Comparison of seven commercial RT-PCR diagnostic kits for COVID-19

Kasteren, Puck B. van; Veer, Bas van der; Brink, Sharon van den; Wijsman, Lisa; Jonge, Jørgen de; Brandt, Anne-Marie van den; Molenkamp, Richard; Reusken, Chantal; Meijer, Adam

doi:10.1016/j.jcv.2020.104412

Cited by 430 publications

(402 citation statements)

References 6 publications

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“…The existence of false negatives in the RT-qPCR test has been inferred in a number of studies that compared clinical test and symptomatic data with RT-qPCR testing information (Kucirka et al, 2020;Li et al, 2020;Xiao et al, 2020). Several studies have compared the performance of different RT-qPCR kits on RNA from clinical samples primarily to assess the performance of the kits, and have found agreement as well as differences that also point to the existence of false negative test results (Hogan et al, 2020;Pujadas et al, 2020;van Kasteren et al, 2020;Xiong et al, 2020). However, direct experimental analysis of RT-qPCR negative RNA samples at testing centres using different but related RT-PCR based tests as a way of estimating detection efficiency has received limited attention likely because of the high demand for diagnostic tests, shortage of testing kits, and cost of testing.…”

Section: Discussionmentioning

confidence: 99%

An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance

Davda

Frank

Prakash

et al. 2020

Preprint

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With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency.

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Section: Discussionmentioning

confidence: 99%

An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance

Davda

Frank

Prakash

et al. 2020

Preprint

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“…2-fold serial dilutions were prepared, and a standard curve was obtained. The parameters such as primer e ciency (94.9%) and R 2 value (0.99) were found within the acceptable range for commercial kits (16) (Fig. 2).…”

Section: Resultsmentioning

confidence: 71%

“…The higher sensibility from the E gene in a normal RT-qPCR is expected because samples can be considered positive up to a Ct ~ 40 [11,16]. Unlikely, other genes in a RT LAMP where there is evidence that a positive sample can be only up to a Ct ~ 30 [24].…”

Section: Discussionmentioning

confidence: 99%

“…We present an in-house protocol which is primarily based on the envelope protein gene E for COVID-19 detection. This gene target is highly recommended by the WHO and the Pan American Health Organization (PAHO) as a diagnostic target and it is considered a highly sensitive probe [11,[15][16][17]. The in-house protocol also includes an internal control for quality of genetic material, the human ribonuclease P (RP).…”

Section: Introductionmentioning

confidence: 99%

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In-House Development, Standardization, and Validation of a RT-qPCR Assay for the Detection of SARS-CoV-2 Virus in Ecuador.

Torre

Pibaque²,

Veloz³

et al. 2020

Preprint

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The World Health Organization (WHO) reported about 30 million cases of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and around 1 million deaths worldwide. Ecuador is the country with the highest mortality rate of confirmed cases in South America where both the poor ability to identify SARS-CoV-2 carriers and shortages in reagent supply have contributed the high infection rate observed. Hence, there is an urgent need to develop, standardize and validate an in-house protocol that cannot only reduces testing costs, but also increase the ability to screen widely the population. Primer-probe sets for the SARS-CoV-2 envelope protein E and the human ribonuclease P (RP) were validated for a duplex quantitative Reverse Transcription Polymerase Chain Reaction (RT-qPCR) for the Coronavirus Disease-19 (COVID-19) detection. Optimal E primers concentration was 400 nM and TaqMan probe 200 nM. The primer efficiency was set at 94.9% and R2 value at 0.99, which was comparable to commercial kits. The lower detection limit was found at 15 copies/ μL (50 copies/rx). In comparison to a Loop-mediated Isothermal Amplification (LAMP) commercial kit, there was a higher detection rate (30%) and results were highly reproducible (95%). We were able to develop a highly sensitive and low-cost duplex in-house RT-qPCR test for COVID-19 detection comparable to other commercially available kits.

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“…Auf Grundlage der früh vorhandenen Sequenzierungsdaten konnten sehr schnell diagnostische PCR-Assays zur Detektion des Virus von Abstrichen der Schleimhaut des Nasenrachenraums, aber auch im Sputum oder Rachenspülwasser sowie anderen Körperflüssigkeiten entwickelt werden [27,28] Die analytische Sensitivität der Teste ist sehr gut (um die 5 RNA-Moleküle/PCR-Ansatz) [27,38], sodass insbesondere symptomatische Patienten in der Frühphase sicher erfasst werden. Da jedoch die Sensitivität des gesamten Diagnoseverfahrens auch von der präanalytischen Phase -in diesem Falle die Durchführung eines Abstriches -maßgeblich beeinflusst wird, sind insbesondere suspekte negative PCR-Ergebnisse durch eine weitere Probenentnahme zu verifizieren.…”

Section: Die Zur Identifizierung Dieses Erregers Durchgeführtenunclassified

Labordiagnostik bei SARS-CoV-2-Infektionen

Roskos

2020

Der Klinikarzt

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ZUSAMMENFASSUNGDie aktuelle COVID-19-Pandemie stellte auch die medizinischen Labore vor große Herausforderungen. Der prinzipiell sehr frühen Kenntnis des primär neuen Erregers und der prinzipiellen Möglichkeit des Nachweises des Virus stand oft eine zunächst unzureichende Verfügbarkeit an Reagenzien und Analysensystemen gegenüber, die aber relativ schnell verbessert werden konnten, sodass nun eine flächendeckende und schnelle Diagnostik dieses Erregers möglich ist. Neben der Erregeridentifizierung liefert die Labordiagnostik jedoch auch wichtige Hinweise bei der Beurteilung der Erkrankung bzw. der Abschätzung des weiteren Verlaufes. Die Wertigkeit einzelner Parameter bzw. Parameterkonstellationen wurde dabei teilweise erst im Verlauf der Pandemie deutlich bzw. ist auch noch in der Evaluierung.

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Comparison of seven commercial RT-PCR diagnostic kits for COVID-19

Cited by 430 publications

References 6 publications

An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance

An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance

In-House Development, Standardization, and Validation of a RT-qPCR Assay for the Detection of SARS-CoV-2 Virus in Ecuador.

Labordiagnostik bei SARS-CoV-2-Infektionen

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