Early induction of SARS-CoV-2 specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients

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   ScreenIT

   Oct 22, 2020

   SciScore for 10.1101/2020.10.15.341958: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All participants provided written informed consent.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Six patients were male, six were female, their median age at time of admission was 52.5 years, ranging from 27 to 78 years.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Luminex analysis: SARS-CoV-2 RBD, S1 and N proteins (Genscript) were conjugated onto MagPlex microsphere (Luminex) using xMAP antibody coupling kit (Luminex).	xMAP suggested: None
   SARS-CoV-2 spike and N proteins specific antibodies were detected by pre-incubation of 100-fold diluted serum (in 1% BSA PBS) with conjugated microspheres (1250 …

   SciScore for 10.1101/2020.10.15.341958: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All participants provided written informed consent.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Six patients were male, six were female, their median age at time of admission was 52.5 years, ranging from 27 to 78 years.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Luminex analysis: SARS-CoV-2 RBD, S1 and N proteins (Genscript) were conjugated onto MagPlex microsphere (Luminex) using xMAP antibody coupling kit (Luminex).	xMAP suggested: None
   SARS-CoV-2 spike and N proteins specific antibodies were detected by pre-incubation of 100-fold diluted serum (in 1% BSA PBS) with conjugated microspheres (1250 beads/antigen) for 1h at room temperature, followed by 1:1000 diluted PE-conjugated anti-human IgG polyclonal antibody (eBioscience) or PE-conjugated anti-human IgM antibody for 1h at room temperature.	anti-human IgG suggested: None anti-human IgM suggested: None
   IFN-γ ELISPOT assay: 15-mer peptides that spanned the entire ORF of genes eight SARS-CoV-2 proteins (NP, M, ORF7, ORF8, ORF3, S, NSP7, NSP13) and antibody responses to two SARS-CoV-2 proteins (NP, S) were synthesised with 10 amino acids overlap and were grouped into pools of approximately 40 peptides (Table S1).	NSP7 suggested: (Abcam Cat# ab21660, RRID:AB_874019) NSP13 suggested: None
   Biotinylated anti-IFN-γ antibody (MabTech) at a 1:2000 dilution in PBS/0.5% FCS was incubated at RT for two hours, followed by six wash steps with PBS and incubation of Streptavidin-AP (MabTech) at a 1:2000 dilution in PBS/0.5% FCS at RT for one hour.	anti-IFN-γ suggested: None
   Cells were stained with the yellow LIVE/DEAD fixable dead cell stain kit (Invitrogen) and anti-CD3 (clone SK7; 3:50), anti-CD4 (clone SK3; 3:50), and anti-CD8 (clone SK1; 3:50) antibodies..	anti-CD3 suggested: None anti-CD4 suggested: None anti-CD8 suggested: None
   Cells were subsequently fixed and permeabilised using the Cytofix/Cytoperm kit (BD Biosciences-Pharmingen) and stained with anti-IFN-γ (clone 25723, R&D Systems; 1:25) and anti-TNF-α (clone MAb11; 1:25) antibodies and analysed on a BD-LSR II FACS Scan.	anti-TNF-α suggested: None
   Software and Algorithms
   Sentences	Resources
   Study design: Patients (n=12) were enrolled in this study after being admitted to the hospital and confirmed to be infected with SARS-CoV-2 based on a positive SARS-CoV-2 RT-PCR test as part of the PROTECT (National Healthcare Group Domain Specific Review Board reference number 2012/00917) and Novel Pathogens (CIRB ref.	National Healthcare suggested: None
   Statistical analysis: Regression analyses were performed using GraphPad Prism v7 software.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Figures were prepared in Adobe Illustrator Creative Cloud.	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)

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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.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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   Read the original source
2. 

   Version published to 10.1101/2020.10.15.341958 on bioRxiv

   Oct 16, 2020