scholarly journals Field performance evaluation of the PanBio rapid SARS-CoV-2 antigen assay in an epidemic driven by 501Y.v2 (lineage B.1.351) in the Eastern Cape, South Africa

2021 ◽  
Author(s):  
Oluwakemi Laguda Akingba ◽  
Kaitlin Sprong ◽  
Diana Ruth Hardie
Keyword(s):  
South Africa ◽  
Test Performance ◽  
Field Performance ◽  
Evaluation Study ◽  
Clinical Samples ◽  
Eastern Cape ◽  
Rt Pcr ◽  
Assay Sensitivity ◽  
Predictive Values ◽  
Mobile Community

AbstractBackgroundSouth Africa was the African country most severely affected by the SARS-CoV-2 pandemic during 2020, experiencing 2 waves of infection. During the first wave, diagnostics were largely based on reverse transcription-linked PCR (RT-PCR). The Abbott PanBio antigen test was deployed during the 2nd wave which was driven by emergence of the 501Y.v2 variant. At the time of evaluation in mid-November 2020, 501Y.v2 was the dominant circulating virus in Nelson Mandela Bay, in the Eastern Cape Province.MethodsA prospective diagnostic evaluation study was undertaken, during a period of high community transmission, to evaluate the field performance of the PanBio antigen RTD. Testing was conducted at mobile community testing centres on 677 ambulant patients seeking SARS-CoV-2 testing. RT-PCR was performed on the original naso-pharyngeal antigen swabs to evaluate test performance.ResultsOf 146 RT-PCR positive individuals, 101 were RTD positive in the clinic. The antigen RTD had an overall sensitivity of 69.2% (95%CI 61.4, 75.8) and specificity of 99.0% (95%CI 98.8, 99.3) in this clinical context. Sensitivity was strongly dependent on the amount of virus in clinical samples, as reflected by the PCR cycle threshold (CT) value, with 100% detection in samples where the CT was <20, 96% with CT between 20-25, 89% with CT between 26-30 and 64% when CT was 31-35.ConclusionsThe assay reliably detected 501Y.v2 infections in ambulatory ill patients. Assay sensitivity was >90% in patients with high viral loads who are expected to be most infectious. Negative and positive predictive values were also >90%.

D-Dimer Testing for Deep Venous Thrombosis: A Metaanalysis

2004 ◽  
Vol 50 (7) ◽  
pp. 1136-1147 ◽  
Author(s):  
Steven W Heim ◽  
Joel M Schectman ◽  
Mir S Siadaty ◽  
John T Philbrick
Keyword(s):  
Venous Thrombosis ◽  
Deep Venous Thrombosis ◽  
Test Performance ◽  
Reference Standard ◽  
Assay Sensitivity ◽  
Predictive Values ◽  
Assay Performance ◽  
Level 1 ◽  
D Dimer ◽  
Rule Out

Abstract Background: The use of D-dimer assays as a rule-out test for deep venous thrombosis (DVT) is controversial. To clarify this issue we performed a systematic review of the relevant literature. Methods: We identified eligible studies, using MEDLINE entries from February 1995 through October 2003, supplemented by a review of bibliographies of relevant articles. Studies reporting accuracy evaluations comparing D-dimer test results with lower extremity ultrasound or venography in symptomatic patients with suspected acute DVT were selected for review. Two reviewers critically appraised each study independently according to previously established methodologic standards for diagnostic test research. Those studies judged to be of highest quality were designated Level 1. Results: The 23 Level 1 studies reported data on 21 different D-dimer assays. There was wide variation in assay sensitivity, specificity, and negative predictive values, and major differences in methodology of reviewed studies. A multivariate analysis of assay performance, controlling for sample size, DVT prevalence, reference standard, and patient mix, found few differences among the assays in effect on test performance as measured by diagnostic odds ratio. Increasing prevalence of DVT was associated with poorer test performance (P = 0.01), whereas the choice of venography as the reference standard was associated with better test performance (P &lt;0.005). Conclusions: Explanations for the wide variation in assay performance include differences in biochemical and technical characteristics of the assays, heterogeneity and small size of patient groups, and bias introduced by choice of reference standards. Assay sensitivity and negative predictive value were frequently &lt;90%, uncharacteristic of a good rule-out test. General use of D-dimer assays as a stand-alone test for the diagnosis of DVT is not supported by the literature.

scholarly journals ASSESSMENT OF PERFORMANCE AND IMPLEMENTATION CHARACTERISTICS OF RAPID POINT OF CARE SARS-CoV-2 ANTIGEN TESTING IN KENYA

