HIV-1 load comparison using four commercial real-time assays

Evaluation of the ELITechGroup solution for plasma HIV-1 RNA quantification

In the last few years, many manufacturers have developed new kits for plasma HIV-1 RNA quantification. Recently, a solution consisting of the ELITe InGenius® instrument and the HIV1 ELITe MGB®kit has been commercialized worldwide. Our aim was to compare its clinical performance with the Aptima® HIV-1 Quant Dx kit by Hologic, on a panel of HIV-1 group M circulating variants, representative of viral load levels found during the pre- and post-treatment follow-up of patients. The linearity was evaluated on the AcroMetrix® HIV-1 Panel. Clinical specificity was evaluated on 100 plasma samples negative for HIV; and clinical sensitivity and sequential follow-up were evaluated on 166 HIV-1 positive plasma samples from 126 patients. The linearity data showed a difference obtained for each point of less than 0.2 Log cp/mL. No amplification was found for the 100 HIV negative clinical specimens. The overall agreement between the two kits was 83.7 %; the differences corresponded to a slightly higher detection for the Aptima kit (with more samples detected below the lower limit of quantification). A Bland & Altman analysis of the quantifiable samples showed a mean difference of -0.05 Log and Spearman's coefficient was 0.975. Only six samples presented discrepancies (above 0.5 Log), but these differences were overall similar between the two kits. Our study has shown that the HIV1 ELITe MGB® Kit can be successfully used for the monitoring of patients infected with various epidemic HIV-1 strains, and for the precise quantification of the viral load.

Correlation between Cepheid GeneXpert and Abbott M2000 assays for HIV viral load measurements

Measurement of HIV viral load (VL) is the best indicator of success of antiretroviral therapy. We investigated the correlation between results by the Cepheid GeneXpert and a standard of care VL assay (Abbott M2000). This was a prospective study of people living with HIV who attended the department for routine VL measurement with the Abbott M2000. Consenting patients agreed to provide one extra blood sample for VL measurement with the Cepheid GeneXpert assay. One hundred patients consented to participate in the study. There were 18 patients with VL ≥ 40 copies/mL and 75 patients with VL < 40 copies on both assays. The two assays had 93% agreement, with a kappa of 0.79 (p < 0.001). Treating VL as a continuous variable found measurements to be significantly higher on the Cepheid GeneXpert assay than the Abbott (p = 0.002). Analysis of samples with VL ≥ 40 copies/mL on either assay (n = 25) found the mean difference between the two assays to be 0.31 log₁₀ copies/mL (95% limits of agreement: -0.63, 1.25). Whilst the measurements on the two assays are relatively highly correlated, there is a clear bias, with the Cepheid GeneXpert tending to give higher VL values.

Accuracy of quantitative HIV-1 RNA test methods at 1000 copies/mL and the potential impact of differences in assay calibration on therapy monitoring of patients

The World Health Organization (WHO) recommends the clinical use of a human immunodeficiency virus 1 (HIV-1) viral load (VL) threshold level of 1000 copies (cp)/mL in patients on antiretroviral therapy (ART) to distinguish between viral control (VL < 1000 cp/mL) and viral failure or poor adherence (VL > 1000 cp/mL). The accuracy of five quantitative HIV-1 RNA assays at this level was compared by replicate testing (n = 24) of 1000 cp/mL samples prepared from the Viral Quality Control (VQC) HIV-1 subtype B standard, which is in use for validation of nucleic acid testing methods since 1995. Until 2004 the VL assays reported geometric mean (95% confidence interval [CI]) values ranging between 449 (188-1067) and 3162 (3057-2367) cp/mL when using the Siemens bDNA 3.0 assay as reference method for an assigned value of 1000 (962-1038) cp/mL. In 2018, the following values (95% CI) were found by 24 replicate tests in each of the VL assays on the 1000 cp/mL samples: Abbott RealTime 1084 (784-1572), BioMerieux EasyQ 1110 (533-2230), Roche CAP/CTM 1277 (892-1828), Hologic Aptima 1616 (1324-1973), and Cepheid GeneXpert 2502 (1713-3655) cp/mL. Calibration studies involving three consecutive WHO replacement standards showed a significant drift in the amount of RNA copies per International Unit overtime. Heat inactivation of HIV-1 standards was found to cause a destandardizing effect. Our study underlines the limitations in HIV-1 RNA assay calibration based on frequently replaced WHO international standards. It is therefore proposed that clinicians interpret the recommended 1000 cp/mL alert level in therapy monitoring with an inaccuracy range of 500 to 2000 cp/mL.

Comparative performance of the Biocentric Generic Viral Load, Roche CAP/CTM v1.5, Roche CAP/CTM v2.0 and m2000 Abbott assays for quantifying HIV-1 B and non-B strains: Underestimation of some CRF02 strains

BACKGROUND

HIV-1 viral load testing is now recommended by the World Health Organization for every patient receiving antiretroviral therapy (ART).

OBJECTIVES

The objective of this study is to evaluate the performance of commercial assays for their ability to quantify HIV-1 strains currently circulating in France.

STUDY DESIGN

The performances of the Generic HIV-RNA assay from Biocentric were compared to those of the Roche CAP/CTM v1.5, Roche CAP/CTM v2.0 and Abbott m2000 RealTime HIV-1 assays. A total of 1885 HIV-1 plasma samples were tested, including 684 samples from patients included in the ANRS-Primo Cohort.

RESULTS

We found a good concordance of quantification between the Roche v2.0 and the Biocentric assays, both of which were superior to the Roche v1.5 assay. We show moderate agreement between techniques; however, CRF02_AG strains and undetermined viruses were underestimated when quantified with the Roche CAP/CTM v2.0. In contrast, a comparison of the Biocentric and Abbott assay results showed strong agreement between assays, indicating that both are well suited for quantification of CRF02_AG strains. Moreover, a 2% underestimation of the B subtypes was observed with the Biocentric assay.

CONCLUSIONS

These results have implications for viral load monitoring in Western Africa, where CRF02_AG strains are highly prevalent. Closer epidemiological surveillance and evaluation of commercial assays are still necessary to better evaluate the impact of the genetic evolution of circulating viruses on HIV-RNA quantification in the regions most affected by the HIV-1 epidemic.

