Establishing diagnostic cut-off criteria for the COBAS AmpliPrep/COBAS TaqMan HIV-1 Qualitative test through validation against the Amplicor DNA test v1.5 for infant diagnosis using dried blood spots

Delays in HIV-1 infant polymerase chain reaction testing may leave children without confirmed diagnoses in the Western Cape province, South Africa

Background

Early diagnosis and confirmation of HIV infection in newborns is crucial for expedited initiation of antiretroviral therapy. Confirmatory testing must be done for all children with a reactive HIV PCR result. There is no comprehensive data on confirmatory testing and HIV PCR test request rejections at National Health Laboratory Service laboratories in South Africa.

Objective

This study assessed the metrics of routine infant HIV PCR testing at the Tygerberg Hospital Virology Laboratory, Cape Town, Western Cape, South Africa, including the proportion of rejected test requests, turn-around time (TAT), and rate of confirmatory testing.

Methods

We retrospectively reviewed laboratory-based data on all HIV PCR tests performed on children ≤ 24 months old (n = 43 346) and data on rejected HIV PCR requests (n = 1479) at the Tygerberg virology laboratory over two years (2017–2019). Data from sample collection to release of results were analysed to assess the TAT and follow-up patterns.

Results

The proportion of rejected HIV PCR requests was 3.3%; 83.9% of these were rejected for various pre-analytical reasons. Most of the test results (89.2%) met the required 96-h TAT. Of the reactive initial test results, 53.5% had a follow-up sample tested, of which 93.1% were positive. Of the initial indeterminate results, 74.7% were negative on follow-up testing.

Conclusion

A high proportion of HIV PCR requests were rejected for pre-analytical reasons. The high number of initial reactive tests without evidence of follow-up suggests that a shorter TAT is required to allow confirmatory testing before children are discharged.

Indeterminate HIV PCR results within South Africa's early infant diagnosis programme, 2010-2019

OBJECTIVES

We describe the extent of, and variables associated with, indeterminate HIV-PCR results and final HIV status within South Africa's early infant diagnosis (EID) programme between 2010 and 2019.

METHODS

Retrospective analysis of routine paediatric HIV-PCR laboratory data from South Africa's National Health Laboratory Service Data Warehouse between 2010 and 2019. Final HIV status was determined by linking patient results (including HIV-PCR, HIV viral load, HIV serology and CD4 counts) using a probabilistic matching algorithm. Multivariate logistic regression was performed to determine variables associated with final HIV status among patients with an indeterminate HIV-PCR result.

RESULTS

Among 4 429 742 specimens registered for HIV-PCR testing from 3 816 166 patients, 113 209 (2.97%) tested positive and 22 899 (0.6%) tested indeterminate. As a proportion of HIV-detected results, 15.7% (23 896/151 832) of total and 31.5% (4900/15 566), 18.8% (11 400/60 794) and 10.1% (7596/75 472) among patients aged <7 days, 7 days-3 months and ≥3 months, respectively, were reported as indeterminate. Overall, 39.7% of patients with an indeterminate result had a linked HIV test to determine HIV status, of which 53.6% were positive with a median time to repeat testing of 30 days (interquartile range 15-69). Among patients who tested indeterminate, variables associated with a significantly higher odds of having a positive HIV status included testing indeterminate at birth (adjusted odds ratio (AOR) 0.63 (0.48-0.83) and 0.52 (0.39-0.69) for testing indeterminate at 7 days-3 months and ≥3 months respectively compared with birth), within a hospital (AOR 2.45 (1.99-3.03)), and in districts with an intra-uterine transmission rate ≥1.1% (AOR 3.14 (1.84-5.35)) (p < 0.001).

DISCUSSION

Indeterminate HIV-PCR results represent a considerable burden of missed diagnostic opportunities, diagnostic dilemmas and delays in making a definite diagnosis among HIV-infected infants within South Africa's EID programme. Alternative EID verification practices are urgently needed.