2021 ◽  
Author(s):  
Jesse Gitaka ◽  
Eva Muthamia ◽  
Samuel Mbugua ◽  
Mary Mungai ◽  
Gama Bandawe ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Test Performance ◽  
Gold Standard ◽  
Point Of Care ◽  
Turnaround Time ◽  
Ease Of Use ◽  
Control Measures ◽  
Antigen Test ◽  
Rt Pcr ◽  
Predictive Values

Abstract Background: The COVID-19 pandemic has resulted in a need for rapid identification of infectious cases. Testing barriers have prohibited adequate screening for SARS COV2, resulting in significant delays in treatment provision and commencement of outbreak control measures. This study aimed to generate evidence on the performance and implementation characteristics of the BD Veritor rapid antigen test as compared to the gold standard test for diagnosis of SARS COV2 in Kenya. Methods: This was a field test performance evaluation in symptomatic and asymptomatic adults undergoing testing for SARS COV2. Recruited participants were classified as SARS-CoV2-positive based on the locally implemented gold standard reverse transcription polymerase chain reaction (RT-PCR) test performed on nasopharyngeal swabs. 272 antigen tests were performed with simultaneous gold standard testing, allowing us to estimate sensitivity, specificity, positive and negative predictive values for the BD Veritor rapid antigen test platform. Implementation characteristics were assessed using the Consolidated Framework for Implementation Research for feasibility, acceptability, turn-around time, and ease-of-use metrics. Results and Discussion: We enrolled 97 PCR negative symptomatic and 128 PCR negative asymptomatic, and 28 PCR positive symptomatic and 19 PCR positive asymptomatic participants. Compared to the gold standard, the sensitivity of the BD Veritor antigen test was 94% (95% confidence interval [CI] 86.6 to 100.0) while the specificity was 98% (95% confidence interval [CI] 96 to 100). The sensitivity of BD Veritor antigen test was higher among symptomatic (100%) compared to asymptomatic (84%) participants, although this difference was not statistically significant. There was also a lack of association between cycle threshold value and sensitivity of BD Veritor test. The BD Veritor test had quick turnaround time and minimal resource requirements, and laboratory personnel conducting testing felt that it was easier to use than the gold standard RT-PCR. Conclusion: The BD Veritor rapid antigen test exhibited excellent sensitivity and specificity when used to detect SARS-CoV-2 infection among both symptomatic and asymptomatic individuals in varied population settings in Kenya. It was feasible to implement and easy to use, with rapid turnaround time.

scholarly journals How to best test suspected cases of COVID-19: an analysis of the diagnostic performance of RT-PCR and alternative molecular methods for the detection of SARS-CoV-2

2021 ◽  
Author(s):  
Adrian Mironas ◽  
David Jarrom ◽  
Evan Campbell ◽  
Jennifer Washington ◽  
Sabine Ettinger ◽  
...  
Keyword(s):  
Diagnostic Test ◽  
Test Performance ◽  
Clinical Utility ◽  
Diagnostic Performance ◽  
Point Of Care ◽  
Alternative Methods ◽  
Rt Pcr ◽  
Predictive Values ◽  
Molecular Assays ◽  
Test Result

AbstractAs COVID-19 testing is rolled out increasingly widely, the use of a range of alternative testing methods will be beneficial in ensuring testing systems are resilient and adaptable to different clinical and public health scenarios. Here, we compare and discuss the diagnostic performance of a range of different molecular assays designed to detect the presence of SARS-CoV-2 infection in people with suspected COVID-19. Using findings from a systematic review of 103 studies, we categorised COVID-19 molecular assays into 12 different test classes, covering point-of-care tests, various alternative RT-PCR protocols, and alternative methods such as isothermal amplification. We carried out meta-analyses to estimate the diagnostic accuracy and clinical utility of each test class. We also estimated the positive and negative predictive values of all diagnostic test classes across a range of prevalence rates. Using previously validated RT-PCR assays as a reference standard, 11 out of 12 classes showed a summary sensitivity estimate of at least 92% and a specificity estimate of at least 99%. Several diagnostic test classes were estimated to have positive predictive values of 100% throughout the investigated prevalence spectrum, whilst estimated negative predictive values were more variable and sensitive to disease prevalence. We also report the results of clinical utility models that can be used to determine the information gained from a positive and negative test result in each class, and whether each test is more suitable for confirmation or exclusion of disease. Our analysis suggests that several tests exist that are suitable alternatives to standard RT-PCR and we discuss scenarios in which these could be most beneficial, such as where time to test result is critical or, where resources are constrained. However, we also highlight methodological concerns with the design and conduct of many included studies, and also the existence of likely publication bias for some test classes. Our results should be interpreted with these shortcomings in mind. Furthermore, our conclusions on test performance are limited to their use in symptomatic populations: we did not identify sufficient suitable data to allow analysis of testing in asymptomatic populations.

