Reduced neutralization of SARS-CoV-2 B.1.617 variant by inactivated and RBD-subunit vaccine

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1. 

   ScreenIT

   Jul 12, 2021

   SciScore for 10.1101/2021.07.09.451732: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: The study was approved by the Ethics Commission of Chongqing Medical University (ref. no. 2020003). Consent: Written informed consent was waived by the Ethics Commission of the designated hospital for emerging infectious diseases.
   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
   Anti-RBD monoclonal antibodies (mAbs) against the SARS-CoV-2 Spike protein were obtained from the blood samples of COVID-19 convalescent patients as described previously.	Anti-RBD suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HEK 293T cells or A549 …

   SciScore for 10.1101/2021.07.09.451732: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: The study was approved by the Ethics Commission of Chongqing Medical University (ref. no. 2020003). Consent: Written informed consent was waived by the Ethics Commission of the designated hospital for emerging infectious diseases.
   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
   Anti-RBD monoclonal antibodies (mAbs) against the SARS-CoV-2 Spike protein were obtained from the blood samples of COVID-19 convalescent patients as described previously.	Anti-RBD suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HEK 293T cells or A549 cells transfected with human ACE2 (293T-ACE2 or A549-ACE2) were cultured under the same conditions with the addition of G418 (0.5 mg/mL) to the medium.	A549 suggested: None
   SARS-CoV-2 Spike-mediated pseudoviral entry assay: To detect Spike variant-mediated viral entry, 293T-ACE2 and A549-ACE2 cells (1.5× 104) grown on 96-well plates were infected with 50 μL pseudoviruses (1 × 104 copies).	A549-ACE2 suggested: None
   Briefly, plasmid pAdTrack-TO4-S, encoding SARS-CoV-2 Spike protein and enhanced green fluorescent protein (eGFP), was transfected into HEK 293T cells using Lipofectamine 3000 (Invitrogen).	HEK 293T suggested: None
   Pseudovirus-based neutralization assay: The 293T-ACE2 cells (1.5 × 104 cells/well) were seeded on 96-well plates.	293T-ACE2 suggested: RRID:CVCL_YZ65)
   Recombinant DNA
   Sentences	Resources
   D614G mutation was introduced using site-directed mutagenesis (denoted as pCMV3-S-D614G).	pCMV3-S-D614G suggested: None
   SARS-CoV-2 B.1.617 and B.1.1.7 variant Spikes were codon-optimized and synthesized by GenScript Inc (Nanjing, China) and cloned into pCMV3 vector.	pCMV3 suggested: RRID:Addgene_161029)
   Vpr luciferase reporter vector (pNL4-3.	pNL4-3 suggested: None
   Briefly, plasmid pAdTrack-TO4-S, encoding SARS-CoV-2 Spike protein and enhanced green fluorescent protein (eGFP), was transfected into HEK 293T cells using Lipofectamine 3000 (Invitrogen).	pAdTrack-TO4-S suggested: None
   In parallel, another group of HEK 293T cells was transfected with hACE2 expressing plasmids.	hACE2 suggested: RRID:Addgene_1786)
   Software and Algorithms
   Sentences	Resources
   Protein bands were visualized using SuperSignal West Pico Chemiluminescent Substrate kits (Bio-Rad, Hercules, CA, USA) and quantified by densitometry using ImageJ software (NCBI, Bethesda, MD, USA).	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   The titers of neutralizing antibodies were calculated as 50% inhibitory dose (ID50), the half-maximal inhibitory concentrations (IC50) of monoclonal antibodies (mAbs) against pseudoviruses was calculated using GraphPad Prism 8.0 software (GraphPad Software, San Diego, CA, USA).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Statistical analyses: Statistical analyses of the data were performed using GraphPad Prism version 8.0 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:

   The limitation of this study include its small sample size, only focus on pseudovirus-basded antibody neutralization in cell culture, and the possibility that mutations may alter neutralization by modulating Spike function rather than its antigenicity. To fully characterize the features of B.1.617 variant, in vivo study with authentic virus and the role of memory T or B cells in protection against this variant will be required. Conclusions about vaccine-mediated protection must be validated by real-world data collected in regions where B.1.617 variant is circulating. Collectively, this study will be helpful for understanding the increased spread of B.1.617 variant and highlight the need to in depth survey of this variant. Given the evolving nature of the SARS-CoV-2 RNA genome, new variant of concern will continue to arise, which may threaten vaccine efficacy. Therefore, antibody therapeutics and vaccine evaluations against new variants are worthy of further investigation.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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 10.1101/2021.07.09.451732v1 on bioRxiv

   Jul 9, 2021