scholarly journals Next Generation Sequencing for HIV-1 Drug Resistance Testing—A Special Issue Walkthrough

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 340
Author(s):  
Rami Kantor
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Resistance Testing ◽  
Next Generation ◽  
Special Issue ◽  
Global Challenge ◽  
Drug Resistance Testing ◽  
Generation Sequencing ◽  
Hiv 1

Drug resistance remains a global challenge in the fight against the HIV pandemic [...]

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 for HIV Drug Resistance Testing: Laboratory, Clinical, and Implementation Considerations

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 617 ◽  
Author(s):  
Santiago Ávila-Ríos ◽  
Neil Parkin ◽  
Ronald Swanstrom ◽  
Roger Paredes ◽  
Robert Shafer ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Clinical Care ◽  
Pcr Amplification ◽  
Resistance Testing ◽  
Sample Type ◽  
Next Generation ◽  
Hiv Drug Resistance ◽  
Drug Resistance Testing ◽  
Generation Sequencing

Higher accessibility and decreasing costs of next generation sequencing (NGS), availability of commercial kits, and development of dedicated analysis pipelines, have allowed an increasing number of laboratories to adopt this technology for HIV drug resistance (HIVDR) genotyping. Conventional HIVDR genotyping is traditionally carried out using population-based Sanger sequencing, which has a limited capacity for reliable detection of variants present at intra-host frequencies below a threshold of approximately 20%. NGS has the potential to improve sensitivity and quantitatively identify low-abundance variants, improving efficiency and lowering costs. However, some challenges exist for the standardization and quality assurance of NGS-based HIVDR genotyping. In this paper, we highlight considerations of these challenges as related to laboratory, clinical, and implementation of NGS for HIV drug resistance testing. Several sources of variation and bias occur in each step of the general NGS workflow, i.e., starting material, sample type, PCR amplification, library preparation method, instrument and sequencing chemistry-inherent errors, and data analysis options and limitations. Additionally, adoption of NGS-based HIVDR genotyping, especially for clinical care, poses pressing challenges, especially for resource-poor settings, including infrastructure and equipment requirements and cost, logistic and supply chains, instrument service availability, personnel training, validated laboratory protocols, and standardized analysis outputs. The establishment of external quality assessment programs may help to address some of these challenges and is needed to proceed with NGS-based HIVDR genotyping adoption.

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