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

Comparison of short-read and long-read next-generation sequencing technologies for determining HIV-1 drug resistance

Accurate HIV-1 genome sequencing is necessary to identify drug resistance mutations (DRMs) in people with HIV-1 (PWH). Next-generation-sequencing (NGS) allows the detection of minor variants and is now available in many laboratories. Our study aimed to compare two NGS approaches, a "short read" sequencing protocol using DeepChek® Whole Genome HIV-1 Assay on Illumina, and a "long read" sequencing protocol of HIV-1 pol and env single-molecule real-time sequencing (SMRT) on Pacific Biosciences (PacBio). We analyzed 16 plasma samples and 13 cellular samples from PWH. HIV-1 whole genome was amplified into five amplicons using DeepChek® Whole Genome HIV-1 Assay and sequenced on an iSeq. 100. In parallel, HIV-1 pol and env genes were separately amplified and sequenced using PacBio SMRT system with the circular consensus sequencing mode on a Sequel IIe. Concordance rates for determining DRMs with both approaches varied depending on the HIV-1 region, with higher concordance in the integrase region compared to the reverse transcriptase and protease regions. DeepChek® Whole Genome HIV-1 Assay exhibited better sensitivity in HIV-1 RNA sequencing of plasmas with lower viral loads. In cell HIV-1 DNA sequencing, the DeepChek® Whole Genome HIV-1 Assay performed better in pol and env sequencing but detected more APOBEC-induced DRMs, which can represent defective proviruses. Our findings indicate that both DeepChek® Whole Genome HIV-1 Assay and PacBio SMRT sequencing exhibit good performance for subtype determination, detection, and quantification of DRMs of the HIV-1 genome. However, some discrepancies were found in cellular samples, highlighting the challenges of interpreting HIV-1 DNA DRMs.

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.

Evaluating the Dual-Target Aptima HIV-1 Quant Dx Assay: Comparison between Viral Loads Measured with pol and LTR Targets in the Same Samples

For effective management of HIV-1 patients, accurate measurement of HIV-1-RNA viral load (VL) is fundamental. The latest generation molecular assays for monitoring VL perform simultaneous detection of two regions of the viral genome, but without specifying the target used for VL quantitation. By using the "open" software (research use only [RUO]) of Aptima HIV-1 Quant Dx Assay (Aptima) which provides both results obtained with the pol and LTR targets, we were able to compare n = 500 plasma samples results from chronically HIV-1-infected patients under antiretroviral therapy (ART). Correlation and concordance were analyzed. By stratifying VL into two groups (<30 and ≥30 copies/mL HIV-1-RNA) according to pol-based results and matching them with their respective LTR values, concordance was substantial (κ = 0.635; 95%CI = 0.569 to 0.700) as expected. Considering the specimens (n = 224) with VL exactly quantified (i.e., ≥30 copies/mL) with both targets, an optimal correlation subsisted (r = 0.8882; P < 0.0001) and Bland-Altman plot showed no significant mean difference between them. However, by stratifying all these data in three ranges (30 to 200, 201 to 1,000, and >1,000 copies/mL) according to pol-based results, concordance analysis showed fair agreement (κ = 0.344; 95%CI = 0.257 to 0.432). Indeed, after excluding mutually concordant VL values in each range (n = 134), the remaining discordant samples (n = 90; 40.1%) showed significant (P < 0.05) difference between VL measured with the two targets. With the Aptima "open" software, samples with pol-based VL <1,000 copies (cp)/mL HIV-1-RNA, the corresponding LTR values were on average 0.5 log₁₀ cp/mL higher. Further studies on these discrepancies and the nature of viral RNA elements detected only with the LTR despite efficient ART are in progress. IMPORTANCE The last generation dual-target platforms for quantification of HIV-1 RNA return a single value of viral load (VL) derived from a combined reading of two HIV-1 genome targets. By using a modified version of Aptima software, providing both the VL results obtained from pol and LTR amplification separately, we observed discordant VL results in some samples from HIV-1-infected patients on antiretroviral therapy. In particular, some samples with pol-based quantified <1,000 copies/mL VL showed the LTR-based value on average 0.5 log₁₀ copies/mL higher, and other samples, always by treated patients, showed VL exclusively quantified with LTR target while the corresponding pol-based VL results were completely undetected. Standard software of double-target based diagnostic systems does not allow recognizing discrepant VL values in these particular, but not rare, clinical specimens. This issue could have implications for clinical management by leading physicians to consider changing antiretroviral regimen based on presumed failure of antiretroviral therapy.

