Comparison of SARS-CoV-2 RT-PCR on a high-throughput molecular diagnostic platform and the cobas SARS-CoV-2 test for the diagnostic of COVID-19 on various clinical samples

Opota, Onya; Brouillet, René; Greub, Gilbert; Jaton, Katia

doi:10.1093/femspd/ftaa061

Cited by 46 publications

(51 citation statements)

References 22 publications

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“…To investigate the impact of the method and operator on Ct estimates, samples containing 1-100’000 SARS-CoV-2-C2 g.c.p.r. were analysed by RT-qPCR in two independent labs using different assays (30,31). We found that the Ct values obtained from these samples using independent methods are highly correlated ( Figure S4A, Additional File 1 ) as previously found (32).…”

Section: Resultsmentioning

confidence: 99%

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

Kubik

Marques

Xing

et al. 2020

Preprint

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Background: SARS-CoV-2 genotyping has been instrumental to monitor virus evolution and transmission during the pandemic. The reliability of the information extracted from the genotyping efforts depends on a number of aspects, including the quality of the input material, applied technology and potential laboratory-specific biases. These variables must be monitored to ensure genotype reliability. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in studies of viral spread and evolution. Results: We used clinical samples and synthetic viral genomes to evaluate the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination using an amplicon-based approach. We found that at least 1000 viral genomes are necessary to confidently detect variants in the genome at frequencies of 10% or higher. The broad applicability of our recommendations was validated in >200 clinical samples from six independent laboratories. The genotypes of clinical isolates with viral load above the recommended threshold cluster by sampling location and period. Our analysis also supports the rise in frequency of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was favoured by travelling during the summer 2020. Conclusions: We present much-needed recommendations for reliable determination of SARS-CoV-2 genome sequence and demonstrate their broad applicability in a large cohort of clinical samples.

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Section: Resultsmentioning

confidence: 99%

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

Kubik

Marques

Xing

et al. 2020

Preprint

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“…Given the uncertainty regarding sensitivity and specificity of RAT, all antigen results were confirmed on one of the following molecular platforms: i) VIASURE SARS-CoV-2 (N1 + N2) Real Time PCR Detection Kit for BD MAX™ (Becton Dickinson, USA) or GeneXpert SARS-CoV-2 test (Cepheid, https://www.cepheid.com) 12 as rapid systems, ii) test cobas 6800® SARS-CoV-2 (Roche, Basel, Switzerland) 13 or our automated high-throughput molecular diagnostic (MDx) platform as classic systems. Our MDx platform uses Magnapure RNA-extraction coupled to applied biosystems 7900 amplification device (Quant Studio 7) and three Hamilton robots, with primers targeting the E- and RdRp-encoding genes 14,15 .…”

Section: Methodsmentioning

confidence: 92%

“…Real Time PCR Detection Kit for BD MAX™ (Becton Dickinson, USA) or GeneXpert SARS-CoV-2 test (Cepheid, https://www.cepheid.com) 12 as rapid systems, ii) test cobas 6800® SARS-CoV-2 (Roche, Basel, Switzerland) 13 or our automated high-throughput molecular diagnostic All rights reserved. No reuse allowed without permission.…”

Section: Routine Confirmation By Rt-pcrmentioning

confidence: 99%

ImplemeNting SARS-CoV-2 Rapid antigen testing in the Emergency wArd of a Swiss univErsity hospital: the INCREASE study

Caruana

Croxatto

Kampouri

et al. 2021

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Background: While facing a second wave in SARS-CoV-2 pandemic, in November 2020 the Swiss Federal Office of Public Health (FOPH) authorized the use of rapid antigen tests (RATs) in addition to the gold-standard reverse transcription-polymerase chain reaction (RT-PCR). Methods: We implemented the use of RAT in the emergency ward of our university hospital for rapid patients' triaging and compared performances of four different antigen tests. All results were compared to SARS-CoV-2 specific RT-PCR (reference standard). Findings: Triaging patients using RAT in association with RT-PCR allowed us to isolate promptly positive patients and to save resources, in a context of rapid RT-PCR reagents shortage. Among 532 patients with valid results, overall sensitivities were 48.3% for One Step Exdia and 41.2% for Standard Q, PanbioTM and BD Veritor. All four antigen tests exhibited specificity above 99%. Sensitivity increased up to 74.6%, 66.2%, 66.2% and 64.8% for One Step Exdia, Standard Q, Panbio, and BD Veritor respectively, when considering viral loads above 105copies/ml, up to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/ml and 100% (for all tests) when considering viral loads above 107 copies/ml. Sensitivity was significantly higher for patients presenting with symptoms onset within 4 days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with evolution of symptoms for more than 4 days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Sensitivities of all RAT assays were of only 33% among hospitalized patients without COVID-19 symptoms. Interpretation: RAT might represent a useful epidemiological resource in selected clinical settings as a complementary tool to the molecular tests for rapid patients triaging, but the lower sensitivity compared to RT-PCR, especially in late presenters and subjects without COVID-19 symptoms, must be taken into account in order to correctly use RAT for triaging.

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“…Viral load were obtained by converting cycle thresholds of the RT-PCR instruments, using the formula logVL=-0.27Ct+13.04, as previously reported. 16,17…”

Section: Methodsmentioning

confidence: 99%

Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: a prospective comparative clinical trial

Schwob

Miauton

Petrović

et al. 2020

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BackgroundNasopharyngeal antigen Rapid Diagnostic Tests (RDTs) and saliva RT-PCR have shown variable performance to detect SARS-CoV-2.MethodsIn October 2020, we conducted a prospective trial involving patients presenting at testing centers with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR.ResultsOut of 949 patients enrolled, 928 patients had all three tests. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) ≥106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively.Sensitivity of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients and 96.5% (93.6-98.3%) for those with VL≥106. Sensitivity of STANDARD-Q®, Panbio™ and COVID-VIRO® Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL≥106, sensitivities were 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%) and ≥4 days (85.7%) after symptoms onset (p=0.6). Sensitivities of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR.ConclusionsThe high performance of RDTs allows rapid identification of COVID cases with immediate isolation of the vast majority of contagious individuals. RDT could be a game changer in primary care practices, and even more so in resource-constrained settings. PCR on saliva can replace NP PCR.ClinicalTrial.gov Identifier: NCT04613310

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Comparison of SARS-CoV-2 RT-PCR on a high-throughput molecular diagnostic platform and the cobas SARS-CoV-2 test for the diagnostic of COVID-19 on various clinical samples

Cited by 46 publications

References 22 publications

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

ImplemeNting SARS-CoV-2 Rapid antigen testing in the Emergency wArd of a Swiss univErsity hospital: the INCREASE study

Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: a prospective comparative clinical trial

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