Prolonged activation of nasal immune cell populations and development of tissue-resident SARS-CoV-2-specific CD8+ T cell responses following COVID-19

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1. Version published to 10.1038/s41590-021-01095-w

   Dec 22, 2021
2. 

   ScreenIT

   Apr 24, 2021

   SciScore for 10.1101/2021.04.19.21255727: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics

   Consent: After informed consent was obtained, longitudinal sampling was performed for the duration of the hospital admission, and one convalescent sample was obtained at the outpatient follow-up appointment, which was scheduled six weeks after hospital discharge. IRB: Ethical approval was obtained from the Medical Ethical Committee Leiden-Den Haag-Delft (NL73740.058.20). Field Sample Permit: Nasal cell collection and storage: Nasal cells were collected by gently scraping the nasal inferior turbinate using curettes (Rhino-Pro®, Arlington Scientific), as described previously42, and placing them in a tube containing pre-cooled 8mL sterile PBS containing 5mM EDTA (Life Technologies).

   Sex as a …

   SciScore for 10.1101/2021.04.19.21255727: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	Consent: After informed consent was obtained, longitudinal sampling was performed for the duration of the hospital admission, and one convalescent sample was obtained at the outpatient follow-up appointment, which was scheduled six weeks after hospital discharge. IRB: Ethical approval was obtained from the Medical Ethical Committee Leiden-Den Haag-Delft (NL73740.058.20). Field Sample Permit: Nasal cell collection and storage: Nasal cells were collected by gently scraping the nasal inferior turbinate using curettes (Rhino-Pro®, Arlington Scientific), as described previously42, and placing them in a tube containing pre-cooled 8mL sterile PBS containing 5mM EDTA (Life Technologies).
   Sex as a biological variable	These were all sixty years or older, and with a male:female ratio of 2:1, in order to match the patient population.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   FCS files were then normalized using the reference PBMCs and the CyTOFBatchAdjust package with 99 percentile scaling for each marker individually 50.	CyTOFBatchAdjust suggested: None
   Clustering of cells into populations was done using hierarchical stochastic neighbor embedding (hSNE) or tSNE with Cytosplore software (v2.3.0, https://www.cytosplore.org/), using all markers minus EpCAM and cPARP 51.	Cytosplore suggested: (Cytosplore Viewer, RRID:SCR_018330)

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   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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. 

   Version published to 10.1101/2021.04.19.21255727 on medRxiv

   Apr 22, 2021