A New Real-Time Quantitative PCR for Diagnosis and Monitoring of HIV-1 Group O Infection

Gueudin, Marie; Leoz, Marie; Lemée, Véronique; Oliveira, Fabienne De; Vessière, Aurélia; Kfutwah, Anfumbom; Plantier, Jean‐Christophe

doi:10.1128/jcm.05669-11

Cited by 31 publications

(23 citation statements)

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“…Currently available real-time HIV RNA PCR assays and the qualitative diagnostic RNA assay have improved sensitivity for detection of non-subtype B HIV infection and the less common Group O strains, compared to older RNA assays that did not detect or appropriately amplify many non-B subtypes and Group O HIV [70][71][72][73][74][75] (see HIV RNA Monitoring in Children: General Considerations in Clinical and Laboratory Monitoring).…”

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Antiretroviral Treatment as Prevention

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2011

N Engl J Med

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Antiretroviral Treatment as Prevention

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2011

N Engl J Med

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“…In most studies, including the ones performed for commercial assays, only 2 to 11 HIV-1 group O samples were tested, which is low to assess the quality of the quantification (18,23,61,62). Plantier and coworkers were the only team able to test a large number of group O samples (77 different strains) to validate their specific HIV-1 group O "in-house" real-time assay (22,26,63). Furthermore, our group O panel covered HIV-1 group O genetic diversity, reflecting that the high genetic diversity of this group did not have an impact on our detection.…”

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“…Due to globalization, this heterogeneity can also be found in different geographic regions in which the common viral load assays may not be able to detect these "unusual" strains (19)(20)(21). Furthermore, highly divergent viruses, such as HIV-1 groups O, N, and P, which also circulate and have a clinical course similar to that of HIV-1 group M, need appropriate monitoring tools that are not often available (22,23). Thus, HIV diversity and molecular epidemiology still impacts on the management and monitoring of HIV-infected patients.…”

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“…However, the main limit of the majority of these tests is that their designed primers and probe have numerous mismatches with HIV-1 groups O, N, and P (alignment with HIV-1 sequences from the HIV.lanl database [data not shown]), implying the possible nondetection or underquantification of these circulating strains (25). On the other hand, a real-time PCR assay developed by Gueudin and coworkers specifically quantifies HIV-1 group O but does not detect HIV-1 group M strains (22,26).…”

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Single Real-Time Reverse Transcription-PCR Assay for Detection and Quantification of Genetically Diverse HIV-1, SIVcpz, and SIVgor Strains

et al. 2013

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Although antiretroviral treatment availability has improved, the virological monitoring of patients remains largely uneven across regions. In addition, viral quantification tests are suffering from human immunodeficiency virus type 1 (HIV-1) genetic diversity, fueled by the emergence of new recombinants and of lentiviruses from nonhuman primates. We developed a real-time reverse transcription-PCR (RT-PCR) assay that is relatively inexpensive and able to detect and quantify all circulating forms of HIV-1 and its simian immunodeficiency virus (SIV) precursors, SIVcpz and SIVgor. Primers and a probe were designed to detect all variants of the HIV-1/SIVcpz/SIVgor lineage. HIV-1 M plasma (n ‫؍‬ 190; 1.68 to 7.78 log 10 copies/ml) representing eight subtypes, nine circulating recombinant forms, and 21 unique recombinant forms were tested. The mean PCR efficiency was 99%, with low coefficients of intra-and interassay variation (<5%) and a limit of quantification of <2.50 log 10 copies/ml, with a 200-l plasma volume. On the studied range, the specificity and the analytical sensitivity were 100 and 97.4%, respectively. The viral loads were highly correlated (r ‫؍‬ 0.95, P < 0.0001) with the reference method (generic HIV assay; Biocentric) and had no systematic difference, irrespective of genotype. Furthermore, 22 HIV-1 O plasmas were screened and were better quantified compared to the gold-standard RealTime HIV-1 assay (Abbott), including four samples that were only quantified by our assay. Finally, we could quantify SIVcpzPtt and SIVcpzPts from chimpanzee plasma (n ‫؍‬ 5) and amplify SIVcpz and SIVgor from feces. Thus, the newly developed real-time RT-PCR assay detects and quantifies strains from the HIV-1/SIVcpz/SIVgor lineage, including a wide diversity of group M strains and HIV-1 O. It can therefore be useful in geographical areas of high HIV diversity and at risk for the emergence of new HIV variants.

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“…Some serological tools are less sensitive to HIV-1/O (30) or HIV-2 (22,31) and may behave similarly with recombinants carrying a group O-derived envelope or with cryptic HIV-1ϩHIV-2 infections (17). Similarly, variants may affect the determination of viral load (VL) by quantitative RT-PCR (32)(33)(34)(35). This justifies the use of nonspecific primers to prevent the misquantification or lack of detection of one of the variants in cases of dual infection or recombinants involving minor variants.…”

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A Multiplex PCR Approach for Detecting Dual Infections and Recombinants Involving Major HIV Variants

et al. 2016

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The cocirculation of different HIV types and groups can lead to dual infections and recombinants, which hinder diagnosis and therapeutic management. We designed two multiplex PCRs (mPCRs) coupled with capillary electrophoresis to facilitate the detection of such infections. The first, MMO2, targets three variants (HIV-1/M, HIV-1/O, and HIV-2), and the second, MMO, targets HIV-1/M and HIV-1/O. These mPCRs were validated on DNA and RNA extracts from 19 HIV-1/M, 12 HIV-1/O, and 13 HIV-2 cultures and from mixtures simulating dual infections. They were then assessed with DNA and RNA extracts from samples of 47 clinical monoinfections and HIV-1/M+O dual infections or infections with HIV-1/MO recombinants. Both mPCRs had excellent specificity. Sensitivities ranged from 80 to 100% forin vitrosamples and from 58 to 100% for clinical samples, with the results obtained depending on the material used and the region of the genome concerned. Sensitivity was generally lower for DNA than for RNA and for amplifications of the integrase and matrix regions. In terms of global detection (at least one target gene for each strain), both mPCRs yielded a detection rate of 100% forin vitrosamples. MMO2detected 100% of the clinical strains from DNA and 97% from RNA, whereas MMOdetected 100% of the strains from both materials. Thus, forin vitroand clinical samples, MMO2was a useful tool for detecting dual infections with HIV-1 and HIV-2 (referred to as HIV-1+HIV-2) and HIV-1/M+O, and MMOwas useful for detecting both MO dual infections and MO mosaic patterns.

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A New Real-Time Quantitative PCR for Diagnosis and Monitoring of HIV-1 Group O Infection

Cited by 31 publications

References 32 publications

Antiretroviral Treatment as Prevention

Antiretroviral Treatment as Prevention

Single Real-Time Reverse Transcription-PCR Assay for Detection and Quantification of Genetically Diverse HIV-1, SIVcpz, and SIVgor Strains

A Multiplex PCR Approach for Detecting Dual Infections and Recombinants Involving Major HIV Variants

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