Performance Evaluation of the New HIV-1 Quantification Assay, Xpert HIV-1 Viral Load, on a Wide Panel of HIV-1 Variants

OBJECTIVE

To evaluate the quantification performance of the new Cepheid GeneXpert HIV-1 viral load assay, on a wide panel of HIV-1 variants.

METHODS

Clinical performance was evaluated relative to the Abbott RealTime HIV-1 assay on 285 HIV-1 seropositive samples selected to cover the assays quantification range (40 copies/mL-10,000,000 copies/mL), and included RNA undetectable or detected seropositive samples. The panel comprised 120 subtype B, 150 non-B, and 15 nontypable clinical samples; serial dilutions of 18 viral supernatants representative of the divergent viruses of HIV-1 groups N, O, and P were also tested.

RESULTS

Based on samples selected according to the Abbott assay viral loads (VL), the Cepheid assay detected or quantified 222/285 (78%) samples and the Abbott assay 240/285 (84%). Xpert yielded VLs for 162 (76%) of the 213 quantifiable samples with Abbott. This difference corresponded to 51 samples with VL >40 copies/mL by the Abbott assay (all below 200 copies/mL) but detected (n = 40) or undetectable (n = 11) by the Cepheid assay. VL of samples quantifiable by both assays (n = 162) showed very strong correlation, with a Spearman correlation coefficient of 0.985 and a Bland-Altman's mean of differences of -0.01. Performance for quantification of the non-M samples showed very good correlation, with significantly higher values with Cepheid for the group N and 2 group O samples.

CONCLUSIONS

Our study showed that the Xpert HIV-1 VL assay offered very good performance for detection and quantification of the current HIV-1 genetic diversity; differences reported at the threshold could be an issue and requires further evaluations. The practicability of this new assay makes it suitable for low-income countries, where it could facilitate and improve follow-up of patients, as well as for high-income regions.

Comparison between Roche and Xpert in HIV-1 RNA quantitation: A high concordance between the two techniques except for a CRF02_AG subtype variant with high viral load titters detected by Roche but undetected by Xpert

BACKGROUND

HIV-1 viral load (VL) testing is important to predict viral progression and to monitor the response to antiretroviral therapy. New HIV-1 VL tests are continuously introduced to the market. Their performance is usually compared to Abbott and/or Roche HIV-1 VL assays, as reference. The Xpert HIV-1 VL test was recently introduced, but its performance compared to Roche has not been sufficiently studied.

OBJECTIVES

To compare the Xpert assay with Roche and to assess its use in the HIV clinical laboratory.

STUDY DESIGN

A total of 383 plasma samples of HIV-1 infected patients previously tested by Roche, were retrospectively tested by Xpert to determine concordance between the two assays. Samples included a diversity of HIV-1 subtypes and a wide range of VLs.

RESULTS

There was a high concordance between the two assays, except for a CRF02_AG subtype variant with high VL titters, that was detected by Roche but undetected by Xpert. The 5' long terminal repeat gene region of this virus, targeted by the Xpert assay, was amplified and sequenced. A 25 nucleotide insert was identified, but was unmatched to any known sequences of HIV-1. This particular insert, however could not explain the false-negativity by the Xpert assay.

CONCLUSIONS

This study underlines the challenge to routine VL testing due to the high genetic diversity of HIV-1. Clinicians should, therefore be advised that a negative VL in cases where the clinical picture does not match the laboratory report, might in fact be, a false-negative result of the VL assay.

Analytical Performances of Human Immunodeficiency Virus Type 1 RNA-Based Amplix® Real-Time PCR Platform for HIV-1 RNA Quantification

Objectives. We evaluated the performances of Amplix real-time PCR platform developed by Biosynex (Strasbourg, France), combining automated station extraction (Amplix station 16 Dx) and real-time PCR (Amplix NG), for quantifying plasma HIV-1 RNA by lyophilized HIV-1 RNA-based Amplix reagents targeting gag and LTR, using samples from HIV-1-infected adults from Central African Republic. Results. Amplix real-time PCR assay showed low limit of detection (28 copies/mL), across wide dynamic range (1.4-10 log copies/mL), 100% sensitivity and 99% specificity, high reproducibility, and accuracy with mean bias < 5%. The assay showed excellent correlations and concordance of 95.3% with the reference HIV-1 RNA load assay (Roche), with mean absolute bias of +0.097 log copies/mL by Bland-Altman analysis. The assay was able to detect and quantify the most prevalent HIV-1 subtype strains and the majority of non-B subtypes, CRFs of HIV-1 group M, and HIV-1 groups N and O circulating in Central Africa. The Amplix assay showed 100% sensitivity and 99.6% specificity to diagnose virological failure in clinical samples from antiretroviral drug-experienced patients. Conclusions. The HIV-1 RNA-based Amplix real-time PCR platform constitutes sensitive and reliable system for clinical monitoring of HIV-1 RNA load in HIV-1-infected children and adults, particularly adapted to intermediate laboratory facilities in sub-Saharan Africa.

Evaluation of the Upgraded Version 2.0 of the Roche COBAS® AmpliPrep/COBAS® TaqMan HIV-1 Qualitative Assay in Central African Children

Background:

Several commercially available molecular techniques were developed based on subtype B of HIV-1, which represents only 10% of HIV strains worldwide. Indeed, in sub-Saharan Africa, non-B subtypes of HIV-1 are predominant. The aim of this study was to evaluate the performances of the COBAS^® AmpliPrep/COBAS^® (CAP/CTM) HIV-1 Qualitative assays to detect the broad range of HIV-1 variants circulating in Central Africa and compare to the outgoing CAP/CTM HIV-1 Quantitative test v2.0 (Roche Molecular Systems), chosen as reference gold standard molecular assay.

Methods:

The CAP/CTM HIV-1 Qualitative tests versions 1.0 and 2.0 (Roche Molecular Systems, Inc., Branchburg, NJ, USA) were evaluated compared to CAP/CTM TaqMan HIV-1 Quantitative test v2.0 (Roche Molecular Systems) on 239 dried plasma spot (DPS) from 133 HIV-1-infected (with detectable plasma HIV RNA load) and 106 uninfected children, followed-up at Complexe Pédiatrique, Bangui, Central African Republic.

