Keywords
Spike, India, West Bengal, Mutations
This article is included in the Emerging Diseases and Outbreaks gateway.
This article is included in the Coronavirus collection.
Spike, India, West Bengal, Mutations
The SARS-CoV2 (a member of Coronaviruses) outbreak occurred in Wuhan, China in the year 2019, and was recently declared a pandemic, which has affected countries worldwide. To design antiviral therapeutics/vaccines it is important to understand the genetic sequence, structure and function of the viral proteins. When a virus tries to adapt to a new environment, in a new host, in a new geographical location and a new population, it may make changes to its genetic make-up which in turn bring slight modifications in viral proteins. Such variations would help the virus to utilize the host’s machinery to best in favour virus survival and propagation. Since the host’s immune system eventually learns to identify an infecting pathogen and starts producing protective antibodies, a virus often changes its structural proteins so that it escapes the host’s immune system and continues to infect the host cells. Coronaviruses have been long known to undergo rapid mutations in its RNA genome1. Such mutations are reflected in changes in the amino acid sequences of its structural and non-structural proteins.
The spike protein is a structural protein of SARS-CoV2 that forms a homotrimer on the surface of the vital lipid envelope2. This trimer is made up of monomers consisting of S1 and S2 subunits. S1 subunit helps in attachment to the host cell receptor, while S2 subunit helps in fusion to host cell and entry. Thus, the spike protein has been an area of interest for designing vaccine and antiviral candidates against SARS-CoV2. Since the spike protein tends to mutate, it is important to obtain a broad mutation profile of this protein from extensive genome sequencing from different geographical locations of the world. Targeting areas of the spike protein that do not undergo mutation, i.e. conserved regions, would be the key to designing effective broad spectrum antivirals or vaccine.
We downloaded the five new SARS-CoV2 sequences from West Bengal (EPI_ISL_430468; EPI_ISL_430467; EPI_ISL_430465; EPI_ISL_430464; EPI_ISL_430466) from the GISAID database under the EpiCov icon by specifying location as India and the spike protein sequences corresponding to Kerala isolates (QIA98583 and QHS34546)3, Gujarat isolate (QJC1949.1)4 and Wuhan isolate (QIS29982.1) from the NCBI virus database. Wuhan isolate was used as the original SARS-CoV-2 sequence for sequence comparisons. For this study we have considered only the complete sequences (>29,000bp) with high coverage.
For the West Bengal isolates, the nucleotide sequences corresponding to the spike protein were selected and then translated on ExPASY Translate tool to obtain the protein sequences.
All the spike protein sequences were aligned using the multiple sequence alignment platform of CLUSTAL Omega. The alignment file was viewed using MView and differences in the sequence or the amino acid changes were recorded.
CFSSP (Chou and Fasman secondary structure prediction) server was used to predict secondary structures of SARS-CoV2 spike protein.
To study the effect of mutation on the conformation, stability and flexibility of the spike protein, the SARS-CoV-2 structure was downloaded from RCSB PDB. We used the available SARS-CoV-2 spike ectodomain structure (open state) (PDB ID: 6VYB). The 6VYB structure was uploaded on DynaMut software (University of Melbourne, Australia)5 and changes in vibrational entropy and the atomic fluctuations and deformation energies due to mutation were determined. For atomic fluctuation and deformation energy calculations, calculations were performed by the software over first ten non-trivial modes of the molecule.
The first set of five sequencing data from clinical isolates of SARS-CoV2 from the state of West Bengal, India was submitted on 27/2/2020 by the National Institute of Biomedical Genomics (NIBMG) in collaboration with ICMR-National Institute of Cholera and Enteric Diseases (ICMR-NICED). The sequences were submitted to the GISAID database.
We downloaded all the sequences from West Bengal (Table 1) and performed a nucleotide translation to obtain respective spike protein sequences. All these spike protein sequences were first aligned in CLUSTAL Omega to check for similarities or differences. We found that at position 723, all the isolates from West Bengal except EPI_ISL_430466 had ‘T’ (other isolates had ‘I’). Also, at position 1124, two of the isolates (EPI_ISL_430468 and EPI_ISL_430464) showed mutation from ‘G’ to ‘V’. We used spike protein sequence translated from one of these sequences (EPI_ISL_430468) as representative of SARS-CoV2 spike from West Bengal for our further comparison with other states.
Since, we had access to sequences for SARS-CoV2 only from three states in India (Kerala, Gujarat and now West Bengal), we compared all those sequences to detect possible changes (Figure 1). We considered the original Wuhan sequence as the wild type for comparison. We found six different amino acid positions that were mutated in these isolates overall. We had recently published the details with respect to the spike protein mutations in Kerala3 and Gujarat isolates4.
Here, we report that in West Bengal isolates there were three mutations in the spike protein. One of these mutations was D614G in the S1 domain. This lies near the receptor bending domain at a downstream position. Another mutation, T723I lie further downstream in the S protein in the S2 domain. Mutation G1124V is the third mutation and lie in the S2 domain. While D614G was also found in the isolate from Gujarat but not in Kerala isolates, T723I and G1124V mutation were exclusively found in the isolates of West Bengal. None of the isolates from other parts of India had this mutation.
Although T723I was also exclusive for West Bengal, it appeared only in one isolate. Thus, we characterized mutation G1124V which appeared in two of the isolates. Both glycine (G) and valine (V) are non-polar amino acids with aliphatic R groups. Glycine has no side chain whereas valine is bulkier due to its side chain. A change from glycine to valine can thus potentially disrupt the local folding of the protein. For example, it was shown that G to V change in a P-glycoprotein changed its drug specificities6.
