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. (Q33622927)

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English	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.	scientific article

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6 March 2020

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 (English)

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6 March 2020

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6 March 2020

Ezequiel Ruiz-Mateos

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6 March 2020

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Felix Feyertag

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Miguel E Quiñones-Mateu

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Miguel E Quiñones-Mateu

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Richard M Gibson

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Ashley M Meyer

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Dane Winner

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Manuel Leal

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David L Robertson

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Christine L Schmotzer

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27 January 2014

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6 March 2020

Antimicrobial Agents and Chemotherapy

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6 March 2020

2167-2185

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6 March 2020

Targeted exome sequencing integrated with clinicopathological information reveals novel and rare mutations in atypical, suspected and unknown cases of Alport syndrome or proteinuria

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HIV-1 tropism testing in subjects achieving undetectable HIV-1 RNA: diagnostic accuracy, viral evolution and compartmentalization

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PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data

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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

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Resistance mutations outside the integrase coding region have an effect on human immunodeficiency virus replicative fitness but do not affect its susceptibility to integrase strand transfer inhibitors

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Update of the drug resistance mutations in HIV-1: March 2013.

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

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

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

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Read length versus depth of coverage for viral quasispecies reconstruction

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

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Effect of maraviroc on HIV disease progression-related biomarkers.

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Phenotyping methods for determining HIV tropism and applications in clinical settings

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HIV population genotypic tropism testing and its clinical significance

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Performance comparison of benchtop high-throughput sequencing platforms

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

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

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

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

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

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2011 update of the drug resistance mutations in HIV-1.

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

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Current tests to evaluate HIV-1 coreceptor tropism

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

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Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy

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Performance of a population-based HIV-1 tropism phenotypic assay and correlation with V3 genotypic prediction tools in recent HIV-1 seroconverters

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Clustal W and Clustal X version 2.0

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Accuracy and quality of massively parallel DNA pyrosequencing

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

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Sensitive oligonucleotide ligation assay for low-level detection of nevirapine resistance mutations in human immunodeficiency virus type 1 quasispecies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Natural variation in the V3 crown of human immunodeficiency virus type 1 affects replicative fitness and entry inhibitor sensitivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Genotypic predictors of human immunodeficiency virus type 1 drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Transmission of HIV-1 drug resistance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Alpha-complementation assay for HIV envelope glycoprotein-mediated fusion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Treatment of antiretroviral-drug-resistant HIV-1 infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Accuracy of the TRUGENE HIV-1 genotyping kit.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Comparative analysis of two commercial phenotypic assays for drug susceptibility testing of human immunodeficiency virus type 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

Drug-resistant strains of AIDS virus found

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

21 June 2018

HIV-1 tropism evolution after short-term maraviroc monotherapy in HIV-1-infected patients

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Discordance in HIV-1 co-receptor use prediction by different genotypic algorithms and phenotype assay: intermediate profile in relation to concordant predictions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Resistance associated mutations to dolutegravir (S/GSK1349572) in HIV-infected patients--impact of HIV subtypes and prior raltegravir experience

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Design and validation of new genotypic tools for easy and reliable estimation of HIV tropism before using CCR5 antagonists.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Minority quasispecies of drug-resistant HIV-1 that lead to early therapy failure in treatment-naive and -adherent patients

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Correlation between genotypic predictions based on V3 sequences and phenotypic determination of HIV-1 tropism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Preexisting resistance to nonnucleoside reverse-transcriptase inhibitors predicts virologic failure of an efavirenz-based regimen in treatment-naive HIV-1-infected subjects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Antivirogram or phenosense: a comparison of their reproducibility and an analysis of their correlation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Correlation between rules-based interpretation and virtual phenotype interpretation of HIV-1 genotypes for predicting drug resistance in HIV-infected individuals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Nested PCR for detection of mutans streptococci in dental plaque

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Nucleotide diversity in three different genomic regions of Venezuelan HIV type 1 isolates: a subtyping update

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4023761

30 October 2018

Prediction of HIV-1 drug susceptibility phenotype from the viral genotype using linear regression modeling

1 reference

https://pubmed.ncbi.nlm.nih.gov/24468782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/24468782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/24468782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/24468782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Analysis of heterogeneous viral populations by direct DNA sequencing

1 reference

https://pubmed.ncbi.nlm.nih.gov/24468782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/24468782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparison of genotyping and phenotyping methods for determining susceptibility of HIV-1 to antiretroviral drugs

1 reference

https://pubmed.ncbi.nlm.nih.gov/24468782

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1128/AAC.02710-13

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24468782%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24468782%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24468782%20AND%20SRC:MED&resulttype=core&format=json

6 March 2020

ResearchGate publication ID

0 references

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