Results:

The version 1.0 showed low sensitivity (93.2%), with 9 (6.8%) false negative results, demonstrating under-detection of non-B HIV-1 subtypes. In contrast, the upgraded version 2.0 showed 100%-sensitivity, 100%-specificity and perfect agreement (κ coefficient, 1.0).

Conclusion:

Our evaluation in the Central African Republic demonstrates the clinical implications of the accuracy and reliability of the CAP/CTM HIV-1 Qualitative assay for early diagnosis of HIV-1 in Central African children.

Detection and quantification of HIV-1 RNA with a fully automated transcription-mediated-amplification assay

BACKGROUND

Nucleic acid testing is the major method used to monitor HIV viral load. Commercial systems based on real-time PCR assays are available for high-volume centralized laboratory testing, but they are not fully automated.

OBJECTIVES AND STUDY DESIGN

We have compared the diagnostic performance of the Hologic Aptima HIV-1 Quant Dx assay (Aptima) (based on real-time TMA) on the Panther instrument, a fully-automated random access platform, to that of, the Roche Cobas Ampliprep Cobas TaqMan (CAP/CTM) HIV-1 version 2.0 (based on real-time PCR).

RESULTS

Probit analysis of replicate dilutions of NIBSC WHO International HIV-1 Standard, gave LODs of 8.6 c/ml for Aptima and 15.2 c/ml for CAP/CTM. The agreement between the assays was excellent when measuring HIV RNA in a calibrated reference (κ=0.90, p<0.001) and good when measuring clinical samples (κ=0.62, p<0.001). The correlation among the samples quantified by the two methods was very good (r=0.95, p<0.001) and the mean difference between the values obtained with the two assays was 0.02 log c/ml for B and non-B subtypes. The vast majority of results showed <0.5 log variance between the two assays (89%); only one sample showed results that differed by over 1.0 log c/ml.

CONCLUSION

The performance of the new fully automated Aptima assay is adequate for clinical monitoring of HIV-1 RNA during infections and treatment. The Aptima assay is well suited for routine laboratory use.

Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites

HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory (EQAPOL) was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS). Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9%) were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative approach, especially for detection of low-abundance DRMs.

Evaluation of the Aptima(®) HIV-1 Quant Dx assay for HIV-1 RNA viral load detection and quantitation in plasma of HIV-1-infected individuals: A comparison with Abbott RealTime HIV-1 assay

The Hologic Aptima^® HIV‐1 Quant Dx assay (Aptima HIV) is a real‐time transcription‐mediated amplification method CE‐approved for use in diagnosis and monitoring of HIV‐1 infection. The analytical performance of this new assay was compared to the FDA‐approved Abbott RealTime HIV‐1 (RealTime). The evaluation was performed using 220 clinical plasma samples, the WHO 3rd HIV‐1 International Standard, and the QCMD HIV‐1 RNA EQA. Concordance on qualitative results, correlation between quantitative results, accuracy, and reproducibility of viral load data were analyzed. The ability to measure HIV‐1 subtypes was assessed on the second WHO International Reference Preparation Panel for HIV‐1 Subtypes. With clinical samples, inter‐assay agreement for qualitative results was high (91.8%) with Cohen's kappa statistic equal to 0.836. For samples with quantitative results in both assays (n = 93), Lin's concordance correlation coefficient was 0.980 (P  < 0.0001) and mean differences of measurement, conducted according to Bland–Altman method, was low (0.115 log₁₀ copies/ml). The Aptima HIV quantified the WHO 3rd HIV‐1 International Standard diluted from 2000 to 31 cp/ml (5,700–88 IU/ml) at expected values with excellent linearity (R² > 0.970) and showed higher sensitivity compared to RealTime being able to detect HIV‐1 RNA in 10 out of 10 replicates containing down to 7 cp/ml (20 IU/ml). Reproducibility was very high, even at low HIV‐1 RNA values. The Aptima HIV was able to detect and accurately quantify all the main HIV‐1 subtypes in both reference panels and clinical samples. Besides excellent performance, Aptima HIV shows full automation, ease of use, and improved workflow compared to RealTime. J. Med. Virol. 88:1535–1544, 2016. © 2016 Wiley Periodicals, Inc.

Comparing Abbott m2000 RealTime HIV test and Roche COBAS Ampliprep/COBAS Taqman HIV test, v2.0 in treated HIV-1 B and non-B subjects with low viraemia

Viral load testing is a valuable tool in HIV clinical care and research. Discrepancies among diverse viral load assays, especially with regard to non-B HIV-1 subtypes have been reported. Our study aimed to explore the impact of HIV subtype (B versus non-B) on the agreement between CAP/CTM, v2.0 and m2000 RealTime in treated HIV patients, focusing on low viral loads (<200 copies/ml). Our findings indicate that there is a significant difference in the performance of the compared assays in the low-viremic range and non-B subtypes, suggesting that a single assay should be used for follow-up.

Evaluation of the RealTime HIV-1, Xpert HIV-1, and Aptima HIV-1 Quant Dx Assays in Comparison to the NucliSens EasyQ HIV-1 v2.0 Assay for Quantification of HIV-1 Viral Load

HIV-1 RNA monitoring, both before and during antiretroviral therapy, is an integral part of HIV management worldwide. Measurements of HIV-1 viral loads are expected to assess the copy numbers of all common HIV-1 subtypes accurately and to be equally sensitive at different viral loads. In this study, we compared for the first time the performance of the NucliSens v2.0, RealTime HIV-1, Aptima HIV-1 Quant Dx, and Xpert HIV-1 viral load assays. Plasma samples (n = 404) were selected on the basis of their NucliSens v2.0 viral load results and HIV-1 subtypes. Concordance, linear regression, and Bland-Altman plots were assessed, and mixed-model analysis was utilized to compare the analytical performance of the assays for different HIV-1 subtypes and for low and high HIV-1 copy numbers. Overall, high concordance (>83.89%), high correlation values (Pearson r values of >0.89), and good agreement were observed among all assays, although the Xpert and Aptima assays, which provided the most similar outputs (estimated mean viral loads of 2.67 log copies/ml [95% confidence interval [CI], 2.50 to 2.84 log copies/ml] and 2.68 log copies/ml [95% CI, 2.49 to 2.86 log copies/ml], respectively), correlated best with the RealTime assay (89.8% concordance, with Pearson r values of 0.97 to 0.98). These three assays exhibited greater precision than the NucliSens v2.0 assay. All assays were equally sensitive for subtype B and AG/G samples and for samples with viral loads of 1.60 to 3.00 log copies/ml. The NucliSens v2.0 assay underestimated A1 samples and those with viral loads of >3.00 log copies/ml. The RealTime assay tended to underquantify subtype C (compared to the Xpert and Aptima assays) and subtype A1 samples. The Xpert and Aptima assays were equally efficient for detection of all subtypes and viral loads, which renders these new assays most suitable for clinical HIV laboratories.

