Next-generation sequencing for HIV drug resistance testing: laboratory, clinical, and implementation considerations

S Ávila-Ríos, N Parkin, R Swanstrom, R Paredes… - Viruses, 2020 - mdpi.com
Higher accessibility and decreasing costs of next generation sequencing (NGS), availability
of commercial kits, and development of dedicated analysis pipelines, have allowed an …

Low-abundance drug-resistant HIV-1 variants in antiretroviral drug-naive individuals: a systematic review of detection methods, prevalence, and clinical impact

HA Mbunkah, S Bertagnolio, RL Hamers… - The Journal of …, 2020 - academic.oup.com
Background The presence of high-abundance drug-resistant HIV-1 jeopardizes success of
antiretroviral therapy (ART). Despite numerous investigations, the clinical impact of low …

[HTML][HTML] Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

JJC de Vries, JR Brown, N Couto, M Beer… - Journal of Clinical …, 2021 - Elsevier
Metagenomic next-generation sequencing (mNGS) is an untargeted technique for
determination of microbial DNA/RNA sequences in a variety of sample types from patients …

Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing

ER Lee, N Parkin, C Jennings, CJ Brumme, E Enns… - Scientific Reports, 2020 - nature.com
Next generation sequencing (NGS) is a trending new standard for genotypic HIV-1 drug
resistance (HIVDR) testing. Many NGS HIVDR data analysis pipelines have been …

Multi-laboratory comparison of next-generation to sanger-based sequencing for HIV-1 drug resistance genotyping

NT Parkin, S Avila-Rios, DF Bibby, CJ Brumme… - Viruses, 2020 - mdpi.com
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 …

Dolutegravir plus lamivudine for maintenance of HIV viral suppression in adults with and without historical resistance to lamivudine: 48-week results of a non …

R De Miguel, D Rial-Crestelo… - …, 2020 - thelancet.com
Background We investigated the efficacy of a switch to dolutegravir plus lamivudine in
aviremic individuals without evidence of persistent lamivudine resistance-associated …

A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance

T Taylor, ER Lee, M Nykoluk, E Enns, B Liang… - Scientific Reports, 2019 - nature.com
Conventional HIV drug resistance (HIVDR) genotyping utilizes Sanger sequencing (SS)
methods, which are limited by low data throughput and the inability of detecting low …

Pre-treatment HIV-drug resistance associated with virologic outcome of first-line NNRTI-antiretroviral therapy: a cohort study in Kenya

IA Beck, M Levine, CJ McGrath, S Bii, RS Milne… - …, 2020 - thelancet.com
Background Pre-treatment HIV-drug-resistance (PDR) to WHO-recommended 1st-line non-
nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral treatment (ART) is …

Pre-treatment integrase inhibitor resistance and natural polymorphisms among HIV-1 subtype C infected patients in Ethiopia

DA Arimide, ZI Szojka, K Zealiyas, A Gebreegziabxier… - Viruses, 2022 - mdpi.com
Dolutegravir-based antiretroviral therapy (ART) has been scaled up in many developing
countries, including Ethiopia. However, subtype-dependent polymorphic differences might …

Interaction of the host and viral genome and their influence on HIV disease

RH Tough, PJ McLaren - Frontiers in Genetics, 2019 - frontiersin.org
The course of Human Immunodeficiency Virus type 1 (HIV) infection is a dynamic interplay in
which both host and viral genetic variation, among other factors, influence disease …