Increased aerosol transmission for B.1.1.7 (alpha variant) over lineage A variant of SARS-CoV-2

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   ScreenIT

   Aug 4, 2021

   SciScore for 10.1101/2021.07.26.453518: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Ethics Statement: All animal experiments were conducted in an AAALAC International-accredited facility and were approved by the Rocky Mountain Laboratories Institutional Care and Use Committee following the guidelines put forth in the Guide for the Care and Use of Laboratory Animals 8th edition, the Animal Welfare Act, United States Department of Agriculture and the United States Public Health Service Policy on the Humane Care and Use of Laboratory Animals.
   Sex as a biological variable	Inoculation experiments: Four to six-week-old female and male Syrian hamsters (ENVIGO) were inoculated (10 animals per virus) intranasally (I.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	no…

   SciScore for 10.1101/2021.07.26.453518: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Ethics Statement: All animal experiments were conducted in an AAALAC International-accredited facility and were approved by the Rocky Mountain Laboratories Institutional Care and Use Committee following the guidelines put forth in the Guide for the Care and Use of Laboratory Animals 8th edition, the Animal Welfare Act, United States Department of Agriculture and the United States Public Health Service Policy on the Humane Care and Use of Laboratory Animals.
   Sex as a biological variable	Inoculation experiments: Four to six-week-old female and male Syrian hamsters (ENVIGO) were inoculated (10 animals per virus) intranasally (I.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: At regular intervals mycoplasma testing was performed. Authentication: The airflow was adjusted for each tube length to be 30 cage changes/hour and the flow was validated prior to starting the experiments by timing a smoke plume through the tubes.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Secondary goat anti-hamster IgG Fc (horseradish peroxidase (HRP)-conjugated, Abcam) spike-specific antibodies were used for detection and visualized with KPL TMB 2-component peroxidase substrate kit (SeraCare, 5120-0047).	Secondary goat anti-hamster IgG Fc suggested: None anti-hamster IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Virus propagation was performed in VeroE6 cells in DMEM supplemented with 2% fetal bovine serum, 1 mM L-glutamine, 50 U/mL penicillin and 50 μg/mL streptomycin (DMEM2).	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Receptor transfection: BHK cells were seeded in black 96-well plates and transfected the next day with 100 ng plasmid DNA encoding human or hamster ACE2, using polyethylenimine (Polysciences).	BHK suggested: None
   Briefly, plates pre-coated with poly-L-lysine (Sigma–Aldrich) were seed with 293T cells and transfected the following day with 1,200 ng of empty plasmid and 400 ng of plasmid encoding coronavirus spike or no-spike plasmid control (green fluorescent protein (GFP)).	293T suggested: None
   Recombinant DNA
   Sentences	Resources
   Human and hamster ACE2 (Q9BYF1.2 and GQ262794.1, respectively), were synthesized and cloned into pcDNA3.1+ (GenScript).	pcDNA3.1+ suggested: RRID:Addgene_117272)
   BHK cells previously transfected with ACE2 plasmid of interest were inoculated with equivalent volumes of pseudotype stocks.	ACE2 suggested: RRID:Addgene_164219)
   Software and Algorithms
   Sentences	Resources
   Mutagenesis to model the residues that differ in the B.1.1.7 RBD and hamster ACE2 was performed in COOT 51.	COOT suggested: (Coot, RRID:SCR_014222)
   The structure figure was generated using the Pymol Molecular Graphics System (	Pymol suggested: (PyMOL, RRID:SCR_000305)
   Amino acid sequence alignments of human ACE2 (BAB40370.1) and hamster ACE2 (XP_005074266.1), and of SARS-CoV-2 RBD from the linage A strain and B.1.1.7 variant, were were generated using Clustal Omega (http://europepmc.org/article/MED/).	Clustal Omega suggested: (Clustal Omega, RRID:SCR_001591)
   Remaining reads were mapped to the SARS-CoV-2 2019-nCoV/USA-WA1/2020 (MN985325.1 using Bowtie2 version 2.2.928 with parameters --local --no-mixed-X 1500.	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   PCR duplicates were removed using picard MarkDuplicates (Broad Institute) and variants were called using GATK HaplotypeCaller version 4.1.2.029 with parameter-ploidy 2.	GATK suggested: (GATK, RRID:SCR_001876)

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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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   Version published to 10.1101/2021.07.26.453518 on bioRxiv

   Jul 26, 2021