Use of an Indeterminate Range in HIV Early Infant Diagnosis: A Systematic Review and Meta-Analysis

BACKGROUND

Expanded access to HIV antiretrovirals has dramatically reduced mother-to-child transmission of HIV. However, there is increasing concern around false-positive HIV test results in perinatally HIV-exposed infants but few insights into the use of indeterminate range to improve infant HIV diagnosis.

METHODS

A systematic review and meta-analysis was conducted to evaluate the use of an indeterminate range for HIV early infant diagnosis. Published and unpublished studies from 2000 to 2018 were included. Study quality was evaluated using GRADE and QUADAS-2 criteria. A random-effects model compared various indeterminate ranges for identifying true and false positives.

RESULTS

The review identified 32 studies with data from over 1.3 million infants across 14 countries published from 2000 to 2018. Indeterminate results accounted for 16.5% of initial non-negative test results, and 76% of indeterminate results were negative on repeat testing. Most results were from Roche tests. In the random-effects model, an indeterminate range using a polymerase chain reaction cycle threshold value of ≥33 captured over 93% of false positives while classifying fewer than 9% of true positives as indeterminate.

CONCLUSIONS

Without the use of an indeterminate range, over 10% of infants could be incorrectly diagnosed as HIV positive if their initial test results are not confirmed. Use of an indeterminate range appears to lead to substantial improvements in the accuracy of early infant diagnosis testing and supports current recommendations to confirm all initial positive tests.

Clinical Consequences of Using an Indeterminate Range for Early Infant Diagnosis of HIV: A Decision Model

BACKGROUND

To minimize false-positive diagnoses of HIV in exposed infants, the World Health Organization recommends confirmatory testing for all infants initiating antiretroviral therapy (ART). In settings where confirmatory testing is not feasible or intermittently performed, clinical decisions may be aided by semi-quantitative cycle thresholds (Cts) that identify positive results most likely to be false-positive.

METHODS

We developed a decision analysis model of HIV-exposed infants in sub-Saharan Africa to estimate the clinical consequences of deferring ART for infants with weakly positive ("indeterminate") results. We assessed the degree to which "indeterminate" results may reduce the number of infants starting ART unnecessarily while missing a small number of HIV-infected infants. Our primary outcome was the ratio of averted unnecessary ART regimens to additional HIV-related deaths (due to false-negative diagnosis) at different Ct cutoffs.

RESULTS

The clinical consequences of adopting an indeterminate range varied with the prevalence of HIV and Ct cutoff. Considering a Ct cutoff ≥33, adopting an indeterminate range could prevent a median of 1.4 infants from receiving ART unnecessarily (95% UR: 1.0-2.0) for each additional HIV-related death. This ratio could be improved by prioritizing infants with indeterminate results for confirmatory testing [median 8.8 (95% UR: 6.0-13.3)] and by adopting a higher cutoff [median 82.3 (95% UR: 49.0-155.8) with Ct ≥36].

CONCLUSIONS

When implemented in settings where confirmatory testing is not universal, the benefits of classifying weakly positive results as "indeterminate" may outweigh the risks. Accordingly, the World Health Organization has recommended Ct values ≥33 be considered indeterminate for infant HIV diagnosis.

HIV diagnostic challenges in breast-fed infants of mothers on antiretroviral therapy

BACKGROUND

Prompt initiation of antiretroviral therapy (ART) for HIV-infected infants is strongly recommended but diagnostic confirmation is important as committing children to life-long ART carries serious health and social implications.

METHODS

Two HIV-exposed infants in Johannesburg, South Africa were identified presenting with unusual trajectories of diagnostic nucleic acid amplification tests (NAAT) and viral load results.

