Rates of and Reasons for Failure of Commercial Human Immunodeficiency Virus Type 1 Viral Load Assays in Brazil

Drexler, Jan Felix; Luna, Luciano Kleber de Souza; Pedroso, Célia; Pedral-Sampaio, Diana; Queiroz, Artur T. L.; Brites, Carlos; Netto, Eduardo Martins; Drosten, Christian

doi:10.1128/jcm.00136-07

Cited by 24 publications

(20 citation statements)

References 19 publications

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“…Therefore, the PCR product of a CTM strongly positive control reaction was cloned into a pGEM-T Easy vector (Promega) and sequenced. The sequence was very similar to the sequences of the Cobas Amplicor Monitor v1.5 assay primers and probe, which have been published earlier (3). Figure 1 shows the 157-bp sequence of the cloned PCR product from the CTM assay (corresponding to nucleotides 1359 to 1515 of the HXB2 reference sequence; GenBank accession no.…”

supporting

confidence: 59%

Single-Point Mutations Causing More than 100-Fold Underestimation of Human Immunodeficiency Virus Type 1 (HIV-1) Load with the Cobas TaqMan HIV-1 Real-Time PCR Assay

et al. 2009

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supporting

confidence: 59%

Single-Point Mutations Causing More than 100-Fold Underestimation of Human Immunodeficiency Virus Type 1 (HIV-1) Load with the Cobas TaqMan HIV-1 Real-Time PCR Assay

et al. 2009

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“…Several reports have noticed differences obtained when quantifying HIV-1 non-B subtypes with different methodologies (5,7,12,14,25,26,28). Moreover, failure to detect non-B subtypes by viral load techniques has been previously described (10,11). The natural polymorphisms associated with genetic non-B subtypes and recombinant strains in the HIV-1 binding sites of primers or probes used in those assays can influence in their efficiency (12,20,25,26).…”

mentioning

confidence: 99%

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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“…This aspect is of major importance, and VL assays should always be validated and further evaluated in different countries with different molecular epidemiological features, as has been done for previous "in-house" assays developed for resource-limited settings (30,45). The later criticisms on commercial viral load assays and their lack of validation on "unusual" strains for developed countries (1,16,17,46,57,58) have induced some changes in the development of industrial assays (2); i.e., the Abbott real-time assay or the last Roche Cobas TaqMan kit were recently validated and evaluated on HIV-1 group M diversity and a few HIV-1 group O strains (18,23,(59)(60)(61)(62). Unlike previously described generic or "in-house" tests, the designed probe did not bear numerous mismatches with described HIV-1 group O sequences, and our RT-qPCR assay was able to detect and quantify HIV-1 group O viruses from plasma samples.…”

Section: Discussionmentioning

confidence: 99%

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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Rates of and Reasons for Failure of Commercial Human Immunodeficiency Virus Type 1 Viral Load Assays in Brazil

Cited by 24 publications

References 19 publications

Single-Point Mutations Causing More than 100-Fold Underestimation of Human Immunodeficiency Virus Type 1 (HIV-1) Load with the Cobas TaqMan HIV-1 Real-Time PCR Assay

Single-Point Mutations Causing More than 100-Fold Underestimation of Human Immunodeficiency Virus Type 1 (HIV-1) Load with the Cobas TaqMan HIV-1 Real-Time PCR Assay

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

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

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