Characterization of immune responses in fully vaccinated individuals after breakthrough infection with the SARS-CoV-2 delta variant

Article activity feed

1. Version published to 10.1126/scitranslmed.abn6150

   Apr 20, 2022
2. 

   ScreenIT

   Oct 23, 2021

   SciScore for 10.1101/2021.10.18.21265113: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: Participants were provided contact information for the Beth Israel Deaconess Medical Center (BIDMC) study team for recruitment and informed consent. IRB: The BIDMC Institutional Review Board approved this study (#2021P000344) as part of a parent biorepository study (#2020P000361).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The plates were again washed 3 times and 50 μL of SULFO-Tagged anti-Human IgG detection antibody diluted to 1x in Diluent 100 was added to each well and incubated shaking at 700 rpm at room temperature for at …

   SciScore for 10.1101/2021.10.18.21265113: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: Participants were provided contact information for the Beth Israel Deaconess Medical Center (BIDMC) study team for recruitment and informed consent. IRB: The BIDMC Institutional Review Board approved this study (#2021P000344) as part of a parent biorepository study (#2020P000361).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The plates were again washed 3 times and 50 μL of SULFO-Tagged anti-Human IgG detection antibody diluted to 1x in Diluent 100 was added to each well and incubated shaking at 700 rpm at room temperature for at least 1 h.	anti-Human IgG suggested: (RevMAb Biosciences Cat# 31-1019-MK, RRID:AB_2783627)
   Intracellular cytokine staining (ICS) assay: 106 peripheral blood mononuclear cells well were re-suspended in 100 µL of R10 media supplemented with CD49d monoclonal antibody (1 µg/mL) and CD28 monoclonal antibody (1 µg/mL) as described previously.	CD49d suggested: (BD Biosciences Cat# 347690, RRID:AB_647457) CD28 suggested: None
   The next day, the cells were washed twice with DPBS, stained with aqua live/dead dye for 10 mins and then stained with predetermined titers of monoclonal antibodies against CD279 (clone EH12.1, BB700), CD4 (clone L200, BV711),	CD279 suggested: (BD Biosciences Cat# 746185, RRID:AB_2743534) CD4 suggested: None BV711 suggested: None
   Cells were washed twice with 1X Perm Wash buffer (BD Perm/WashTM Buffer 10X in the CytoFix/CytoPerm Fixation/ Permeabilization kit diluted with MilliQ water and passed through 0.22µm filter) and stained with intracellularly with monoclonal antibodies against IFN-γ (clone B27; BUV395), and CD3 (clone SP34.2, Alexa 700), for 30 min.	IFN-γ suggested: (BD Biosciences Cat# 563563, RRID:AB_2738277) CD3 suggested: (BD Biosciences Cat# 556610, RRID:AB_396483)
   Enzyme-linked immunospot (ELISPOT) assay: ELISPOT plates were coated with mouse anti-human IFN-γ monoclonal antibody from MabTech at 1 µg/well and incubated overnight at 4°C.	anti-human IFN-γ suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene) and spike protein expressing pcDNA3.1-SARS-CoV-2 SΔCT were co-transfected into HEK293T cells (ATCC CRL_3216) with lipofectamine 2000 (ThermoFisher Scientific).	HEK293T suggested: ATCC Cat# CRL-3216, RRID:CVCL_0063)
   The mixture was incubated at 37 °C for 1 h before adding to HEK293T-hACE2 cells.	HEK293T-hACE2 suggested: RRID:CVCL_A7UK)
   Recombinant DNA
   Sentences	Resources
   Pseudovirus neutralizing antibody assay: The SARS-CoV-2 pseudoviruses expressing a luciferase reporter gene were used to measure pseudovirus neutralizing antibodies as described previously.5,6 In brief, the packaging construct psPAX2 (AIDS Resource and Reagent Program)	psPAX2 suggested: RRID:Addgene_12260)
   luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene) and spike protein expressing pcDNA3.1-SARS-CoV-2 SΔCT were co-transfected into HEK293T cells (ATCC CRL_3216) with lipofectamine 2000 (ThermoFisher Scientific).	pLenti-CMV Puro-Luc suggested: None pcDNA3.1-SARS-CoV-2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Pseudovirus neutralizing antibody assay: The SARS-CoV-2 pseudoviruses expressing a luciferase reporter gene were used to measure pseudovirus neutralizing antibodies as described previously.5,6 In brief, the packaging construct psPAX2 (AIDS Resource and Reagent Program)	AIDS Resource and Reagent Program suggested: None
   Fixed cells were transferred to 96-well round bottom plate and analyzed by BD FACSymphony™ system.	BD FACSymphony™ suggested: None
   Data were analyzed using FlowJo v9.9	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Statistical analysis: Descriptive statistics were calculated using GraphPad Prism 8.4.3, (	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   (GraphPad Software, San Diego, California).	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: We detected the following sentences addressing limitations in the study:

   One limitation of this study is the relatively small number of individuals in this immunologic analysis compared with the large total number of individuals in this outbreak. Nevertheless, the magnitude and consistency of the immunologic differences observed between vaccinated infected and vaccinated uninfected individuals suggest the generalizability of the conclusions. Another limitation is the fact that the vaccinated infected group was generally younger than the vaccinated uninfected group, which may reflect different risk behaviors or exposures based on age. However, age did not appear to correlate with the magnitude of binding or neutralizing antibody titers in this cohort (Fig. S2). In conclusion, we describe humoral and cellular immune responses in the first large, well described cluster of breakthrough infections with the SARS-CoV-2 delta variant in fully vaccinated individuals in the United States. Breakthrough infection led to a large increase in antibody and T cell responses in vaccinated individuals, suggesting important immunologic benefits of vaccination even when infection was not prevented. Moreover, anamnestic antibody responses in breakthrough infections were similar in magnitude regardless of the length of time from vaccination (Fig. S3), suggesting the possibility of protection against severe disease for a prolonged period of time even after serum antibody titers decline. These data provide unique insights into the immunology of breakthrough infections wit...

   ---

   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: We did not find any issues relating to colormaps.

   ---

   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.

   ---

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

   ---

   Read the original source
3. 

   Version published to 10.1101/2021.10.18.21265113 on medRxiv

   Oct 20, 2021