RESULTS

Case 1 had repeat indeterminate NAAT results during the first 3 weeks of life; repeat testing thereafter was negative with undetectable viral load including after daily nevirapine prophylaxis ended. ART was not initiated at this time. Case 2 had a single positive NAAT result at 1 month of age that prompted initiation of ART. Subsequent results were negative and ART was discontinued. Repeat negative NAAT with viral load below the limit of quantification or undetectable continued to be obtained. Shortly after and around weaning, positive NAAT results with high viral load (7.1 and 6.03 log10 copies/ml for Cases 1 and 2, respectively) were observed in both children. Both mothers were treated with tenofovir, emtricitabine and efavirenz during breastfeeding. Testing with ultrasensitive assays on early samples conclusively revealed HIV-1 proviral DNA in Case 1. Testing with ultrasensitive assays after the early period but prior to weaning did not detect HIV in either infant.

CONCLUSION

We hypothesize that breast milk from the mothers of these two rare cases had HIV-specific or nonspecific factors that led to the undetectable results in already infected infants until breastfeeding ended. Our results raise the importance of repeat testing of HIV-exposed breast-fed infants after complete cessation of all breastfeeding.

Pooled PCR testing of dried blood spots for infant HIV diagnosis is cost efficient and accurate

Background

Access to qualitative HIV PCRs for early infant diagnosis (EID) is restricted in resource-limited settings due to cost. We hypothesised that pooling of dried blood spots (DBS), defined as combining multiple patient samples in a single test with subsequent individual testing of positive pools, would be cost saving while retaining clinical accuracy compared to individual patient testing.

Methods

Cost savings: A model was developed to simulate reagent and consumable cost saving of pooled compared to individual sample testing. Daily sample/result data of a public health laboratory in South Africa were used to illustrate outputs from the model. Samples were randomly allocated to pools and the process was repeated 1000 times to measure variation in estimates due to this stochasticity.

Clinical accuracy: 1170 patient samples were tested using the Roche CAP/CTM Qual assay in pools of five 50 μl DBS. Negative pools comprised DBS previously tested in single reactions; positive pools included 1 positive sample.

Results

Pooling would have saved 64% of laboratory costs in 2015. The model is published as an R-based web tool, into which the user enters sample/positivity estimates and workflow management parameters to obtain cost saving estimates at an optimal pool size.

Sensitivity of pooled testing was 98.8% overall; 100% for strongly reactive pools. One pool tested false positive which would not impact clinical specificity as individual patient testing is performed prior to reporting.

Conclusions

Pooled PCR testing for EID remains accurate and dramatically reduces costs in settings with moderate to low prevalence rates and sufficient sample numbers.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3767-z) contains supplementary material, which is available to authorized users.

Interpretation of indeterminate HIV-1 PCR results are influenced by changing vertical transmission prevention regimens

BACKGROUND

Suppression of HIV by antiretroviral drugs may be one of the reasons that indeterminate HIV-1 PCR results are obtained from testing HIV-exposed infants. This complicates the early identification of infected infants, potentially delaying initiating treatment early. There is uncertainty as to how different vertical HIV transmission prevention regimens (VTP) affect the rate and predictive value of indeterminate PCR results.

OBJECTIVES

To investigate rates of indeterminate PCR results, outcomes of subsequent samples and the predictive value of an indeterminate PCR for a later positive result in the setting of intensifying VTP in the Western Cape province of South Africa.

STUDY DESIGN

Retrospective laboratory data analysis. Diagnostic PCR data of a public health laboratory from June 2009 to October 2014 was analysed and categorised by South African VTP regimens. First indeterminate HIV-1 PCRs in patients younger than 12 months were linked with follow-up HIV-1 PCRs and/or serological tests. Linked results sets were analysed by PCR amplification characteristics and subsequent patient outcome.

RESULTS

Over intensified VTP regimens, the rate of indeterminate and positive PCRs decreased significantly (5.6-3.2% and 2.4-0.4%, respectively; both p<0.001). Most notably, significantly more patients with indeterminate results had positive PCRs on subsequent samples during WHO Option B+ use compared to older regimens (64.1% vs. 14.7%, p<0.001) at a median 28days later.

