Evaluation of NucliSens EasyQ™ HIV-1 assay for quantification of HIV-1 subtypes prevalent in South-east Asia

Lam, Hoyin; Chen, J.H.K.; Wong, Ka-Hing; Chan, Kenny Chi-Wai; Li, P.; Lee, M.P.; Tsang, Dnc; Yuen, Kwok‐Yung; Yam, Wing-Cheong

doi:10.1016/j.jcv.2006.10.002

Cited by 11 publications

(5 citation statements)

References 20 publications

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“…In agreement with our findings, a recent evaluation testing the Roche Cobas TaqMan and Abbott RealTime extraction-quantification systems for HIV-1 subtype quantification also reported large viremia differences in non-B subtypes, particularly in CRF02_AG variants (14). As for other HIV-1 variants, a recent study showed the versatility of both the NucliSens EasyQ v1.1 and the Cobas Amplicor tests in monitoring subtype B and recombinant CRF01_AE viruses prevalent in Southeast Asia (21). It should be noted that neither of these variants was included in our study.…”

Section: Discussionsupporting

confidence: 91%

Performance of Three Commercial Viral Load Assays, Versant Human Immunodeficiency Virus Type 1 (HIV-1) RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2, Testing HIV-1 Non-B Subtypes and Recombinant Variants

Holguín

López²,

Molinero³

et al. 2008

J Clin Microbiol

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Monitoring antiretroviral therapy requires that human immunodeficiency virus type 1 (HIV-1) viremia assays are applicable to all distinct variants. This study evaluates the performance of three commercial viral load assays-Versant HIV-1 RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2-in testing 83 plasma specimens from patients carrying HIV-1 non-B subtypes and recombinants previously defined by phylogenetic analysis of the pol gene. All 28 specimens from patients under treatment presented viremia values below the detection limit with the three methods. In the remaining 55 specimens from naive individuals viremia could not be detected in 32.7, 20, and 14.6% using the NucliSens, Versant, or TaqMan tests, respectively, suggesting potential viral load underestimation of some samples by all techniques. Only 32 (58.2%) samples from naive subjects were quantified by the three methods; the NucliSens test provided the highest HIV RNA values (mean, 4.87 log copies/ml), and the Versant test provided the lowest (mean, 4.16 log copies/ml). Viremia differences of greater than 1 log were seen in 8 (14.5%) of 55 specimens, occurring in 10.9, 7.3, and 5.4%, respectively, of the specimens in comparisons of Versant versus NucliSens, Versant versus TaqMan, and TaqMan versus NucliSens. Differences greater than 0.5 log, considered significant for clinicians, occurred in 45.5, 27.3, and 29% when the same assays were compared. Some HIV-1 strains, such as subtype G and CRF02_AG, showed more discrepancies in distinct quantification methods than others. In summary, an adequate design of primers and probes is needed for optimal quantitation of plasma HIV-RNA in non-B subtypes. Our data emphasize the need to use the same method for monitoring patients on therapy and also the convenience of HIV-1 subtyping.

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Section: Discussionsupporting

confidence: 91%

Performance of Three Commercial Viral Load Assays, Versant Human Immunodeficiency Virus Type 1 (HIV-1) RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2, Testing HIV-1 Non-B Subtypes and Recombinant Variants

Holguín

López²,

Molinero³

et al. 2008

J Clin Microbiol

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“…Automated data analysis and reporting is achieved by using Windows ® -based software. Comparative evaluation studies demonstrated a relatively good concordance of the result values with the Roche Cobas Monitor v1.5 assay [32]. However, the disparity between the results of the two assays was highly significant in subtype C samples; in the vast majority of these samples, higher VL values were obtained by the Roche assay [33].…”