scholarly journals Molecular Detection of Carbapenemase-Encoding Genes in Multidrug-Resistant Acinetobacter baumannii Clinical Isolates in South Africa

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Yaw Adjei Anane ◽  
Teke Apalata ◽  
Sandeep Vasaikar ◽  
Grace Emily Okuthe ◽  
Sandile Songca
Keyword(s):  
South Africa ◽  
Acinetobacter Baumannii ◽  
Multidrug Resistant ◽  
Clinical Samples ◽  
Eastern Cape ◽  
Healthcare Facilities ◽  
Microdilution Method ◽  
Broth Microdilution Method ◽  
High Level ◽  
Encoding Genes

Introduction. Carbapenem-resistant Acinetobacter baumannii has been responsible for an increasing number of hospital-acquired infections globally. The study investigated the prevalence of carbapenemase-encoding genes in clinical multidrug-resistant A. baumannii strains. Materials and Methods. A total of 100 nonduplicate multidrug-resistant A. baumannii strains were cultured from clinical samples obtained from healthcare facilities in the O. R. Tambo district. The strains were confirmed by detecting the intrinsic blaOXA-51-like gene. Antimicrobial susceptibility testing was performed by VITEK® 2 and autoSCAN-4 systems. The MIC of imipenem and meropenem was rechecked by E-test. Colistin MIC was confirmed by the broth microdilution method. Real-time PCR was performed to investigate the presence of carbapenemase-encoding genes. Results. Most strains showed high resistance rates (>80%) to the antibiotics tested. Resistance to amikacin, tetracycline, and tigecycline were 50%, 64%, and 48%, respectively. All strains were fully susceptible to colistin. The blaOXA-51-like was detected in all strains whilst blaOXA-23-like, blaOXA-58-like, blaOXA-24-like, blaIMP-1, blaVIM, and blaNDM-1 were found in 70%, 8%, 5%, 4%, 3%, and 2% of strains, respectively. None of the tested strains harboured the genes blaSIM and blaAmpC. The coexistence of blaOXA-23-like, and blaIMP-1 or blaOXA-58-like was detected in 1% and 2% strains, respectively. A distinct feature of our findings was the coharbouring of the genes blaOXA-23-like, blaOXA-58-like, and blaIMP-1 in 2% strains, and this is the first report in the Eastern Cape Province, South Africa. The intI1 was carried in 80% of tested strains whilst ISAba1/blaOXA-51-like and ISAba1/blaOXA-23-like were detected in 15% and 40% of the strains, respectively. The detection of blaOXA-23-like, ISAba1/blaOXA-51-like, ISAba1/blaOXA-23-like, and blaOXA-23-like, blaOXA-58-like, and blaIMP-1 carbapenemases in strains had a significant effect on both imipenem and meropenem MICs. Conclusions. Results showed a high level of oxacillinases producing A. baumannii circulating in our study setting, highlighting the need for local molecular surveillance to inform appropriate management and prevention strategies.

scholarly journals Field performance and public health response using the BinaxNOW TM Rapid SARS-CoV-2 antigen detection assay during community-based testing

2020 ◽  
Author(s):  
Genay Pilarowski ◽  
Carina Marquez ◽  
Luis Rubio ◽  
James Peng ◽  
Jackie Martinez ◽  
...  
Keyword(s):  
Public Health ◽  
Community Setting ◽  
Field Performance ◽  
Rt Pcr ◽  
Public Health Response ◽  
Public Health Action ◽  
Assay Sensitivity ◽  
Detection Assay ◽  
Health Response ◽  
Health Action

Abstract Among 3,302 persons tested for SARS-CoV-2 by BinaxNOW TM and RT-PCR in a community setting, rapid assay sensitivity was 100%/98.5%/89% using RT-PCR Ct thresholds of 30, 35 and none. The specificity was 99.9%. Performance was high across ages and those with and without symptoms. Rapid resulting permitted immediate public health action.

scholarly journals Comparative Evaluation of Six Molecular Assays based on RT-PCR and Cross Primer Isothermal Amplification for SARS-CoV-2 Detection

2020 ◽  
Author(s):  
Shuang Wu ◽  
Xiaolu Shi ◽  
Qiongcheng Chen ◽  
Yixiang Jiang ◽  
Le Zuo ◽  
...  
Keyword(s):  
Comparative Study ◽  
Clinical Diagnosis ◽  
Isothermal Amplification ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Predictive Values ◽  
Health Crisis ◽  
Pcr Assays ◽  
Sensitivity Specificity