CONCLUSIONS

Indeterminate HIV PCRs, although decreasing in frequency with Option B+, should be regarded with a high index of suspicion for being representative of true HIV-1 infections. Additional virological testing is required to arrive at a definitive diagnosis.

Differentiating clearly positive from indeterminate results: A review of irreproducible HIV-1 PCR positive samples from South Africa's Early Infant Diagnosis Program, 2010-2015

We describe the extent of and variables associated with irreproducible HIV-1 PCR positive results within South Africa's Early Infant Diagnosis (EID) program from 2010 to 2015 and propose criteria for differentiating indeterminate from clearly positive results using the COBAS® AmpliPrep/COBAS® TaqMan HIV-1 Qualitative Test version 2.0 (CAP/CTM Qual v2.0). Fourteen percent of specimens with an instrument-positive result that were repeat-tested yielded a negative result for which cycle threshold (Ct) proved to be the only predictive variable. A Ct <33.0 was found to be the most accurate threshold value for differentiating clearly positive from irreproducible cases, correctly predicting 96.8% of results. Among 70 patients with an irreproducible positive result linked to a follow up HIV-1 PCR test, 67 (95.7%) were negative and 3 (4.3%) were instrument-positive. Criteria differentiating clearly positive from indeterminate results need to be retained within EID services and infants with indeterminate results closely monitored and final HIV status determined.

Prevalence and outcomes of HIV-1 diagnostic challenges during universal birth testing - an urban South African observational cohort

Introduction: HIV‐1 polymerase chain reaction (PCR) testing at birth aims to facilitate earlier initiation of antiretroviral therapy (ART) for HIV‐infected neonates. Data from two years of universal birth testing implementation in a high‐burden South African urban setting are presented to demonstrate the prevalence and outcomes of diagnostic challenges in this context.

Methods: HIV‐exposed neonates born at Rahima Moosa Mother and Child Hospital between 5 June 2014 and 31 August 2016 were routinely screened at birth for HIV‐1 on whole blood samples using the COBAS® AmpliPrep/COBAS® TaqMan (CAP/CTM) HIV‐1 Qualitative Test, version 2.0 (Roche Molecular Systems, Inc., Branchburg, NJ, USA). Virological results were interpreted according to standard operating procedures with the South African National Health Laboratory Service. All neonates with non‐negative results were actively followed‐up and categorized according to HIV infection status as positive, negative, uncertain and lost to follow‐up (LTFU).

Results: 104 (1.8%) of 5743 HIV‐exposed neonates received a non‐negative birth PCR result, for which laboratory data were available for 102 (98%) cases – 78 (76%) tested positive and 24 (24%) indeterminate. HIV infection status was confirmed positive in 83 (81%) infants, negative in 8 (8%), uncertain in 5 (5%) and LTFU in 6 (6%) cases. The positive predictive value (excluding cases of uncertain diagnosis and inadequate testing) following a non‐negative HIV‐1 PCR screening test at birth was 0.91 (83/91; 95% confidence interval: 0.85–0.96). Neonates testing positive at birth had significantly higher viral load (VL) results than those testing indeterminate at birth of 4.5 and 3.0 log copies/ml (p = 0.0007), respectively. Similarly, mothers of neonates with positive as compared to indeterminate birth test results had higher VLs of 4.5 and 2.7 log copies/ml (p = 0.0013), respectively. Half of neonates with an indeterminate birth test were shown to be HIV‐infected on subsequent confirmatory testing, with time to final diagnosis 30 days longer for these neonates (p < 0.0001).

Conclusion: Indeterminate HIV‐1 PCR results accounted for a quarter of non‐negative results at birth and were associated with a high risk of infection in comparison to the risk of in utero transmission. Indeterminate birth results with positive HIV PCR results on repeat testing were associated with later final diagnosis. The HIV‐1 status remains uncertain in a minority of cases because of repeatedly indeterminate results, highlighting the need for more sensitive and specific virological tests.

