Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies

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   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.12.430472: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   IACUC: This study was approved by the ILE DE FRANCE IV ethical committee. Consent: At enrolment written informed consent was collected and participants completed a questionnaire which covered sociodemographic characteristics, virological findings (SARS-CoV-2 RT-PCR results including date of testing), clinical data (date of symptom onset, type of symptoms, hospitalization), and data related to anti-SARS-CoV-2 vaccination if ever (brand product, date of first and second vaccination).

   Randomization

   The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment Orléans Cohort of convalescent and …

   SciScore for 10.1101/2021.02.12.430472: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: This study was approved by the ILE DE FRANCE IV ethical committee. Consent: At enrolment written informed consent was collected and participants completed a questionnaire which covered sociodemographic characteristics, virological findings (SARS-CoV-2 RT-PCR results including date of testing), clinical data (date of symptom onset, type of symptoms, hospitalization), and data related to anti-SARS-CoV-2 vaccination if ever (brand product, date of first and second vaccination).
   Randomization	The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment Orléans Cohort of convalescent and vaccinated individuals: Orleans’ Cohort of convalescent and/or vaccinated individuals: since April 2020, a prospective, monocentric, longitudinal, cohort clinical study enrolling 170 SARS-CoV-2-infected individuals and 30 non-infected healthy controls is on-going, aiming to describe the persistence of specific and neutralizing antibodies over a 24-months period.
   Blinding	The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment Orléans Cohort of convalescent and vaccinated individuals: Orleans’ Cohort of convalescent and/or vaccinated individuals: since April 2020, a prospective, monocentric, longitudinal, cohort clinical study enrolling 170 SARS-CoV-2-infected individuals and 30 non-infected healthy controls is on-going, aiming to describe the persistence of specific and neutralizing antibodies over a 24-months period.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	Contamination: Cells were tested negative for mycoplasma.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The vaccine recipients were tested for anti-S antibodies at Hôpital Européen Georges Pompidou (Paris) with the following assays: Abbott SARS-CoV-2 IgG assays (Des Plaines, IL, USA) targeting SARS-CoV-2 nucleoprotein (N) were performed on Architect™ i2000SR analyzer (Abbott)	anti-S suggested: None
   Antibodies and ACE-2 ectodomain: Human anti-SARS-CoV2 monoclonal antibodies were cloned from S-specific blood memory B cells of Covid19 convalescents (Planchais et al, manuscript in preparation).	anti-SARS-CoV2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Titration of viral stocks was performed on Vero E6, with a limiting dilution technique allowing a calculation of TCID50, or on S-Fuse cells.	Vero E6 suggested: None
   Viruses were sequenced directly on nasal swabs, and after one or two passages on Vero cells.	Vero suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
   Briefly, HEK293T (referred as 293T) cells were acquired from ATCC (ATCC® CRL-3216™) and tested negative for mycoplasma.	HEK293T suggested: None
   293T Cells were transfected with the indicated Spike expression plasmids or a control plasmid using Lipofectamine 2000 (Life technologies).	293T suggested: None
   Human anti-S IgG mAbs and His-tagged recombinant ACE2 ectodomain (amino acids 19-615) cloned into pcDNA3.1 vector were produced by transient transfection of Freestyle™ 293-F cells and purified by affinity chromatography as previously described 37	293-F suggested: None
   Software and Algorithms
   Sentences	Resources
   Commercial serological assays: The serum samples from the Strasbourg cohort were first tested at Hôpital de Strasbourg using two commercial assays: 1) a CE-Marked LFA for detection of IgM and IgG against the SARS-CoV-2 RBD of the S protein developed by Biosynex® (	Biosynex® suggested: None
   The vaccine recipients were tested for anti-S antibodies at Hôpital Européen Georges Pompidou (Paris) with the following assays: Abbott SARS-CoV-2 IgG assays (Des Plaines, IL, USA) targeting SARS-CoV-2 nucleoprotein (N) were performed on Architect™ i2000SR analyzer (Abbott)	Abbott suggested: (Abbott, RRID:SCR_010477) Architect™ suggested: None
   Results were analysed with FlowJo 10.7.1 (Becton Dickinson).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Figures were drawn on Prism 9 (GraphPad Software).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Statistical analysis was conducted using GraphPad Prism 9.	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:

   Potential limitations of our study are the relatively low number of individuals analyzed and the short time frame of analysis after vaccination. Furthermore, we have not investigated the impact of pre-existing cellular immunity, which may be more cross-reactive against variants than the humoral response. Future work with more vaccine recipients that have or haven’t been previously infected, and longer periods of survey, will help characterizing the role of local and systemic humoral responses in vaccine efficacy. In conclusion, our results demonstrate that suboptimal or declining antibody responses are associated with a loss of cross-reactivity against novel emerging viral strains.

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04750720	Recruiting	Study of the Kinetics of COVID-19 Antibodies for 24 Months i…
   NCT04441684	Recruiting	Seroprevalence of SARS-CoV-2 in Strasbourg University Hospit…

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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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   Version published to 10.1101/2021.02.12.430472 on bioRxiv

   Feb 12, 2021