Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India
India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences fr...
Published in: | F1000Research |
---|---|
Main Authors: | , , , , , , |
Format: | Text |
Language: | English |
Published: |
F1000 Research Limited
2020
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309413/ https://doi.org/10.12688/f1000research.23805.1 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:7309413 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:7309413 2023-05-15T15:34:29+02:00 Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India Begum, Feroza Mukherjee, Debica Thagriki, Dluya Das, Sandeepan Tripathi, Prem Prakash Banerjee, Arup Kumar Ray, Upasana 2020-05-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309413/ https://doi.org/10.12688/f1000research.23805.1 en eng F1000 Research Limited http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309413/ http://dx.doi.org/10.12688/f1000research.23805.1 Copyright: © 2020 Begum F et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY F1000Res Brief Report Text 2020 ftpubmed https://doi.org/10.12688/f1000research.23805.1 2020-06-28T00:33:40Z India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on GISAID, a global initiative for sharing avian flu data. In this study, we have analysed the spike protein sequences from all five isolates and also compared their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and another at 1124 in the S2 domain of spike protein of the isolates from West Bengal only. There was one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of the mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding. Text Avian flu PubMed Central (PMC) The Spike ENVELOPE(-37.317,-37.317,-54.017,-54.017) F1000Research 9 371 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Brief Report |
spellingShingle |
Brief Report Begum, Feroza Mukherjee, Debica Thagriki, Dluya Das, Sandeepan Tripathi, Prem Prakash Banerjee, Arup Kumar Ray, Upasana Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India |
topic_facet |
Brief Report |
description |
India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on GISAID, a global initiative for sharing avian flu data. In this study, we have analysed the spike protein sequences from all five isolates and also compared their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and another at 1124 in the S2 domain of spike protein of the isolates from West Bengal only. There was one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of the mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding. |
format |
Text |
author |
Begum, Feroza Mukherjee, Debica Thagriki, Dluya Das, Sandeepan Tripathi, Prem Prakash Banerjee, Arup Kumar Ray, Upasana |
author_facet |
Begum, Feroza Mukherjee, Debica Thagriki, Dluya Das, Sandeepan Tripathi, Prem Prakash Banerjee, Arup Kumar Ray, Upasana |
author_sort |
Begum, Feroza |
title |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India |
title_short |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India |
title_full |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India |
title_fullStr |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India |
title_full_unstemmed |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India |
title_sort |
analyses of spike protein from first deposited sequences of sars-cov2 from west bengal, india |
publisher |
F1000 Research Limited |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309413/ https://doi.org/10.12688/f1000research.23805.1 |
long_lat |
ENVELOPE(-37.317,-37.317,-54.017,-54.017) |
geographic |
The Spike |
geographic_facet |
The Spike |
genre |
Avian flu |
genre_facet |
Avian flu |
op_source |
F1000Res |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7309413/ http://dx.doi.org/10.12688/f1000research.23805.1 |
op_rights |
Copyright: © 2020 Begum F et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.12688/f1000research.23805.1 |
container_title |
F1000Research |
container_volume |
9 |
container_start_page |
371 |
_version_ |
1766364864293371904 |