Reference : Concordance between HIV-1 genotypic coreceptor tropism predictions based on plasma RNA a...
Scientific journals : Article
Human health sciences : Immunology & infectious disease
http://hdl.handle.net/2268/111364
Concordance between HIV-1 genotypic coreceptor tropism predictions based on plasma RNA and proviral DNA.
English
Verhofstede, C. [> > > >]
Brudney, D. [> > > >]
Reynaerts, J. [> > > >]
VAIRA, Dolorès mailto [Centre Hospitalier Universitaire de Liège - CHU > > Microbiologie médicale]
Fransen, K. [> > > >]
De Bel, A. [> > > >]
Seguin-Devaux, C. [> > > >]
De Wit, S. [> > > >]
Vandekerckhove, L. [> > > >]
Geretti, A*-M [> > > >]
2011
HIV Medicine
Blackwell Publishing
12
9
544-52
Yes (verified by ORBi)
International
1464-2662
1468-1293
[en] Algorithms ; DNA, Viral/blood ; Gene Amplification ; Genotype ; HIV Infections/virology ; HIV-1/genetics ; Humans ; Phenotype ; RNA, Viral/blood ; Viral Load/genetics ; Viral Tropism/genetics ; Viremia/virology
[en] OBJECTIVE: The aim of the study was to evaluate the use of proviral DNA as a source of viral genetic material for genotypic coreceptor tropism testing (GTT). METHODS: GTT consisted of bulk V3 sequencing followed by geno2pheno interpretation with the interpretative cut-off [false positive rate (FPR)] set at 5 and 10%. GTT was performed for 165 patients with a viral load of >500 HIV-1 RNA copies/mL on simultaneously collected plasma RNA and proviral DNA, and for 126 patients with a viral load of <500 copies/mL on current proviral DNA and pretreatment plasma RNA. Phenotypic tropism testing (PTT) results were available for 142 samples. RESULTS: In the simultaneous RNA/DNA comparison, concordance in prediction was 95.2% (at FPR 10%) and 96.4% (at FPR 5%). Six RNA-R5/DNA-X4 and two RNA-X4/DNA-R5 discordances were observed at an FPR of 10%, and six RNA-R5/DNA-X4 discordances were observed at an FPR of 5%. In the longitudinal RNA/DNA comparison, concordance was 88.1% (at FPR 10%) and 90.5% (at FPR 5%). Eight RNA-X4/DNA-R5 and seven RNA-R5/DNA-X4 discordances were seen at an FPR of 10%, and 10 RNA-R5/DNA-X4 and two RNA-X4/DNA-R5 discordances at an FPR of 5%. The overall concordance of RNA GTT with PTT was 82% (at FPR 10%) and 83% (at FPR 5%). The overall concordance of DNA GTT with PTT was 85% (at both 10 and 5% FPRs). CONCLUSIONS: GTT produced highly concordant tropism predictions for proviral DNA and plasma RNA. GTT on proviral DNA offers a promising approach for tropism prediction in clinical practice, particularly for the assessment of treated patients with low or suppressed viraemia.
http://hdl.handle.net/2268/111364
10.1111/j.1468-1293.2011.00922.x
(c) 2011 British HIV Association.

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Restricted access
HIV Med 2011.pdfPublisher postprint128.55 kBRequest copy

Bookmark and Share SFX Query

All documents in ORBi are protected by a user license.