Comparison of the bioMérieux NucliSENS EasyQ HIV-1 v2.0-HIV-1 RNA quantification assay versus Abbott RealTime HIV-1 and Roche Cobas TaqMan HIV-1 v2.0 on current epidemic HIV-1 variants

BACKGROUND

An improved version of the bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 has been introduced to overcome the underquantification observed with previous versions, especially with non-B HIV-1 subtypes.

OBJECTIVES

Comparing bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 versus Roche Cobas CA/CTM v2.0 and Abbott RealTime HIV-1 assays for HIV-1 group M and non-M (N, O, P) viral load measurement.

STUDY DESIGN

The three assays were tested in parallel on 103HIV-1 group M plasma samples, and on non-group M HIV-1 culture supernatants.

RESULTS

Values obtained for the 103HIV-1 group M plasma samples tested with bioMérieux assay showed good overall correlation compared to the 2 others. The Roche Cobas assay gave higher values than the bioMérieux assay, while Abbott and bioMérieux both displayed similar results. However, analysis showed a wider dispersion in results when comparing the bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 and the other 2 techniques. All data taken into account, we observed frequent discrepancies in quantification, of the plasma samples and major differences above 1log in 10/72 (13.8%). The quantification of non-M HIV groups in culture supernatant has shown variable results, with better quantification of HIV-O and of HIV-N respectively with the Abbott assay and the bioMérieux assay.

CONCLUSIONS

The bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 showed improved sensitivity to non-B HIV-M subtypes compared to previous versions. Notwithstanding, we observed frequent discrepancies and a wide dispersion in results when comparing bioMérieux NucliSENS(®) EasyQ(®) HIV-1 v2.0 and the other 2 techniques.

Comparison of four commercial viral load techniques in an area of non-B HIV-1 subtypes circulation

The aim of this study was to compare four HIV-1 viral quantitation platforms, Nuclisens EasyQ v2.0(®) (EQ), COBAS AmpliPreP/Cobas Taqman(®) HIV-1 test v 2.0 (CTM), GENERIC HIV CHARGE VIRALE(®) (GEN), with Abbott Real Time HIV-1(®) (m2000sp/rt) as reference technique. The study had first evaluated m2000sp/rt performances and then compared quantitation between techniques. Discordant samples were genotyped on gag and pol gene and sequences were analyzed using Sequence locator and SeqPublish to detect eventual mismatches. Performance analysis of m2000sp/rt showed good results with coefficients of variation values (CV) of 1.35%, 0.65%, and 0.54% for repeatability testing of low, intermediate and high concentrations, respectively. Reproducibility tests showed low CV values with 2.36% and 1.42% for low and high concentration levels, respectively and contamination test was very low value with 0.94%. Correlation and concordance between techniques ranged from r(2)=0.98 and bias=-0.00185 (for m2000sp/rt vs CTM) to r(2)=0.90 and bias=-0.135 (for EQ vs GEN). Discrepancies were observed on 37 samples mostly CRF02_AG but despite some mismatches, sequence analysis (26/37) did not show any remarkable differences between CRF02_AG queries and references. This study showed good correlation and good concordance between techniques. However, EQ yielded under-quantitation of CRF02_AG.

Comparative performance of the new Aptima HIV-1 Quant Dx assay with three commercial PCR-based HIV-1 RNA quantitation assays

BACKGROUND

Quantitative measurement of HIV-1 RNA levels in plasma ('viral load') plays a central role in clinical management. The choice of assay platform can influence results and treatment decisions.

OBJECTIVE

To compare the analytical performance of the new TMA-based Hologic Aptima(®) HIV-1 Quant Dx assay with that of three PCR-based assays: Abbott RealTime HIV-1, Qiagen Artus(®) HI Virus-1 QS-RGQ, and Roche CAP/CTM HIV-1 Test v2.

STUDY DESIGN

Assay performance was evaluated using Acrometrix HIV-1 RNA Standard panels; the 3rd WHO HIV-1 RNA International Standard (12-500 copies/ml; 6 dilutions; 9 replicates); and plasma samples from 191 HIV-positive patients.

RESULTS

Aptima showed high (>0.99) precision, accuracy and concordance with the Acrometrix Standards across a wide dynamic range (2.0-6.7 log10copies/ml). Variance caused up to 2.1 (Aptima), 1.7 (RealTime), 7.5 (Artus), and 1.9 (CAP/CTM) fold changes in the International Standard quantifications at 50-500 copies/ml. HIV-1 RNA detection rates in plasma samples were 141/191 (74%), 119/191 (62%), 108/191 (57%), and 145/191 (76%) for Aptima, RealTime, Artus and CAP/CTM, respectively. For categorising samples either side of 50 copies/ml, Aptima had excellent agreement with RealTime (kappa 0.92; 95% CI 0.87-0.98); lowest agreement was with Artus (kappa 0.79; 95%CI 0.70-0.88). Aptima quantifications were mean 0.12 and 0.06 log10copies/ml higher compared with RealTime and CAP/CTM, respectively, and 0.05 log10copies/ml lower compared with Artus. Limits of agreement were narrowest when comparing Aptima to RealTime.

CONCLUSIONS

The new Aptima HIV assay is sensitive, precise, and accurate. HIV assays exhibit discordance at low HIV-1 RNA copy numbers.

