Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use? (Q42234370)

19 October 2017

Next-Generation Sequencing to Help Monitor Patients Infected with HIV: Ready for Clinical Use? (English)

1 reference

19 October 2017

Richard M Gibson

1

1 reference

PubMed ID

24585216

19 October 2017

Christine L Schmotzer

series ordinal

2

1 reference

PubMed ID

24585216

19 October 2017

Miguel E Quiñones-Mateu

series ordinal

3

1 reference

19 October 2017

1 April 2014

1 reference

Current infectious disease reports

19 October 2017

1 reference

19 October 2017

16

1 reference

19 October 2017

401

1 reference

19 October 2017

4

1 reference

Drug-resistant strains of AIDS virus found

19 October 2017

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

The evolution of HIV treatment guidelines: current state-of-the-art of ART.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Current tests to evaluate HIV-1 coreceptor tropism

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Genotypic resistance testing in routine clinical care

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

The use of resistance testing in the management of HIV-1-infected patients

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Performance of the applied biosystems ViroSeq human immunodeficiency virus type 1 (HIV-1) genotyping system for sequence-based analysis of HIV-1 in pediatric plasma samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Accuracy of the TRUGENE HIV-1 genotyping kit.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Genotypic antiretroviral resistance testing for human immunodeficiency virus type 1 integrase inhibitors by use of the TruGene sequencing system

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

HIV population genotypic tropism testing and its clinical significance

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Sensitivity of the ViroSeq HIV-1 genotyping system for detection of the K103N resistance mutation in HIV-1 subtypes A, C, and D.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Next-generation sequencing to assess HIV tropism

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Insights into hominid evolution from the gorilla genome sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Bats are a major natural reservoir for hepaciviruses and pegiviruses

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Challenges of bringing next generation sequencing technologies to clinical molecular diagnostic laboratories

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Clinical integration of next-generation sequencing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Rapid deep sequencing of patient-derived HIV with ion semiconductor technology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Analysis of low-frequency mutations associated with drug resistance to raltegravir before antiretroviral treatment

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Concordance between two phenotypic assays and ultradeep pyrosequencing for determining HIV-1 tropism

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Phenotyping methods for determining HIV tropism and applications in clinical settings

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Standardized peripheral blood mononuclear cell culture assay for determination of drug susceptibilities of clinical human immunodeficiency virus type 1 isolates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

A rapid method for simultaneous detection of phenotypic resistance to inhibitors of protease and reverse transcriptase in recombinant human immunodeficiency virus type 1 isolates from patients treated with antiretroviral drugs

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Recombinant virus assay: a rapid, phenotypic assay for assessment of drug susceptibility of human immunodeficiency virus type 1 isolates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Novel method for simultaneous quantification of phenotypic resistance to maturation, protease, reverse transcriptase, and integrase HIV inhibitors based on 3'Gag(p2/p7/p1/p6)/PR/RT/INT-recombinant viruses: a useful tool in the multitarget era of ant

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Analysis of HIV cross-resistance to protease inhibitors using a rapid single-cycle recombinant virus assay for patients failing on combination therapies

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Clinical management of HIV-1 resistance

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Rationale and uses of a public HIV drug-resistance database

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

HIV-1 Entry Cofactor: Functional cDNA Cloning of a Seven-Transmembrane, G Protein-Coupled Receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Identification of a major co-receptor for primary isolates of HIV-1

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Determination of coreceptor usage of human immunodeficiency virus type 1 from patient plasma samples by using a recombinant phenotypic assay

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Alpha-complementation assay for HIV envelope glycoprotein-mediated fusion

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Expression plasmids are only useful for the investigation of co-receptor tropism and fusion capacity of short HIV-1 envelope domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Structural basis for coreceptor selectivity by the HIV type 1 V3 loop

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Molecular switch for alternative conformations of the HIV-1 V3 region: implications for phenotype conversion

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Sequencing technologies - the next generation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

An integrated semiconductor device enabling non-optical genome sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Real-time DNA sequencing from single polymerase molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Sequence-specific detection of individual DNA strands using engineered nanopores.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Development of a low bias method for characterizing viral populations using next generation sequencing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Viral population estimation using pyrosequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Frequency and implications of HIV superinfection

