Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact

Minority and majority pre-treatment HIV-1 drug resistance associated with failure of 1st-line NNRTI ART in Kenyan women

(2019) Ross S. Milne et al.   AIDS

Presence, persistence and effects of pre-treatment HIV-1 drug resistance variants detected using next generation sequencing: A Retrospective longitudinal study from rural coastal Kenya

(2019) Amin S. Hassan et al.   PLoS One

Impact of Human Immunodeficiency Virus Type 1 Minority Variants on the Virus Response to a Rilpivirine-Based First-line Regimen

(2018) Stéphanie Raymond et al.   CLINICAL INFECTIOUS DISEASES

Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society–USA Panel

(2018) Huldrych F Günthard et al.   CLINICAL INFECTIOUS DISEASES

Primary resistance to integrase strand transfer inhibitors in patients infected with diverse HIV-1 subtypes in sub-Saharan Africa

(2018) Seth C Inzaule et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Low prevalence of transmitted HIV-1 drug resistance detected by a dried blood spot (DBS)-based next-generation sequencing (NGS) method in newly diagnosed individuals in Cameroon in the years 2015–16

(2018) Herbert A Mbunkah et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Insights about minority HIV-1 strains in transmitted drug resistance mutation dynamics and disease progression

(2018) Ana Rachel Leda et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Pretreatment drug resistance in a large countrywide Ethiopian HIV-1C cohort: a comparison of Sanger and high-throughput sequencing

(2018) Nigus Fikrie Telele et al.   Scientific Reports

Assessment of Transmitted HIV-1 Drug Resistance Mutations Using Ultra-Deep Pyrosequencing in A Turkish Cohort

(2018) Uluhan Sili   CURRENT HIV RESEARCH

Clinically relevant thresholds for ultrasensitive HIV drug resistance testing: a multi-country nested case-control study

(2018) Seth C Inzaule et al.   Lancet HIV

Impact of Next-generation Sequencing Defined Human Immunodeficiency Virus Pretreatment Drug Resistance on Virological Outcomes in the ANRS 12249 Treatment-as-Prevention Trial

(2018) Anne Derache et al.   CLINICAL INFECTIOUS DISEASES

Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors

(2018) Ronit R. Dalmat et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

(2018) Hezhao Ji et al.   Journal of the International AIDS Society

Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay

(2018) Nicholas Silver et al.   AIDS Research and Therapy

Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes

(2018) Bin Su et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Disparities in HIV-1 transmitted drug resistance detected by ultradeep sequencing between men who have sex with men and heterosexual populations

(2017) E Todesco et al.   HIV MEDICINE

No impact of HIV-1 protease minority resistant variants on the virological response to a first-line PI-based regimen containing darunavir or atazanavir

(2017) Marine Perrier et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Multimethod Longitudinal HIV Drug Resistance Analysis in Antiretroviral-Therapy-Naive Patients

(2017) Aubin J. Nanfack et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Ultradeep sequencing of B and non-B HIV-1 subtypes: Viral diversity and drug resistance mutations before and after one month of antiretroviral therapy in naive patients

(2017) Olivier Epaulard et al.   JOURNAL OF CLINICAL VIROLOGY

Prevalence of Drug-Resistant Minority Variants in Untreated HIV-1–Infected Individuals With and Those Without Transmitted Drug Resistance Detected by Sanger Sequencing

(2017) Dana S Clutter et al.   JOURNAL OF INFECTIOUS DISEASES

MinVar: A rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing

(2017) Michael Huber et al.   JOURNAL OF VIROLOGICAL METHODS

No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men

(2017) Antoine Chaillon et al.   JOURNAL OF VIROLOGY

Comparison between next-generation and Sanger-based sequencing for the detection of transmitted drug-resistance mutations among recently infected HIV-1 patients in Israel, 2000-2014

(2017) Roy Moscona et al.   Journal of the International AIDS Society

Survival of HIV-positive patients starting antiretroviral therapy between 1996 and 2013: a collaborative analysis of cohort studies

