Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection

Article activity feed

1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.11.25.399139: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   IRB: Ethics statement: The study of migrant workers was approved by the Singapore Ministry of Health under Section 59A of the Infectious Diseases Act (2015), thus institutional review board approval was not required and all participants gave verbal consent to participate. Consent: All COVID-19 patients provided written informed consent and their study was approved by the Institutional Review Boards of NUS (H-20-006), SingHealth (CIRB/F/2018/2387 and CIRB/F/2018/3045) and the National Healthcare Group Domain Specific Review Board (2012/00917).

   Randomization

   Study population: The asymptomatic cohort comprised 541 men aged 19-59 years (median 35 years) recruited from …

   SciScore for 10.1101/2020.11.25.399139: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethics statement: The study of migrant workers was approved by the Singapore Ministry of Health under Section 59A of the Infectious Diseases Act (2015), thus institutional review board approval was not required and all participants gave verbal consent to participate. Consent: All COVID-19 patients provided written informed consent and their study was approved by the Institutional Review Boards of NUS (H-20-006), SingHealth (CIRB/F/2018/2387 and CIRB/F/2018/3045) and the National Healthcare Group Domain Specific Review Board (2012/00917).
   Randomization	Study population: The asymptomatic cohort comprised 541 men aged 19-59 years (median 35 years) recruited from randomly-selected rooms within a SARS-CoV-2 affected dormitory housing over 4000 migrant workers and followed up prospectively from May to July 2020.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody quantification: Sera were tested for anti-nucleoprotein (NP) IgG antibodies (CMIA, Abbott Laboratories) on an Abbott Architect i2000SR automated instrument; a signal to cutoff ratio of ≥1.4 was defined as a positive result following the manufacturer’s recommendation.	anti-nucleoprotein (NP) IgG suggested: None
   ELISpot plates (Millipore) were coated with human IFN-γ antibody (1-D1K, Mabtech) overnight at 4ºC.	IFN-γ suggested: None
   ), anti-IL-6 (MQ2-13A5), anti-IL-10 (JES3-19F1) and anti-TNF-α (MAb11) antibodies and analyzed on a BD-LSR II FACS Scan.	anti-IL-6 suggested: None anti-IL-10 suggested: None anti-TNF-α suggested: None
   Software and Algorithms
   Sentences	Resources
   All COVID-19 patients provided written informed consent and their study was approved by the Institutional Review Boards of NUS (H-20-006), SingHealth (CIRB/F/2018/2387 and CIRB/F/2018/3045) and the National Healthcare Group Domain Specific Review Board (2012/00917).	National Healthcare suggested: None
   Antibody quantification: Sera were tested for anti-nucleoprotein (NP) IgG antibodies (CMIA, Abbott Laboratories) on an Abbott Architect i2000SR automated instrument; a signal to cutoff ratio of ≥1.4 was defined as a positive result following the manufacturer’s recommendation.	Abbott Laboratories suggested: None Abbott Architect suggested: (Abbott ARCHITECT i1000sr System, RRID:SCR_019328)
   Data were analyzed by FlowJo (BD Biosciences).	FlowJo suggested: (FlowJo, RRID:SCR_008520)

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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: We detected the following sentences addressing limitations in the study:

   Clearly, this whole blood cytokine assay has limitations, since it does not enable distinction of the cellular source of the different cytokines. However, it provides a holistic snapshot of the virus-specific cellular immunity and can be performed in a large group of asymptomatic individuals tested in a limited time. The results obtained with unsupervised clustering were extremely clear in describing distinct cytokine secretion patterns in symptomatic versus asymptomatic individuals and revealed possible features of SARS-CoV-2-specific T cell responses that are worthy of more detailed characterization in future studies. We observed a high secretion of TNF-α, IL-6, IL-1β and IL-10 exclusively in the blood of a subset of patients who recently recovered from COVID-19, especially in patients with severe COVID-19. The high secretion of pro-inflammatory cytokines was, however, neither proportional to the quantity of IFN-γ and IL-2 detected in the same assay nor to the number of IFN-γ spots detected in the same patients analyzed in parallel with ELISpot. These findings seem to confirm that myeloid cells present in patients who recovered from symptomatic COVID-19 disease have been reprogrammed to promote inflammatory signals and are hyper-responsive to IFNs (30). Secretion of the pro-inflammatory cytokines IL-6, TNF-α, IL-1β was also detected in peptide-stimulated blood of asymptomatic individuals. Yet, their quantity was directly proportional to the quantity of T cell cytokines (IL-...

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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 10.1084/jem.20202617

   Mar 1, 2021
3. 

