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.

Nextera XT protocol for MiSeq HIVPR-RT sequencing v1

2021 ◽  
Author(s):  
Paula Aulicino
Keyword(s):  
Drug Resistance ◽  
Illumina Miseq ◽  
Hiv 1

The protocol allows amplification and NGS sequencing of a PR-RT HIV-1 sequence using tagmentation strategy and Illumina MiSeq equipment, followed by analysis of drug-resistance associated mutations by HyDRA

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 More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Alison F Feder ◽  
Soo-Yon Rhee ◽  
Susan P Holmes ◽  
Robert W Shafer ◽  
Dmitri A Petrov ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Hiv Treatment ◽  
Adaptive Mutation ◽  
Selective Sweeps ◽  
Resistance Mutations ◽  
Consensus Sequences ◽  
Adaptive Mutations ◽  
Slow Evolution ◽  
Effective Drugs ◽  
Hiv 1

In the early days of HIV treatment, drug resistance occurred rapidly and predictably in all patients, but under modern treatments, resistance arises slowly, if at all. The probability of resistance should be controlled by the rate of generation of resistance mutations. If many adaptive mutations arise simultaneously, then adaptation proceeds by soft selective sweeps in which multiple adaptive mutations spread concomitantly, but if adaptive mutations occur rarely in the population, then a single adaptive mutation should spread alone in a hard selective sweep. Here, we use 6717 HIV-1 consensus sequences from patients treated with first-line therapies between 1989 and 2013 to confirm that the transition from fast to slow evolution of drug resistance was indeed accompanied with the expected transition from soft to hard selective sweeps. This suggests more generally that evolution proceeds via hard sweeps if resistance is unlikely and via soft sweeps if it is likely.

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 Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals

2020 ◽  
Vol 75 (11) ◽  
pp. 3319-3326
Author(s):  
Benjamin Chimukangara ◽  
Jennifer Giandhari ◽  
Richard Lessells ◽  
Nonhlanhla Yende-Zuma ◽  
Benn Sartorius ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Virological Failure ◽  
Statistical Significance ◽  
Drug Resistant ◽  
Resistance Mutations ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
The Impact ◽  
Hiv 1 ◽  
Control Study

Abstract Objectives To determine the impact of pretreatment low-abundance HIV-1 drug-resistant variants (LA-DRVs) on virological failure (VF) among HIV-1/TB-co-infected individuals treated with NNRTI first-line ART. Methods We conducted a case–control study of 170 adults with HIV-1/TB co-infection. Cases had at least one viral load (VL) ≥1000 RNA copies/mL after ≥6 months on NNRTI-based ART, and controls had sustained VLs <1000 copies/mL. We sequenced plasma viruses by Sanger and MiSeq next-generation sequencing (NGS). We assessed drug resistance mutations (DRMs) using the Stanford drug resistance database, and analysed NGS data for DRMs at ≥20%, 10%, 5% and 2% thresholds. We assessed the effect of pretreatment drug resistance (PDR) on VF. Results We analysed sequences from 45 cases and 125 controls. Overall prevalence of PDR detected at a ≥20% threshold was 4.7% (8/170) and was higher in cases than in controls (8.9% versus 3.2%), P = 0.210. Participants with PDR at ≥20% had almost 4-fold higher odds of VF (adjusted OR 3.7, 95% CI 0.8–18.3) compared with those without, P = 0.104. PDR prevalence increased to 18.2% (31/170) when LA-DRVs at ≥2% were included. Participants with pretreatment LA-DRVs only had 1.6-fold higher odds of VF (adjusted OR 1.6, 95% CI 0.6–4.3) compared with those without, P = 0.398. Conclusions Pretreatment DRMs and LA-DRVs increased the odds of developing VF on NNRTI-based ART, although without statistical significance. NGS increased detection of DRMs but provided no additional benefit in identifying participants at risk of VF at lower thresholds. More studies assessing mutation thresholds predictive of VF are required to inform use of NGS in treatment decisions.

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
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