scholarly journals Effect of storage conditions of dried plasma and blood spots on HIV-1 RNA quantification and PCR amplification for drug resistance genotyping

2010 ◽  
Vol 65 (8) ◽  
pp. 1562-1566 ◽  
Author(s):  
M. Monleau ◽  
C. Butel ◽  
E. Delaporte ◽  
F. Boillot ◽  
M. Peeters
Keyword(s):  
Drug Resistance ◽  
Pcr Amplification ◽  
Storage Conditions ◽  
Blood Spots ◽  
Rna Quantification ◽  
Drug Resistance Genotyping ◽  
Hiv 1

Dried blood spots for HIV-1 drug resistance genotyping in decentralized settings in Senegal

2013 ◽  
Vol 86 (1) ◽  
pp. 45-51 ◽  
Author(s):  
Abou Abdallah Malick Diouara ◽  
Halimatou Diop-Ndiaye ◽  
Khady Kebe-Fall ◽  
Edmond Tchiakpè ◽  
Ousseynou Ndiaye ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Dried Blood Spots ◽  
Blood Spots ◽  
Drug Resistance Genotyping ◽  
Hiv 1

scholarly journals HIV-1 drug resistance genotyping from dried blood spots stored for 1 year at 4 C

2008 ◽  
Vol 61 (6) ◽  
pp. 1217-1220 ◽  
Author(s):  
A. S. Youngpairoj ◽  
S. Masciotra ◽  
C. Garrido ◽  
N. Zahonero ◽  
C. de Mendoza ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Dried Blood Spots ◽  
Blood Spots ◽  
Drug Resistance Genotyping ◽  
Hiv 1

Development and evaluation of an assay for HIV-1 protease and reverse transcriptase drug resistance genotyping of all major group-M subtypes

2012 ◽  
Vol 54 (1) ◽  
pp. 21-25 ◽  
Author(s):  
Susan C. Aitken ◽  
Aletta Kliphuis ◽  
Carole L. Wallis ◽  
Mei Ling Chu ◽  
Quirine Fillekes ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Reverse Transcriptase ◽  
Major Group ◽  
Drug Resistance Genotyping ◽  
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.

Evaluation of an affordable HIV-1 virological failure assay and antiretroviral drug resistance genotyping protocol

2013 ◽  
Vol 194 (1-2) ◽  
pp. 300-307 ◽  
Author(s):  
M. Bronze ◽  
S.C. Aitken ◽  
C.L. Wallis ◽  
K. Steegen ◽  
L.J. Stuyver ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Virological Failure ◽  
Antiretroviral Drug Resistance ◽  
Drug Resistance Genotyping ◽  
Antiretroviral Drug ◽  
Hiv 1

scholarly journals Estimation of HIV-1 DNA Level Interfering with Reliability of HIV-1 RNA Quantification Performed on Dried Blood Spots Collected from Successfully Treated Patients

2016 ◽  
Vol 54 (6) ◽  
pp. 1641-1643 ◽  
Author(s):  
Sylvie Zida ◽  
Edouard Tuaillon ◽  
Makoura Barro ◽  
Arnaud Kwimatouo Lekpa Franchard ◽  
Thérèse Kagoné ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Dried Blood Spots ◽  
Peripheral Blood Mononuclear ◽  
Rna Detection ◽  
Blood Spots ◽  
Hiv Rna ◽  
Rna Quantification ◽  
Blood Mononuclear Cells ◽  
The Impact ◽  
Hiv 1

The impact of HIV-1 DNA coamplification during HIV-1 RNA quantification on dried blood spots (DBS) was explored. False-positive HIV RNA detection (22/62, 35%) was associated with high HIV-1 DNA levels. Specificity of HIV-1 RNA assays on DBS should be evaluated following manufacturer protocols on samples with HIV-1 DNA levels of ≥1,000 copies/106peripheral blood mononuclear cells.

scholarly journals MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing

2017 ◽  
Vol 240 ◽  
pp. 7-13 ◽  
Author(s):  
Michael Huber ◽  
Karin J. Metzner ◽  
Fabienne D. Geissberger ◽  
Cyril Shah ◽  
Christine Leemann ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Deep Sequencing ◽  
Drug Resistance Genotyping ◽  
Versatile Tool ◽  
Hiv 1
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