SARS‐CoV‐2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate?
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Abstract
Lineage B.1.617+, also known as G/452R.V3 and now denoted by WHO with the Greek letters δ and κ, is a recently described SARS‐CoV‐2 variant under investigation first identified in October 2020 in India. As of May 2021, three sublineages labeled as B.1.617.1 (κ), B.1.617.2 (δ), and B.1.617.3 have been already identified, and their potential impact on the current pandemic is being studied. This variant has 13 amino acid changes, three in its spike protein, which are currently of particular concern: E484Q, L452R, and P681R. Here, we report a major effect of the mutations characterizing this lineage, represented by a marked alteration of the surface electrostatic potential (EP) of the receptor‐binding domain (RBD) of the spike protein. Enhanced RBD‐EP is particularly noticeable in the B.1.617.2 (δ) sublineage, which shows multiple replacements of neutral or negatively charged amino acids with positively charged amino acids. We here hypothesize that this EP change can favor the interaction between the B.1.617+ RBD and the negatively charged ACE2, thus conferring a potential increase in the virus transmission.
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SciScore for 10.1101/2021.06.08.445535: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. 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 PyMol (PyMol, version 2.4) suite was utilized for in-silico mutagenesis and its Adaptive Poisson–Boltzmann Solver (APBS) plugin (13) has been used to calculate the electrostatic potential of the wild-type and VOCs SARS-CoV-2 Spike Receptor Binding Domain (RBD) and evaluate potential differences in terms of molecular interaction with ACE2 receptor. PyMolsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open …
SciScore for 10.1101/2021.06.08.445535: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. 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 PyMol (PyMol, version 2.4) suite was utilized for in-silico mutagenesis and its Adaptive Poisson–Boltzmann Solver (APBS) plugin (13) has been used to calculate the electrostatic potential of the wild-type and VOCs SARS-CoV-2 Spike Receptor Binding Domain (RBD) and evaluate potential differences in terms of molecular interaction with ACE2 receptor. PyMolsuggested: (PyMOL, RRID:SCR_000305)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).
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.
- 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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