Missed diagnostic opportunities within South Africa's early infant diagnosis program, 2010-2015

BACKGROUND

Samples submitted for HIV PCR testing that fail to yield a positive or negative result represent missed diagnostic opportunities. We describe HIV PCR test rejections and indeterminate results, and the associated delay in diagnosis, within South Africa's early infant diagnosis (EID) program from 2010 to 2015.

METHODS

HIV PCR test data from January 2010 to December 2015 were extracted from the National Health Laboratory Service Corporate Data Warehouse, a central data repository of all registered test-sets within the public health sector in South Africa, by laboratory number, result, date, facility, and testing laboratory. Samples that failed to yield either a positive or negative result were categorized according to the rejection code on the laboratory information system, and descriptive analysis performed using Microsoft Excel. Delay in diagnosis was calculated for patients who had a missed diagnostic opportunity registered between January 2013 and December 2015 by means of a patient linking-algorithm employing demographic details.

RESULTS

Between 2010 and 2015, 2 178 582 samples were registered for HIV PCR testing of which 6.2% (n = 134 339) failed to yield either a positive or negative result, decreasing proportionally from 7.0% (n = 20 556) in 2010 to 4.4% (n = 21 388) in 2015 (p<0.001). Amongst 76 972 coded missed diagnostic opportunities, 49 585 (64.4%) were a result of pre-analytical error and 27 387 (35.6%) analytical error. Amongst 49 694 patients searched for follow-up results, 16 895 (34.0%) had at least one subsequent HIV PCR test registered after a median of 29 days (IQR: 13-57), of which 8.4% tested positive compared with 3.6% of all samples submitted for the same period.

CONCLUSIONS

Routine laboratory data provides the opportunity for near real-time surveillance and quality improvement within the EID program. Delay in diagnosis and wastage of resources associated with missed diagnostic opportunities must be addressed and infants actively followed-up as South Africa works towards elimination of mother-to-child transmission.

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.

Improved Sensitivity of a Dual-Target HIV-1 Qualitative Test for Plasma and Dried Blood Spots

The use of nucleic acid detection for HIV type 1 (HIV-1) detection is strongly recommended in infants <18 months of age, in whom serology is unreliable. This study evaluated the Cobas AmpliPrep/Cobas TaqMan HIV-1 Qualitative Test v2.0 (TaqMan HIV-1 Qual Test, v2.0), a dual-target total nucleic acid real-time PCR assay. The limit of detection (LOD) of the new test in plasma and dried blood spots (DBS) was determined with the 2nd International HIV-1 RNA WHO standard. The specificity of the assay was tested with EDTA plasma (n = 1,301) and DBS from HIV-negative adults (n = 1,000). The sensitivity was determined using HIV-1-positive samples (n = 169 adult EDTA plasma, n = 172 adult DBS, and n = 100 infant DBS) that included group M, subtypes A to H, CRF01_AE, CRF02_AG, and groups O and N. All positive specimens and a subset of the negative specimens were also tested with the Abbott RealTime HIV-1 Qual assay (RealTime). The LOD of the TaqMan assay was 20 copies/ml in plasma and 300 copies/ml in DBS, with specificities of 99.8% in plasma and 99.9% in DBS. The TaqMan assay results were 100% concordant with RealTime results in EDTA plasma samples and in 100 HIV-1-negative adult DBS. Among 172 HIV-1-positive DBS from adults, the TaqMan assay showed positive results for all DBS while RealTime missed five DBS with low target concentrations. Infant DBS results were 100% concordant. The improved sensitivity of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Qualitative Test, v2.0, compared to current commercially available assays may enable earlier diagnosis and treatment in adults and infants. The dual-target test may ensure HIV-1 detection even if a mutation is present in one of the two target regions. The DBS sample matrix facilitates virological testing in remote areas.

Recommendations for the management of indeterminate HIV PCR results within South Africa's early infant diagnosis programme

Indeterminate HIV PCR results represent missed diagnostic opportunities within South Africa’s early infant diagnosis programme. These results not only delay diagnosis and appropriate management but are also a source of confusion and apprehension amongst clinicians and caregivers. We describe the extent of indeterminate HIV PCR results within South Africa’s early infant diagnosis programme and provide recommendations for the management of these cases, both in terms of laboratory practice and the clinical care of the infants.

