Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway

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   ScreenIT

   Nov 19, 2021

   SciScore for 10.1101/2021.10.23.465542: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Rhesus Macaque Model, Immunizations, and Delta Challenge: All experiments conducted according to NIH regulations and standards on the humane care and use of laboratory animals as well as the Animal Care and Use Committees of the NIH Vaccine Research Center and Bioqual, Inc. (Rockville, Maryland).
   Sex as a biological variable	6-week-old male Syrian hamsters (Envigo) were housed at Bioqual, Inc.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Total IgG and IgA antigen-specific antibodies to variant SARS-CoV-2 RBD-derived antigens were determined by enzyme-linked immunosorbent assay …

   SciScore for 10.1101/2021.10.23.465542: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Rhesus Macaque Model, Immunizations, and Delta Challenge: All experiments conducted according to NIH regulations and standards on the humane care and use of laboratory animals as well as the Animal Care and Use Committees of the NIH Vaccine Research Center and Bioqual, Inc. (Rockville, Maryland).
   Sex as a biological variable	6-week-old male Syrian hamsters (Envigo) were housed at Bioqual, Inc.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Total IgG and IgA antigen-specific antibodies to variant SARS-CoV-2 RBD-derived antigens were determined by enzyme-linked immunosorbent assay (ELISA) using MULTI-ARRAY 384-well streptavidin-coated plates (Meso Scale Discovery, MSD).	IgA suggested: None
   Total IgG antibody titers in the BAL were quantitated by using the Human/NHP IgG Kit (MSD) and antibody titers to measles were quantitated by using the Monkey Anti-Measles IgG ELISA Kit (Alpha Diagnostics International) according to the manufacturer’s instructions.	Total IgG suggested: None Anti-Measles IgG suggested: None
   Cells were incubated with an anti-SARS-CoV S primary antibody directly conjugated to biotin (CR3022-biotin) for 1 hour at room temperature.	anti-SARS-CoV S suggested: None CR3022-biotin suggested: None
   Briefly, anti-histidine antibody was immobilized on Series S Sensor Chip CM5 (Cytiva) through primary amine coupling using a His capture kit (Cytiva), allowing His-tagged SARS-CoV-2 S protein containing 2 proline stabilization mutations (S-2P) to be captured on active sensor surface.	anti-histidine suggested: None
   The following antibodies were used (monoclonal unless indicated): IgD FITC (goat polyclonal, Southern Biotech), IgM PerCP-Cy5.5 (clone G20-127, BD Biosciences), IgA Dylight 405 (goat polyclonal, Jackson Immunoresearch Inc), CD20 BV570 (clone 2H7, Biolegend), CD27 BV650 (clone O323, Biolegend), CD14 BV785 (clone M5E2, Biolegend), CD16 BUV496 (clone 3G8, BD Biosciences), IgG Alexa 700 (clone G18-145, BD Biosciences), CD3 APC-Cy7 (clone SP34.2, BD Biosciences), CD38 PE (clone OKT10, Caprico Biotechnologies), CD21 PE-Cy5 (clone B-ly4, BD Biosciences), and CXCR5 PE-Cy7 (clone MU5UBEE, Thermo Fisher Scientific).	CD20 suggested: (BioLegend Cat# 348805, RRID:AB_2889063) CD27 suggested: (BioLegend Cat# 124241, RRID:AB_2800595) CD14 suggested: (BD Biosciences Cat# 750381, RRID:AB_2874552) CD16 suggested: (BD Biosciences Cat# 564653, RRID:AB_2744294) CD21 suggested: None CXCR5 suggested: None
   The following monoclonal antibodies were used: CD3 APC-Cy7 (clone SP34.2, BD Biosciences), CD4 PE-Cy5.5 (clone S3.5, Invitrogen), CD8 BV570 (clone RPA-T8, BioLegend), CD45RA PE-Cy5 (clone 5H9, BD Biosciences), CCR7 BV650 (clone G043H7, BioLegend), CXCR5 PE (clone MU5UBEE, Thermo Fisher), CXCR3 BV711 (clone 1C6/CXCR3, BD Biosciences), PD-1 BUV737 (clone EH12.1, BD Biosciences), ICOS Pe-Cy7 (clone C398.4A, BioLegend), CD69 ECD (cloneTP1.55.3, Beckman Coulter), IFN-g Ax700 (clone B27, BioLegend), IL-2 BV750 (clone MQ1-17H12, BD Biosciences), IL-4 BB700 (clone MP4-25D2, BD Biosciences), TNF-FITC (clone Mab11, BD Biosciences), IL-13 BV421 (clone JES10-5A2, BD Biosciences), IL-17 BV605 (clone BL168, BioLegend), IL-21 Ax647 (clone 3A3-N2.1, BD Biosciences), and CD154 BV785 (clone 24-31, BioLegend).	CD4 suggested: (Thermo Fisher Scientific Cat# 8822-6853-41, RRID:AB_2575278) CCR7 suggested: (GenWay Biotech Inc. Cat# GWB-EA1DA7, RRID:AB_10269678) CXCR3 suggested: (BD Biosciences Cat# 741866, RRID:AB_2871195) PD-1 BUV737 suggested: (BD Biosciences Cat# 565299, RRID:AB_2739167) CD69 suggested: (BD Biosciences Cat# 747520, RRID:AB_2744097) IL-2 suggested: (BioLegend Cat# 500347, RRID:AB_2566470) IL-4 suggested: (BD Biosciences Cat# 745925, RRID:AB_2871637) IL-13 BV421 suggested: (BioLegend Cat# 501916, RRID:AB_2616748) IL-17 suggested: (BioLegend Cat# 512326, RRID:AB_2563887) CD154 suggested: (BioLegend Cat# 310842, RRID:AB_2572187)
   A rabbit polyclonal anti-SARS-CoV-2 antibody (GeneTex, GTX135357) at a dilution of 1:2000 was used for IHC.	anti-SARS-CoV-2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells and Viruses: VeroE6 cells were obtained from ATCC (clone E6, ATCC, #CRL-1586) and cultured in complete DMEM medium consisting of 1x DMEM (VWR, #45000-304), 10% FBS, 25mM HEPES Buffer (Corning Cellgro), 2mM L-glutamine, 1mM sodium pyruvate, 1x Non-essential Amino Acids, and 1x antibiotics.	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   VeroE6-TMPRSS2 cells were generated at Vaccine Research Center, NIH, Bethesda, MD.	VeroE6-TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   The antibody-virus mixture was then added to Vero cells and incubated at 37°C for 1 hour.	Vero suggested: None
   Briefly, HEK293T/17 cells (ATCC CRL-11268) were transfected with the following: plasmids encoding S proteins from Wuhan-Hu-1 strain (GenBank no. MN908947.3) with a p.Asp614Gly mutation, a luciferase reporter, lentivirus backbone, and the human transmembrane protease serine 2 (TMPRSS2) genes.	HEK293T/17 suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
   TCID50 Assay: Vero-TMPRSS2 cells (obtained from Adrian Creanga, Vaccine Research Center-NIAID) were plated at 25,000 cells/well in DMEM with 10% FBS and gentamicin, and the cultures were incubated at 37°C, 5.0% CO2.	Vero-TMPRSS2 suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
   Software and Algorithms
   Sentences	Resources
   IC50 titers were calculated using a log(agonist) versus normalized-response (variable slope) nonlinear regression model in Prism v9.0.2 (GraphPad).	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   The following antibodies were used (monoclonal unless indicated): IgD FITC (goat polyclonal, Southern Biotech), IgM PerCP-Cy5.5 (clone G20-127, BD Biosciences), IgA Dylight 405 (goat polyclonal, Jackson Immunoresearch Inc), CD20 BV570 (clone 2H7, Biolegend), CD27 BV650 (clone O323, Biolegend), CD14 BV785 (clone M5E2, Biolegend), CD16 BUV496 (clone 3G8, BD Biosciences), IgG Alexa 700 (clone G18-145, BD Biosciences), CD3 APC-Cy7 (clone SP34.2, BD Biosciences), CD38 PE (clone OKT10, Caprico Biotechnologies), CD21 PE-Cy5 (clone B-ly4, BD Biosciences), and CXCR5 PE-Cy7 (clone MU5UBEE, Thermo Fisher Scientific).	BD Biosciences suggested: (BD Biosciences, RRID:SCR_013311)
   Samples were acquired on an BD FACSymphony cytometer and analyzed using FlowJo version 10.7.2 (BD, Ashland, OR).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   All analyses are conducted using R version 4.0.2 and GraphPad Prism version 8.2.0 unless otherwise specified.	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:

   A potential limitation relates to the extent of viral replication following B.1.617.2 challenge. The challenge stock used here was passaged once and fully matched the canonical B.1.617.2 S sequences obtained from humans. However, we did not observe greater sgRNA copy numbers in the upper airway than in previous challenges with B.1.351 or WA1 (Corbett et al., 2021b; Corbett et al., 2021c). Clinical reports have described substantially higher viral titers in the upper respiratory tract from B.1.617.2 infections compared to ancestral strains (Ong et al., 2021; Williams et al., 2021). It is possible that the NHP model does not precisely recapitulate human infection. We and others have previously shown that antibodies are a correlate of protection (Corbett et al., 2021b; Gilbert et al., 2021). These studies are based on a short interval between vaccination and virus exposure or challenge. Here, we did not find a clear immune correlate of protection between binding or neutralizing antibody responses in the blood at the peak of the response or the time of challenge one year later. Additional analysis from human clinical trials with much larger numbers of vaccinated individuals than the 8 NHP in this study will be important for determining whether serum antibody titers remain as a correlate of protection in the long term. Indeed, the data presented here raise the possibility that the correlate of protection may lie in the ability of tissue-resident memory B cells to expand after infe...

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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 10.1101/2021.10.23.465542 on bioRxiv

   Oct 24, 2021