(2017) Adam Trickey et al.   Lancet HIV

High prevalence of HIV-1 transmitted drug-resistance mutations from proviral DNA massively parallel sequencing data of therapy-naïve chronically infected Brazilian blood donors

(2017) Rodrigo Pessôa et al.   PLoS One

Sensitive sentinel mutation screening reveals differential underestimation of transmitted HIV drug resistance among demographic groups

(2016) Jin-fen Li et al.   AIDS

Enhanced surveillance of HIV-1 drug resistance in recently infected MSM in the UK

(2016) Emma Cunningham et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations

(2016) David Seifert et al.   JOURNAL OF MOLECULAR BIOLOGY

Pre-treatment minority HIV-1 drug resistance mutations and long term virological outcomes: is prediction possible?

(2016) M. L. Mzingwane et al.   Virology Journal

Pretreatment HIV-drug resistance in Mexico and its impact on the effectiveness of first-line antiretroviral therapy: a nationally representative 2015 WHO survey

(2016) Santiago Ávila-Ríos et al.   Lancet HIV

A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing

(2016) Elizabeth P. St. John et al.   PLoS One

Clinical value of ultradeep HIV-1 genotyping and tropism testing in late presenters with advanced disease

(2015) Maria Casadellà et al.   AIDS

High Prevalence of HIV Low Abundance Drug-Resistant Variants in a Treatment-Naive Population in North Rift Kenya

(2015) Winfrida Cheriro et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain

(2015) Jessica R. Keys et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Primary resistance to integrase strand-transfer inhibitors in Europe: Table 1.

(2015) M. Casadellà et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Minority resistant HIV-1 variants and the response to first-line NNRTI therapy

(2015) F. Nicot et al.   JOURNAL OF CLINICAL VIROLOGY

Deep sequencing analysis of HIV-1 reverse transcriptase at baseline and time of failure in patients receiving rilpivirine in the phase III studies ECHO and THRIVE

(2015) Veerle Van Eygen et al.   JOURNAL OF MEDICAL VIROLOGY

Emergent HIV-1 Drug Resistance Mutations Were Not Present at Low-Frequency at Baseline in Non-Nucleoside Reverse Transcriptase Inhibitor-Treated Subjects in the STaR Study

(2015) Danielle Porter et al.   Viruses-Basel

Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq

(2015) Hirotaka Ode et al.   Frontiers in Microbiology

Minor viral population with drug-resistant mutation and risk of persistent low-level viremia or ‘blips’ in HIV-1 subtype C

(2014) Ujjwal Neogi et al.   AIDS

Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients

(2014) Karin J. Metzner et al.   AIDS

Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism

(2014) Richard M. Gibson et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Virological failure after 1 year of first-line ART is not associated with HIV minority drug resistance in rural Cameroon 

(2014) A. Zoufaly et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case–control study using centralized ultrasensitive 454 pyrosequencing

(2014) Alessandro Cozzi-Lepri et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2014) H. Ekici et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

HIV Reverse-Transcriptase Drug Resistance Mutations During Early Infection Reveal Greater Transmission Diversity Than in Envelope Sequences

(2014) Jonathan T. Lipscomb et al.   JOURNAL OF INFECTIOUS DISEASES

Low-Frequency Nevirapine (NVP)–Resistant HIV-1 Variants Are Not Associated With Failure of Antiretroviral Therapy in Women Without Prior Exposure to Single-Dose NVP

(2014) Valerie F. Boltz et al.   JOURNAL OF INFECTIOUS DISEASES

An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing

(2014) Birgitte B. Simen et al.   JOURNAL OF VIROLOGICAL METHODS

Prevalence of WHO Transmitted Drug Resistance Mutations by Deep Sequencing in Antiretroviral-Naïve Subjects in Hunan Province, China

(2014) Zou Xiaobai et al.   PLoS One

Minority Drug-Resistant HIV-1 Variants in Treatment Naïve East-African and Caucasian Patients Detected by Allele-Specific Real-Time PCR

