Distinct sensitivities to SARS-CoV-2 variants in vaccinated humans and mice

Version published to 10.1016/j.celrep.2022.111299

Aug 1, 2022

SciScore for 10.1101/2022.02.07.479468: (What is this?)

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

Table 1: Rigor

Ethics	IACUC: Animal procedures were performed under the approvals of the Institutional Animal Care and Use Committee (IACUC) of University of Washington, Seattle, WA. Euthanasia Agents: Mice were injected intramuscularly into the quadriceps muscle of each hind leg using a 27-gauge needle (BD, San Diego, CA) with 50 μL per injection site (100 μL total) of immunogen under isoflurane anesthesia. IRB: This study was approved by the University of Washington Human Subjects Division Institutional Review Board (STUDY00010350)
Sex as a biological variable	BALB/c mice for RBD-NP, S ‘2P’, and HexaPro immunizations: Female BALB/c mice (Stock # 000651, BALB/c cByJ mice) four weeks old were obtained from Jackson Laboratory, Bar Harbor, Maine, and maintained at the Comparative Medicine Facility at the University of Washington, Seattle, WA, accredited by the American Association for the Accreditation of Laboratory Animal Care International (AAALAC).
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
One day post-transfection, cells were infected with VSV(G*ΔG-luciferase)29 and after 2 h were washed five times with DMEM before adding medium supplemented with anti-VSV-G antibody (I1-mouse hybridoma supernatant, CRL-2700, ATCC)	anti-VSV-G suggested: (LSBio (LifeSpan Cat# LS-C51761-50, RRID:AB_1277784)
Experimental Models: Cell Lines
Sentences	Resources
Briefly, HEK293T cells in DMEM supplemented with 10% FBS, 1% PenStrep seeded in 10-cm dishes were transfected with the plasmid encoding for the corresponding S glycoprotein using lipofectamine 2000 (Life Technologies) following manufacturer’s indications.	HEK293T suggested: None
Pseudovirus Neutralization: HEK293-hACE2 cells15 or VeroE6-TMPRSS214 were cultured in DMEM with 10% FBS (Hyclone) and 1% PenStrep and 8ug/mL puromycin for TMPRSS2 maintenance with 5% CO2 in a 37°C incubator (ThermoFisher).	VeroE6-TMPRSS214 suggested: None
To generate VSVΔG-based SARS-CoV-2 pseudovirus, BHK-21/WI-2 cells were transfected with the spike expression plasmid and infected by VSVΔG-firefly-luciferase as previously described30.	BHK-21/WI-2 suggested: RRID:CVCL_HB78)
Lentivirus encoding hACE2-P2A-TMPRSS2 was made to generate A549-hACE2-TMPRSS2 cells which were maintained in DMEM supplemented with 10% fetal bovine serum and 1µg/mL puromycin.	A549-hACE2-TMPRSS2 suggested: RRID:CVCL_A5KB)
Both viruses were propagated on Vero-TMPRSS2 cells and subjected to deep sequencing to confirm the presence of expected substitutions.	Vero-TMPRSS2 suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
Immune complexes were added to VeroE6-TMPRSS2 cell monolayers and incubated for 1 h at 37°C prior to the addition of 1% (w/v) methylcellulose in MEM.	VeroE6-TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
Experimental Models: Organisms/Strains
Sentences	Resources
BALB/c mice for mRNA-1273 immunizations: Female BALB/c mice (6 to 8 weeks old) were obtained from Charles River Laboratories.	BALB/c suggested: None
1292S mice for mRNA-1273 immunizations: 129S2 mice (strain: 129S2/SvPasCrl, Cat # 287) were obtained from Charles River Laboratories and housed in a pathogen-free animal facility at Washington University in St. Louis.	129S2 suggested: RRID:IMSR_CRL:287) 129S2/SvPasCrl suggested: RRID:IMSR_CRL:287)
Recombinant DNA
Sentences	Resources
Plasmid construction: The SARS-CoV-2-RBD-Avi construct was synthesized by GenScript into pcDNA3.1-with an N-terminal mu-phosphatase signal peptide and a C-terminal octa-histidine tag, flexible linker, and avi tag (GHHHHHHHHGGSSGLNDIFEAQKIEWHE).	pcDNA3.1-with suggested: None
The SARS-CoV-2 S ‘2P’ ectodomain trimer (GenBank: YP_009724390.1, BEI NR-52420) was synthesized by GenScript into pCMV with an N-terminal mu-phosphatase signal peptide and a C-terminal TEV cleavage site (GSGRENLYPQG)	pCMV suggested: RRID:Addgene_16459)
The RBD-16GS-I53-50A fusion was cloned into pCMV/R using the Xba1 and AvrII restriction sites and Gibson assembly25.	pCMV/R suggested: None
Pseudovirus Neutralization Assay for BALB/c mRNA-1273 samples: Codon-optimized full-length spike genes (Wuhan-Hu-1 with G614, Beta, or Gamma) were cloned into pCAGGS vector.	pCAGGS suggested: RRID:Addgene_127347)
Software and Algorithms
Sentences	Resources
Animals were housed and maintained at the New Iberia Research Center (NIRC) of the University of Louisiana at Lafayette, an AAALAC International accredited institution, in accordance with the rules and regulations of the Guide for the Care and Use of Laboratory Animal Resources.	NIRC suggested: None
Relative luciferase units were plotted and normalized in Prism (GraphPad).	Prism suggested: (PRISM, RRID:SCR_005375)
Antibody-dose response curves were analyzed using non-linear regression analysis (with a variable slope) (GraphPad Software).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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).

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.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 10. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

Results from rtransparent:

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No protocol registration statement was detected.

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

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Distinct sensitivities to SARS-CoV-2 variants in vaccinated humans and mice

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