Abbott RealTime Research Articles

Cervical Precancerous Lesions and Associated Factors Among Women Screened in Two Hospitals in the City of Douala, Cameroon.

Cervical cancer remains the second leading cause of death amongwomen in Cameroon despite the new strategies put in place. This study was conducted in order to determine the prevalence of precancerous cervical lesions and its associated factors in Douala (Cameroon). A cross-sectional study was conducted over a period of nine months in two hospitals of the city of Douala, Cameroon (Laquintinie Hospital and Gyneco-Ostetric and Pediatric Hospital). Cervico-vaginal and endocervical samples were taken from women attending the above-mentioned hospitals in order to identify and characterize precancerous lesions by cytological examinationand to genotype for human papillomavirus (HPV) using the Abbott RealTime High-Risk (HR) HPVkit. Data of sociodemographic characteristics, clinical history, and knowledge about cervical cancer were collected using a questionnaire. Of the 196 women included in this study, 17% had precancerous lesions, including 1.53% for atypical glandular cells (AGC), 4.53% for atypical squamous cells (ASC), 4.53% for low-grade squamous intraepithelial lesion (LSIL), 5.61% for high-grade squamous intraepithelial lesion (HSIL), 0.51% for atypical squamous cells of undetermined significance (ASC-US), and 0.51% for atypical squamous cellscannot exclude HSIL (ASC-H). In addition, the prevalence of HPV infection was 18%, of which 2% was for HPV 16, 2% for HPV 18, and 14% for undetermined HPV. A positive association was recorded between the occurrence of precancerous lesions and HPV infection (P=0.01), age, and school level. Moreover, the occurrence of precancerous lesions was positively associated with the participants' level of knowledge (P=0.01). Precancerous lesions were predominantly HSIL, and the factor most associated with these lesions was HPV infection. This study demonstrates that diagnosis is made at a relatively late stage due to a low level of knowledge about cervical cancer in the population.

Evaluation of a Quantitative Dual-Target EBV DNA Test on a Fully Automated Molecular Testing System.

The measurement of Epstein-Barr virus (EBV) deoxyribonucleic acid (DNA) is key to diagnosing and managing EBV-associated complications in transplant recipients. The performance of the new Conformité Européenne (CE) and Food and Drug Administration (FDA)-cleared quantitative Roche cobas EBV real-time PCR assay was determined by using EDTA-plasma dilution panels and clinical samples that were spiked with either the World Health Organization's EBV international standard or high-titer EBV lambda stock. Correlation with the Abbott Realtime EBV assay was assessed in clinical specimens and conducted at two independent laboratories. An in silico analysis revealed that the dual-target test (EBNA1 and BMRF2) was 100% inclusive for the known diversity of EBV. The overall limit of detection (LoD) was 16.6 IU/mL for genotype 1 (GT1). GT2 LoD was verified at 18.8 IU/mL. The linear ranges were from 1.40 × 101 to 2.30 × 108 IU/mL and from 2.97 × 101 to 9.90 × 107 IU/mL for GT1 and GT2, respectively. Accuracy was confirmed across the linear range (mean difference not exceeding ±0.18 log10). Precision was not influenced by the factors analyzed (standard deviation of 0.02 to 0.17 log10), including the presence of potentially interfering endogenous or exogenous substances. Plasma samples were stable under several conditions (variable time points, storage, and freeze/thaw cycles). In clinical EBV DNA-positive samples, correlation between the cobas EBV test and the comparator was high (n = 126 valid results; R2 = 0.96) with a 0.1 mean log10 titer difference. The cobas EBV test is an accurate, sensitive, specific, and reproducible assay for the detection of EBV DNAemia in plasma. In general, high levels of automation and calibration to the international standard will lead to improvements in the harmonization of quantitative EBV DNA test results across laboratories.

Comparison between the Roche Cobas 4800 Human Papillomavirus (HPV), Abbott RealTime High-Risk HPV, Seegene Anyplex II HPV28, and Novel Seegene Allplex HPV28 Assays for High-Risk HPV Detection and Genotyping in Mocked Self-Samples.

