High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2

Gorzalski, Andrew; Tian, Honglin; Laverdure, Chris; Morzunov, Sergey P.; Verma, Subhash C.; VanHooser, Stephanie; Pandori, Mark

doi:10.1016/j.jcv.2020.104501

Cited by 95 publications

(97 citation statements)

References 8 publications

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“…When analytical test sensitivity is low, failure to confirm may represent a false negative confirmatory test. However, our data on repeatability, coupled with validation literature indicating SARS-CoV-2 tests have high analytical sensitivity [ 17 , 18 ], suggest lower reported overall clinical sensitivity predominantly arises during sampling: confirmation tests of an initially positive sample would not reflect such insensitivity. Any clinical sensitivity issues must be considered when making prevalence estimates in a population of people, rather than the population of samples they have produced.…”

Section: Discussionmentioning

confidence: 77%

Specificity and positive predictive value of SARS-CoV-2 nucleic acid amplification testing in a low-prevalence setting

Skittrall

Wilson

Smielewska

et al. 2021

Clinical Microbiology and Infection

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Objectives When SARS-CoV-2 prevalence is low, many positive test results are false positives. Confirmatory testing reduces overdiagnosis and nosocomial infection and enables real-world estimates of test specificity and positive predictive value. This study estimates these parameters to evaluate the impact of confirmatory testing, and to improve clinical diagnosis, epidemiological estimation and interpretation of vaccine trials. Methods Over one month, we took all respiratory samples from our laboratory with a patient’s first detection of SARS-CoV-2 RNA (Hologic Aptima SARS-CoV-2 assay or in-house RT-PCR platform), and repeated testing using two platforms. Samples were categorised by source, and by whether clinical details suggested COVID-19 or corroborative testing from another laboratory. We estimated specificity and positive predictive value using maximum likelihood-based approaches. Results Of 19,597 samples, SARS-CoV-2 RNA was detected in 107. 52 corresponded to first-time detection (0.27% of tests on samples without previous detection); further testing detected SARS-CoV-2 RNA ≥1 time (“confirmed”) in 29 (56%), and failed to detect SARS-CoV-2 RNA (“not confirmed”) in 23 (44%). Depending upon assumed parameters, point estimates for specificity and positive predictive value were 99.91%–99.98% and 61.8%–89.8% respectively using the Hologic Aptima SARS-CoV-2 assay, and 97.4%–99.1% and 20.1%–73.8% respectively using an in-house assay. Conclusions Nucleic acid amplification testing for SARS-CoV-2 is highly specific. Nevertheless, when prevalence is low a significant proportion of initially positive results fail to confirm and confirmatory testing substantially reduces false positive detections. Omitting additional testing in samples with higher prior detection probabilities focuses testing where clinically impactful and minimises delay.

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Section: Discussionmentioning

confidence: 77%

Specificity and positive predictive value of SARS-CoV-2 nucleic acid amplification testing in a low-prevalence setting

Skittrall

Wilson

Smielewska

et al. 2021

Clinical Microbiology and Infection

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“…A Hologic APTIMA transcription TMA assay was compared to the RT-PCR method in 116 nasopharyngeal swabs. Superior sensitivity (98.15%) of TMA assay (52/53) compared to 96.25% of RT-PCR (51/53) with a detection limit of 5.5 × 10 2 copies in 1 out of 5 samples were reported [ 81 ]. RCA is another promising isothermal amplification technique that received considerable attention in recent years because of its sensitivity and capability to amplify up to 10 9 fold within 90 min [ 82 ].…”

Section: Current Detection Methods For Sars-cov-2mentioning

confidence: 99%

“…1 h faster results than RT-PCR 80 [ 78 ] RT-LAMP CPA PSR N & Orf1ab 10 DNAcopiesμl −1 Simulated OP/NP LAMP had better LOD result for SARS-CoV-2 extracted RNA, Specific, Primer pairs designed for LAMP, CPA and PSR targeting N -sequence Excellent for a real diagnosis.LOD Lyophilized LAMP kit for Orf1ab 21.57 & N 43.14 copies/reaction 431.47 & 862.9 of CPA and PSR copies/reaction. [ 77 ] Hologic transcription TMA 5.5 × 10 2 copies in 1 out of 5 NP Sensitivity 98.1% (52/53) for TMA and 96.2% (51/53) for RT-PCR 116 [ 81 ] RT-RAA ORF1ab gene 2 copies/reaction NP/OP sputum, Nasal swab, BAL, Stool, Whole blood Sensitivity and specificity of RT-RAA was 97.63% (330/338) and 97.87% (596/609), Ultrafast speed of detection, 16 samples per run, A single person can finish 16 samples in 40 min by working with automatic DNA extraction. 947 [ 115 ] CRISPR-Cas12DETETER lateral flow E & N genes 1 copies μL −1 NP/OP Low-cost, Relatively rapid positive predictive agreement and negative predictive agreement of SARS-CoV-2 DETECTR relative to the CDC qRT–PCR assay were 95% and 100%, respectively 83 [ 85 ] Dual CRISPR -Cas12a N gene 1.2 copies of DNA targets HIV 4.6 copies RNA targets SARS-CoV-2 40 min incubation time, Fast, One-pot, Robust [ 86 ] C2CA RdRp …”