Comparison of the performance of Aptima HIV-1 Quant Dx Assay with Abbott RealTime HIV Assay for viral load monitoring using plasma and Dried Blood Spots collected in Kenya

Introduction

HIV-1 viral Load (VL) testing is recommended for the monitoring of antiretroviral treatment. Dried Blood Spots (DBS) are an effective sample type in resource limited settings, where safe phlebotomy and reliable shipping are hard to guarantee. In HIV high burden countries, high throughput assays can improve access to testing services. The Hologic Aptima HIV-1 Quant Dx Assay (Aptima Assay) is a high throughput assay that runs on the CE-IVD approved Panther platform. The objectives of this study were to assess the performance characteristics of Aptima for VL monitoring using plasma and venous DBS specimens and to determine the stability of HIV-1 RNA in DBS.

Materials and methods

This was a cross-sectional study of 2227 HIV infected adults visiting health facilities in Nairobi and Busia, Kenya. Each provided a venous blood sample; plasma was prepared from 1312 samples while paired DBS samples and plasma were prepared from the remaining 915 samples. The agreement between the Aptima assay and the Abbott RealTime HIV-1 Assay (Abbott RT) was analysed by comparing the HIV-1 VL in both assays at the medical decision point of 1000 copies/mL. To assess stability of HIV-1 RNA in DBS, VL in DBS spotted on day 0 were compared with that from the same DBS card after 21 days of storage at room temperature.

Results

Overall, 436 plasma samples had quantifiable results in both Aptima and Abbott RT. The agreement between the two assays at 1000 copies/mL was 97.48% with a Pearson’s correlation coefficient (r) of 0.9589 and gave a mean bias of 0.33 log copies/mL on Bland-Altman analysis. For fresh DBS, the agreement in both assays was 94.64% at 1000 copies/mL, with an r of 0.8692 and a mean bias of 0.35 log copies/mL. The overall agreement between DBS tested in Aptima on day 0 versus day 21 was 95.71%, with a mean bias of -0.154.

Conclusion

The Aptima HIV-1 Quant Dx assay is an accurate test for VL monitoring of HIV-1 using DBS and plasma sample types in Kenya.

Performance Evaluation of the Aptima Assays in Comparison with the cobas 6800 Assays for the Detection of HIV-1, HBV, and HCV in Clinical Samples

Background

Accurate and consistent viral load (VL) quantitation of HIV type 1 (HIV-1), hepatitis B virus (HBV), and hepatitis C virus (HCV) is important for diagnosis and clinical monitoring. Assay results have to be concordant and compatible across laboratories. We evaluated the performance of three Aptima assays (Hologic, San Diego, CA, USA) and compared their VL values with corresponding cobas 6800 assay (Roche Diagnostics, Mannheim, Germany) results, using 840 clinical samples.

Methods

The correlation between VL results obtained using the two assays was evaluated in terms of analytical sensitivity, precision/reproducibility, linearity, and cross-reactivity. Agreement rates were determined using kappa statistics. The overall agreement of VL values was examined using Passing–Bablok regression analysis.

Results

All CVs were within 5%; the assays had good precision for detecting all three viruses. The linearity of quantitation assessed using three AccuSpan linearity panels (Seracare, Milford, MA, USA), was excellent for the Aptima assays. For HIV-1 and HCV, the results of both assays showed excellent agreement (κ=0.89 and 0.90, respectively) while for HBV, the results showed good agreement (κ=0.69). For analytical sensitivity, the VLs required for a 100% detection rate of HIV-1, HBV, and HCV were 20 copies/mL, 7.5 IU/mL, and 5.0 IU/mL, respectively. The results for HIV-1, HBV, and HCV obtained using both assays correlated strongly (R²=0.97, 0.93, and 0.95, respectively).

Conclusions

The cobas 6800 and Aptima assays, with fully automated and high-throughput molecular platforms for HIV-1, HBV, and HCV VL measurements, show good analytical performance and a strong correlation between results. The study results suggest that the assays can be used interchangeably for long-term monitoring of chronic infections.