Secondary structure prediction showed changes in and around the site of mutation (Figure 2). In the mutant spike there was a loss of turn structure from position 1124 and addition of four helices at positions 1123, 1124, 1125 and 1126. This change in secondary structure might lead to change in function of S2. S2 helps in fusion process of the spike protein and thus mutation in S2 may have altered receptor spike interactions and thus infectivity.
To correlate if changes in secondary structure are also reflected in the dynamics of the protein in its tertiary structure, we performed normal mode analyses and studied protein stability and flexibility. Change in vibrational entropy energy (ΔΔSVib ENCoM) between the wild type Wuhan isolate and the West Bengal isolate was -4.445 kcal.mol-1.K-1 (Figure 3). The ΔΔG was 0.905 kcal/mol and the ΔΔG ENCoM was 4.756 kcal/mol. All these suggested a stabilizing mutation in this type of spike. The interatomic interactions have been shown in Figure 4.
Analyses of atomic fluctuations and deformation energies showed visible changes (Figure 5). Atomic fluctuations calculate the measure of absolute atomic motion whereas deformation energies detect the measure of flexibility of a protein. Figure 5 shows the visual representations of the atomic fluctuation and deformation energies where positions that could be visibly detected to be different have been marked.
This is the first report of mutations of such types in the isolates of the state of West Bengal and further sequencing followed by sequence analyses would help expanding the knowledge about variations of spike protein in human SARS-CoV. These variations might lead to virus diversification and eventual emergence of variants, antibody escape mutants, strains and serotypes. Also, mutations might help the virus to expand its tissue tropism and adjust with the host environment better. Therefore, elaborate studies on sequence variations should be done, which would in turn help in better therapeutic targeting.
Accession numbers for sequences used in this study can be found in Table 1 and the test. GSAID is a free-to-use resource, but requires registration prior to accessing.
Figshare: Figure F1000corrected.pdf, https://doi.org/10.6084/m9.figshare.12254033.v27.
This project contains the following extended data:
- Images raw images as created on DynaMut software:
○ Deformation_protein_158809623989_wild_type
○ Deformation_protein_G943V_158809623989_mutant_1124
○ Diff_A_G943V_158809623989_Kolkata_1124_mutation_6VYB23805-V1-1-fluctuation_protein_158809623989wild_type
○ Fluctuation_protein_G943V_158809623989_mutant_1124
○ Protein_cleanedcontacts_A_943_158809623989_wild_type
○ Protein_G943Vcontacts_A_943_158809623989_Mutant_Kolkata_1124
We thank NIBMG, Kalyani, West Bengal and ICMR-NICED for depositing the sequences in public database and making it openly available. We thank CSIR, AcSIR and North Bengal Medical College and Hospital for other necessary support and input.
A previous version of this article is available on bioRxiv: https://biorxiv.org/cgi/content/short/2020.04.28.066985v1
Views | Downloads | |
---|---|---|
F1000Research | - | - |
PubMed Central
Data from PMC are received and updated monthly.
|
- | - |
Is the work clearly and accurately presented and does it cite the current literature?
Partly
Is the study design appropriate and is the work technically sound?
Yes
Are sufficient details of methods and analysis provided to allow replication by others?
Yes
If applicable, is the statistical analysis and its interpretation appropriate?
Not applicable
Are all the source data underlying the results available to ensure full reproducibility?
Yes
Are the conclusions drawn adequately supported by the results?
Partly
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: I have limited expertise on computational approaches for protein structure prediction
Is the work clearly and accurately presented and does it cite the current literature?
Yes
Is the study design appropriate and is the work technically sound?
Yes
Are sufficient details of methods and analysis provided to allow replication by others?
Partly
If applicable, is the statistical analysis and its interpretation appropriate?
Not applicable
Are all the source data underlying the results available to ensure full reproducibility?
Yes
Are the conclusions drawn adequately supported by the results?
Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Host-pathogen interaction, Biochemical characterization of mutant versions of proteins, Cancer biology using organoid and mouse models
Is the work clearly and accurately presented and does it cite the current literature?
Yes
Is the study design appropriate and is the work technically sound?
Yes
Are sufficient details of methods and analysis provided to allow replication by others?
Yes
If applicable, is the statistical analysis and its interpretation appropriate?
Yes
Are all the source data underlying the results available to ensure full reproducibility?
Yes
Are the conclusions drawn adequately supported by the results?
Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Clinical Biochemistry
Alongside their report, reviewers assign a status to the article:
Invited Reviewers | |||
---|---|---|---|
1 | 2 | 3 | |
Version 2 (revision) 27 Sep 23 |
|||
Version 1 18 May 20 |
read | read | read |
Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. Consider the following examples, but note that this is not an exhaustive list:
Sign up for content alerts and receive a weekly or monthly email with all newly published articles
Already registered? Sign in
The email address should be the one you originally registered with F1000.
You registered with F1000 via Google, so we cannot reset your password.
To sign in, please click here.
If you still need help with your Google account password, please click here.
You registered with F1000 via Facebook, so we cannot reset your password.
To sign in, please click here.
If you still need help with your Facebook account password, please click here.
If your email address is registered with us, we will email you instructions to reset your password.
If you think you should have received this email but it has not arrived, please check your spam filters and/or contact for further assistance.
Comments on this article Comments (0)