(2014) Halime Ekici et al.   PLoS One

Low-Frequency NNRTI-Resistant HIV-1 Variants and Relationship to Mutational Load in Antiretroviral-Naïve Subjects

(2014) Shaili Gupta et al.   Viruses-Basel

Detection of Low-Frequency HIV Type 1 Reverse Transcriptase Drug Resistance Mutations by Ultradeep Sequencing in Naive HIV Type 1-Infected individuals

(2013) Pantxika Bellecave et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing

(2013) Vijay Bansode et al.   BMC INFECTIOUS DISEASES

Evaluation of a Benchtop HIV Ultradeep Pyrosequencing Drug Resistance Assay in the Clinical Laboratory

(2013) Boaz Avidor et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Origin of Minority Drug-Resistant HIV-1 Variants in Primary HIV-1 Infection

(2013) Karin J. Metzner et al.   JOURNAL OF INFECTIOUS DISEASES

Clinical and analytical relevance of NNRTIs minority mutations on viral failure in HIV-1 infected patients

(2013) Sofiane Mohamed et al.   JOURNAL OF MEDICAL VIROLOGY

Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination

(2013) Francesca Di Giallonardo et al.   PLoS One

Highly-Sensitive Allele-Specific PCR Testing Identifies a Greater Prevalence of Transmitted HIV Drug Resistance in Japan

(2013) Masako Nishizawa et al.   PLoS One

Deep sequencing does not reveal additional transmitted mutations in patients diagnosed with HIV-1 variants with single nucleoside reverse transcriptase inhibitor resistance mutations

(2012) M Pingen et al.   HIV MEDICINE

Minority variants associated with resistance to HIV-1 nonnucleoside reverse transcriptase inhibitors during primary infection

(2012) F. Nicot et al.   JOURNAL OF CLINICAL VIROLOGY

Minority HIV-1 resistant variants in recent infection and in patients who failed first-line antiretroviral therapy with no detectable resistance-associated mutations in Thailand

(2012) Hai Le Nguyen et al.   JOURNAL OF MEDICAL VIROLOGY

Low abundance drug resistance variants in transmitted HIV drug resistance surveillance specimens identified using tagged pooled pyrosequencing

(2012) Hezhao Ji et al.   JOURNAL OF VIROLOGICAL METHODS

Ultra-Deep Sequencing of HIV-1 Reverse Transcriptase Before Start of an NNRTI-based Regimen in Treatment-naive Patients

(2012) Peter Messiaen et al.   VIROLOGY

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

Prevalence of low-level HIV-1 variants with reverse transcriptase mutation K65R and the effect of antiretroviral drug exposure on variant levels

(2011) Michael J Kozal et al.   ANTIVIRAL THERAPY

Low-Frequency HIV-1 Drug Resistance Mutations and Risk of NNRTI-Based Antiretroviral Treatment Failure

(2011) Jonathan Z. Li   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Detection of Low-Level K65R Variants in Nucleoside Reverse Transcriptase Inhibitor–Naive Chronic and Acute HIV-1 Subtype C Infections

(2011) Jin-fen Li et al.   JOURNAL OF INFECTIOUS DISEASES

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

(2011) S. Gianella et al.   JOURNAL OF VIROLOGY

Prevalence and Impact of Minority Variant Drug Resistance Mutations in Primary HIV-1 Infection

(2011) Joanne D. Stekler et al.   PLoS One

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High frequency of integrase Q148R minority variants in HIV-infected patients naive of integrase inhibitors

(2010) Charlotte Charpentier et al.   AIDS

Low level of the K103N HIV-1 above a threshold is associated with virological failure in treatment-naive individuals undergoing efavirenz-containing therapy

(2010) Derrick D Goodman et al.   AIDS

Impact of Low Abundance HIV Variants on Response to Ritonavir-Boosted Atazanavir or Fosamprenavir Given Once Daily with Tenofovir/Emtricitabine in Antiretroviral-Naive HIV-Infected Patients

