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Research Article
Genetic diversity and structural characterization of spike glycoprotein of newly emerged SARS-CoV-2
S. Acharya
Department of Zoology, Vidyasagar University, Midnapore-721102, West Bengal
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
A new beta Coronavirus (SARS-CoV-2) infection was first identified in the Wuhan City, China in December 2019 and after that it had spread rapidly throughout the globe and subsequently WHO have announced it as a pandemic. So, SARS-CoV-2 has now become a global threat to human civilization. Recent studies showed that the proteomic data of SARS-CoV-2 is closely related with other beta Coronavirus. The phylogenetic tree revealed the closeness of recently reported SAR-CoV2 with SARS-CoV by using MEGA 7 along with the suitable protocol of Neighbor joining algorithm. The spike glycoprotein plays the most important role during the onset of infection. Several mutations have been reported across the globe in the S Proteins. In this research, molecular docking between the SARS-CoV-2 spike glycoprotein and ACE2 protein was carried out in PatchDock web servers. [email protected] calculated the molecular simulation using Normal Mode Analysis (NMA) along with lowest deformation energy value which signifies the domain motions. Also during multiple sequence analysis, variations were observed within the Spike protein reported globally. 3- Dimensional structure of protein molecules were designed using homology modeling and the structure were validated through Q mean score and Ramachandran plot. All of the designed sequences were having around 91% of the amino acid in the favored region of Ramachandran plot. In order to check the binding affinity difference between the mutated and non-mutated strains, the generated models were docked with human ACE2 molecules. The non mutated strains have given the similar ACE value. However, there were variations in ACE value of the mutated strains. This observation provides evidence of Phylogenetic diversity and evolution.
Keywords
SARS-CoV-2, COVID19, homology modeling, molecular docking, Phylogenetic analysis.
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BIPUL CHANDRA KARMAKAR
commented on 27 May, 2020
First of all this information put on some crucial and important knowledge to existing knowledge. Not only that this article tells whole history of COVID19 infection and its outcome but also the bioinformative interation study provide clues for developing vaccine against the virus to scientic communities. I think these information will open up a way to save our valuable life from this infection..
Rudra Narayan Saha
ORCiDcommented on 28 May, 2020
This is an interesting study and is an important addition to the literature. The title and abstract are appropriate for the content of the text. Furthermore, the article is well constructed, the experiments were well conducted, and analysis was well performed. I like the conceptualization of the study as it illustrates the variations in different mutated strains which led to evidences in phylogenetic diversity and evolution. The main strength of this paper lies in the fact that it addresses a relevant topic. The authors have used a selected set of excellent and elegant bioinformatic approaches which will almost certainly influence our way of thinking about variations in the Spike proteins of the novel SARS-CoV 2. The GIS data set availability and the use of GPS coordinates in monitoring viral disease epidemiology will open up new avenues on predicting future outbreaks.
Sangita Paul
commented on 28 May, 2020
This article seems to be quite promising for opening up new avenues in CORONA VIRUS research and help in combating this dreadful scenario all over the world. To stop the nuisance created by this virus it is important to develop some strategies which would shatter its activity and lessen the transmissibility all around. Likewise the bioinformatics analysis done and the approach of this study (comparison with mutant forms ) are quite potent in culminating this hostile situation.
TANMOY KUMAR DEY
ORCiDcommented on 28 May, 2020
This piece of work reported critical features of SARS-nCov2 related disease etiology. The authors demonstrated polymorphism in the spike protein configurations, sampled globally. The data suggested that the polymorphisms seem to have influenced the SARS-nCov2 spike protein binding to the human ACE2 receptor. Also the paper has logically explained the mutations in the light of evolution and the phylogenetic diversity of the betacoronavirus family. In my opinion the novel findings of this work hold significant clinical relevance. The bioinformatics-based datasets presented in the paper would help the scientists worldwide to understand the significance of these polymorphisms in vaccine development and controlling the rampaging spread of SARS-nCov2 virus.
Avishek Ghosh
commented on 29 May, 2020
A nice elucidation & description of introduction of SARS CoV 2 genetic diversity is portrayed here. These findings would always illuminate the area of research related to Spike protein of SARS CoV2 which can provide the platform for further studies in evolutionary aspect of COVID 19.