   ScreenIT

   Nov 28, 2020

   SciScore for 10.1101/2020.11.25.399139: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   All COVID-19 patients provided written informed consent and their study was approved by the Institutional Review Boards of NUS (H-20-006), SingHealth (CIRB/F/2018/2387 and CIRB/F/2018/3045) and the National Healthcare Group Domain Specific Review Board (

   Randomization

   Study population The asymptomatic cohort comprised 541 men aged 19-59 years (median 35 years) recruited from randomly-selected rooms within a SARS-CoV-2 affected dormitory housing over 4000 migrant workers and followed up prospectively from May to July 2020.

   Blinding

   not detected.

   Power Analysis

   not detected.

   Sex as a biological variable

   not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody …

   SciScore for 10.1101/2020.11.25.399139: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   All COVID-19 patients provided written informed consent and their study was approved by the Institutional Review Boards of NUS (H-20-006), SingHealth (CIRB/F/2018/2387 and CIRB/F/2018/3045) and the National Healthcare Group Domain Specific Review Board (

   Randomization

   Study population The asymptomatic cohort comprised 541 men aged 19-59 years (median 35 years) recruited from randomly-selected rooms within a SARS-CoV-2 affected dormitory housing over 4000 migrant workers and followed up prospectively from May to July 2020.

   Blinding

   not detected.

   Power Analysis

   not detected.

   Sex as a biological variable

   not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody quantification Sera were tested for anti-nucleoprotein (NP) IgG antibodies (CMIA, Abbott Laboratories) on an Abbott Architect i2000SR automated instrument; a signal to cutoff ratio of ≥1.4 was defined as a positive result following the manufacturer’s recommendation.	anti-nucleoprotein ( NP ) IgG suggested: None
   ELISpot plates (Millipore) were coated with human IFN-γ antibody (1-D1K, Mabtech) overnight at 4ºC.	IFN-γ suggested: None
   ), anti-IL-6 (MQ2-13A5), anti-IL-10 (JES3-19F1) and anti-TNF-α (MAb11) antibodies and analyzed on a BD-LSR II FACS Scan.	anti-IL-6 suggested: None anti-IL-10 suggested: None anti-TNF-α suggested: None
   Software and Algorithms
   Sentences	Resources
   All COVID-19 patients provided written informed consent and their study was approved by the Institutional Review Boards of NUS (H-20-006), SingHealth (CIRB/F/2018/2387 and CIRB/F/2018/3045) and the National Healthcare Group Domain Specific Review Board (	National Healthcare suggested: None
   Antibody quantification Sera were tested for anti-nucleoprotein (NP) IgG antibodies (CMIA, Abbott Laboratories) on an Abbott Architect i2000SR automated instrument; a signal to cutoff ratio of ≥1.4 was defined as a positive result following the manufacturer’s recommendation.	Abbott Laboratories suggested: None Abbott Architect suggested: (Abbott ARCHITECT i1000sr System, RRID:SCR_018371)
   Antibodies were purchased from BD Biosciences- Pharmingen unless otherwise stated.	BD Biosciences- suggested: None
   The results obtained from UMAP analyses were incorporated as additional parameters and converted to .fcs files, which were then loaded into FlowJo to generate heatmaps of cytokine secretion on the reduced dimensions.	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: We detected the following sentences addressing limitations in the study:

   Clearly, this whole blood cytokine assay has limitations, since it does not enable distinction of the cellular source of the different cytokines. However, it provides a holistic snapshot of the virus- specific cellular immunity and can be performed in a large group of asymptomatic individuals tested in a limited time. The results obtained with unsupervised clustering were extremely clear in describing distinct cytokine secretion patterns in symptomatic versus asymptomatic individuals and revealed possible features of SARS-CoV-2-specific T cell responses that are worthy of more detailed characterization in future studies. We observed a high secretion of TNF-α, IL-6, IL-1β and IL-10 exclusively in the blood of a subset of patients who recently recovered from COVID-19, especially in patients with severe COVID-19. The high secretion of pro-inflammatory cytokines was, however, neither proportional to the quantity of IFN-γ and IL-2 detected in the same assay nor to the number of IFN-γ spots detected in the same patients analyzed in parallel with ELISpot. These findings seem to confirm that myeloid cells present in patients who recovered from symptomatic COVID-19 disease have been reprogrammed to promote inflammatory signals and are hyper-responsive to IFNs (30). Secretion of the pro-inflammatory cytokines IL-6, TNF-α, IL-1β was also detected in peptide- stimulated blood of asymptomatic individuals. Yet, their quantity was directly proportional to the quantity of T cell cytokines (I...

   ---

   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.

   ---

   About SciScore

   SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

   Read the original source
4. 

   Version published to 10.1101/2020.11.25.399139v1 on bioRxiv

   Nov 27, 2020