olivier Robineau ◽  
Agnès Meybeck ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Resistance Testing ◽  
Next Generation ◽  
Proviral Dna ◽  
Drug Resistance Testing ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Next generation sequencing of HIV-1 protease in the PIVOT trial of protease inhibitor monotherapy

2018 ◽  
Vol 101 ◽  
pp. 63-65 ◽  
Author(s):  
David T. Dunn ◽  
Wolfgang Stöhr ◽  
Alejandro Arenas-Pinto ◽  
Anna Tostevin ◽  
Jean L. Mbisa ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Protease Inhibitor ◽  
Next Generation ◽  
Protease Inhibitor Monotherapy ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

Viruses ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 694 ◽  
Author(s):  
Neil T. Parkin ◽  
Santiago Avila-Rios ◽  
David F. Bibby ◽  
Chanson J. Brumme ◽  
Susan H. Eshleman ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Illumina Miseq ◽  
Next Generation ◽  
Sequence Comparisons ◽  
Consensus Sequences ◽  
Drug Resistance Genotyping ◽  
Next Generation Sequencing Ngs ◽  
Sequence Quality ◽  
Average Sequence Identity ◽  
Hiv 1

Next-generation sequencing (NGS) is increasingly used for HIV-1 drug resistance genotyping. NGS methods have the potential for a more sensitive detection of low-abundance variants (LAV) compared to standard Sanger sequencing (SS) methods. A standardized threshold for reporting LAV that generates data comparable to those derived from SS is needed to allow for the comparability of data from laboratories using NGS and SS. Ten HIV-1 specimens were tested in ten laboratories using Illumina MiSeq-based methods. The consensus sequences for each specimen using LAV thresholds of 5%, 10%, 15%, and 20% were compared to each other and to the consensus of the SS sequences (protease 4–99; reverse transcriptase 38–247). The concordance among laboratories’ sequences at different thresholds was evaluated by pairwise sequence comparisons. NGS sequences generated using the 20% threshold were the most similar to the SS consensus (average 99.6% identity, range 96.1–100%), compared to 15% (99.4%, 88.5–100%), 10% (99.2%, 87.4–100%), or 5% (98.5%, 86.4–100%). The average sequence identity between laboratories using thresholds of 20%, 15%, 10%, and 5% was 99.1%, 98.7%, 98.3%, and 97.3%, respectively. Using the 20% threshold, we observed an excellent agreement between NGS and SS, but significant differences at lower thresholds. Understanding how variation in NGS methods influences sequence quality is essential for NGS-based HIV-1 drug resistance genotyping.

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