Practical approach to method verification in plasma and validation in cerebrospinal fluid under accreditation using a flexible scope in molecular virology: setting up the HIV, HBV and HCV Aptima™ Quant Dx assays

Background Our laboratory obtained the ISO 15189 accreditation for the plasmatic HIV-1, HBV and HCV viral load (VL) using the m2000 RealTime™ system, which was recently changed for the platform Panther®. Here, we discuss a strategy for performing method validation/verification very quickly. Methods We performed the mandatory (repeatability, internal quality assessment [IQA], measurement uncertainty [MU]) and optional technical verifications for CE/IVD assays using the flexible scope range A. We also performed the mandatory assays for the validation of HIV-1 VL in the cerebrospinal fluid (CSF) using the flexible scope range B. The change was checked by following up on the turnaround time (TAT). Results The coefficient of variation (CV%) for repeatability and IQA complied with the limit of 0.25 log. The MU results ranged from 0.04 to 0.25 log copies or IU/mL. The comparisons of methods showed excellent correlations (R2 = 0.96 for the three parameters) but a delayed centrifugation on HCV VL showed variations of up to 2 log IU/mL. An excellent linearity for HIV-1 in the CSF was obtained from 1.5 to 5 log copies/mL with R2 = 0.99. The TAT increased (84%-98%) in routine usage. Conclusions The three Aptima assays are well suited for routine laboratory use and can be integrated within less than 2 weeks in accordance with flexible scope range A. Our data allows us to confidently perform HIV-1 VL in CSF following flexible scope range B. Finally, we provide an organizational guide for flexible scope management in molecular virology within a short time frame.

Prospective evaluation of accuracy of HIV viral load monitoring using the Aptima HIV Quant Dx assay with fingerstick and venous dried blood spots prepared under field conditions in Kenya

Quantification of HIV-1 RNA is essential for clinical management of HIV patients. The limited throughput and significant hands-on time required by most HIV Viral load (VL) tests makes it challenging for laboratories with high test volume, to turn around patient results quickly. The Hologic Aptima HIV-1 Quant Dx Assay (Aptima), has the potential to alleviate this burden as it is high throughput and fully automated. This assay is validated for both plasma and dried blood spots (DBS), which are commonly used in resource limited settings. The objective of this study was to compare the performance of Aptima to Abbott RealTime HIV-1 Assay (Abbott RT), which was used as reference. This was a cross-sectional prospective study where HIV VL in finger stick (FS) DBS, venous blood (VB) DBS and plasma, collected from 258 consenting adults visiting 5 medical facilities in Kenya, Africa were tested in Aptima. The results were compared to plasma VL in Abbott RT at the medical decision point (MDP) of 1000 copies/mL and across Aptima assay range. The total agreement at MDP between plasma HIV VL in Abbott RT and plasma, FS and VB DBS tested in Aptima were 97.7%, 92.2% and 95.3% respectively with kappa statistic of 0.95, 0.84 and 0.90. The positive and negative agreement for all 3 sample types were >92%. Regression analysis between VL in Abbott RT plasma and various sample types tested in Aptima had a Pearson's correlation coefficient ≥0.91 with systematic bias of < 0.20 log copies/mL on Bland-Altman analysis. The high level of agreement in Aptima HIV VL results for all 3 sample types with Abbott RT plasma VL along with the high throughput, complete automation, and ease of use of the Panther platform makes Aptima a good option for HIV VL monitoring for busy laboratories with high volume of testing.

Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures

OBJECTIVES

Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is key to the clinical and epidemiological assessment of CoVID-19. We cross-validated manual and automated high-throughput testing for SARS-CoV-2-RNA, evaluated SARS-CoV-2 loads in nasopharyngeal-oropharyngeal swabs (NOPS), lower respiratory fluids, and plasma, and analyzed detection rates after lockdown and relaxation measures.

METHODS

Basel-S-gene, Roche-E-gene, and Roche-cobas®6800-Target1 and Target2 were prospectively validated in 1344 NOPS submitted during the first pandemic peak (Week 13). Follow-up cohort (FUP) 1, 2, and 3 comprised 10,999, 10,147, and 19,389 NOPS submitted during a 10-week period until Weeks 23, 33, and 43, respectively.

RESULTS

Concordant results were obtained in 1308 cases (97%), including 97 (9%) SARS-CoV-2-positives showing high quantitative correlations (Spearman's r > .95; p < .001) for all assays and high precision by Bland-Altman analysis. Discordant samples (N = 36, 3%) had significantly lower SARS-CoV-2 loads (p < .001). Following lockdown, detection rates declined to <1% in FUP-1, reducing single-test positive predictive values from 99.3% to 85.1%. Following relaxation, rates flared up to 4% and 12% in FUP-2 and -3, but infected patients were younger than during lockdown (34 vs. 52 years, p < .001). In 261 patients providing 936 NOPS, SARS-CoV-2 loads declined by three orders of magnitude within 10 days postdiagnosis (p < .001). SARS-CoV-2 loads in NOPS correlated with those in time-matched lower respiratory fluids or in plasma but remained detectable in some cases with negative follow-up NOPS, respectively.