Infection with high-risk human papillomavirus (hrHPV) is well recognized as the main cause of cervical cancer. The recently developed Seegene Allplex HPV28 assay is a novel quantitative PCR (qPCR) assay designed to separately detect and quantify 28 distinct HPV genotypes in a fully automated and user-friendly manner. This study evaluated and compared the performance of this new assay with the performance of the Roche Cobas 4800, the Abbott RealTime high-risk HPV, and the Seegene Anyplex II HPV28 assays. A total of 114 mocked self-samples, i.e., semicervical samples collected by gynecologists using the Viba-Brush, were analyzed with all four HPV assays. Agreement in terms of detecting and genotyping HPV was assessed by the mean of the Cohen's kappa (κ) coefficient. Results of all four HPV assays agreed in 85.9% of the cases when using the Abbott RealTime manufacturer's recommended quantification cycle (Cq) cutoff for positivity (<32.00) and 91.2% when using an adapted range (32.00 to 36.00). An intercomparison of the included assays demonstrated an overall agreement ranging from 85.9 to 100.0% (κ = 0.42 to 1.00) when using the manufacturer's guidelines and 92.9 to 100.0% (κ = 0.60 to 1.00) with the adapted range. For all assays, highly significant, strongly positive Pearson correlations were shown between the Cq values of positive test results. This study thereby shows high concordance between results of the included HPV assays on mocked self-samples. Based on these findings, we imply that the novel Allplex HPV28 assay demonstrates a comparable performance to those of available qPCR HPV assays, potentially providing opportunities for the simplification and standardization of future large-scale testing. IMPORTANCE This study proves that the novel Allplex HPV28 assay has a good diagnostic performance in comparison with the well-known, validated, and frequently used Roche Cobas 4800, Abbott RealTime, and Anyplex II HPV28 assays. According to our experience, the novel Allplex HPV28 assay had a user-friendly and automated workflow with short hands-on time, had an open platform which facilitates the use of add-on assays, and provided quick and easy-to-interpret results. Together with its ability to detect and quantify 28 HPV genotypes, the Allplex HPV28 assay could therefore potentially provide opportunities for the simplification and standardization of future diagnostic testing programs.

A protocol for feasibility of plasma based GeneXpert platform and Dried Blood Spot (DBS) based Abbott platform for HIV-1 viral load testing among the people living with HIV attending ART centers in India.

HIV-1 Viral load (VL) measures efficiency of the antiretroviral therapy (ART) after treatment initiation and helps to diagnose virological failures at an early stage. Current VL assays require sophisticated laboratory facilities. As well as there are other challenges pertaining to insufficient laboratory access, cold-chain management and sample transportation. Hence the number of HIV-1 VL testing laboratories is inadequate in the resource limited settings. The revised national tuberculosis elimination programme (NTEP) in India has developed a vast network of point of care (PoC) testing facilities for diagnosis of tuberculosis and several GeneXpert platforms are functional under this programme. Both the GeneXpert HIV-1 assay and HIV-1 Abbott real time assay are comparable and GeneXpert HIV-1 assay can be used as PoC for HIV-1 Viral load testing. Also, the dried blood spot (DBS) as a sample type has been considered as a good option for HIV-1 VL testing in hard to reach areas. This protocol is therefore developed to assess the feasibility of integrating HIV-1 VL testing among people living with HIV (PLHIV) attending ART centres using the two public health models under the current programme: 1. HIV-1 VL testing using GeneXpert platform and plasma as a sample type, and 2. HIV-1 VL testing using Abbott m2000 platform and DBS as a sample type. This ethically approved feasibility study will be implemented at two moderate to high burden ART centres where VL testing facility is not available in the town. Under Model-1, arrangements will be made to carry out VL testing on the adjacent GeneXpert facility and under Model-2, DBS will be prepared on site and couriered to identified viral load testing laboratories. In order to assess the feasibility, data will be collected on pretested questionnaire pertaining to number of samples tested for VL testing, number of samples tested for tuberculosis (TB) diagnosis and the turnaround time (TAT). In-depth interviews will be conducted among the service providers at ART centre and different laboratories for addressing any issues regarding the model implementation. The proportion of PLHIV tested for VL at ART centres, total TAT for both models including TAT for sample transportation, sample testing and receipt of results as well as proportion of sample rejections and reasons for the same, correlation coefficient between DBS based and plasma based VL testing will be estimated using various statistical tools. If found promising, these public health approaches will be helpful for the policy makers and program implementation in scaling up HIV-1 viral load testing within India.

Comparison of Two Molecular Tests, Roche COBAS&amp;lt;sup&amp;gt;®&amp;lt;/sup&amp;gt;AmpliPrep/COBAS&amp;lt;sup&amp;gt;®&amp;lt;/sup&amp;gt;TaqMan&amp;lt;sup&amp;gt;®&amp;lt;/sup&amp;gt; and Abbott-RealTime in the HIV-1 Early Infants Diagnosis

