Serological responses to human virome define clinical outcomes of Italian patients infected with SARS-CoV-2

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1. Version published to 10.7150/ijbs.78002

   Jan 1, 2022
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.09.04.20187088: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After overnight incubation, the blocking buffer was aspirated and sera samples containing 2 µg of total IgG were mixed with 2×1010 pfu T7 library in 1mL dilution buffer (20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 6 mM MgSO4) supplemented with 50 µg/mL chloramphenicol and 50µg/mL kanamycin into the deep well plate, and rotated at 4°C for 20 hours for the phage to form complex with the antibodies from sera.	total IgG suggested: None
   Software and Algorithms
   Sentences	Resources
   The fastq files were mapped to the virome library sequence with Bowtie.	Bowtie suggested: (Bowtie, RRID:SCR_005476)
   Sequence alignment: …

   SciScore for 10.1101/2020.09.04.20187088: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After overnight incubation, the blocking buffer was aspirated and sera samples containing 2 µg of total IgG were mixed with 2×1010 pfu T7 library in 1mL dilution buffer (20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 6 mM MgSO4) supplemented with 50 µg/mL chloramphenicol and 50µg/mL kanamycin into the deep well plate, and rotated at 4°C for 20 hours for the phage to form complex with the antibodies from sera.	total IgG suggested: None
   Software and Algorithms
   Sentences	Resources
   The fastq files were mapped to the virome library sequence with Bowtie.	Bowtie suggested: (Bowtie, RRID:SCR_005476)
   Sequence alignment: Protein sequences of SARS-CoV and SARS-CoV-2 are aligned with the EBI Clustal Omega Multiple Sequence Alignment tool (https://www.ebi.ac.uk/Tools/msa/clustalo/) and NCBI BLASTP tool (https://blast.ncbi.nlm.nih.gov/).	https://www.ebi.ac.uk/Tools/msa/clustalo/ suggested: (Clustal Omega, RRID:SCR_001591) BLASTP suggested: (BLASTP, RRID:SCR_001010)
   Since ROSE package is very good at dealing with binary dataset, we used the epitope binding score VirScan data of moderate and critical groups.	ROSE suggested: (ROSE, RRID:SCR_017390)
   The survival risk prediction tool of the BRB-ArrayTools Stable Version 4.6.1 was used for survival analysis.	BRB-ArrayTools suggested: (BRB-ArrayTools, RRID:SCR_010938)
   Additional Statistical Methods: All other analysis was performed with GraphPad Prism 8 or R 3.6.3.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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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:

   The main limitation of this study is the inclusion of only 156 COVID-19 patients without asymptomatic individuals or patients with mild symptoms infected with SARS-CoV-2. While we observed a consistent and clear elevation of individual’s immune memory antibody repertoires linked to trajectories of disease severity over time, there remains a substantial heterogeneity within each patient group, which will require expanding our analysis in the future to larger cohorts with increased time resolution in order to gain a deeper understanding of the complex interplay between host immunity and SARS-CoV-2 infection.

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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.
   • Thank you for including a protocol registration statement.

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3. 

   Version published to 10.1101/2020.09.04.20187088v1 on medRxiv

   Sep 7, 2020