Section: Available Assays In Detailmentioning

confidence: 88%

Molecular assays for monitoring HIV infection and antiretroviral therapy

Wittek

Stürmer

Doerr

et al. 2007

Expert Review of Molecular Diagnostics

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Infection with HIV results in lifelong persistence of the virus in the body of infected persons, independent of antiretroviral treatment. Therefore, efficient and meaningful therapy monitoring has been developed since its introduction in the 1980s. Whereas, primarily, the measurement of the CD4 cell count was the most important clinical marker of disease progression, nowadays the estimation of plasma viral load with molecular methods plays a major role as a marker of therapy success. To optimize therapy changes in patients failing on antiretroviral therapy regimen, HIV-1 genotyping has been introduced and is now widely accepted as an additional diagnostic tool. Due to this increase in diagnostic parameters, clinicians and virologists have to cope with many different methods. This review should give a brief overview of the current commercially available assays for detection and quantification of HIV, as well as for HIV-1 genotypic resistance testing. Quantitative reverse transcriptase PCR, real-time PCR, nucleic acid sequence-based amplification and the branched DNA system are described in detail, and the advantages and disadvantages are discussed. In addition, two commercially available HIV-1 genotyping assays are compared. However, a general recommendation to favor one system over the other cannot be given, because the final decision of which system to use should be decided on the individual requirements.

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“…Consistent with most of findings concerning the HIV genome in South East Asia, our results confirmed presence of the subtype CRF01_AE in all patients in the present study. 23 Extensive studies have been conducted to investigate the association between HIV subtype and disease progression; however, the results have been inconsistent. 24 Saina et al .…”

Section: Discussionmentioning

confidence: 99%

Molecular genotypes of gag sequences in HIV-1 infected children treated with antiretroviral therapy in Vietnam

Dang

Pham

Dinh

et al. 2020

Therapeutic Advances in Infection

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Background: Gag protein of human immunodeficiency virus (HIV) has been reported to play a crucial role in establishing infection, viral replication, and disease progression; thus, gag might be related to treatment response. The objective of this study was to investigate molecular genotypes of the gag gene, particularly the important functional binding domains in relation to treatment outcomes. Methods: HIV-infected children enrolled and treated at Vietnam National Children’s Hospital were recruited in the study. A total of 25 gag sequences were generated and used to construct phylogenetic trees and aligned with a reference sequence comparing 17 functional domains. Results: We found that all patients in a treatment failure (TF) group belonged to one cluster of the phylogenetic tree. In addition, the rate of mutations was significantly higher in TF compared with a treatment success (TS) group, specifically the PIP2 recognition motif, and the nucleocapsid basic and zinc motif 2 domains [median and (interquartile range (IQR): 12.5 (6.25–12.5) versus 50 (25–50), p < 0.01; 0 (0–0) versus 0 (0–21.43), p = 0.03 and 0 (0–7.14) versus 7.14 (7.14–7.14), p = 0.04, respectively]. When analyzing gag sequences at different time points in seven patients, we did not observe a consistent mutation pattern related to treatment response. Conclusion: Gag mutations in certain domains might be associated with increased viral load; therefore, studying the molecular genotype of the gag gene might be beneficial in monitoring treatment response in HIV-infected children.

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Evaluation of NucliSens EasyQ™ HIV-1 assay for quantification of HIV-1 subtypes prevalent in South-east Asia

Cited by 11 publications

References 20 publications

Performance of Three Commercial Viral Load Assays, Versant Human Immunodeficiency Virus Type 1 (HIV-1) RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2, Testing HIV-1 Non-B Subtypes and Recombinant Variants

Performance of Three Commercial Viral Load Assays, Versant Human Immunodeficiency Virus Type 1 (HIV-1) RNA bDNA v3.0, Cobas AmpliPrep/Cobas TaqMan HIV-1, and NucliSens HIV-1 EasyQ v1.2, Testing HIV-1 Non-B Subtypes and Recombinant Variants

Molecular assays for monitoring HIV infection and antiretroviral therapy

Molecular genotypes of gag sequences in HIV-1 infected children treated with antiretroviral therapy in Vietnam

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