RT‐PCR/MALDI‐TOF mass spectrometry‐based detection of SARS‐CoV‐2 in saliva specimens
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Abstract
As severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infections continue, there is a substantial need for cost‐effective and large‐scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS‐CoV‐2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT‐PCR/MALDI‐TOF mass spectrometry‐based assay (Agena MassARRAY®) to detect SARS‐CoV‐2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS‐CoV‐2 RNA in saliva by the cobas® 6800/8800 SARS‐CoV‐2 real‐time RT‐PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS‐CoV‐2 detection on the novel Agena system as well as on a conventional real‐time RT‐PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS‐CoV‐2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.
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SciScore for 10.1101/2021.03.11.21253234: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Statistical analyses: For comparison of outcomes across both platforms, percent agreement and Cohen’s kappa (κ) statistic were calculated using the attribute agreement analysis on Minitab Statistical Software (19.2020.2.0). Minitabsuggested: (Minitab, RRID:SCR_014483)Normality was assessed by D’Agostino and Pearson test for continuous variables (e.g., Ct values) (GraphPad Prism 9.0.2). GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not …
SciScore for 10.1101/2021.03.11.21253234: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Statistical analyses: For comparison of outcomes across both platforms, percent agreement and Cohen’s kappa (κ) statistic were calculated using the attribute agreement analysis on Minitab Statistical Software (19.2020.2.0). Minitabsuggested: (Minitab, RRID:SCR_014483)Normality was assessed by D’Agostino and Pearson test for continuous variables (e.g., Ct values) (GraphPad Prism 9.0.2). GraphPad Prismsuggested: (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:Our study does have limitations in that our saliva collection methods did not occur at one time point but rather at any point in the day within two days of initial NP/AN collection. While the utility of standardized collection methods (e.g., early morning collection) remain to be further clarified, this is not a variable we controlled in this study. In addition, we utilized a pooled positive NP specimen to serve as our analyte to assess sensitivity. As a result, the sensitivities measured are based on a potentially heterogenous mixture of viral variants. We addressed this by pooling specimens isolated from two consecutive days to ensure a sampling of the predominant circulating clade virus at the given time period. Overall, we demonstrate comparable analytical performance across two unique diagnostic platforms for detection of SARS-CoV-2 nucleic acids in saliva specimens. Given the continued spread and rise of new SARS-CoV-2 variants, there is a critical need to understand the analytic capabilities of these technologies. This is especially relevant in large-scale screening efforts where saliva has the potential to be further exploited for its utility as a clinical specimen. This greater understanding of assay and target sensitivity is essential to informing both effective detection efforts and broader public health measures to ultimately quell the COVID-19 pandemic.
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.
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