A dynamic COVID-19 immune signature includes associations with poor prognosis

Article activity feed

1. Version published to 10.1038/s41591-020-1038-6

   Aug 17, 2020
2. 

   ScreenIT

   Jun 10, 2020

   SciScore for 10.1101/2020.06.08.20125112: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Patients above 18 years of age and with capacity to consent were approached for informed consent to serial blood sampling by the research nursing team if they met the criteria of a positive PCR result for SARS-CoV-2 or strong clinical suspicion of infection. IRB: Both approvals are granted under the terms of the Infectious Disease Biobank’s ethics permission (reference 19/SC/0232) granted by the South Central Hampshire B Research Ethics Committee in 2019.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Cell…

   SciScore for 10.1101/2020.06.08.20125112: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Patients above 18 years of age and with capacity to consent were approached for informed consent to serial blood sampling by the research nursing team if they met the criteria of a positive PCR result for SARS-CoV-2 or strong clinical suspicion of infection. IRB: Both approvals are granted under the terms of the Infectious Disease Biobank’s ethics permission (reference 19/SC/0232) granted by the South Central Hampshire B Research Ethics Committee in 2019.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Cell Sorting by Flow Cytometry: PBMCs were stained with the following antibodies from the panels found in Supplementary Table 3; CD3-FITC (P5), TCR γδ-PE-Cy7 (P3), CD4-BV711 (P5), CD8-PerCP-Cy5.5 (P3), CD25-PE (P1: 2A3 & M-A251), CD45RA-BV786 (P3), CCR7-PE-CF594 (P3), and CD127-BV421 (Sort).	CD4-BV711 suggested: None P5 suggested: None CD8-PerCP-Cy5.5 suggested: None CD25-PE suggested: None CD45RA-BV786 suggested: None P3 suggested: None CCR7-PE-CF594 suggested: None CD127-BV421 suggested: None
   The Protein G Sepharose beads (251µl of 4% suspension, Creative BioMart) were used to capture the immune complexes of anti-SARS-CoV-2 antibodies and NanoLuc fusion proteins.	anti-SARS-CoV-2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   This protein was expressed in 500 mL HEK-293F cells (Invitrogen) at a density of 1.5 million cells/mL.	HEK-293F suggested: RRID:CVCL_6642)
   ) RBD domain of S (aa 329-538) and N (aa 2-419) gene fragments were cloned into pNanoLuc vector, transfected into HEK293 cells, the cell lysates containing NanoLuc-fusion proteins were probed with plasma samples (0.5 - 11×1106 luminescence units; LU) for 1 hr at RT.	HEK293 suggested: None
   Software and Algorithms
   Sentences	Resources
   Flow Cytometry Data Analysis: FCS files were analysed using FlowJo (10.6.2, Treestar).	FlowJo suggested: (FlowJo, RRID:SCR_008520)

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2020.06.08.20125112v1 on medRxiv

   Jun 9, 2020