Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein

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1. Version published to 10.1016/j.cell.2022.05.019

   Jun 1, 2022
2. 

   ScreenIT

   Nov 19, 2021

   SciScore for 10.1101/2021.10.25.465646: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Most of the human sera was collected from prospective bone marrow donors in Seattle with approval from the Human Subjects Institutional Review Board in the 1980s and were stored in the Infectious Disease Sciences Biospecimen Repository at the Vaccine and Infectious Disease Division of the Fred Hutch Cancer Center.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: None of the cell lines used were routinely tested for mycoplasma contamination

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After 2 h, virus inoculum was removed and cells were washed five times with DMEM prior addition of …

   SciScore for 10.1101/2021.10.25.465646: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Most of the human sera was collected from prospective bone marrow donors in Seattle with approval from the Human Subjects Institutional Review Board in the 1980s and were stored in the Infectious Disease Sciences Biospecimen Repository at the Vaccine and Infectious Disease Division of the Fred Hutch Cancer Center.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: None of the cell lines used were routinely tested for mycoplasma contamination

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After 2 h, virus inoculum was removed and cells were washed five times with DMEM prior addition of DMEM supplemented with anti-VSV-G antibody [Il-mouse hybridoma supernatant diluted 1 to 25 (v/v), from CRL-2700, ATCC] to minimize parental background.	anti-VSV-G suggested: None
   After 1 h, the fusion-peptide-specific S2S8 monoclonal antibody was added at 1:250 dilution and incubated ON at 4°C with agitation.	S2S8 suggested: None
   Next day, the membrane was washed three times with TBS-T and an Alexa Fluor 680-conjugated goat antihuman secondary antibody (1:50,000 dilution, Jackson ImmunoResearch, 109-625-098) was added and incubated during 1 h at room temperature.	antihuman suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: Cell lines used in this study were obtained from ATCC: Human cells epithelial embryo (HEK293T, CRL-3216), Felis catus (CRFK, CCL-94), Canis familiaris epithelial kidney cells (MDCK, CCL-34), Canis familiaris tumor fibroblast cells (A-72, CRL-1542) and Sus scrofa pig testis fibroblast cells (ST, CRL-1746) or ThermoFisher Scientific: ExpiCHO cells and Expi293F™ cells.	MDCK suggested: None
   Pseudotyped virus infections and neutralizations: For pseudotyped VSV infections and neutralizations, HEK293T cells were transfected with plasmids encoding for the different fulllength APN orthologs (flAPN) following the protocol described by (Eguia et al., 2021).	HEK293T suggested: None
   Recombinant DNA
   Sentences	Resources
   Plasmids: Genes used in this study were synthesized by GenScript, codon optimized for expression in mammalian cells, cloned into pcDNA3.1 (+) between KpnI and XhoI, in frame with a Kozak’s sequence to direct translation and with the signal peptide derived from the μ phosphatase: MGILPSPGMPALLSLVSLLSVLLMGCVAETGT (except for the full-length genes in which the original signal peptide was used).	pcDNA3.1 ( + ) suggested: None
   The 1AF10 Fab light and heavy sequences were obtained from Reguera et al., 2012 and cloned separately into pcDNA3.1.	pcDNA3.1 suggested: RRID:Addgene_79663)
   Software and Algorithms
   Sentences	Resources
   Cell lines: Cell lines used in this study were obtained from ATCC: Human cells epithelial embryo (HEK293T, CRL-3216), Felis catus (CRFK, CCL-94), Canis familiaris epithelial kidney cells (MDCK, CCL-34), Canis familiaris tumor fibroblast cells (A-72, CRL-1542) and Sus scrofa pig testis fibroblast cells (ST, CRL-1746) or ThermoFisher Scientific: ExpiCHO cells and Expi293F™ cells.	ThermoFisher Scientific suggested: None
   The introduction of the desired mutation R to T was verified by sequencing purified plasmids by GENEWIZ.	GENEWIZ suggested: (GENEWIZ, RRID:SCR_003177)
   Data were plotted in Graphpad Prism (v.9.0.2).	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Relative luciferase units were plotted and normalized in Prism (GraphPad): cells alone without pseudovirus was defined as 0 % infection, and cells with virus only (no sera) was defined as 100 % infection.	Prism suggested: (PRISM, RRID:SCR_005375)
   3D refinements were carried out using non-uniform refinement in cryoSPARC (Punjani et al., 2020).	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   CryoEM model building and analysis: UCSF Chimera (Pettersen et al., 2004) and Coot (Emsley et al., 2010) were used to fit atomic models (PDB 5SZS) into the cryoEM maps and Domain 0 was manually built.	Coot suggested: (Coot, RRID:SCR_014222)

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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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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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3. 

   Version published to 10.1101/2021.10.25.465646v1 on bioRxiv

   Oct 26, 2021