<i>Background: </i>Prompt diagnosis and treatment of infants born to parents living with HIV is essential to reduce infant mortality. The availability of several high-throughput automated molecular tests is necessary to increase the services of early diagnosis tests in infants, especially in countries with limited resources such as Senegal. <i>Objective: </i>The objective of this study was to compare two automated molecular tests, Roche COBAS^®AmpliPrep/COBAS^® TaqMan^®HIV-1 Qualitative and Abbott RealTime HIV-1 Qualitative in the early diagnosis of HIV-1 infection in children born to HIV-positive mothers in Senegal. Methods: The study was conducted exclusively at the molecular biology laboratory of the armed forces AIDS programme at the Ouakam Military Hospital, Dakar, Senegal, between September 2020 and December 2021. It involved 136 children aged between 1 and 18 months born to HIV-1 infected mothers. The samples were taken from blood obtained from the baby's heel, dried on blotting paper (DBS) and sent to the molecular biology laboratory. They were then stored at room temperature before being tested for the study. After these samples were analysed on both molecular techniques, the Abbott Qualitative results were compared to diagnostic tests performed with Roche COBAS^®AmpliPrep/COBAS^®TaqMan^®HIV-1 Qualitative, which is the reference molecular technique. R Studio software version 099.902, 2016 was used to calculate specificity and sensitivity and Kappa coefficient. For statistical tests, they are considered significant when the P-value is less than 5%. <i>Results:</i> Out of a total of 136 samples tested, the overall positive and negative concordance was 94.84%, 79.41% and 93.58% respectively. The concordance coefficient, Cohen's Kappa coefficient, was also analysed. It gave a value of 0.853 (95% CI: [74.7-95.8]). A discrepancy was found between the two tests. Seven samples, which had previously tested positive on Roche Cobas, tested negative on Abbott Qualitative. <i>Conclusion: </i>The result showed a comparable performance characterized by very good negative, positive and global concordances and also, a very high Cohen's Kappa coefficient κ. The present study showed that the two molecular tests are comparable and that the Abbott Qualitative is a practical alternative for the diagnosis of HIV in infants.

Comparison of four commercial EBV DNA quantitative tests to a new test at an early stage of development.

Regular screening for Epstein-Barr virus (EBV) DNA using quantitative RT-PCR is recommended for early intervention in at-risk patients. Harmonization of quantitative RT-PCR assays is critical to avoid misinterpretation of results. Here, we compare quantitative results of the cobas® EBV assay to four commercial RT-qPCR assays. The cobas EBV, EBV R-Gene, artus EBV RG PCR, RealStar EBV PCR kit 2.0 and Abbott EBV RealTime assays were compared for analytic performance using a 10-fold dilution series of EBV reference material, normalized to the WHO standard. For clinical performance, their quantitative results were compared using anonymized, leftover EBV-DNA-positive EDTA plasma samples. For analytic accuracy, the cobas EBV deviated -0.0097 log10 from target values. The other tests showed deviations between 0.0037 and -0.12 log10. For clinical performance, accuracy and linearity of cobas EBV data from both study sites were excellent. Bland-Altman bias and Deming regression analyses showed statistical correlation for cobas EBV to both EBV R-Gene and Abbott RealTime assays but an offset of cobas EBV to artus EBV RG PCR and RealStar EBV PCR kit 2.0. The cobas EBV showed the closest correlation to the reference material, followed closely by EBV R-Gene and Abbott EBV RealTime. Values obtained are stated in IU/mL, facilitating comparison across testing sites and potentially improving utilization of guidelines for diagnosis, monitoring, and treatment of patients.

Genetic diversity of the human immunodeficiency virus of type 1 in Gabonese transfusional settings

BackgroundThe high endemicity of transfusion-transmissible infections (TTIs) in sub-Saharan Africa is a real public health problem. To reduce the risk of HIV transmission through blood donation, the NBTC of Gabon has launched in recent years a reorganization of its blood transfusion system. This study aims to characterize the molecular strains of HIV-1 circulating in donors and to estimate the risk of viral transmission.Materials and methodsA cross-sectional study was carried out during the period from August 2020 to August 2021 among 381 donors who had agreed to donate blood at the National Blood Transfusion Center (NBTC). Viral load was determined by Abbott Real-Time (Abbott m2000®, Abbott) and sequencing by the Sanger method (ABI 3500 Hitachi®). The phylogenetic tree was constructed by MEGA X software. Data were checked, entered, and analyzed using SPSS version 21.0 software, with p ≤ 0.05 considered statistically significant.ResultsA total of 381 donors were enrolled in the study. Among the 359 seronegative donors, five (5) seronegative donors were detected positive for HIV-1 using Real-Time PCR. The residual risk was 648 per 1,000,000 donations. The prevalence of residual infection was 1.4% [0,01; 0,03]. Sixteen (16) samples were sequenced. The strains obtained were CRF02_AG (50%), subtype A1 (18.8%), subtype G (12.5%), CRF45_cpx (12.5%) and subtype F2 (6.2%). Six sequences clustered with A1, G, CRF02_AG, and CRF45_cpx subtypes.ConclusionThe residual risk of HIV-1 transmission by blood transfusion remains a concern in the Gabonese transfusional settings. A policy based on improving the current screening strategy would involve the implementation of the nucleic acid test (NAT) in order to optimize the safety of the donation by detecting the HIV-1 subtypes in circulation in the donors.

