Multifactorial seroprofiling dissects the contribution of pre-existing human coronaviruses responses to SARS-CoV-2 immunity

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1. Version published to 10.1038/s41467-021-27040-x

   Nov 18, 2021
2. 

   ScreenIT

   Apr 24, 2021

   SciScore for 10.1101/2021.04.21.21255410: (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
   In the final protocol, five million anti-His antibody coupled magnetic beads were incubated with His-tagged antigens diluted in PBS at a concentration of 320 nM.	anti-His suggested: None
   Phycoerythrin (PE)-labeled secondary antibodies specific to IgG, IgA or IgM were used as detector antibodies (Supplementary Table 13).	Phycoerythrin (PE)-labeled suggested: None secondary antibodies specific to IgG, IgA or IgM suggested: None
   50 µl diluted plasma were incubated with 50 µl of the ABCORA antigen bead cocktail for 30 minutes at room temperature in 96-well plates, washed three times with PBS-BSA 1% and …

   SciScore for 10.1101/2021.04.21.21255410: (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
   In the final protocol, five million anti-His antibody coupled magnetic beads were incubated with His-tagged antigens diluted in PBS at a concentration of 320 nM.	anti-His suggested: None
   Phycoerythrin (PE)-labeled secondary antibodies specific to IgG, IgA or IgM were used as detector antibodies (Supplementary Table 13).	Phycoerythrin (PE)-labeled suggested: None secondary antibodies specific to IgG, IgA or IgM suggested: None
   50 µl diluted plasma were incubated with 50 µl of the ABCORA antigen bead cocktail for 30 minutes at room temperature in 96-well plates, washed three times with PBS-BSA 1% and incubated in separate reactions with phycoerythrin (PE)-labeled detector antibodies for IgG, IgA or IgM at a final concentration of 1/500 in PBS-BSA 1%.	phycoerythrin (PE)-labeled detector antibodies for IgG suggested: None
   Antibody status of plasma from SARS-CoV-2 positive individuals (N=171) were analyzed with the following test systems: Included test systems targeted the N protein (Elecsys® Anti-SARS-CoV-2 (Roche Diagnostics GmbH)), the RBD region of the S protein (Elecsys® Anti-SARS-CoV-2 S assay (Roche Diagnostics GmbH)), and the S1 subunit (EUROIMMUN Anti-SARS-CoV-2 ELISA (IgG)) (Supplementary Table 7).	Anti-SARS-CoV-2 suggested: None Anti-SARS-CoV-2 ELISA (IgG) suggested: None
   The first was based on the S1/RBD specific antibody CR3022 (37 and Supplementary Table 13).	S1/RBD suggested: None
   We used this approach to quantify the concentration of RBD and S1 antibody reactivity in the positive donor control, and used titrations of the donor pool included on each ABCORA plate to calculate the S1 and RBD content of plasma samples in relation to it.	S1 suggested: None
   Association between HCoVs and SARS-CoV-2 reactivities: To explore the association between HCoVs and SARS-CoV-2 reactivities, we defined a new HCoV response variable (HCoV high/low) for each antibody class (IgG, IgA, IgM) as follows: a patient had high HCoV Ig reactivity for a given antibody class if its measurements were higher than the population median in at least three out of the four HCoV measurements (HKU1, OC43, NL63, 229E).	antibody class (IgG suggested: None IgA, IgM suggested: None NL63 suggested: (Virostat Cat# 3879, RRID:AB_2889994)
   Experimental Models: Cell Lines
   Sentences	Resources
   293-T cells were obtained from the American Type Culture Collection (ATCC CRL-11268) 61.	293-T suggested: None
   HT1080/ACE2cl.14 cells 32 were kindly provided by P. Bieniasz, Rockefeller University, NY.	HT1080/ACE2cl.14 suggested: None
   ABCORA 2.0 included in addition S1 of HCoV-HKU1, ABCORA 5.0 included S1 of all circulating HCoVs (HCoV-NL63, HCoV-229E, HCoV-HKU1, HCoV-OC43).	HCoV-NL63 suggested: RRID:CVCL_RW88)
   Recombinant DNA
   Sentences	Resources
   The env-inactivated HIV-1 reporter construct pHIV-1NL4-3 ΔEnv-NanoLuc (pHIV-1Nanoluc) and HT1080/ACE2cl.14 cells were kindly provided by P. Bieniasz, Rockefeller University, NY, USA.	pHIV-1NL4-3 suggested: None
   To create a SARS-CoV-2 spike expression plasmid (P_CoV2_Wuhan), a codon-optimized C terminal truncated (AA 1255-1273) spike encoding gene of strain Wuhan-Hu-1 (GenBank accession no. MN908947) was synthesized (GeneArt, Thermo Fisher Scientific, Waltham, MA) and cloned into pcDNA.3.1.	pcDNA.3.1 suggested: None
   Pseudotyped SARS-CoV-2 spike expressing viruses were generated by co-transfecting 293-T cells with a mixture of pHIV-1Nanoluc, P_CoV2_Wuhan and PEI Max (Polysciences Europe GmbH, Hirschberg, Germany).	pHIV-1Nanoluc suggested: None
   Software and Algorithms
   Sentences	Resources
   Plasma neutralization titers causing 50%, 80% and 90% reduction in viral infectivity (NT50, NT80 and NT90, respectively) compared to controls without plasma were calculated by fitting a sigmoid dose–response curve (variable slope) to the RLU data, using GraphPad Prism with constraints (bottom=0, top=100).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Figures were made using the ggplot2 package70.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)

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   Results from OddPub: Thank you for sharing your code and data.

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   As others and we have shown, SARS-CoV-2 and HCoV immunity to infection is often not long-lasting (Fig. 5, Supplementary Fig. 10) 5,60, a limitation that SARS-CoV-2 vaccines hope to overcome. Should SARS-CoV-2 responses in turn provide a degree of defense against HCoV infection, broad protection against coronaviruses may be in reach.

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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 10.1101/2021.04.21.21255410 on medRxiv

   Apr 21, 2021