Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations
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Abstract
Clinical evidence for asymptomatic cases of coronavirus disease (COVID-19) has reinforced the significance of effective surveillance testing programs. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays are considered the ‘gold standard’ for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. However, the labor and resource requirements can be prohibitive with respect to large testing volumes associated with the pandemic. Pooled testing algorithms may serve to increase testing capacity with more efficient resource utilization. Due to the lack of carefully curated cohorts, there is limited evidence for the applicability of RT-PCR pooling in asymptomatic COVID-19 cases. In this study, we compared the analytical sensitivity of the TaqMan™ SARS-CoV-2 Pooling Assay to detect one positive sample in a pool of five anterior nares swabs in symptomatic and asymptomatic cohorts at an institute of higher education. Positive pools were deconvoluted and each individual sample was retested using the TaqPath™ COVID-19 Combo Kit. Both assays target the open reading frame ( ORF ) 1ab , nucleocapsid ( N ), and spike ( S ) gene of the strain that originated in Wuhan, Hubei, China. Qualitative results demonstrated absolute agreement between pooled and deconvoluted samples in both cohorts. Independent t-test performed on C t shifts supported an insignificant difference between cohorts with p-values of 0.306 ( Orf1ab ), 0.147 ( N ), and 0.052 ( S ). All negative pools were correctly reported as negative. Pooled PCR testing up to five samples is a valid method for surveillance testing of students and staff in a university setting, especially when the prevalence is expected to be low.
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SciScore for 10.1101/2021.05.20.21257523: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Sample Collection, Storage, and Preanalytical Processing: The study was conducted at the Northeastern University COVID-19 response laboratory, the Life Science Testing Center (LSTC; Burlington, MA, USA), which performs population testing for university affiliates. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Resulting threshold cycle (Ct) values were extracted using COVID-19 Interpretive Software and analyzed using Microsoft Excel® and GraphPad Prism version 9 for Windows (GraphPad Software, San Diego, CA, USA). Microsoft Excel®suggested: …SciScore for 10.1101/2021.05.20.21257523: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Sample Collection, Storage, and Preanalytical Processing: The study was conducted at the Northeastern University COVID-19 response laboratory, the Life Science Testing Center (LSTC; Burlington, MA, USA), which performs population testing for university affiliates. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Resulting threshold cycle (Ct) values were extracted using COVID-19 Interpretive Software and analyzed using Microsoft Excel® and GraphPad Prism version 9 for Windows (GraphPad Software, San Diego, CA, USA). Microsoft Excel®suggested: (Microsoft Excel, RRID:SCR_016137)GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:It is important to note, significant dilution effects observed in all genes was a result of interpreting one positive per pool of five and may indicate a limitation of the experimental design due to probability of more than one positive per pool in practice [9]. Thus, the practical significance observed by the average Ct shifts and negligible impact to qualitative agreement supports retention of RT-qPCR sensitivity at a minimum. This strategy of increased extraction and elution volumes for group tests reported absolute qualitative agreement to the deconvoluted counterpart, including a 1/3 gene positive case, and produced a more conserved Ct shift [7,9]. Since symptomatic subjects tend to have a significantly higher prevalence of COVID-19 in a pandemic setting, from a resource efficiency standpoint, it is advisable to consider pooling samples when testing subjects who are non-symptomatic such as in vaccinated populations, where the prevalence rates are expected to be significantly lower.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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