Immunogenicity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and Ad26.CoV2.S Vaccination in People Living With Human Immunodeficiency Virus (HIV)

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1. Version published to 10.1093/cid/ciab1008

   Dec 10, 2021
2. 

   ScreenIT

   Oct 13, 2021

   SciScore for 10.1101/2021.10.08.21264519: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: These participants are enrolled in a prospective cohort study approved by the Biomedical Research Ethics Committee at the University of KwaZulu–Natal (reference BREC/00001275/2020).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: Cell lines have not been authenticated. Contamination: The cell lines have been tested for mycoplasma contamination and are mycoplasma negative.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   For experiments, plasma was serially diluted and the the GenScript A02051 anti-spike monoclonal antibody was added as a positive control to one column of wells.	anti-spike

   SciScore for 10.1101/2021.10.08.21264519: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: These participants are enrolled in a prospective cohort study approved by the Biomedical Research Ethics Committee at the University of KwaZulu–Natal (reference BREC/00001275/2020).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: Cell lines have not been authenticated. Contamination: The cell lines have been tested for mycoplasma contamination and are mycoplasma negative.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   For experiments, plasma was serially diluted and the the GenScript A02051 anti-spike monoclonal antibody was added as a positive control to one column of wells.	anti-spike suggested: None
   Secondary goat anti-rabbit horseradish peroxidase (Abcam ab205718) antibody was added at 1 μg/mL and incubated for 2 h at room temperature with shaking.	anti-rabbit suggested: (Abcam Cat# ab205718, RRID:AB_2819160)
   Multi-epitope protein microarray: ImmuSAFE COVID-19 Array slides (Sengenics Corporation, Singapore) were used to measure the anti-SARS CoV-2 IgG and IgA antibodies against N and S proteins.	anti-SARS CoV-2 IgG suggested: None
   Arrays were then incubated simultaneously with two detection antibodies: AF647 anti-human IgG and AF555 anti-human IgA (ThermoFisher; 1.25µg/ml each in 3ml assay buffer) for 30 min at RT with gentle agitation and dried by centrifugation at 1200× g for 2 min.	anti-human IgG suggested: None anti-human IgA suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   H1299 cells were passaged every second day.	H1299 suggested: NCI-DTP Cat# NCI-H1299, RRID:CVCL_0060)
   ACE2-expressing H1299-E3 cells were seeded at 1.5 × 105 cells per mL and incubated for 18–20 h.	H1299-E3 suggested: None
   The viral supernatant (P2 stock) was aliquoted and stored at −80 °C and further passaged in Vero E6 cells to obtain the P3 stock used in experiments as follows: a T25 flask (Corning) was seeded with Vero E6 cells at 2 × 105 cells per mL and incubated for 18–20 h.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   For microscopy images, automated image analysis was performed using a custom script in MATLAB v.	MATLAB suggested: (MATLAB, RRID:SCR_001622)
   Arrays were then incubated simultaneously with two detection antibodies: AF647 anti-human IgG and AF555 anti-human IgA (ThermoFisher; 1.25µg/ml each in 3ml assay buffer) for 30 min at RT with gentle agitation and dried by centrifugation at 1200× g for 2 min.	ThermoFisher suggested: (ThermoFisher; SL 8; Centrifuge, RRID:SCR_020809)

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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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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
3. 

   Version published to 10.1101/2021.10.08.21264519v1 on medRxiv

   Oct 10, 2021