Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction
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SciScore for 10.1101/2021.09.10.21262695: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All participants included in this study provided written informed consent. 2. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Additionally, S gene dropout samples with cycle threshold less than 30 (Ct < 30.0) were submitted to whole genome sequencing (WGS) using the Illumina MiSeq high-throughput. WGSsuggested: NoneLibrary preparation was conducted using QIAseq QIAseqsuggested: (QIAGEN GeneGlobe Data Analysis Center, RRID:SCR_021211)Fifty-nine Brazilian SARS-CoV-2 complete genomes and the reference sequence (EPI_ISL_402124) (>29 kb) were retrieved from the … SciScore for 10.1101/2021.09.10.21262695: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All participants included in this study provided written informed consent. 2. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Additionally, S gene dropout samples with cycle threshold less than 30 (Ct < 30.0) were submitted to whole genome sequencing (WGS) using the Illumina MiSeq high-throughput. WGSsuggested: NoneLibrary preparation was conducted using QIAseq QIAseqsuggested: (QIAGEN GeneGlobe Data Analysis Center, RRID:SCR_021211)Fifty-nine Brazilian SARS-CoV-2 complete genomes and the reference sequence (EPI_ISL_402124) (>29 kb) were retrieved from the GISAID database using Clustal Omega. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)T-cell epitopes: The search in Immune Epitope Database (IEDB) considered T-cells epitopes for SARS-CoV-2 spike protein (region of 10 residues flanking the Y380Q) with 70% similarity in BLAST. BLASTsuggested: (BLASTX, RRID:SCR_001653)Physicochemical properties: Electrostatic potential (EP) was verified through Delphi web server calculations and PIPSA [20,21]. Delphisuggested: (DelPhi, RRID:SCR_008669)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has some limitations. The small sample size in which WGS was feasible may limit any conclusion about the clinical severity related to the mutations found. Moreover, individuals were enrolled in a single city in Southern Brazil, which may limit the generality of our findings. Nonetheless, despite such limitations, a novel mutation (Y380Q) in the RBD region of SARS-CoV-2 spike protein was described. The analysis based on crystal structures reinforces the importance of the Y380 and C379 residues in the NAbs binding, and thus mutations in these regions may affect the interaction effectiveness between the NAbs and SARS-CoV-2 protein, as inferred by computational analysis.
Results from TrialIdentifier: No clinical trial numbers were referenced.
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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