A virus that has gone viral: amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding, and thus, infectivity
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Abstract
Since 2002, β coronaviruses (CoVs) have caused three zoonotic outbreaks, SARS-CoV in 2002, MERS-CoV in 2012, and the recent outbreak of SARS-CoV-2 late in 2019 (also named as COVID-19 or novel coronavirus 2019 or nCoV2019). Spike (S) protein, one of the structural proteins of this virus plays key role in receptor (ACE2) binding and thus virus entry. Thus, this protein has attracted scientists for detailed study and therapeutic targeting. As the nCoV2019 takes its course throughout the world, more and more sequence analyses are being done and genome sequences are being deposited in various databases. From India, two clinical isolates have been sequenced and the full genome has been deposited in GenBank. We have performed sequence analyses of the Spike protein of the Indian isolates and compared with that of the Wuhan, China (where the outbreak was first reported). While all the sequences of Wuhan isolates are identical, we found point mutations in the Indian isolates. Out of the two isolates, one was found to harbor a mutation in its receptor-binding domain (RBD) at position 407. At this site, arginine (a positively charged amino acid) was replaced by isoleucine (a hydrophobic amino acid that is also a C-β branched amino acid). This mutation has been seen to change the secondary structure of the protein at that region and this can potentially alter receptor binding of the virus. Although this finding needs further validation and more sequencing, the information might be useful in rational drug designing and vaccine engineering.
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SciScore for 10.1101/2020.04.07.029132: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For our sequence alignments we have used NCBI BLAST, CLUSTAL W and CLUSTAL OMEGA. BLASTsuggested: (BLASTX, RRID:SCR_001653)CLUSTAL OMEGAsuggested: (Clustal Omega, RRID:SCR_001591)JMol and ConSurf tools were used to predict the structure of the proteins. JMolsuggested: (Jmol, RRID:SCR_003796)PyMoL standalone software was used to visualize the structure and understand the pattern of bonding. PyMoLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
R…SciScore for 10.1101/2020.04.07.029132: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For our sequence alignments we have used NCBI BLAST, CLUSTAL W and CLUSTAL OMEGA. BLASTsuggested: (BLASTX, RRID:SCR_001653)CLUSTAL OMEGAsuggested: (Clustal Omega, RRID:SCR_001591)JMol and ConSurf tools were used to predict the structure of the proteins. JMolsuggested: (Jmol, RRID:SCR_003796)PyMoL standalone software was used to visualize the structure and understand the pattern of bonding. 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.
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