Cutting epitopes to survive: the case of lambda variant
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
This manuscript concisely reports an in-silico study on the potential impact of the Spike protein mutations on immuno-escape ability of SARS-CoV-2 lambda variant. Biophysical and bioinformatics data suggest that a combination of shortening immunogenic epitope loops and generation of potential N-glycosylation sites may be a viable adaptation strategy potentially allowing this emerging viral variant escaping host immunity.
Article activity feed
-
SciScore for 10.1101/2021.08.14.456353: (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
Software and Algorithms Sentences Resources The reference Wuhan Spike sequence is labelled by the RefSeq [6] code yp_009724390. RefSeqsuggested: (RefSeq, RRID:SCR_003496)The servers Dynamut and GlycoPred [9] and NetNGlyc [10] were used to predict point mutations impact onto the Spike structure, and glycosylation sites, respectively. NetNGlycsuggested: (NetNGlyc, RRID:SCR_001570)Structural analysis and visualization have been carried out with PyMOL [12] or UCSF Chimera [7]. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the …SciScore for 10.1101/2021.08.14.456353: (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
Software and Algorithms Sentences Resources The reference Wuhan Spike sequence is labelled by the RefSeq [6] code yp_009724390. RefSeqsuggested: (RefSeq, RRID:SCR_003496)The servers Dynamut and GlycoPred [9] and NetNGlyc [10] were used to predict point mutations impact onto the Spike structure, and glycosylation sites, respectively. NetNGlycsuggested: (NetNGlyc, RRID:SCR_001570)Structural analysis and visualization have been carried out with PyMOL [12] or UCSF Chimera [7]. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
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.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.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
