Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia

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1. Version published to 10.1038/s41564-022-01135-7

   May 30, 2022
2. 

   Version published to 10.21203/rs.3.rs-1210846/v1 on Research Square

   Jan 13, 2022
3. 

   ScreenIT

   Dec 18, 2021

   SciScore for 10.1101/2021.12.14.21267772: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All human serum samples were obtained with written informed consent from the participants (2020/ETH00964; 2020/ETH02068).
   Sex as a biological variable	not detected.
   Randomization	The parameters of a logistic function representing the (log10) normalised neutralisation titre parameters σ = 0.46 (representing the spread of neutralisation titres in vaccinated individuals), x50 = log10 0.20 and k = 3.1 were estimated previously by fitting vaccine efficacy data from randomised control trials across 7 SARS-CoV-2 vaccines4.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Other immunoglobulin …

   SciScore for 10.1101/2021.12.14.21267772: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All human serum samples were obtained with written informed consent from the participants (2020/ETH00964; 2020/ETH02068).
   Sex as a biological variable	not detected.
   Randomization	The parameters of a logistic function representing the (log10) normalised neutralisation titre parameters σ = 0.46 (representing the spread of neutralisation titres in vaccinated individuals), x50 = log10 0.20 and k = 3.1 were estimated previously by fitting vaccine efficacy data from randomised control trials across 7 SARS-CoV-2 vaccines4.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Other immunoglobulin products: For monoclonal antibodies, DNA sequences encoding the variable domain sequences of the therapeutic monoclonal antibodies sotrovimab, casirivimab, imdevimab, bamlanivimab, cilgavimab and tixagevimab were generated by gene synthesis, cloned into human IgG1 expression vectors, and produced in CHO cells 7.	CHO suggested: CLS Cat# 603479/p746_CHO, RRID:CVCL_0213)
   Cell culture: Hek293T cells stably expressing human ACE2 and TMPRSS2 were generated by lentiviral transductions as previously described 10.	Hek293T suggested: None
   HAT-24 cells and VeroE6-TMPRSS2 (CellBank Australia, JCRB1819) were cultured in DMEM-10%FBS and VeroE6 cells (ATCC® CRL-1586™) in MEM-10%FBS.	HAT-24 suggested: None VeroE6 suggested: None
   The supernatant was cleared by centrifugation (2000 xg for 5 minutes), frozen at -80 °C (passage 2), then thawed and titrated to determine median tissue culture infective dose (TCID50) on VeroE6 or VeroE6-TMPRSS2 cells according to the Spearman-Karber method 14.	VeroE6-TMPRSS2 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   For the latter Omicron was expanded only in the VeroE6 line, as lower titers were observed when expanding virus using the VeroE6-TMPRSS2 line.	VeroE6-TMPRSS2 suggested: None
   Software and Algorithms
   Sentences	Resources
   The Adapting to Pandemic Threats (ADAPT) cohort is composed of RT-PCR–confirmed convalescent individuals (incl. some subsequently vaccinated) recruited in Australia since 2020 10.	ADAPT suggested: (ADAPT, RRID:SCR_006769)
   Data was normalised to generate sigmoidal dose-response curves (average counts for mock-infected controls = 100%, and average counts for highest viral concentration = 0%) and median lethal dose (LD50) values were obtained with GraphPad Prism software.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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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4. 

   Version published to 10.1101/2021.12.14.21267772 on medRxiv

   Dec 15, 2021