Performance of Roche CAP/CTM HIV-1 qualitative test version 2.0 using dried blood spots for early infant diagnosis

In the context of early infant diagnosis (EID) decentralization in sub-Saharan Africa, dried blood spot (DBS) is now widely used for HIV proviral DNA detection in resource-limited settings. A new version of CAP/CTM (version 2) has been introduced, recently by Roche Diagnosis as a new real-time PCR assay to replace previous technologies on qualitative detection of HIV-1 DNA using whole blood and DBS samples. The objective of this study was to evaluate CAP/CTM version 2 compared to CAP/CTM version 1 and Amplicor on DBS. A total of 261 DBS were collected from children aged 4 weeks to 17 months born from HIV-seropositive mothers and tested by the three techniques. CAP/CTM version 2 showed 100% of agreement with Amplicor including 74 positive results and 187 negative results. CAP/CTM version 2 versus CAP/CTM version 1 as well as CAP/CTM version 1 versus Amplicor showed two discordant results giving a sensitivity of 98.6%, specificity of 99.5%, positive predictive value of 98.6% and negative predictive value of 99.5%. The concordance was 99.12% (95% of confidence interval) giving a Kappa coefficient of 0.97 (p<0.001). These findings confirmed the expected good performance of CAP/CTM version 2 for HIV-1 EID.

Performance of an Early Infant Diagnostic Test, AmpliSens DNA-HIV-FRT, Using Dried Blood Spots Collected from Children Born to Human Immunodeficiency Virus-Infected Mothers in Ukraine

An accurate accessible test for early infant diagnosis (EID) is crucial for identifying HIV-infected infants and linking them to treatment. To improve EID services in Ukraine, dried blood spot (DBS) samples obtained from 237 HIV-exposed children (≤18 months of age) in six regions in Ukraine in 2012 to 2013 were tested with the AmpliSens DNA-HIV-FRT assay, the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 Qual test, and the Abbott RealTime HIV-1 Qualitative assay. In comparison with the paired whole-blood results generated from AmpliSens testing at the oblast HIV reference laboratories in Ukraine, the sensitivity was 0.99 (95% confidence interval [CI], 0.95 to 1.00) for the AmpliSens and Roche CAP/CTM Qual assays and 0.96 (95% CI, 0.90 to 0.98) for the Abbott Qualitative assay. The specificity was 1.00 (95% CI, 0.97 to 1.00) for the AmpliSens and Abbott Qualitative assays and 0.99 (95% CI, 0.96 to 1.00) for the Roche CAP/CTM Qual assay. McNemar analysis indicated that the proportions of positive results for the tests were not significantly different (P > 0.05). Cohen's kappa (0.97 to 0.99) indicated almost perfect agreement among the three tests. These results indicated that the AmpliSens DBS and whole-blood tests performed equally well and were comparable to the two commercially available EID tests. More importantly, the performance characteristics of the AmpliSens DBS test meets the World Health Organization EID test requirements; implementing AmpliSens DBS testing might improve EID services in resource-limited settings.

HIV-1 variability and viral load technique could lead to false positive HIV-1 detection and to erroneous viral quantification in infected specimens

OBJECTIVES

Viral load (VL) testing is used for early HIV diagnosis in infants (EID) and for detecting early therapeutic failure events, but can be affected by HIV genetic variability. Dried blood samples (DBS) increase VL access and EID in remote settings and when low blood volume is available.

METHODS

This study compares VL values using Siemens VERSANT HIV-1 RNA 1.0 kPCR assay (kPCR) and Roche CAP/CTM Quantitative test v2.0 (CAP/CTM v2.0) in 176 DBS carrying different HIV-1 variants collected from 69 Equatoguinean mothers and their infants with known HIV-1 status (71 infected, 105 uninfected).

