Waning immune responses against SARS-CoV-2 among vaccinees in Hong Kong

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1. 

   ScreenIT

   Dec 30, 2021

   SciScore for 10.1101/2021.12.22.473934: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: This study was approved by the Institutional Review Board of the University of Hong Kong/Hospital Authority Hong Kong West Cluster (Ref No. UW 21-452). Consent: Written informed consent was obtained from all study subjects
   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 50% inhibitory concentrations (IC50) of each specimen were calculated using non-linear regression in GraphPad Prism v8 to reflect anti-SARS-CoV-2 antibody potency.	anti-SARS-CoV-2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Briefly, SARS-CoV-2 …

   SciScore for 10.1101/2021.12.22.473934: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: This study was approved by the Institutional Review Board of the University of Hong Kong/Hospital Authority Hong Kong West Cluster (Ref No. UW 21-452). Consent: Written informed consent was obtained from all study subjects
   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 50% inhibitory concentrations (IC50) of each specimen were calculated using non-linear regression in GraphPad Prism v8 to reflect anti-SARS-CoV-2 antibody potency.	anti-SARS-CoV-2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Briefly, SARS-CoV-2 pseudoviruses were generated by co-transfection of 293T cells with a pair of plasmids, the S-expression plasmid for wildtype or VOCs and the pNL4-3Luc_Env_Vpr plasmid in a human immunodeficiency virus type 1 backbone (15, 16).	293T suggested: None
   The plasma-virus mixtures were then added into pre-seeded HEK 293T-hACE2 cells.	HEK 293T-hACE2 suggested: None
   Recombinant DNA
   Sentences	Resources
   Briefly, SARS-CoV-2 pseudoviruses were generated by co-transfection of 293T cells with a pair of plasmids, the S-expression plasmid for wildtype or VOCs and the pNL4-3Luc_Env_Vpr plasmid in a human immunodeficiency virus type 1 backbone (15, 16).	pNL4-3Luc_Env_Vpr suggested: None
   Software and Algorithms
   Sentences	Resources
   Study subjects: Participants who completed two doses of SARS-CoV-2 vaccination (either BioNTech or Sinovac) before June 2021 were recruited for this study.	BioNTech suggested: None
   For intracellular staining, cells were fixed and permeabilized with BD Cytofix/Cytoperm (BD Biosciences) prior to staining with the mAbs against cytokines (PE anti-IFN-γ, AF488 anti-TNF-α and PE-Cy7 anti-IL-2) (Biolegend) with Perm/Wash buffer (BD Biosciences).	BD Cytofix/Cytoperm suggested: None
   Statistical analysis: Flow cytometric data were analysed using FlowJo 10.6.0.	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Statistical analysis was performed using the GraphPad Prism v8 Software.	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:

   This study has some limitations. Due to lack of a spreading epidemic in Hong Kong, we could not determine vaccine-mediated protective efficacy. The sample size of this study was relatively small and most of our subjects have not reached 6 months for follow-up testing. Extend the follow-up to 6 months and one year or longer is necessary for future study. While NAbs have been indicated as correlates of protection (23, 30), the protective role of vaccine-induced T cell responses remains to be further investigated. During acute SARS-CoV-2 infection, we and others demonstrated that antigen-specific T cell responses have likely been associated with viral control and limited pathogenesis(13) (38). In this study, while we consistently found antigen-specific CD4+T cells after vaccinations by both types of vaccines as previously reported by others (19, 39, 40), majority of our subjects did not show measurable RBD-specific CD4+ T cells. The difference between spike- and RBD-specific CD4 responses and why only spike-specific CD4 responses correlated to NAbTs but not to CD8+ T cells remain unclear. VOC spike-specific T cell responses were not explored due to limited cells received, although some studies indicated that the mutations in VOCs might modify single T cell specificities but could not fully escape the whole repertoire of spike-specific T cells (41, 42). Future studies are needed to address these 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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2. 

   Version published to 10.1101/2021.12.22.473934v1 on bioRxiv

   Dec 23, 2021