Evaluation of the NucliSens EasyQ v2.0 assay in comparison with the Roche Amplicor v1.5 and the Roche CAP/CTM HIV-1 Test v2.0 in quantification of C-clade HIV-1 in plasma

Human immunodeficiency virus type 1 (HIV-1) genetic diversity poses a challenge to reliable viral load monitoring. Discrepancies between different testing platforms have been observed, especially for non-clade-B virus. Therefore we compare, in antiretroviral therapy (ART)-naïve South African subjects predominantly infected with HIV-1 clade-C, three commercially available assays: the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test version 2.0 by Roche (CAP/CTM v2.0), the BioMérieux NucliSens Version 2.0 Easy Q/Easy Mag (NucliSens v2.0) and the Roche COBAS Amplicor HIV-1 Monitor Test Version 1.5 (Amplicor v1.5). Strong linear correlation was observed and Bland-Altman analyses showed overall good agreement between the assays with mean viral load differences of 0.078 log cp/ml (NucliSens v2.0 – Amplicor v1.5), 0.260 log cp/ml (CAP/CTM v2.0 – Amplicor v1.5) and 0.164 log cp/ml (CAP/CTM v2.0 – NucliSens v2.0), indicating lower mean viral load results for the Amplicor v1.5 and higher mean readings for the CAP/CTM v2.0. Consistent with observations following previous comparisons of CAP/CTM v2.0 versus Amplicor v1.5, the CAP/CTM v2.0 assay detected low-level viremia (median 65 cp/ml) in more than one-third of those in whom viremia had been undetectable (<20 cp/ml) in assays using the NucliSens platform. These levels of viremia are of uncertain clinical significance but may be of importance in early detection of ART resistance in those on treatment. Overall the three assays showed good comparability of results but with consistent, albeit relatively small, discrepancies for HIV-1 clade-C samples, especially in the low-viremic range that should be taken into account when interpreting viral load data.

Ability of two commercially available assays (Abbott RealTime HIV-1 and Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Version 2.0) to quantify low HIV-1 RNA Levels (<1,000 copies/milliliter): comparison with clinical samples and NIBSC working reagent for nucleic acid testing assays

Concordance between molecular assays may be suboptimal at low HIV-1 viremia levels (<1,000 copies/ml); therefore, it may be difficult to define and compare virologic endpoints for successful and failed therapy. We compared two commercial assays (the Abbott RealTime HIV-1 and the Roche Cobas AmpliPrep/TaqMan HIV-1 version 2.0) for their ability to detect and quantify low viral loads. A comparison was performed using 167 residual clinical samples (with values ranging from "not detected" to 1,000 copies/ml, as measured by the Abbott assay) and the National Institute and Biological Standards and Control (NIBSC) HIV-1 RNA working reagent 1 for nucleic acid amplification techniques (NAT) assays (serially diluted to a range from 1 to 1,000 copies/ml). Quantitative results were compared using Lin's concordance correlation coefficient and a Bland-Altman plot. Concordance with the qualitative results was measured by Cohen's kappa statistic. With clinical samples, the degree of interassay concordance of the qualitative results at a 40-copies/ml HIV-1 RNA threshold was substantial (κ = 0.762); the correlation among the quantified samples was suboptimal (concordance correlation coefficient, 0.728; P < 0.0001); the mean difference of the values between the Roche and Abbott assays was 0.193 log10 copies/ml. Using the HIV-1 RNA working reagent 1 for NAT assays, the results provided by the Roche assay were, on average, 3 times higher than expected, while the Abbott assay showed high accuracy. The Roche assay was highly sensitive, being able to detect a level as low as 3.5 copies/ml HIV-1 RNA with 95% probability. The performance characteristics of each molecular assay should be taken into account when HIV-1 RNA threshold values for "virologic suppression," "virologic failure," "persistent low viral loads," etc., are defined and indicated in the support of clinical decisions.

Comparative performances of HIV-1 RNA load assays at low viral load levels: results of an international collaboration

Low-level viremia during antiretroviral therapy and its accurate measurement are increasingly relevant. Here, we present an international collaboration of 4,221 paired blood plasma viral load (pVL) results from four commercial assays, emphasizing the data with low pVL. The assays compared were the Abbott RealTime assay, the Roche Amplicor assay, and the Roche TaqMan version 1 and version 2 assays. The correlation between the assays was 0.90 to 0.97. However, at a low pVL, the correlation fell to 0.45 to 0.85. The observed interassay concordance was higher when detectability was defined as 200 copies/ml than when it was defined as 50 copies/ml. A pVL of ∼100 to 125 copies/ml by the TaqMan version 1 and version 2 assays corresponded best to a 50-copies/ml threshold with the Amplicor assay. Correlation and concordance between the viral load assays were lower at a low pVL. Clear guidelines are needed on the clinical significance of low-level viremia.

Therapeutic vaccination using cationic liposome-adjuvanted HIV type 1 peptides representing HLA-supertype-restricted subdominant T cell epitopes: safety, immunogenicity, and feasibility in Guinea-Bissau

We have designed a therapeutic HIV-1 vaccine concept based on peptides together with the adjuvant CAF01. Peptides represented 15 HLA-supertype-restricted subdominant and conserved CD8 T cell epitopes and three CD4 T-helper cell epitopes. In this phase I clinical trial, safety and immunogenicity were assessed in untreated HIV-1-infected individuals in Guinea-Bissau, West Africa. Twenty-three HIV-1-infected individuals were randomized to receive placebo (n=5) or vaccine (n=18). Safety was appraised by clinical follow-up combined with monitoring of biochemistry, hematology, CD4 T cell counts, and HIV-1 viral loads. T cell immunogenicity was monitored longitudinally by interferon (IFN)-γ ELISpot. New vaccine-specific T cell responses were induced in 6/14 vaccinees for whom ELISpot data were valid. CD4 T cell counts and viral loads were stable. The study shows that therapeutic immunization is feasible and safe in Guinea-Bissau and that it is possible to redirect T cell immunity with CAF01-adjuvanted HIV-1 peptide vaccine during untreated HIV-1 infection in some patients. However, relatively few preexisting and vaccine-induced HIV-1 T cell responses to CD8 T cell epitopes were detected against HIV-1 using IFN-γ ELISpot in this chronically infected African population.

Cobas ampliprep/cobas TaqMan HIV-1 v2.0 assay: consequences at the cohort level

Background

High-sensitive real-time PCR assays are routinely used to monitor HIV-1 infected subjects. Inter-assay discrepancies have been described at the low viral load (VL) end, where clinical decisions regarding possible virological rebound are based.

