Concordance between Two Phenotypic Assays and Ultradeep Pyrosequencing for Determining HIV-1 Tropism

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Published inAntimicrobial Agents and Chemotherapy Vol. 55; no. 6; pp. 2831 - 2836
Main Authors SALIOU, Adrien, DELOBEL, Pierre, DUBOIS, Martine, NICOT, Florence, RAYMOND, Stéphanie, CALVEZ, Vincent, MASQUELIER, Bernard, IZOPET, Jacques
Format Journal Article
LanguageEnglish
Published Washington, DC American Society for Microbiology 01.06.2011
Subjects
Adult
Antibiotics. Antiinfectious agents. Antiparasitic agents
Antiviral Agents
Biological and medical sciences
CCR5 Receptor Antagonists
Genotyping
HIV-1
HIV-1 - genetics
HIV-1 - physiology
Human immunodeficiency virus 1
Human viral diseases
Humans
Immunodeficiencies
Immunodeficiencies. Immunoglobulinopathies
Immunopathology
Infectious diseases
Life Sciences
Medical sciences
Microbiology and Parasitology
Middle Aged
Pharmacology. Drug treatments
Phenotype
Phenotyping
Receptors, CCR5
Receptors, CXCR4
Receptors, CXCR4 - physiology
Sequence Analysis, DNA
Tropism
Viral diseases
Viral diseases of the lymphoid tissue and the blood. Aids
Viral Tropism
Tropism
Immunopathology
HIV-1 virus
Retroviridae
AIDS
Immune deficiency
Lentivirus
Infection
Virus
Phenotype
Viral disease
Concordance
Human immunodeficiency virus
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Abstract Classifications Services AAC Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue AAC About AAC Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy AAC RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0066-4804 Online ISSN: 1098-6596 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to AAC .asm.org, visit: AAC       
AbstractList There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The sensitivity of ultradeep pyrosequencing combined with genotyping tools is similar to that of phenotypic assays for detecting minor CXCR4-using variants. We evaluated the agreement between two phenotypic assays, the Toulouse tropism test (TTT) and the Trofile assay, and ultradeep pyrosequencing for determining the tropism of HIV-1 quasispecies. The concordance between the TTT and Trofile assays was assessed for 181 samples successfully phenotyped by both assays. The TTT was 86% concordant with the standard Trofile assay and 91.7% with its enhanced-sensitivity version. The concordance between phenotypic characterization of HIV-1 tropism and ultradeep pyrosequencing genotypic prediction was further studied in selected samples. The HIV-1 tropism inferred from ultradeep pyrosequencing of 11 samples phenotyped as X4 and dualtropic and 12 phenotyped as R5-tropic agreed closely with the results of phenotyping. However, ultradeep pyrosequencing detected minor CXCR4-using variants in 3 of 12 samples phenotyped as R5-tropic. Ultradeep pyrosequencing also detected minor CXCR4-using variants that had been missed by direct sequencing in 6 of 9 samples phenotyped as X4-tropic but genotyped as R5-tropic by direct sequencing. Ultradeep pyrosequencing was 87% concordant with the Trofile and TTT phenotypic assays and was in the same range of sensitivity (0.4%) than these two phenotypic assays (0.3 to 0.5%) for detecting minor CXCR4-using variants. Ultradeep pyrosequencing provides a new way to improve the performance of genotypic prediction of HIV-1 tropism to match that of the phenotypic assays.
ABSTRACT There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The sensitivity of ultradeep pyrosequencing combined with genotyping tools is similar to that of phenotypic assays for detecting minor CXCR4-using variants. We evaluated the agreement between two phenotypic assays, the Toulouse tropism test (TTT) and the Trofile assay, and ultradeep pyrosequencing for determining the tropism of HIV-1 quasispecies. The concordance between the TTT and Trofile assays was assessed for 181 samples successfully phenotyped by both assays. The TTT was 86% concordant with the standard Trofile assay and 91.7% with its enhanced-sensitivity version. The concordance between phenotypic characterization of HIV-1 tropism and ultradeep pyrosequencing genotypic prediction was further studied in selected samples. The HIV-1 tropism inferred from ultradeep pyrosequencing of 11 samples phenotyped as X4 and dualtropic and 12 phenotyped as R5-tropic agreed closely with the results of phenotyping. However, ultradeep pyrosequencing detected minor CXCR4-using variants in 3 of 12 samples phenotyped as R5-tropic. Ultradeep pyrosequencing also detected minor CXCR4-using variants that had been missed by direct sequencing in 6 of 9 samples phenotyped as X4-tropic but genotyped as R5-tropic by direct sequencing. Ultradeep pyrosequencing was 87% concordant with the Trofile and TTT phenotypic assays and was in the same range of sensitivity (0.4%) than these two phenotypic assays (0.3 to 0.5%) for detecting minor CXCR4-using variants. Ultradeep pyrosequencing provides a new way to improve the performance of genotypic prediction of HIV-1 tropism to match that of the phenotypic assays.
Classifications Services AAC Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue AAC About AAC Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy AAC RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0066-4804 Online ISSN: 1098-6596 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to AAC .asm.org, visit: AAC       
Author Jacques Izopet
the ANRS AC11 Resistance Study Group
Pierre Delobel
Bernard Masquelier
Stéphanie Raymond
Adrien Saliou
Martine Dubois
Florence Nicot
Vincent Calvez
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Issue 6
Keywords Tropism
Immunopathology
HIV-1 virus
Retroviridae
AIDS
Immune deficiency
Lentivirus
Infection
Virus
Phenotype
Viral disease
Concordance
Human immunodeficiency virus
Language English
License CC BY 4.0
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There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The...
ABSTRACT There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage....
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SourceType Open Access Repository
Aggregation Database
Index Database
Publisher
StartPage 2831
SubjectTerms Adult
Antibiotics. Antiinfectious agents. Antiparasitic agents
Antiviral Agents
Biological and medical sciences
CCR5 Receptor Antagonists
Genotyping
HIV-1
HIV-1 - genetics
HIV-1 - physiology
Human immunodeficiency virus 1
Human viral diseases
Humans
Immunodeficiencies
Immunodeficiencies. Immunoglobulinopathies
Immunopathology
Infectious diseases
Life Sciences
Medical sciences
Microbiology and Parasitology
Middle Aged
Pharmacology. Drug treatments
Phenotype
Phenotyping
Receptors, CCR5
Receptors, CXCR4
Receptors, CXCR4 - physiology
Sequence Analysis, DNA
Tropism
Viral diseases
Viral diseases of the lymphoid tissue and the blood. Aids
Viral Tropism
Title Concordance between Two Phenotypic Assays and Ultradeep Pyrosequencing for Determining HIV-1 Tropism
URI http://aac.asm.org/content/55/6/2831.abstract
https://www.ncbi.nlm.nih.gov/pubmed/21464245
https://journals.asm.org/doi/10.1128/AAC.00091-11
https://search.proquest.com/docview/875717598
https://search.proquest.com/docview/911158951
https://hal.science/hal-00675722
https://pubmed.ncbi.nlm.nih.gov/PMC3101380
Volume 55
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