Section: Novel Developed Technologies For Sars-cov-2 Detectionmentioning

confidence: 99%

Diagnostic techniques for COVID-19 and new developments

Sheikhzadeh

Eissa

Ismail

et al. 2020

Talanta

127

129

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COVID-19 pandemic is a serious global health issue today due to the rapid human to human transmission of SARS-CoV-2, a new type of coronavirus that causes fatal pneumonia. SARS -CoV-2 has a faster rate of transmission than other coronaviruses such as SARS and MERS and until now there are no approved specific drugs or vaccines for treatment. Thus, early diagnosis is crucial to prevent the extensive spread of the disease. The reverse transcription-polymerase chain reaction (RT-PCR) is the most routinely used method until now to detect SARS-CoV-2 infections. However, several other faster and accurate assays are being developed for the diagnosis of COVID-19 aiming to control the spread of infection through the identification of patients and immediate isolation. In this review, we will discuss the various detection methods of the SARS-CoV-2 virus including the recent developments in immunological assays, amplification techniques as well as biosensors.

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“…Isothermal amplification methods have been developed to replace the thermal cycling steps needed in PCR to simplify, lower the cost of, and reduce the footprint of PCR platforms. 42 Isothermal amplification techniques including loop-mediated isothermal amplification (LAMP), 43 nucleic acid sequence-based amplification (NASBA), 42 transcription-mediated amplification (TMA), 44 rolling circle amplification (RCA), 45 and recombinase polymerase amplification (RPA) 46 have been used for developing COVID-19 diagnostic tests ( Table S2 ).…”

Section: Viral Nucleic Acid Testsmentioning

confidence: 99%

“…In these modes, a higher clinical sensitivity (98.1% (52/53) versus 96.2% (51/53) for RT-PCR) and lower LOD (5.5 × 10 3 copies/mL (1.98 × 10 3 copies/reaction) versus 5.5 × 10 4 copies/mL (1.1 × 10 4 copies/reaction) for RT-PCR) were obtained for TMA compared to RT-PCR. 44 …”

Section: Viral Nucleic Acid Testsmentioning

confidence: 99%

Roadmap to the Bioanalytical Testing of COVID-19: From Sample Collection to Disease Surveillance

et al. 2020

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The disease caused by SARS-CoV-2, coronavirus disease 2019 (COVID-19), has led to a global pandemic with tremendous mortality, morbidity, and economic loss. The current lack of effective vaccines and treatments places tremendous value on widespread screening, early detection, and contact tracing of COVID-19 for controlling its spread and minimizing the resultant health and societal impact. Bioanalytical diagnostic technologies have played a critical role in the mitigation of the COVID-19 pandemic and will continue to be foundational in the prevention of the subsequent waves of this pandemic along with future infectious disease outbreaks. In this Review, we aim at presenting a roadmap to the bioanalytical testing of COVID-19, with a focus on the performance metrics as well as the limitations of various techniques. The state-of-the-art technologies, mostly limited to centralized laboratories, set the clinical metrics against which the emerging technologies are measured. Technologies for point-of-care and do-it-yourself testing are rapidly emerging, which open the route for testing in the community, at home, and at points-of-entry to widely screen and monitor individuals for enabling normal life despite of an infectious disease pandemic. The combination of different classes of diagnostic technologies (centralized and point-of-care and relying on multiple biomarkers) are needed for effective diagnosis, treatment selection, prognosis, patient monitoring, and epidemiological surveillance in the event of major pandemics such as COVID-19.

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High-Throughput Transcription-mediated amplification on the Hologic Panther is a highly sensitive method of detection for SARS-CoV-2

Cited by 95 publications

References 8 publications

Specificity and positive predictive value of SARS-CoV-2 nucleic acid amplification testing in a low-prevalence setting

Specificity and positive predictive value of SARS-CoV-2 nucleic acid amplification testing in a low-prevalence setting

Diagnostic techniques for COVID-19 and new developments

Roadmap to the Bioanalytical Testing of COVID-19: From Sample Collection to Disease Surveillance

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