Methods

A retrospective study was performed to analyze frequencies of viral blips after transition to the COBAS Ampliprep/COBAS TaqMan v2.0 HIV-1 assay (Taqman v2.0) in patients with prior undetectable VLs as measured with the Roche Cobas Ampliprep Amplicor HIV-1 Monitor Test, v1.5 (Amplicor) and was evaluated in comparison to a group of patients monitored with the Abbott Real-time HIV-1 assay (Abbott RT) during the same period of time.

Results

85 of 373 patients with VLs below the limit of quantification with Amplicor had VLs >50 copies/mL after transition to the TaqMan v2.0 assay. Among these 74.1% had VLs ranging from 50–499 copies/mL, 22.9% had VLs >500 copies/mL. From 22 patients with initial Taqman v2.0 based VLs exceeding 500 copies/mL, 6 patients had VLs <20 copies/mL after novel VL measurement on a next visit. In our control group with VL quantification using the Abbott RT assay, only 1 patient became detectable and showed a VL of <40 copies/mL after new measurement.

Conclusions

Transition to the Taqman v2.0 assay was accompanied by an increase of quantifiable HIV-1 VLs in patients with long term viral suppression under antiretroviral therapy that might be attributed to technical shortcomings of the Taqman v2.0 assay. A high test variability at the low VL end but also beyond was observed, making meaningful clinical interpretation of viral blips derived from different assays difficult.

An in-house assay for BK polyomavirus quantification using the Abbott m2000 RealTime system

BK polyomavirus (BKPyV) quantification is useful for monitoring renal transplant patient response to therapy. The Abbott m2000 RealTime System employed by some clinical laboratories to perform US Food and Drug Administration-approved assays can also be used to develop in-house assays such as the one presented here. This study aimed to validate an in-house quantitative real-time PCR assay targeting the BKPyV major capsid VP1 gene for assessment of viral load using the Abbott m2000 RealTime System. BKPyV load was measured in 95 urine and plasma samples previously tested for BKPyV by one of three laboratories (46 BKPyV-positive samples consisting of 35 plasma and 11 urine samples; 49 samples negative for BKPyV consisting of 47 plasma and two urine samples). Two additional plasma specimens from the College of American Pathologists proficiency testing survey were also analysed. Precision studies were performed by diluting a high-viral-titre patient sample into BKPyV-negative pooled plasma to create high-positive (6.16 log10 copies ml(-1)) and low-positive (3.16 log10 copies ml(-1)) samples. For precision studies of inter-assay variability, a high-positive (7.0 log10 copies ml(-1)) and a low-positive (3.0 log10 copies ml(-1)) sample were measured in 20 separate runs. The assay's limit of quantification and limit of detection were 2.70 and 2.25 log10 copies ml(-1), respectively. The assay was linear from 2.70 to 9.26 log10 copies ml(-1). Of the 48 known positives, 43 were detected as positive, with three reported by the reference laboratory as values lower than the limit of detection. Two known positives at 3.27 and 3.80 log10 copies ml(-1) tested negative by the m2000 BKPyV assay. Of the 49 known negative samples, 48 were negative by the m2000 BKPyV load assay, with one sample confirmed positive by a reference laboratory. Qualitative analysis prior to discrepancy testing demonstrated a sensitivity of 89.58 % and a specificity of 97.96 %. Precision studies demonstrated inter-assay coefficients of variation of 0.63 % (high positive) and 4.38 % (low positive). Genotyping was performed on 22 patient samples, of which 21 (95.45 %) were type I and one (4.55 %) was type II. In conclusion, the m2000 BKPyV viral load assay sensitivity, specificity, linear range, precision and cost effectiveness make it an attractive methodology for clinical laboratories using the Abbott m2000 RealTime System.

Advances in detection and monitoring of plasma viremia in HIV-infected individuals receiving antiretroviral therapy

PURPOSE OF REVIEW

This review will describe advances in detection and results of monitoring persistent viremia in patients on long-term suppressive therapy. In addition, the review explores the usefulness of these methods in determining the effectiveness of new HIV-1 eradication strategies in purging persistent HIV-1 reservoirs.

RECENT FINDINGS

Quantification of plasma HIV-1 RNA levels remains essential for determining the success of combination antiretroviral therapy (cART) in treated patients. Recently, several new platforms with improved sensitivity for quantifying HIV-1 RNA have been developed and the application of these assays has revealed that low-level viremia persists in patients on suppressive therapy. In addition, new technological advances such as digital PCR have been proposed to increase the sensitivity of measuring and characterizing persistent HIV-1 viremia. The application of these assays will be important in determining the effectiveness of future HIV-1 eradication strategies.

SUMMARY

The level of HIV-1 RNA in patient plasma remains an important marker for determining the success of cART. New sensitive assays have found that HIV-1 persists in the plasma of patients on suppressive therapy that may have implications for the clinical management of this disease and strategies for eliminating HIV-1 infection.

Sequencing assays for failed genotyping with the versant hepatitis C virus genotype assay (LiPA), version 2.0

For optimal antiviral therapy, the hepatitis C virus (HCV) genotype needs to be determined, as it remains a strong predictor of sustained viral response. In this study, we assessed the number of HCV genotyping results that could not be determined using the commercially available line probe assay (LiPA) (Versant hepatitis C virus genotype 2.0 assay) in a large international panel of samples from 9,874 HCV-positive patients. In-house sequencing assays targeting the 5' untranslated region (UTR), core region, NS3 region, and NS5B region of the HCV genome and phylogenetic analyses were used to resolve these LiPA failures. Among all cases, the genotypes of 51 samples (0.52%) could not be determined with the LiPA. These undetermined results were observed more frequently among samples from non-European regions (mainly the Arabian Peninsula). The use of sequencing assays coupled with phylogenetic analysis provided reliable genotype results for 86% of the LiPA failures, which exhibited higher rates of genotypes 4, 5, and 6 than did LiPA-resolved genotypes. As expected, the 5' UTR was not sufficiently variable for clear discrimination between genotypes 1 and 6, but it also resulted in errors in classification of some genotype 3 and 4 cases using well-known Web-based BLAST programs. This study demonstrates the low frequency of genotyping failures with the Versant hepatitis C virus genotype 2.0 assay (LiPA) and also underlines the need for a complex combination of sequences and phylogenetic analyses in order to genotype these particular HCV strains correctly.