Pre-existing immunity to SARS-CoV-2 before the COVID-19 pandemic era in Cameroon: A comparative analysis according to HIV-status.

The lower burden of COVID-19 in tropical settings may be due to preexisting cross-immunity, which might vary according to geographical locations and potential exposure to other pathogens. We sought to assess the overall prevalence of SARS-CoV-2 antibodies and determine SARS-CoV-2 seropositivity according to HIV-status before the COVID-19 pandemic era. A cross-sectional and comparative study was conducted at the Chantal BIYA International Reference Centre (CIRCB) on 288 stored plasma samples (163 HIV-positive versus 125 HIV-negative); all collected in 2017-2018, before the COVID-19 pandemic era. Abbott Panbio™ COVID-19 IgG/IgM assay was used for detecting SARS-CoV-2 immunoglobulin G (IgG) and M (IgM). Among people living with HIV (PLHIV), HIV-1 viral load and TCD4 cell count (LTCD4) were measured using Abbott Real Time PCR and BD FACSCalibur respectively. Statistical analyses were performed, with p<0.05 considered statistically significant. The median [IQR] age was 25 [15-38] years. Overall seropositivity to SARS-CoV-2 antibodies was 13.5% (39/288) of which 7.3% (21) was IgG, 7.3% (21) IgM and 1.0% (3) IgG/IgM. According to HIV-status in the study population, SARS-CoV-2 seropositivity was 11.0% (18/163) among HIV-positive versus 16.8% (21/125) among HIV-negative respectively, p=0.21. Specifically, IgG was 6.1% (10/163) versus 8.8% (11/125), p=0.26; IgM was 5.5% (9/163) versus 9.6%, (12/125), p=0.13 and IgG/IgM was 0.6% (1/163) versus 1.6% (2/125) respectively. Among PLHIV, SARS-CoV-2 seropositivity according to CD4 count was 9.2% (≥500 cells/µL) versus 1.8% (200-499 cells/µL), (OR=3.5; p=0.04) and 0.6% (<200 cells/µL), (OR=17.7; p<0.01). According to viral load, SARS-CoV-2 seropositivity was 6.7% (≥40 copies/mL) versus 4.9% (<40 copies/mL), (OR= 3.8; p<0.01). Before COVID-19 in Cameroon, cross-reactive antibodies to SARS-CoV-2 were in circulation, indicating COVID-19 preexisting immunity. This preexisting immunity may contribute in attenuating disease severity in tropical settings like Cameroon. Of relevance, COVID-19 preexisting immunity is lower with HIV-infection, specifically with viral replication and poor CD4-cell count. As poor CD4-count leads to lower cross-reactive antibodies (regardless of viral load), people living with HIV appear more vulnerable to COVID-19 and should be prioritized for vaccination.

Evaluation of Performance Characteristics of the Aptima CMV Quant Assay for the Detection and Quantitation of CMV DNA in Plasma Samples.

Quantification of Cytomegalovirus (CMV) DNA has become the standard of care in the diagnosis and management of CMV infection in transplant recipients. The objective of the study was to evaluate performance characteristics of the Aptima CMV Quant assay in comparison to Abbott RealTime CMV assay, Qiagen Artus CMV RGQ MDx assay, and Roche cobas CMV test using plasma samples. The performance of the Aptima assay was evaluated by comparing the Exact Diagnostics CMV verification panel and positive controls, Hologic CMV internal reproducibility panel, and SeraCare CMV DNA qualification panel to the RealTime assay. Clinical agreement was evaluated using 389 clinical plasma samples comparing the Aptima assay to three comparator assays. The Aptima assay demonstrated good linearity and strong linear correlation between the assays (R2 = 0.99); the intra- and interassay reproducibility was excellent overall (SD = 0.09 to 0.14 and SD = 0.04 to 0.14, respectively); 95% limit of detection (LOD) is 32 IU/mL and LOQ is 45 IU/mL. The SeraCare qualification panel yielded a strong linear correlation (R2 = 0.99). A total of 262 positive samples were analyzed to compare Aptima and Realtime assays using Deming regression and Bland-Altman analysis and demonstrated a mean bias of 0.092 Log10 IU/mL. Artus (85) and cobas (159) positive samples were compared to the Aptima assay using Deming regression and Bland-Altman analyses and showed mean bias of 0.184 and -0.208 Log10 IU/mL, respectively. The findings demonstrate that the Aptima assay is sensitive and accurate in quantifying CMV in plasma specimens on the fully automated Panther system and that the results were comparable to the other FDA-approved CMV assays.

