Residual SARS-CoV-2 viral antigens detected in GI and hepatic tissues from five recovered patients with COVID-19

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1. Version published to 10.1136/gutjnl-2021-324280

   Jun 2, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.10.28.20219014: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: This study was approved by the SingHealth Centralised Institutional Review Board (reference number: 2019/2653). Consent: Written informed consent was obtained from both patients 1 and 2.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Study cohort: Patient 1 was a middle-aged male who was diagnosed with COVID-19 in April 2020.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Multiplex immunohistochemistr: Multiplex immunohistochemistry was performed using an Opal Multiplex fIHC kit (Akoya Bioscience, USA), as we previously described.(7-9) In brief, FFPE tissue samples (4 µm-thick) were labelled with primary …

   SciScore for 10.1101/2020.10.28.20219014: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: This study was approved by the SingHealth Centralised Institutional Review Board (reference number: 2019/2653). Consent: Written informed consent was obtained from both patients 1 and 2.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Study cohort: Patient 1 was a middle-aged male who was diagnosed with COVID-19 in April 2020.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Multiplex immunohistochemistr: Multiplex immunohistochemistry was performed using an Opal Multiplex fIHC kit (Akoya Bioscience, USA), as we previously described.(7-9) In brief, FFPE tissue samples (4 µm-thick) were labelled with primary antibodies against the SARS-CoV-2 nucleocapsid (Polyclonal), ACE2 (EPR4435(2)), CD14 (EPR3653) and CD68 (PG-M1) (Table 1), followed by appropriate secondary antibodies and Opal fluorophore-conjugated tyramide signal amplification (Akoya Bioscience, USA).	ACE2 suggested: None CD14 suggested: (LSBio (LifeSpan Cat# LS-C105589, RRID:AB_2275679) CD68 suggested: None PG-M1 ) ( Table 1 suggested: None
   Next, cells were surface stained with antibody cocktail containing Pacific Orange-anti CD45 (HI30), BV605-anti CD103 (Ber-ACT8), BV750-anti CD4 (SK3), Alexa 532-anti CD3 (UCHT1), PerCP-eFluor 710-anti CD38 (HB7) and PE-CF594-anti CD39 (TU66) (Table 1) in Brilliant Stain Buffer (BD Biosciences, USA), followed by incubation for 30 min at 4°C in the dark.	CD45 suggested: (RayBiotech Cat# CS-11-0123, RRID:AB_1228026) HI30 suggested: None BV605-anti CD103 suggested: None Ber-ACT8 suggested: None BV750-anti CD4 suggested: None CD3 suggested: None UCHT1 suggested: None CD38 suggested: None PE-CF594-anti suggested: None CD39 suggested: None TU66 suggested: None
   Software and Algorithms
   Sentences	Resources
   Data analysis was performed using FlowJo V.10 software (FlowJo LLC, USA).	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: 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 10.1101/2020.10.28.20219014v1 on medRxiv

   Nov 3, 2020