Current assays for HIV-1 diagnostics and antiretroviral therapy monitoring: challenges and possibilities

In 2011, there were over 34 million people living with HIV infections, placing a heavy burden on public health sectors. HIV infection is a lifelong threat that cannot be prevented by vaccination or cured by antiretroviral drugs. The infected patients rely on daily antiretroviral therapy to suppress HIV viral replication. Hence, it is important to diagnose HIV infections as early as possible and to monitor the efficacy of antiretroviral therapy every 3–6 months. Different immunoassays detecting HIV antigens and antibodies have been modified to offer better sensitivity and more rapid diagnosis. Several clinical and virological parameters, including CD4+ cell counts, viral load and drug resistance mutations, are also used for treatment monitoring. Many molecular assay optimizations are now being utilized to improve patient care. This review will focus on the most updated HIV diagnostic assays, as well as discussing the upcoming possibilities of other advanced technologies.

Quantification of viral loads lower than 50 copies per milliliter by use of the Cobas AmpliPrep/Cobas TaqMan HIV-1 test, version 2.0, can predict the likelihood of subsequent virological rebound to >50 copies per milliliter

After 1 year of follow-up, patients on HAART with a baseline viral load (VL) of <20 copies/ml showed significantly lower odds of virological rebound to two consecutive VLs of >50 copies/ml than those with baseline VLs of 20 to 39 and 40 to 49 (P < 0.001). The time to virological rebound was also significantly shorter (P < 0.001) for the groups with baseline VLs of 20 to 39 and 40 to 49.

Digitally programmable microfluidic automaton for multiscale combinatorial mixing and sample processing

A digitally programmable microfluidic Automaton consisting of a 2-dimensional array of pneumatically actuated microvalves is programmed to perform new multiscale mixing and sample processing operations. Large (μL-scale) volume processing operations are enabled by precise metering of multiple reagents within individual nL-scale valves followed by serial repetitive transfer to programmed locations in the array. A novel process exploiting new combining valve concepts is developed for continuous rapid and complete mixing of reagents in less than 800 ms. Mixing, transfer, storage, and rinsing operations are implemented combinatorially to achieve complex assay automation protocols. The practical utility of this technology is demonstrated by performing automated serial dilution for quantitative analysis as well as the first demonstration of on-chip fluorescent derivatization of biomarker targets (carboxylic acids) for microchip capillary electrophoresis on the Mars Organic Analyzer. A language is developed to describe how unit operations are combined to form a microfluidic program. Finally, this technology is used to develop a novel microfluidic 6-sample processor for combinatorial mixing of large sets (>2(6) unique combinations) of reagents. The digitally programmable microfluidic Automaton is a versatile programmable sample processor for a wide range of process volumes, for multiple samples, and for different types of analyses.

Generation of dried tube specimen for HIV-1 viral load proficiency test panels: a cost-effective alternative for external quality assessment programs

Participation in external quality assessment programs is critical to ensure quality clinical laboratory testing. Commercially available proficiency test panels for HIV-1 virus load testing that are used commonly in external quality assessment programs remain a financial obstacle to resource-limited countries. Maintaining cold-chain transportation largely contributes to the cost of traditional liquid proficiency test panels. Therefore, we developed and evaluated a proficiency test panel using dried tube specimens that can be shipped and stored at ambient temperature. This dried tube specimens panel consisted of 20 μl aliquots of a HIV-1 stock that were added to 2 ml tubes and left uncapped for drying, as a preservation method. The stability of dried tube specimens at concentrations ranging from 10² to 10⁶·⁵ RNA copies/ml was tested at different temperatures over time, showing no viral load reduction at 37 °C and a decrease in viral load smaller than 0.5 Log₁₀ at 45 °C for up to eight weeks when compared to initial results. Eight cycles of freezing-thawing had no effect on the stability of the dried tube specimens. Comparable viral load results were observed when dried tube specimen panels were tested on Roche CAPTAQ, Abbott m2000, and Biomerieux easyMAG viral load systems. Preliminary test results of dried proficiency test panels shipped to four African countries at ambient temperature demonstrated a low inter assay variation (SD range: 0.29-0.41 Log₁₀ RNA copies/ml). These results indicated that HIV-1 proficiency test panels generated by this methodology might be an acceptable alternative for laboratories in resource-limited countries to participate in external quality assessment programs.

Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections

Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics.

Comparison of HIV-1 viral load assay performance in immunological stable patients with low or undetectable viremia

The goal of antiretroviral therapy is reduction in morbidity and mortality via suppression of human immunodeficiency virus (HIV) viral load (VL) to undetectable levels. VL assay sensitivity has improved over time, but the reproducibility and clinical importance of VL results marginally higher than the limit of detection (LoD) are uncertain. We assessed the reproducibility and concordance of low VL results obtained with the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 version 2.0 (CAP-CTM) and the Abbott RealTime (m2000) HIV-1 assays, using longitudinal specimens from HIV-1-infected patients with low VL (<300 copies/ml) and stable CD4+ cell counts. Based on replicate testing of 3 specimens, coefficients of variation for log-transformed VL results were 5-8 % for m2000 and 9-10 % for CAP-CTM. The concordance between assays in specimens from patients with previously undetectable, detectable but not quantifiable VL, or variable (undetectable/detectable but not quantifiable VL) results over time was 90, 56, and 56 %, respectively. Correlation between results for specimens with quantifiable VL (initially 40-300 copies/ml) was moderate (R (2) = 0.48) with significantly higher results for CAP-CTM and a mean difference (CAP-CTM minus m2000) of 0.10 log(10) copies/ml. T-cell activation (CD8+/CD38+ percentage) in patients with low VL was initially higher than in patients with undetectable VL, and then decreased to equivalent levels over time. These results indicate that residual viremia at levels slightly above the LoD have no negative effect on T-cell activation.