Abstract SARS-CoV-2 is a newly emerged coronavirus that was isolated from human infections in recent months. Since drugs and vaccines of Covid-19 are still being developed, accurate pathogen detection plays a crucial role in the current public health crisis. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay has been reliably used for the detection and confirmation of SARS-CoV-2 since the beginning of outbreak, whereas isothermal nucleic acid amplification based point of care automated assays has also been considered as a simpler and rapid alternative. However, since these assays have only been developed and applied for clinical use within a short timeframe, their analytical performance has not been adequately compared to-date. We describe a comparative study between a newly developed cross primer isothermal amplification (CPA) assay (Kit A) and five RT-PCR assays (Kits B to F), using clinical diagnosis as the reference standard to evaluate their sensitivity, specificity, predictive values and accuracy analysis. Clinical samples used (n=52) included throat swabs (n=30), nasal swabs (n=7), nasopharyngeal swabs (n=7) and sputum specimens (n=8), comprised of positive (n=26) and cleared cases (n=26) by clinical diagnosis. For the CPA assay (Kit A), the sensitivity, specificity, positive and negative predictive values and accuracy were 100%. Among the five RT-PCR kits, Kits B, C and F had good agreement with clinical diagnosis (Kappa≥0.75), Kits D and E were less congruent (0.4≤Kappa<0.75). Differences between all assays were statistically significant (P<0.001). The reproducibility of RT-PCR assays was determined using a positive sample that was verified by all assays, with standard deviations (SD) between 0.35 and 0.87, and coefficients of variation (CV) between 0.95% and 2.57%, indicating good reproducibility. To further evaluate the CPA assay (Kit A) compared to Kits B and F, throat swabs from close contacts of cases (n=200) were analyzed. All three kits identified the same positive samples and showed total agreement. This is the first comparative study to evaluate a CPA assay and RT-PCR assays for SARS-CoV-2 detection, which could serve as a reference for clinical laboratories and inform testing protocols amid the rapidly evolving COVID-19 pandemic.

scholarly journals Clinical Evaluation of Sofia Rapid Antigen Assay for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 among Emergency Department to Hospital Admissions

2021 ◽  
pp. 1-22
Author(s):  
Richard D. Smith ◽  
J. Kristie Johnson ◽  
Colleen Clay ◽  
Leo Girio-Herrera ◽  
Diane Stevens ◽  
...  
Keyword(s):  
Emergency Department ◽  
Hospital Admissions ◽  
False Negative ◽  
Symptom Assessment ◽  
Rt Pcr ◽  
Cross Sectional ◽  
Assay Sensitivity ◽  
Predictive Values ◽  
Asymptomatic Patients ◽  
Antigen Assay

Abstract Objective To determine the utility of the Sofia® SARS rapid antigen fluorescent immunoassay (FIA) to guide hospital bed placement of patients being admitted through the emergency department (ED). Design Cross-sectional analysis of a clinical quality improvement study. Setting Two community hospitals in Maryland. From 9/21/2020 to 12/3/2020, 2887 patients simultaneously received the Sofia® SARS rapid antigen FIA and SARS-CoV-2 RT-PCR assays on admission through the ED. Methods Rapid antigen results and symptom assessment guided initial patient placement while confirmatory RT-PCR was pending. The sensitivity, specificity, positive and negative predictive values of the rapid antigen assay were calculated relative to RT-PCR, overall and separately for symptomatic and asymptomatic patients. Assay sensitivity was compared to RT-PCR cycle threshold (Ct) values. Assay turnaround times were compared. Clinical characteristics of RT-PCR positive patients and potential exposures from false-negative antigen assays were evaluated. Results Overall agreement, sensitivity, and specificity for all patients was 97.9%, 76.6% (95% confidence interval (CI): 71%, 82%), and 99.7% (95% CI: 99%, 100%), respectively. No differences in performance were seen between asymptomatic and symptomatic individuals. As RT-PCR Ct increased, sensitivity of the antigen assay decreased. Mean turnaround time for the antigen assay and RT-PCR was 1.2 (95% CI: 1.0, 1.3) and 20.1 (95% CI: 18.9, 40.3) hours, respectively (p<0.001). No transmission from antigen-negative/RT-PCR-positive patients was identified. Conclusions While not a replacement for RT-PCR for detection of all SARS-CoV-2 infections, the Sofia® SARS antigen FIA has clinical utility for potential initial timely patient placement.

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