Comparison of Two Molecular Diagnostic Tests for COVID-19: Abbott RealTime SARS-CoV-2 and Allplex&amp;amp;#8482; 2019-nCoV, in the Epidemic Context in Senegal

Background: The persistence of the rapid spread of the COVID-19 pandemic is linked to the appearance of several variants of SARS-CoV2 with an impact on biological diagnosis, treatment and vaccination. The United States Food and Drug Administration (FDA) has granted several SARS-CoV-2 detection tests Emergency Use Authorization (EUA) for diagnosis and better epidemiological surveillance. Thus, multiple RT-PCR tests have been developed and brought to market in order to meet the urgent need for the diagnosis of COVID-19. However, comparative data between these tests in clinical laboratories are scarcely available to assess their performance. Objective: To compare two molecular methods for detecting SARS-CoV-2: the RT-PCR, Allplex™ 2019-nCoV tests on CFX96 Bio-Rad and the Abbott m2000sp/rt RealTime SARS-CoV-2. Materials and Methods: Nasopharyngeal and oropharyngeal swabs were taken from patients to diagnose SARS-CoV-2 infection. For each sample, we searched for the virus with two different RT-PCR tests: 1) first on Abbott m2000 SARS-CoV-2 targeting the N and RdRp genes, 2) then on Allplex™ 2019-nCoV Assay looking for the E, N and RdRp genes. Results: Percentages of the agreement were calculated. A total of 100 samples that tested negative and 90 positives on Abbott m2000 SARS-CoV-2 were retested on Allplex™ 2019-nCoV. Overall agreement was 74.74% on all samples. The specific agreement was 84% and 64.4% respectively for negative and positive samples with the RealTime SARS-CoV-2 test. A positive correlation (r2 = 0.63; p ™ 2019-nCoV and Abbott RealTime SARS-CoV-2 tests in the diagnosis of COVID-19. As the concordance is low for small viremias, the RT-PCR Allplex™ 2019-nCoV Assay would be better indicated during the acute and symptomatic phase of the disease.

Comparison of the diagnostic efficacy of the Abbott RealTime SARS-CoV-2 assay and the BGI real-time fluorescent RT-PCR kit for the RT-PCR-based detection of Severe Acute Respiratory Syndrome Coronavirus-2

Introduction/Objective. Based on the WHO Organization guidelines, the current gold standard to diagnose Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR). The objective of this study was to compare and analyze the detection performance of two different authorized SARS-CoV-2 nucleic acid detection assays: the Abbott RealTime SARS-CoV-2 (ACOV) assay and the BGI Real-Time Fluorescent RT-PCR (BGI) kit. Methods. Our study included 384 randomly selected nasopharyngeal and oropharyngeal swabs previously tested by the ACOV and subsequently tested by the BGI kit for detecting SARS-CoV-2. All patients were adult individuals with symptoms of or suspected Coronavirus disease 2019 (COVID-19). Results. We found that the ACOV assay detected more cases of COVID-19 infection than the BGI assay. The positive percent agreement was 98.3% (95% confidence intervals (95% CI): 95.7?99.3%), while Cohen?s Kappa coefficient was 0.86 (95% CI: 0.80?0.91), indicating a strong level of agreement between these two tests. The negative percent agreement was 85.1% (95% CI: 78.3?90%), while 5.47% of cases were false negative using the BGI test to detect SARS-CoV-2. The sensitivity of the BGI test compared to ACOV was 91.73% (95% CI: 87.64?94.81%), and the specificity of the BGI test was 96.77% (95% CI: 91.95?99.11%). Conclusion. The ACOV showed a bit better diagnostic performance, and due to possible false negative results using the BGI test, we recommend complete testing with the ACOV test.

Evaluation of a multiplex real-time PCR assay for the diagnosis of sexually-transmitted infections

Diagnostic methods with simultaneous multi-targeting are applied for the accurate identification of sexually transmitted infections (STIs). The aim of this study was to evaluate a molecular real-time PCR-based assay (Vivalytic STI assay) for the diagnosis of STIs in comparison with other routine methods. Fifteen individuals suspected of having an STI were tested with the Vivalytic STI assay. As a routine testing, 8/15 patients were tested with the Abbott RealTime CT/NG PCR Assay, 5 specimens were tested with the Simplexa HSV 1 and 2 Direct Kit. Two samples were not tested with a routine assay. Clinical specimens were of different origin (rectal, vaginal, pharyngeal, urine, cerebrospinal fluid (CSF)). Ten out of 15 specimens were positive according to routine diagnostic assays. Three were positive for C. trachomatis (CT) and 2 for N. gonorrhoeae (NG) in single infection, one showed a coinfection with CT and NG. Two samples each were tested positive for Herpes simplex virus 1 (HSV 1) and Herpes simplex virus 2 (HSV 2). All the pathogens detected by routine molecular methods were also detected with Vivalytic STI except for one invalid sample. The Vivalytic STI assay additionally detected M. hominis and U. urealyticum each in one sample. The assay in the focus of the study showed good agreement with other molecular assays and proved to be a simple and a reliable method for the diagnosis of STIs that could improve the diagnostic methods used at our institution.