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This is a preprint. It has not completed peer review.
Research Article
Genetic diversity and structural characterization of spike glycoprotein of newly emerged SARS-CoV-2
S. Acharya
Department of Zoology, Vidyasagar University, Midnapore-721102, West Bengal
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 26 May, 2020
Community comments: 5
Metrics
Comments: 5
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
A new beta Coronavirus (SARS-CoV-2) infection was first identified in the Wuhan City, China in December 2019 and after that it had spread rapidly throughout the globe and subsequently WHO have announced it as a pandemic. So, SARS-CoV-2 has now become a global threat to human civilization. Recent studies showed that the proteomic data of SARS-CoV-2 is closely related with other beta Coronavirus. The phylogenetic tree revealed the closeness of recently reported SAR-CoV2 with SARS-CoV by using MEGA 7 along with the suitable protocol of Neighbor joining algorithm. The spike glycoprotein plays the most important role during the onset of infection. Several mutations have been reported across the globe in the S Proteins. In this research, molecular docking between the SARS-CoV-2 spike glycoprotein and ACE2 protein was carried out in PatchDock web servers. [email protected] calculated the molecular simulation using Normal Mode Analysis (NMA) along with lowest deformation energy value which signifies the domain motions. Also during multiple sequence analysis, variations were observed within the Spike protein reported globally. 3- Dimensional structure of protein molecules were designed using homology modeling and the structure were validated through Q mean score and Ramachandran plot. All of the designed sequences were having around 91% of the amino acid in the favored region of Ramachandran plot. In order to check the binding affinity difference between the mutated and non-mutated strains, the generated models were docked with human ACE2 molecules. The non mutated strains have given the similar ACE value. However, there were variations in ACE value of the mutated strains. This observation provides evidence of Phylogenetic diversity and evolution.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
BIPUL CHANDRA KARMAKAR
commented on 27 May, 2020
First of all this information put on some crucial and important knowledge to existing knowledge. Not only that this article tells whole history of COVID19 infection and its outcome but also the bioinformative interation study provide clues for developing vaccine against the virus to scientic communities. I think these information will open up a way to save our valuable life from this infection..
Rudra Narayan Saha
ORCiDcommented on 28 May, 2020
This is an interesting study and is an important addition to the literature. The title and abstract are appropriate for the content of the text. Furthermore, the article is well constructed, the experiments were well conducted, and analysis was well performed. I like the conceptualization of the study as it illustrates the variations in different mutated strains which led to evidences in phylogenetic diversity and evolution. The main strength of this paper lies in the fact that it addresses a relevant topic. The authors have used a selected set of excellent and elegant bioinformatic approaches which will almost certainly influence our way of thinking about variations in the Spike proteins of the novel SARS-CoV 2. The GIS data set availability and the use of GPS coordinates in monitoring viral disease epidemiology will open up new avenues on predicting future outbreaks.
Sangita Paul
commented on 28 May, 2020
This article seems to be quite promising for opening up new avenues in CORONA VIRUS research and help in combating this dreadful scenario all over the world. To stop the nuisance created by this virus it is important to develop some strategies which would shatter its activity and lessen the transmissibility all around. Likewise the bioinformatics analysis done and the approach of this study (comparison with mutant forms ) are quite potent in culminating this hostile situation.
TANMOY KUMAR DEY
ORCiDcommented on 28 May, 2020
This piece of work reported critical features of SARS-nCov2 related disease etiology. The authors demonstrated polymorphism in the spike protein configurations, sampled globally. The data suggested that the polymorphisms seem to have influenced the SARS-nCov2 spike protein binding to the human ACE2 receptor. Also the paper has logically explained the mutations in the light of evolution and the phylogenetic diversity of the betacoronavirus family. In my opinion the novel findings of this work hold significant clinical relevance. The bioinformatics-based datasets presented in the paper would help the scientists worldwide to understand the significance of these polymorphisms in vaccine development and controlling the rampaging spread of SARS-nCov2 virus.
Avishek Ghosh
commented on 29 May, 2020
A nice elucidation & description of introduction of SARS CoV 2 genetic diversity is portrayed here. These findings would always illuminate the area of research related to Spike protein of SARS CoV2 which can provide the platform for further studies in evolutionary aspect of COVID 19.