SARS‐CoV‐2 RNA screening in routine pathology specimens
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Abstract
Virus detection methods are important to cope with the SARS‐CoV‐2 pandemics. Apart from the lung, SARS‐CoV‐2 was detected in multiple organs in severe cases. Less is known on organ tropism in patients developing mild or no symptoms, and some of such patients might be missed in symptom‐indicated swab testing. Here, we tested and validated several approaches and selected the most reliable RT‐PCR protocol for the detection of SARS‐CoV‐2 RNA in patients’ routine diagnostic formalin‐fixed and paraffin‐embedded (FFPE) specimens available in pathology, to assess (i) organ tropism in samples from COVID‐19‐positive patients, (ii) unrecognized cases in selected tissues from negative or not‐tested patients during a pandemic peak, and (iii) retrospectively, pre‐pandemic lung samples. We identified SARS‐CoV‐2 RNA in seven samples from confirmed COVID‐19 patients, in two gastric biopsies, one small bowel and one colon resection, one lung biopsy, one pleural resection and one pleural effusion specimen, while all other specimens were negative. In the pandemic peak cohort, we identified one previously unrecognized COVID‐19 case in tonsillectomy samples. All pre‐pandemic lung samples were negative. In conclusion, SARS‐CoV‐2 RNA detection in FFPE pathology specimens can potentially improve surveillance of COVID‐19, allow retrospective studies, and advance our understanding of SARS‐CoV‐2 organ tropism and effects.
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SciScore for 10.1101/2021.01.25.21250082: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study was given ethical approval by the ethics committee at the medical faculty of RWTH Aachen University (EK 304/20, EK 119/20, and EK 092/20). 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 RNA isolation from FFPE specimens and SARS-CoV-2 RNA detection: We extracted RNA from FFPE tissue using a Maxwell® 16 LEV RNA FFPE Purification Kit (Promega GmbH, Walldorf, Germany) on the Maxwell® 16 IVD instrument (Promega GmbH) or with the ReliaPrep™ FFPE Total RNA Miniprep System (Promega GmbH) according to the manufacturer’s … SciScore for 10.1101/2021.01.25.21250082: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study was given ethical approval by the ethics committee at the medical faculty of RWTH Aachen University (EK 304/20, EK 119/20, and EK 092/20). 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 RNA isolation from FFPE specimens and SARS-CoV-2 RNA detection: We extracted RNA from FFPE tissue using a Maxwell® 16 LEV RNA FFPE Purification Kit (Promega GmbH, Walldorf, Germany) on the Maxwell® 16 IVD instrument (Promega GmbH) or with the ReliaPrep™ FFPE Total RNA Miniprep System (Promega GmbH) according to the manufacturer’s instructions. FFPEsuggested: (ffpe, RRID:SCR_001307)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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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