Performance Evaluation of the Fully Automated NeuMoDx RT-PCR Platform for the Quantification of CMV and EBV DNA in EDTA Plasma: Implications for Clinical Management and Establishment of a Conversion Formula.

The NeuMoDx96 platform is a fully automated real-time PCR (RT-PCR) system. To provide continued testing quality with the introduction of new assays, the primary aim of this study was to evaluate the analytical and clinical performance of the NeuMoDx platform for the detection and quantification of CMV and EBV DNA in EDTA plasma. As no conversion from log10 international units per milliliter to copies per milliliter was provided, the secondary aim was to calculate and establish a conversion factor for the output of results in copies per milliliter for CMV and EBV. Archived ETDA plasma samples (cytomegalovirus [CMV], n = 290; Ebstein-Barr virus [EBV], n = 254) were used to evaluate the analytical performance of the NeuMoDx96 platform against the routine real-time quantitative PCR (qPCR) assays. Additionally, the first WHO international standards (WHO-IS) for CMV (n = 70) and EBV (n = 72) were used for the calculation of the intra- and interassay variation. WHO-IS qualitative agreement between the assays was 100%. Intra-assay variability was low for both CMV assays (coefficient of variation [CV], phosphate-buffered saline [PBS], 3 log10 IU/mL NeuMoDx, 3.67%; Abbott RealTime, CMV, 3.35%) and NeuMoDx EBV assay (CV, PBS, 3 log10 IU/mL, 3.05%) but high for the Altona EBV assay (CV, PBS, 3 log10 IU/mL, 26.13%). The overall qualitative concordance in clinical samples was 96.8% (270/279) for CMV and 96.7% (237/245) for EBV. The mean difference between the assays was -0.2 log10 IU/mL (CMV) and -0.18 log10 IU/mL (EBV). High qualitative concordance and a significant correlation of quantitative values for both assays make NeuMoDx CMV and EBV assays suitable for routine diagnostic testing. The new RT-PCR system and conversion formulas to report results in copies per milliliter are now applied in clinical routine testing. IMPORTANCE Clinical management of solid organ transplant (SOT) patients requires the careful monitoring of immunosuppression and viral infection or reactivation. qPCR is the gold standard for the detection and quantification of very small amounts of viral DNA and allows for an early assessment of viral load kinetics. The tested NeuMoDx 96 platform provides faster results than the previously used RT-PCR workflows for CMV (Abbott m2000 and RealTime CMV assay) and EBV (LightCycler 480 II, Roche high pure extraction, and Altona RealStar EBV assay) DNA detection. The implemented conversion formulas allow the continued reporting in clinically established copies per milliliter, important for long-term care of SOT patients.

Feasibility, Ease-of-Use, and Operational Characteristics of World Health Organization–Recommended Moderate-Complexity Automated Nucleic Acid Amplification Tests for the Detection of Tuberculosis and Resistance to Rifampicin and Isoniazid

Four moderate-complexity automated nucleic acid amplification tests for the diagnosis of tuberculosis are reported as having laboratory analytical and clinical performance similar to that of the Cepheid Xpert MTB/RIF assay. These assays are the Abbott RealTime MTB and RealTime MTB RIF/INH Resistance, Becton Dickinson MAX MDR-TB, the Hain Lifescience/Bruker FluoroType MTBDR, and the Roche cobas MTB and MTB RIF/INH assays. The study compared feasibility, ease of use, and operational characteristics of these assays/platforms. Manufacturer input was obtained for technical characteristics. Laboratory operators were requested to complete a questionnaire on the assays' ease of use. A time-in-motion analysis was also undertaken for each platform. For ease-of-use and operational requirements, the BD MAX MDR-TB assay achieved the highest scores (86% and 90%) based on information provided by the user and manufacturer, respectively, followed by the cobas MTB and MTB-RIF/INH assay (68% and 86%), the FluoroType MTBDR assay (67% and 80%), and the Abbott RT-MTB and RT MTB RIF/INH assays (64% and 76%). The time-in-motion analysis revealed that for 94 specimens, the RealTime MTB assay required the longest processing time, followed by the cobas MTB assay and the FluoroType MTBDR assay. The BD MAX MDR-TB assay required 4.6 hours for 22 specimens. These diagnostic assays exhibited different strengths and weaknesses that should be taken into account, in addition to affordability, when considering placement of a new platform.

HPV Tests Comparison in the Detection and Follow-Up after Surgical Treatment of CIN2+ Lesions.

