Early computational detection of potential high-risk SARS-CoV-2 variants
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SciScore for 10.1101/2021.12.24.474095: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources After incubation for 1 hour at 37 °C, the inoculum was removed, and cells were washed with PBS before medium supplemented with anti-VSV-G antibody (clone 8G5F11, Kerafast) was added to neutralise residual input virus. anti-VSV-Gsuggested: (Absolute Antibody Cat# Ab01401-2.0, RRID:AB_2883992)Carboxyl groups on the CM5 sensor chip matrix were activated with a mixture of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) to form active esters for the reaction with amine groups. anti-mouse-Fc-antibody (BR100838, Cytiva) was diluted in 10 mM sodium acetate … SciScore for 10.1101/2021.12.24.474095: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources After incubation for 1 hour at 37 °C, the inoculum was removed, and cells were washed with PBS before medium supplemented with anti-VSV-G antibody (clone 8G5F11, Kerafast) was added to neutralise residual input virus. anti-VSV-Gsuggested: (Absolute Antibody Cat# Ab01401-2.0, RRID:AB_2883992)Carboxyl groups on the CM5 sensor chip matrix were activated with a mixture of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) to form active esters for the reaction with amine groups. anti-mouse-Fc-antibody (BR100838, Cytiva) was diluted in 10 mM sodium acetate buffer pH 5 (30 μg/mL) for covalent coupling to immobilisation level of ~6,000 response units (RU). anti-mouse-Fc-antibody (BR100838suggested: NoneTo compute this score, we enumerate the number of unique epitopes involving altered positions, as measured across all the antibody-Spike complex structures deposited in Protein Data Bank. antibody-Spikesuggested: NoneThis allows to approximate the expected weight of mutations, and to ascribe importance to non-RBD mutations, if and only if sufficient escape potential with regard to RBD-targeting antibodies is achieved. RBD-targetingsuggested: NoneIt too changes with time with new discoveries of anti-Spike antibodies, but to a lesser extent and is expected to converge to a stable value. anti-Spikesuggested: NoneExperimental Models: Cell Lines Sentences Resources Serum dilutions were mixed 1:1 with pseudovirus for 30 minutes at room temperature prior to addition to Vero 76 cell monolayers and incubation at 37 °C for 24 hours. Vero 76suggested: NoneRecombinant DNA Sentences Resources In brief, HEK293T/17 monolayers transfected to express SARS-CoV-2 S with the C-terminal cytoplasmic 19 amino acids truncated (SARS-CoV-2-S[CΔ19]) were inoculated with the VSVΔG-GFP/Luc vector. VSVΔG-GFP/Lucsuggested: NoneResults from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:However, we would like to point out that a limitation for the calculation of the latter score for Omicron is the relatively small number of variants that have such a high number of mutations. The Early Warning System can sensitively detect HRVs months ahead of the official WHO designation, sometimes within the same week a sequenced variant enters the database. The only variant with delayed flagging by the EWS compared with WHO designation, the Delta variant, suffers from significant underrepresentation of the lineage in GISAID. This partial and delayed representation of the lineage in the database prevents even growth-based detection, emphasising the importance of extensive, robust, and timely sequencing of SARS-CoV-2 genomic samples globally. Combining comprehensive sequencing with structural modelling and AI can provide unprecedented insights into the COVID-19 pandemic which could be harnessed by public health authorities and governments worldwide to increase their preparedness to HRVs and potentially alleviate the associated human and economic costs. Future development of our approach could be extended to further functionalities such as assessment of known and predicted T cell epitopes, as well as the projection of prospective variant evolution scenarios.
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04380701 Recruiting A Trial Investigating the Safety and Effects of Four BNT162 … 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.
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