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Human immunodeficiency virus type 1 drug resistance testing: Evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Virologic failures on initial boosted-PI regimen infrequently possess low-level variants with major PI resistance mutations by ultra-deep sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Prevalence and impact of minority variant drug resistance mutations in primary HIV-1 infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Impact of minority nonnucleoside reverse transcriptase inhibitor resistance mutations on resistance genotype after virologic failure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Relationship between minority nonnucleoside reverse transcriptase inhibitor resistance mutations, adherence, and the risk of virologic failure

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Archived HIV-1 minority variants detected by ultra-deep pyrosequencing in provirus may be fully replication competent.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Correlation of the virological response to short-term maraviroc monotherapy with standard and deep-sequencing-based genotypic tropism prediction methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Improved V3 genotyping with duplicate PCR amplification for determining HIV-1 tropism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

A comparison of HIV-1 drug susceptibility as provided by conventional phenotyping and by a phenotype prediction tool based on viral genotype

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

TROCAI (tropism coreceptor assay information): a new phenotypic tropism test and its correlation with Trofile enhanced sensitivity and genotypic approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS11908-014-0401-5

Detection of low-frequency HIV type 1 reverse transcriptase drug resistance mutations by ultradeep sequencing in naive HIV type 1-infected individuals

21 January 2018

1 reference

12 December 2020

Frequency of CXCR4-using viruses in primary HIV-1 infections using ultra-deep pyrosequencing

1 reference

12 December 2020

Development and performance of a new recombinant virus phenotypic entry assay to determine HIV-1 coreceptor usage

1 reference

12 December 2020

Tenofovir (TDF)-selected or abacavir (ABC)-selected low-frequency HIV type 1 subpopulations during failure with persistent viremia as detected by ultradeep pyrosequencing

1 reference

12 December 2020

Analysis of pol gene heterogeneity, viral quasispecies, and drug resistance in individuals infected with group O strains of human immunodeficiency virus type 1.

1 reference

12 December 2020

Low-abundance resistant mutations in HIV-1 subtype C antiretroviral therapy-naive individuals as revealed by pyrosequencing.

1 reference

12 December 2020

Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism

1 reference

12 December 2020

Switching between raltegravir resistance pathways analyzed by deep sequencing

1 reference

12 December 2020

HIV tropism: diagnostic tools and implications for disease progression and treatment with entry inhibitors

1 reference

12 December 2020

Genotypic determination of HIV tropism - clinical and methodological recommendations to guide the therapeutic use of CCR5 antagonists

1 reference

12 December 2020

Predicting HIV coreceptor usage on the basis of genetic and clinical covariates.

1 reference

12 December 2020

HIV type 1 tropism and inhibitors of viral entry: clinical implications.

1 reference

12 December 2020

Evaluation of a benchtop HIV ultradeep pyrosequencing drug resistance assay in the clinical laboratory

1 reference

12 December 2020

Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations

1 reference

12 December 2020

Comparison of genotypic and phenotypic HIV type 1 tropism assay: results from the screening samples of Cenicriviroc Study 202, a randomized phase II trial in treatment-naive subjects

1 reference

12 December 2020

Analysis of heterogeneous viral populations by direct DNA sequencing

1 reference

12 December 2020

Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients

1 reference

12 December 2020

Comparison of next-generation sequencing systems

1 reference

12 December 2020

Deep V3 Sequencing for HIV Type 1 Tropism in Treatment-Naive Patients: A Reanalysis of the MERIT Trial of Maraviroc

1 reference

12 December 2020

Genome sequencing in microfabricated high-density picolitre reactors

1 reference

12 December 2020

Understanding HIV phenotypic resistance testing: usefulness in managing treatment-experienced patients.

1 reference

12 December 2020

A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients

1 reference

12 December 2020

10.1007/S11908-014-0401-5

Identifiers

DOI

1 reference

19 October 2017

1 reference

PubMed ID

24585216