Background: HPV tests differ for technology, targets, and information on genotyping of high risk (HR) HPV. In this study, we evaluated the performance of 6 HPV DNA tests and one mRNA test in the detection of cervical intraepithelial lesions (CIN) and as a test-of-cure in the follow-up after surgical conservative treatment. Methods: One hundred seventy-two women referred to the European Institute of Oncology, Milan, for surgical treatment of pre-neoplastic cervical lesions, were enrolled in this study (IEO S544) from January 2011 to June 2015. For all women, a cervical sample was taken before treatment (baseline) and at the first follow-up visit (range 3 to 9 months): on these samples Qiagen Hybrid Capture 2 (HC2), Roche Linear Array HPV Test (Linear Array), Roche Cobas 4800 HPV test (Cobas), Abbott RealTime High Risk HPV test (RT), BD Onclarity HPV assay (Onclarity), Seegene Anyplex II HPV HR Detection (Anyplex), and Hologic Aptima HPV Assay (Aptima) histology and cytology were performed at baseline, and the same tests and cytology were performed at follow-up. Results: At baseline 158/172 (92%), histologies were CIN2+, and 150/172 (87%) women were recruited at follow-up. Assuming HC2 as a comparator, the concordance of HPV tests ranges from 91% to 95% at baseline and from 76% to 100% at follow-up (PABAK ranging from 0.81 to 0.90 at baseline and PABAK ranging from 0.53 to 1 at follow-up). All HPV showed a very good sensitivity in CIN2+ detection at baseline, more than 92%, and a very good specificity at follow-up, more than 89%. Conclusions: HPV tests showed a good concordance with HC2 and a very good and comparable sensitivity in CIN2+ detection. Hence, an HPV test represents a valid option as test-of-cure in order to monitor patients treated for CIN2+ lesions during follow-up.

Clinical Performance of the RealTime High Risk HPV Assay on Self-Collected Vaginal Samples within the VALHUDES Framework.

ABSTRACTThe VALHUDES framework (NCT03064087) was established to evaluate the clinical accuracy of HPV testing on self-samples compared with HPV testing on matched clinician-taken cervical samples. Women referred to colposcopy due to previous cervical abnormalities were recruited at five Belgian colposcopy centers. A total of 486 pairs of matched cervical samples and vaginal self-samples were included in the analysis (228 collected with Evalyn Brush and 258 with Qvintip). The dry vaginal brushes were transferred into 20 mL ThinPrep PreservCyt solution. All specimens were tested with the Abbott RealTime High Risk HPV assay (Abbott RT). Testing on vaginal and cervical specimens was considered the index and comparator tests, respectively, and colposcopy and histology as the reference standard. The clinical sensitivity for CIN2+ of Abbott RT (cutoff ≤32 cycle number [CN]) on vaginal self-samples (Evalyn Brush and Qvintip combined) was 8% lower than on the cervical clinician-collected samples (ratio = 0.92 [95% CI, 0.87 to 0.98]), while the specificity was similar (ratio = 1.04 [95% CI, 0.97 to 1.12]). Sensitivity (ratio = 0.95 [95% CI, 0.89 to 1.02]) and specificity (ratio = 1.11 [95% CI, 0.995 to 1.23]) on Evalyn Brush samples was similar to cervical, while on Qvintip samples, the sensitivity was 12% lower than cervical samples (ratio = 0.88 [95% CI, 0.78 to 0.998]) with similar specificity (0.99 [95% CI, 0.90 to 1.10]). Exploratory cutoff optimization (cutoff ≤35 CN) resulted in an improvement of the relative sensitivity (self-sampling versus clinician sampling: ratio = 0.96 [95% CI, 0.91 to 1.02]) but yielded a loss in relative specificity (ratio = 0.92 [0.85 to 1.00]). The clinical accuracy of Abbott RT differed from the self-sampling device. However, after cutoff optimization, the sensitivity on self-samples taken with either of two vaginal brushes became similar to clinician-collected samples.IMPORTANCE Self-samples are becoming a crucial part of HPV-based cervical cancer screening programs to reach nonattendee women and increase screening coverage. Therefore, the VALHUDES framework was established to validate and evaluate HPV tests and devices on self-samples. Here, in the present manuscript, we evaluated the accuracy of the RealTime High Risk HPV assay (Abbott RT) on two different vaginal devices to detect cervical intraepithelial neoplasia grade two or higher (CIN2+). The study results demonstrated that the Abbott RT assay is similarly accurate on vaginal self-samples as on matched clinician-taken cervical samples after adjusting cutoff values. Moreover, we observed that some vaginal devices perform better than others in CIN2+ detection. We also underline the necessity of standardization and validation of general workflow and sample handling procedures for vaginal self-samples.

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.

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. 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. 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. 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.

