HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies

Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, fo...

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Bibliographic Details
Published in:Viruses 2021-06, Vol.13 (6), p.1125
Main Authors: Manyana, Sontaga, Gounder, Lilishia, Pillay, Melendhran, Manasa, Justen, Naidoo, Kogieleum, Chimukangara, Benjamin
Format: Article
Language:English
Subjects:
Antiretroviral therapy
Costs
Data analysis
Drug resistance
FDA approval
Flexibility
Genes
Genotyping
GLP-1 receptor agonists
HIV
HIV-1 drug resistance
Human immunodeficiency virus
Laboratories
Methods
Mutation
Next-generation sequencing
Quality of life
resource limited settings
Review
Sanger sequencing
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Summary:Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
ISSN:1999-4915
1999-4915
DOI:10.3390/v13061125