Deep sequencing: becoming a critical tool in clinical virology

ME Quiñones-Mateu, S Avila, G Reyes-Teran… - Journal of clinical …, 2014 - Elsevier
Population (Sanger) sequencing has been the standard method in basic and clinical DNA
sequencing for almost 40 years; however, next-generation (deep) sequencing …

Current drugs for HIV-1: from challenges to potential in HIV/AIDS

Y Peng, Y Zong, D Wang, J Chen, ZS Chen… - Frontiers in …, 2023 - frontiersin.org
The human immunodeficiency virus (HIV) persists in latently infected CD4+ T cells and
integrates with the host genome until cell death. Acquired immunodeficiency syndrome …

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 …

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 …

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 …

Bioinformatic data processing pipelines in support of next‐generation sequencing‐based HIV drug resistance testing: the Winnipeg consensus

H Ji, E Enns, CJ Brumme, N Parkin… - Journal of the …, 2018 - Wiley Online Library
Introduction Next‐generation sequencing (NGS) has several advantages over conventional
Sanger sequencing for HIV drug resistance (HIVDR) genotyping, including detection and …

HIV-1 Drug Resistance Detected by Next-Generation Sequencing among ART-Naïve Individuals: A Systematic Review and Meta-Analysis

F Ouyang, D Yuan, W Zhai, S Liu, Y Zhou, H Yang - Viruses, 2024 - mdpi.com
Background: There are an increasing number of articles focused on the prevalence and
clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing …

[HTML][HTML] Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations

H Ji, RA Kozak, MJ Biondi, R Pilon, D Vallee, BB Liang… - Virology, 2015 - Elsevier
Identifying HCV drug resistance mutations (DRMs) is increasingly important as new direct
acting antiviral therapies (DAA) become available. Tagged pooled pyrosequencing (TPP) …

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low-and middle-income countries

H Ekici, SD Rao, A Sönnerborg… - Journal of …, 2014 - academic.oup.com
Objectives Increased trends of primary drug resistance mutations (DRMs) among treatment-
naive HIV-1-infected patients in low-and middle-income countries (LMICs) and the non …

Sensitive testing of plasma HIV-1 RNA and Sanger sequencing of cellular HIV-1 DNA for the detection of drug resistance prior to starting first-line antiretroviral therapy …

AM Geretti, T Conibear, A Hill… - Journal of …, 2014 - academic.oup.com
Objectives This study investigated strategies that may increase the yield of drug resistance
testing prior to starting antiretroviral therapy (ART), and whether transmitted and …