Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

Smith, Elizabeth; Wei, Zhen; Manji, Ryhana; Schron, Deborah; Duong, Scott; Berry, Gregory J.

doi:10.1101/2020.05.14.097311

Cited by 25 publications

(34 citation statements)

References 7 publications

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“…Our evaluation of three different external RNA control materials demonstrated comparable analytical sensitivity with both the SARS-CoV-2 TMA assay and the SARS-CoV-2 RT-PCR assay, with LOD values of between 83 c/ml of 194 c/ml. These analytical sensitivity values correlate with previously reported LOD values by Smith et al ( 16 ). However, using LOD values as determined by external control material to assess or compare assay performance warrants some caution, as different control materials may give considerably different results for the absolute LOD value ( 16 ), and the reported RNA or DNA stock concentrations of these materials may differ from true concentrations ( 17 ).…”

Section: Discussionsupporting

confidence: 91%

Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection

et al. 2020

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The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther System to directly amplify and detect two separate target sequences in the ORF1ab region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 TCID50/ml using inactivated virus, and 25 c/ml using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 – 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross reactivity or interference was observed with testing six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titer. Clinical nasopharyngeal swab specimen testing (N=140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription PCR NAAT for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2.

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Section: Discussionsupporting

confidence: 91%

Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection

et al. 2020

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“…The Cepheid assay has a manufacturer claim of 250 copies/ml for nasopharyngeal swab specimens ( 26 ), and one study demonstrated an even lower LoD of 100 copies/ml ( 25 ). The Hologic assay has a claimed LoD of 0.01 50% tissue culture infective dose (TCID 50 )/ml ( 27 ), and an LoD of 62.5 copies/ml or 1,000 copies/ml was obtained using synthetic RNA reference material or whole inactivated virus, respectively ( 32 ). The higher LoD for stool than upper respiratory specimens may be due to the presence of PCR inhibitors ( 33 ).…”

Section: Discussionmentioning

confidence: 99%

Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms

et al. 2020

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The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after two to three weeks post symptom onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than four weeks suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance. We utilized remnant stool specimens (n=79) from 77 patients with gastrointestinal symptoms. Forty-eight patients had PCR-confirmed COVID-19 and 29 were either nasopharyngeal/oropharyngeal PCR negative or presented for reasons unrelated to COVID-19 and were not tested. Positive percent agreement between the Cepheid and Hologic assays was 93% (95% CI: 81.1%-98.2%) and negative percent agreement was 96% (95% CI: 89%-0.99%). Four discrepant specimens (Cepheid positive only, n=2; Hologic positive only, n=2) exhibited average Ct values of >37 for the targets detected. Of the 48 patients with PCR-confirmed COVID-19, 23 were positive by both assays (47.9%). For the negative patient group, 2/29 were positive by both assays (6.9%). The two stool PCR positive, nasopharyngeal/oropharyngeal PCR negative patients were SARS-CoV-2 IgG positive. Our results demonstrate acceptable agreement between two commercially available molecular assays and support the use of stool PCR to confirm diagnosis when SARS-CoV-2 is undetectable in the upper respiratory tract.

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“…The most widely used technique is PCR and TMA, that has subsequently been incorporated. The sensitivity and specificity of these techniques is very high, both around 99%, which makes them very useful for diagnosing infection [19].…”

Section: Capacity and Current Value Of The Main Microbiological Technmentioning

confidence: 99%

Recommendations for use of antigenic tests in the diagnosis of acute SARS-CoV-2 infection in the second pandemic wave: attitude in different clinical settings

Candel

Barreiro²,

Román³

et al. 2020

Rev Esp Quimioter

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The high transmissibility of SARS-CoV-2 before and shortly after the onset of symptoms suggests that only diagnosing and isolating symptomatic patients may not be sufficient to interrupt the spread of infection; therefore, public health measures such as personal distancing are also necessary. Additionally, it will be important to detect the newly infected individuals who remain asymptomatic, which may account for 50% or more of the cases. Molecular techniques are the “gold standard” for the diagnosis of SARS-CoV-2 infection. However, the massive use of these techniques has generated some problems. On the one hand, the scarcity of resources (analyzers, fungibles and reagents), and on the other the delay in the notification of results. These two facts translate into a lag in the application of isolation measures among cases and contacts, which favors the spread of the infection. Antigen detection tests are also direct diagnostic methods, with the advantage of obtaining the result in a few minutes and at the very “pointof-care”. Furthermore, the simplicity and low cost of these tests allow them to be repeated on successive days in certain clinical settings. The sensitivity of antigen tests is generally lower than that of nucleic acid tests, although their specificity is comparable. Antigenic tests have been shown to be more valid in the days around the onset of symptoms, when the viral load in the nasopharynx is higher. Having a rapid and real-time viral detection assay such as the antigen test has been shown to be more useful to control the spread of the infection than more sensitive tests, but with greater cost and response time, such as in case of molecular tests. The main health institutions such as the WHO, the CDC and the Ministry of Health of the Government of Spain propose the use of antigenic tests in a wide variety of strategies to respond to the pandemic. This document aims to support physicians involved in the care of patients with suspected SC2 infection, in the context of a growing incidence in Spain since September 2020, which already represents the second pandemic wave of COVID-19.

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Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

Abstract: 16

Cited by 25 publications

References 7 publications

Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection

Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection

Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms

Recommendations for use of antigenic tests in the diagnosis of acute SARS-CoV-2 infection in the second pandemic wave: attitude in different clinical settings

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