RESULTS

CAP/CTM v2.0 provided false positive VLs in 11 (10.5%) cases. VL differences above 0.5 log10 were observed in 42/49 (87.5%) DBS, and were above 1 log10 in 18 cases. CAP/CTM v2.0 quantified all the 41 specimens with previously inferred HIV-1 variant by phylogenetic analysis (68.3% recombinants) whereas kPCR only identified 90.2% of them, and was unable to detect 14.3% of 21 CRF02_AG viruses. CAP/CTM v2.0 showed higher sensitivity than kPCR (95.8% vs. 70.1%), quantifying a higher rate of viruses in infected DBS from subjects under antiretroviral exposure at sampling time compared to kPCR (94.7% vs. 96.2%, p-value<0.001). kPCR showed maximum specificity (100%) whereas for CAP/CTM v2.0 was 89.5%.

CONCLUSIONS

VL assays should increase their sensitivity and specificity to avoid overestimated HIV-1 quantifications, which could be interpreted as virological failure events, or false negative diagnostic results due to genetic variability. We recommend using the same VL technique for each patient during antiretroviral therapy monitoring.

Equipment-free incubation of recombinase polymerase amplification reactions using body heat

The development of isothermal amplification platforms for nucleic acid detection has the potential to increase access to molecular diagnostics in low resource settings; however, simple, low-cost methods for heating samples are required to perform reactions. In this study, we demonstrated that human body heat may be harnessed to incubate recombinase polymerase amplification (RPA) reactions for isothermal amplification of HIV-1 DNA. After measuring the temperature of mock reactions at 4 body locations, the axilla was chosen as the ideal site for comfortable, convenient incubation. Using commonly available materials, 3 methods for securing RPA reactions to the body were characterized. Finally, RPA reactions were incubated using body heat while control RPA reactions were incubated in a heat block. At room temperature, all reactions with 10 copies of HIV-1 DNA and 90% of reactions with 100 copies of HIV-1 DNA tested positive when incubated with body heat. In a cold room with an ambient temperature of 10 degrees Celsius, all reactions containing 10 copies or 100 copies of HIV-1 DNA tested positive when incubated with body heat. These results suggest that human body heat may provide an extremely low-cost solution for incubating RPA reactions in low resource settings.

Field evaluation of Abbott Real Time HIV-1 Qualitative test for early infant diagnosis using dried blood spots samples in comparison to Roche COBAS Ampliprep/COBAS TaqMan HIV-1 Qual test in Kenya

Timely diagnosis and treatment of infants infected with HIV are critical for reducing infant mortality. High-throughput automated diagnostic tests like Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Qual Test (Roche CAPCTM Qual) and the Abbott Real Time HIV-1 Qualitative (Abbott Qualitative) can be used to rapidly expand early infant diagnosis testing services. In this study, the performance characteristics of the Abbott Qualitative were evaluated using two hundred dried blood spots (DBS) samples (100 HIV-1 positive and 100 HIV-1 negative) collected from infants attending the antenatal facilities in Kisumu, Kenya. The Abbott Qualitative results were compared to the diagnostic testing completed using the Roche CAPCTM Qual in Kenya. The sensitivity and specificity of the Abbott Qualitative were 99.0% (95% CI: 95.0-100.0) and 100.0% (95% CI: 96.0-100.0), respectively, and the overall reproducibility was 98.0% (95% CI: 86.0-100.0). The limits of detection for the Abbott Qualitative and Roche CAPCTM Qual were 56.5 and 6.9copies/mL at 95% CIs (p=0.005), respectively. The study findings demonstrate that the Abbott Qualitative test is a practical option for timely diagnosis of HIV in infants.