Cross-platform analysis of HIV-1 RNA data generated by a multicenter assay validation study with wide geographic representation

HIV-1 RNA quantitation continues to be extremely important for monitoring patients infected with HIV-1, and a number of assays have been utilized for this purpose. Differences in assay performance with respect to log(10) recovery and HIV-1 subtype specificity have been well documented for commercially available assays, although comparisons are usually limited to one or two assay platforms. Two new FDA-approved assays, the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test (RT) and the Abbott RealTime HIV-1 assay (AR), that utilize real-time PCR have replaced previous HIV-1 RNA platforms. Inadequate detection of some strains of HIV-1 resulted in the addition of a new primer/probe set and the introduction of a second version of the RT assay. In this study, comparisons of assay performance between the different FDA-approved HIV-1 RNA assay platforms (both new and existing) were performed by using validation data that included both well-characterized virus stock and locally collected clinical samples. Laboratories across diverse geographical regions performed the validation testing and submitted data to the Virology Quality Assurance program (VQA) for analysis. Correlation values for clinical sample testing varied across the assay platforms (r = 0.832 to 0.986), and average log(10) recoveries for HIV-1 RNA controls (compared to the nominal value) ranged from -0.215 to 0.181. These data demonstrate the need for use of one assay platform for longitudinal patient monitoring, but the data also reinforce the notion that no one assay is superior and that testing across platforms may be required for discordance reconciliation.

Large-scale comparison of Roche Cobas AmpliPrep/Cobas TaqMan and Abbott RealTime HIV assays

Significant underquantitation of HIV RNA has been reported with the Roche Cobas AmpliPrep/Cobas TaqMan HIV Test (Version 1) compared to other assays. However, these studies have generally involved limited numbers of samples from select patient populations or analysis of samples that were undetectable in the TaqMan assay. Random plasma samples submitted from throughout the United States for HIV RNA quantitation (n=1263) were compared in the Roche TaqMan and Abbott RealTime assays. Twenty-four samples (1.9%) were discrepant, with a maximum difference between the two assays of 1.9logcopies/mL. These data indicate that both tests may be susceptible to underquantitation, but the incidence is low in this large cohort of samples from across the United States.

Comparison between the automated Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 assay and its version 1 and Nuclisens HIV-1 EasyQ version 2.0 assays when measuring diverse HIV-1 genotypes in China

BACKGROUND

Several commercially available HIV-1 viral load assays based on real-time detection technology and automated platforms are available. It is not clear how the diversity of HIV-1 genotypes impacts the ability to consistently detect HIV-1 viral loads.

OBJECTIVES

To examine whether the diversity of HIV-1 genotypes impacts the ability of the Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0), its version 1.0 (CAP/CTM v1.0) and the NucliSens EasyQ HIV-1 version 2.0 (EasyQ v2.0) assays to consistently determine the viral loads.

STUDY DESIGN

The three assays were used to measure the viral load in 178 plasma samples with diverse genotypes from treatment-naive patients.

RESULTS

CAP/CTM v2.0 showed significant correlation and high agreement with CAP/CTM v1.0 and EasyQ v2.0. CAP/CTM v2.0 showed excellent detection of clade B samples compared with CAP/CTM v1.0 and EasyQ v2.0. However, significant differences were observed when using CAP/CTM v2.0 to test clade BC and AE samples. The HIV-1 load measured by CAP/CTM v2.0 differed by >0.5logIU/ml in 59.52% and 72.62% of clade BC samples, and in 57.14% and 85.71% of clade AE samples, compared with CAP/CTM v1.0 and EasyQ v2.0, respectively. CAP/CTM v2.0 was more precise (13.18%) than EasyQ v2.0 (29.21%), and both assays showed good linearity (R≥0.9926).

CONCLUSIONS

The three assays may not deliver consistent results for samples belonging to clades BC and AE. It is strongly suggested that the version of the HIV-1 viral load assay used initially is also used at follow-up.

Comparative frequencies of HIV low-level viremia between real-time viral load assays at clinically relevant thresholds

BACKGROUND

The introduction of new real-time PCR HIV-1 assays with higher sensitivity and broader dynamic range has resulted in detection of low-level viremia (LLV) (≥ 50 copies/mL) in some patients who previously had undetectable HIV-1 viral load (VL) (<50 copies/mL) with end-point PCR assays. It is therefore important to compare the performance of end-point and newer real-time PCR assays at medically relevant decision points.

OBJECTIVES

The study compared the results obtained with the end-point COBAS(®) AMPLICOR HIV-1 MONITOR Test, v1.5 to those obtained by three real-time PCR assays COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HIV-1 Test; the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HIV-1 Test, v2.0; and the Abbott RealTime™ HIV-1 test.

STUDY DESIGN

A total of 391 plasma specimens from HIV-1-infected patients from three US cities were tested with all four assays. The correlation and concordance of results between real-time and end-point PCR assays were calculated.

RESULTS

There was a consistent and similar proportion (11.8-14.0%) of HIV-1 VL ≥ 50 copies/mL with the three real-time PCR assays for specimens recording <50 copies/mL on the end-point PCR assay. The real-time PCR assays correlated with the end-point PCR assay within generally accepted limits, but consistently quantified higher than the end-point PCR assay between 50 and 200 copies/mL. Discrepancies in results were associated with patient CD4+ cell count and antiviral medication class.

CONCLUSIONS

The clinical interpretation of VL results from real-time PCR assays should take into account their higher sensitivity at the lower quantitation range when assessing patients for disease progression and monitoring response to therapy in HIV-1-infected patients, in line with current treatment guidelines.

Mechanisms and factors that influence high frequency retroviral recombination

With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development.

Current challenges to viral load testing in the context of emerging genetic diversity of HIV-1

INTRODUCTION

One of the major characteristics of HIV-1 is its extreme genetic diversity. A key factor in assessing the sensitivity of a molecular-based assay measuring HIV-1 RNA viral load (VL) in plasma is its ability to detect/quantify all (or most of) relevant HIV-1 genetic subtype/recombinant forms accurately.

AREAS COVERED

This review provides an overview of the current commercially available quantitative real-time assays (the Abbott RealTime HIV-1, Roche TaqMan HIV-1 versions 1.0 and 2.0, BioMérieux Nuclisens EasyQ HIV-1, Siemens VERSANT HIV-1 RNA 1.0 kinetic PCR, and Biocentric Generic HIV Viral Load assays). For each assay, studies from 2005 to 2010 assessing the impact of HIV-1 genetic diversity on the reliability of HIV-1 RNA quantification are described.

EXPERT OPINION

In light of HIV-1 genetic diversity, a general recommendation to favor one test over the other cannot categorically be made. Larger field evaluations of HIV-1 RNA assays should be conducted in areas where HIV-1 genetic diversity is the highest. The large-scale implementation of HIV-1 VL testing is urgently required in the developing world to change HIV infection from a likely death sentence into a manageable chronic infection, as done in Northern countries.