High prevalence of and factors associated with human papillomavirus infection among women attending a tertiary hospital in Gauteng Province, South Africa

BackgroundPersistent high-risk (hr) human papillomavirus (HPV) infection is a necessary cause of cervical cancer. Cervical cancer is a major public health problem in Sub-Saharan Africa including South Africa. This study investigated the prevalence of and factors associated with hr-HPV infection among women attending a tertiary hospital in Gauteng Province, South Africa.MethodsCervical samples were collected from 526 participants aged ≥ 18 years using a Cervex Brush® Combi and tested for hr-HPV types on the Abbott m2000 analyzer using the Abbott RealTime HR HPV assay. Samples that tested hr-HPV deoxyribonucleic acid (DNA)-positive were further tested for hr-HPV E6/E7 messenger ribonucleic acid (mRNA) using the APTIMA® HPV assay on the Panther system (Hologic, Inc.). Sociodemographic data were collected using a self-administered questionnaire. Binomial regression analysis was used to assess factors associated with hr-HPV infection.ResultsOverall hr-HPV DNA prevalence was 48.1% (95%CI: 43.8–52.4%). Of the hr-HPV DNA-positives, 24.5% (95%CI: 19.3–30.1) had HPV-16; 12.3% (95%CI: 8.5–16.9) had HPV-18 and 87.4% (95%CI: 82.6–91.2) had other 12 h-HPVs. Of the samples positive for hr-HPV DNA, 84.2% (95%CI: 79.1–88.5) (213/253) were positive for hr-HPV E6/E7 mRNA. Advanced age was an important factor linked to hr-HPV E6/E7 mRNA positivity. Based on multivariate binomial regression analysis, unemployment (PR: 1.50; 95%CI: 1.23–1.83) and being married (PR: 0.61; 95%CI: 0.47–0.81) were identified as statistically significant (p < 0.0001) predictive and protective factors, respectively, for hr-HPV infection.ConclusionsThe prevalence of hr-HPV infection was high. Furthermore, hr-HPV DNA-positive samples had a high hr-HPV E6/E7 mRNA prevalence. The presence of hr-HPV E6/E7mRNA indicates active infection and thus a greater risk of developing the cervical disease. Therefore, HPV mRNA testing could be a better test to monitor women who are positive with Pap smear before colposcopy is performed to reduce the burden of referrals.

Clinical Evaluation of Severe Acute Respiratory Syndrome Coronavirus 2 Rapid Antigen Tests During the Omicron Wave in South Africa.

We evaluated the performance of nasal and nasopharyngeal Standard Q COVID-19 [coronavirus disease 2019] Ag tests (SD Biosensor) and the Panbio COVID-19 Ag Rapid Test Device (nasal; Abbott) against the Abbott RealTime severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay during the Omicron (clades 21M, 21K, and 21L) wave in South Africa. Overall, all evaluated tests performed well, with high sensitivity (range, 77.78%–81.42%) and excellent specificity values (>99%). The sensitivity of rapid antigen tests increased above 90% in samples with cycle threshold <20, and all 3 tests performed best within the first week after symptom onset.

Evaluation of SAMBA II: A Qualitative and Semiquantitative HIV Point-of-Care Nucleic Acid Test.

Point-of-care (POC) nucleic acid tests (NATs) have potential to diagnose acute HIV infection and monitor persons taking pre-exposure prophylaxis or antiretroviral therapy (ART). POC NATs have not yet been evaluated in the US. From June 2018-March 2019, we conducted a cross-sectional evaluation of the Simple Amplification-Based Assay version II (SAMBA II) POC NAT. People with HIV (PWH) and persons testing for HIV were tested with the SAMBA II qualitative (Qual) whole blood (WB) test. From April-September 2019, the Qual test was used on persons who were ART-naive, and SAMBA II Semi-quantitative (Semi-Q) WB was used with ART-experienced PWH. Both were performed on unprocessed venipuncture (VP) and, when indicated by protocol, fingerstick (FS) WB and plasma. SAMBA results were compared with Abbott RealTime HIV-1 polymerase chain reaction results on plasma. We calculated sensitivity, specificity, and concordance between tests. SAMBA was used in 330 visits among 280 participants: 202 (61.2%) visits from PWH, and 128 (38.8%) from HIV-negative persons. Qual test sensitivity with ART-naive participants was 91.4% [32/35, 95% confidence interval (CI): 77.6% to 97.0%] using VP WB and 100% (27/27, 95% CI: 87.5% to 100%) using FS WB. Specificity was 100% using both specimen types. Concordance between the gold standard and Semi-Q at 1000 copies/mL among PWH on ART was 97.7% (86/88, 95% CI: 92.1% to 99.4%) and 100% (30/30, 95% CI: 88.7% to 100%) using VP and FS WB, respectively. The SAMBA II POC NATs showed high sensitivity, specificity, and concordance with the gold standard assay, indicating its potential use in diagnostics and monitoring. Future work will evaluate POC NAT implementation in the US.