(2010) Lisa L. Ross et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Transmission of HIV‐1 Drug‐Resistant Variants: Prevalence and Effect on Treatment Outcome

(2010) Martin R. Jakobsen et al.   CLINICAL INFECTIOUS DISEASES

Increased detection of the HIV-1 reverse transcriptase M184V mutation using mutation-specific minority assays in a UK surveillance study suggests evidence of unrecognized transmitted drug resistance*

(2010) AJ Buckton et al.   HIV MEDICINE

Prevalence of key resistance mutations K65R, K103N, and M184V as minority HIV-1 variants in chronically HIV-1 infected, treatment-naïve patients

(2010) Karin J. Metzner et al.   JOURNAL OF CLINICAL VIROLOGY

Efficient Suppression of Minority Drug‐Resistant HIV Type 1 (HIV‐1) Variants Present at Primary HIV‐1 Infection by Ritonavir‐Boosted Protease Inhibitor–Containing Antiretroviral Therapy

(2010) Karin J. Metzner et al.   JOURNAL OF INFECTIOUS DISEASES

Minority Variants of Drug‐Resistant HIV

(2010) Sara Gianella et al.   JOURNAL OF INFECTIOUS DISEASES

Prevalence and Clinical Significance of HIV Drug Resistance Mutations by Ultra-Deep Sequencing in Antiretroviral-Naïve Subjects in the CASTLE Study

(2010) Max Lataillade et al.   PLoS One

Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy

(2009) Olivia Peuchant et al.   AIDS

Detection of Human Immunodeficiency Virus (HIV) Type 1 M184V and K103N Minority Variants in Patients with Primary HIV Infection

(2009) T. A. Toni et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Persistent Minority K103N Mutations among Women Exposed to Single‐Dose Nevirapine and Virologic Response to Nonnucleoside Reverse‐Transcriptase Inhibitor–Based Therapy

(2009) Ashraf Coovadia et al.   CLINICAL INFECTIOUS DISEASES

Difference in drug resistance patterns between minor HIV-1 populations in cerebrospinal fluid and plasma

(2009) T Bergroth et al.   HIV MEDICINE

Low-Frequency K103N Strengthens the Impact of Transmitted Drug Resistance on Virologic Responses to First-Line Efavirenz or Nevirapine-Based Highly Active Antiretroviral Therapy

(2009) Anna Maria Geretti et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Minority Variants Associated with Transmitted and Acquired HIV-1 Nonnucleoside Reverse Transcriptase Inhibitor Resistance: Implications for the Use of Second-Generation Nonnucleoside Reverse Transcriptase Inhibitors

(2009) Vici Varghese et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure

(2009) Melanie Balduin et al.   JOURNAL OF CLINICAL VIROLOGY

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

Sensitive detection of the K103N non-nucleoside reverse transcriptase inhibitor resistance mutation in treatment-naïve HIV-1 infected individuals by rolling circle amplification

(2009) Bin Wang et al.   JOURNAL OF VIROLOGICAL METHODS

Antiretroviral Drug Resistance Testing in Adult HIV‐1 Infection: 2008 Recommendations of an International AIDS Society–USA Panel

(2008) Martin S. Hirsch et al.   CLINICAL INFECTIOUS DISEASES

Minority Quasispecies of Drug‐Resistant HIV‐1 That Lead to Early Therapy Failure in Treatment‐Naive and ‐Adherent Patients

(2008) Karin J. Metzner et al.   CLINICAL INFECTIOUS DISEASES

Minority Human Immunodeficiency Virus Type 1 Variants in Antiretroviral-Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations

(2008) Y. Mitsuya et al.   JOURNAL OF VIROLOGY

Minority HIV-1 Drug Resistance Mutations Are Present in Antiretroviral Treatment–Naïve Populations and Associate with Reduced Treatment Efficacy

(2008) Jeffrey A Johnson et al.   PLOS MEDICINE