Irreproducible positive results on the Cobas AmpliPrep/Cobas TaqMan HIV-1 Qual test are different qualitatively from confirmed positive results

Criteria that define low positive results on the COBAS® AmpliPrep/COBAS® TaqMan (CAP/CTM) HIV-1 Qual test as inconclusive have been adopted by all academic centres in South Africa that conduct infant HIV PCR, following previous investigations that showed poor specificity of these results. Retesting all inconclusive specimens has considerable cost implications. Therefore, it was attempted to characterise such inconclusive results, by comparing those that prove to be either negative or positive on follow-up testing. This retrospective, laboratory-based study found that 193 of 211 (91.5%) patients with previous inconclusive results (defined as reported positive by CAP/CTM but with cycle threshold [Ct ] values of >32 and/or fluorescence intensity [FI] values of <5) tested negative and only 18 (8.5%) tested positive using independently obtained follow-up samples after a median of 28 days. The only significant independent predictor of a later positive result was a higher FI value (3.326 vs. 0.495, P < 0.0001), whereas Ct values were not predictive independently. Specimens from patients negative on follow-up testing differed qualitatively from specimens that proved to be true positives. As the lower FI values in false-positive compared to true-positive results probably are indicative of a non-specific signal, the incorporation of stringent amplification slope criteria in the assay's test definition file may improve correct classification and thus reduce the need for repeat testing of a large number of inconclusive specimens.

An integrated chip capable of performing sample pretreatment and nucleic acid amplification for HIV-1 detection

This study reports on a microfluidic system equipped with a sample pretreatment device and a nucleic acid amplification device for the rapid diagnosis of the human immunodeficiency virus-1 (HIV-1). The system analyzed proviral deoxyribonucleic acid (DNA) from an HIV-infected Jurkat T cell line. In order to ensure accurate diagnosis among other prevalent B-type strains, simultaneous detections of four conserved HIV-1 B-type DNA fragments were performed in this integrated microfluidic system. The entire protocol including cell lysis, extraction of DNA, polymerase chain reaction (PCR), and optical detection were successfully integrated in order to perform a rapid, automated diagnosis. Experimental results showed that four primer sets with conserved HIV-1 B-type sequences specific for the 167-bp RU5 promoter region, the 424-bp int, the 117-bp tat, and the 162-bp vpr coding regions were successfully amplified from the respective regions of the proviral DNA, even from a single infected cell. This accurate real-time detection was achieved within 95 min using the integrated optical system.

A simple method to quantitate IP-10 in dried blood and plasma spots

BACKGROUND

Antigen specific release of IP-10 is an established marker for infection with M.tuberculosis. Compared to IFN-γ, IP-10 is released in 100-fold higher concentrations enabling the development of novel assays for detection. Dried blood spots are a convenient sample for high throughput newborn screening.

AIM

To develop a robust and sensitive ELISA-based assay for IP-10 detection in plasma, dried blood spots (DBS) and dried plasma spots (DPS); to validate the ELISA in clinically relevant samples; and to assess the performance of the assay for detection of Cytomegalovirus (CMV) and M.tuberculosis specific immune responses.

METHOD

We raised mice and rat monoclonal antibodies against human IP-10 and developed an ELISA. The assay was validated and applied to the detection of CMV and M.tuberculosis specific responses in 18 patients with immune reactivity towards M.tuberculosis and 32 healthy controls of which 22 had immune reactivity towards CMV and none towards M.tuberculosis. We compared the performance of this new assay to IFN-γ.

RESULTS

The ELISA was reliable for IP-10 detection in both plasma and filter paper samples. The linear range of the ELISA was 2.5-600 pg/ml. IFN-γ was not readily detectable in DPS samples. IP-10 was stabile in filter paper samples for at least 4 weeks at 37 °C. The correlation between IP-10 detected in plasma, DPS and DBS samples was excellent (r(2)>0.97).

CONCLUSIONS

This newly developed assay is reliable for IP-10 quantification in plasma, DBS and DPS samples from antigen stimulated and non-stimulated whole blood. The filter paper assays enable easy sample acquisition and transport at ambient temperature e.g. via the postal system. The system can potentially simplify diagnostic assays for M.tuberculosis and CMV infection.