CONCLUSION

Manual and automated assays significantly correlated qualitatively and quantitatively. Following a successful lockdown, declining positive predictive values require independent dual-target confirmation for reliable assessment. Confirmatory and quantitative follow-up testing should be obtained within <5 days and consider lower respiratory fluids in symptomatic patients with SARS-CoV-2-negative NOPS.

Performance evaluation of the Aptima HIV-1 RNA Quant assay on the Panther system using the standard and dilution protocols

BACKGROUND

Currently, FDA-approved HIV-1 viral load (VL) assays use venipuncture-derived plasma. The Hologic Panther system uses 0.7 mL total volume for the Aptima HIV-1 Quant Assay standard (APT-Quant-std) and dilution (APT-Quant-dil) protocols. However, smaller plasma volumes from fingerstick whole blood (FSB) collected in EDTA-microtainer tubes (MCT) could provide an easier sample collection method for HIV-1 VL testing.

OBJECTIVES

To evaluate the performance of the APT-Quant-std compared to the Roche CAP/CTM and Abbott m2000RT VL assays and an alternative APTQuant 1:7 dilution protocol, the latter using 100 μL of MCT-derived plasma from FSB.

STUDY DESIGN

Linearity was determined using commercial HIV-1 RNA plasma controls. Dilutions ranging 1.56-2.95 log10 copies/mL were prepared to determine the APT-Quant-dil Limit of Quantitation (LOQ) using Probit analysis. Specificity of APT-Quant-std was calculated using 326 HIVnegative samples. To evaluate agreement, 329 plasma specimens were tested with APT-Quant-std, CAP/CTM, and m2000RT. Forty-seven matched venipuncture and MCT-derived plasma specimens were tested with APT-Quant-std and APT-Quant-dil.

RESULTS

Among the RNA controls, specificity was 99.69 % for APT-Quant-std. The R2 values were 0.988 (APT-Quant-std/CAP/CTM), 0.980 (APT-Quant-std/ m2000RT), and 0.997 (APT-Quant-std/APT-Quant-dil). The APT-Quant-dil LOQ was estimated at 2.7 log10 copies/mL (500 copies/mL) (95 %CI 2.62-2.87). At 2.3 log10 copies/mL (200 copies/mL), the overall agreement was 91.0 % for APT-Quant-std/CAP/CTM, 85.7 % for APT-Quant-std/m2000RT, and 82.9 % for APT-Quant-std/APT-Quant-dil. Quantified APT-Quant-std results were on average 0.2 log10 copies/mL higher than CAP/CTM and m2000RT and 0.14 log10 copies/mL higher than APT-Quant-dil.

CONCLUSION

APT-Quant showed similar performance compared to the CAP/CTM and m2000RT assays and remains sensitive and accurate using the dilution protocol.

Could HIV-1 RNA Testing be an Option as the Second Step in the HIV Diagnostic Algorithm?

BACKGROUND

There is benefit to early HIV-1 diagnosis and treatment, but there is no Food and Drug Administration-approved quantitative assay with a diagnostic claim. We compared the performance of the Hologic Aptima HIV-1 Quant (APT-Quant) and Aptima HIV-1 Qual (APT-Qual) assays for diagnostic use and the performance of a diagnostic algorithm consisting of Bio-Rad BioPlex 2200 HIV Ag-Ab assay (BPC) followed by APT-Quant (2-test) compared with BPC followed by Geenius HIV-1/2 supplemental assay (Geenius) with reflex to APT-Qual (3-test).

METHODS

Five hundred twenty-four plasma, which included 419 longitudinal specimens from HIV-1 seroconverters (78 were after initiating antiretroviral therapy [ART]) and 105 from ART-naive persons with established HIV-1 infections, were used to evaluate APT-Quant performance for diagnostic use. Specimens from 200 HIV-negative persons were used to measure specificity. For the algorithm comparison, BPC-reactive specimens were evaluated with the 2-test or 3-test algorithm. McNemar's test was used to compare performance.

RESULTS

The APT-Quant detected more samples early in infection compared with APT-Qual. The APT-Quant specificity was 99.8%. Before ART initiation, the algorithms performed similarly among samples from different stages of infection. After ART initiation, the 3-test algorithm performed significantly better (P = 0.0233).

CONCLUSIONS

The APT-Quant has excellent performance for diagnostic use. The 2-test algorithm works well in ART-naive samples, but its performance decreases after the IgG response is elicited and with ART-induced suppressed viremia. Providing confirmation and viral load assay with 1 test result could be advantageous for patient care. However, additional factors and challenges associated with the implementation of this 2-test algorithm, such as cost, specimen type, and collection need further evaluation.

Multicenter Evaluation of Two Next-Generation HIV-1 Quantitation Assays, Aptima Quant Dx and Cobas 6800, in Comparison to the RealTime HIV-1 Reference Assay

High accuracy and precision at the lower end of quantification are crucial requirements of a modern HIV viral load (VL) assay, since some clinically relevant thresholds are located at 50 and 200 copies/ml. In this study, we compared the performance of two new fully automated HIV-1 VL assays, Aptima HIV-1 Quant Dx and Cobas HIV-1 (Cobas 6800), with the established RealTime m2000 assay. Assay precision and accuracy were evaluated in a retrospective evaluation out of excess plasma material from four HIV-1+ individuals (subtypes B, C, CRF01_AE, and CRF02_AG). Native plasma samples were diluted to nominal concentrations at 50 and 200 copies/ml (according to the RealTime m2000 assay). All dilutions were tested in triplicate in five independent runs over 5 days and in three labs per system. Assay concordance was determined using 1,011 surplus clinical routine samples, as well as selected retrospective longitudinal samples from 7 patients on treatment. The three assays yielded highly concordant results for individual clinical samples (R2 > 0.98; average difference, ≤0.2 log copies/ml) and retrospective longitudinal samples from patients on treatment. The Aptima and RealTime assays showed similar high precision, meeting the 5σ criterion for the majority of samples across all labs and subtypes. The Cobas assay was less precise, missing the 5σ criterion for the majority of samples at low concentrations. In this analysis, results from the Cobas assay appeared less reliable near the clinically relevant cutoff and should be interpreted with more caution in this context. Due to high precision, full automation, and high concordance with the RealTime assay, the Aptima assay represents a good alternative in routine VL monitoring.

Comparison of the Aptima HIV-1 Quant Dx assay with the COBAS AmpliPrep/COBAS TaqMan HIV-1 v2.0 Test for HIV-1 viral load quantification in plasma samples from HIV-1-infected patients

BACKGROUND AND AIMS

HIV-1 RNA viral load (VL) in plasma samples of HIV-1-positive patients is used to assess the level of viral replication, the risk of disease progression, and the response and efficacy to antiretroviral treatment. Knowing the performance of different tests for HIV-1 RNA detection is, therefore, important for clinical care. This study compared the performance of the recently introduced Aptima HIV-1 Quant Dx assay (Hologic, Inc) and the standard COBAS AmpliPrep/COBAS TaqMan HIV-1 v2.0 Test (CAP/CTM2) (Roche Molecular System, Inc) for HIV-1 RNA quantitation.

METHODS

Assay performance was assessed using 335 clinical samples, a standard HIV-1 low VL panel, and 2 diluted samples from well-characterized patients infected with different HIV-1 subtypes tested in 5 replicates over 3 days. All samples were tested on both assays to evaluate inter-assay agreement, both qualitatively and quantitively. Altogether, we evaluated assay sensitivity, linearity, accuracy, precision, repeatability, and reproducibility.

RESULTS

Assay agreement for qualitative results in 335 clinical samples was fair (80.6%). Correlation of quantitative assay results (n = 164) was excellent (R 2 = 0.97), with 96.3% of the results within the 95% limit of assay agreement (-0.42 to +0.86 log), and 98.8% within 1 log of each other. Aptima-HIV-1 yielded results, on average, 0.22 log higher than CAP/CTM2. Both assays accurately quantitated the HIV-1 standard at low VL (R 2 ≥ 0.94), with all samples within 0.5 log of the target.

CONCLUSION

Aptima-HIV-1 assay demonstrated sensitivity, accuracy, reproducibility, and precision for the detection and quantitation of HIV-1 RNA across a wide dynamic range of VLs. Its performance, together with full automation and high throughput, suggests that Aptima-HIV-1 could be a suitable assay for reliable monitoring of HIV-1 VL in patients undergoing treatment.