Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations]
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...
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ftdoajarticles:oai:doaj.org/article:abd01f784fdc4247b0a897633e019844 2023-05-15T15:34:31+02:00 Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations] Feroza Begum Debica Mukherjee Dluya Thagriki Sandeepan Das Prem Prakash Tripathi Arup Kumar Banerjee Upasana Ray 2020-05-01T00:00:00Z https://doi.org/10.12688/f1000research.23805.1 https://doaj.org/article/abd01f784fdc4247b0a897633e019844 EN eng F1000 Research Ltd https://f1000research.com/articles/9-371/v1 https://doaj.org/toc/2046-1402 2046-1402 doi:10.12688/f1000research.23805.1 https://doaj.org/article/abd01f784fdc4247b0a897633e019844 F1000Research, Vol 9 (2020) Medicine R Science Q article 2020 ftdoajarticles https://doi.org/10.12688/f1000research.23805.1 2022-12-31T03:03:17Z 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. Article in Journal/Newspaper Avian flu Directory of Open Access Journals: DOAJ Articles The Spike ENVELOPE(-37.317,-37.317,-54.017,-54.017) F1000Research 9 371 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Feroza Begum Debica Mukherjee Dluya Thagriki Sandeepan Das Prem Prakash Tripathi Arup Kumar Banerjee Upasana Ray Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations] |
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Medicine R Science Q |
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 |
Article in Journal/Newspaper |
author |
Feroza Begum Debica Mukherjee Dluya Thagriki Sandeepan Das Prem Prakash Tripathi Arup Kumar Banerjee Upasana Ray |
author_facet |
Feroza Begum Debica Mukherjee Dluya Thagriki Sandeepan Das Prem Prakash Tripathi Arup Kumar Banerjee Upasana Ray |
author_sort |
Feroza Begum |
title |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations] |
title_short |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations] |
title_full |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations] |
title_fullStr |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations] |
title_full_unstemmed |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 1; peer review: 2 approved, 1 approved with reservations] |
title_sort |
analyses of spike protein from first deposited sequences of sars-cov2 from west bengal, india [version 1; peer review: 2 approved, 1 approved with reservations] |
publisher |
F1000 Research Ltd |
publishDate |
2020 |
url |
https://doi.org/10.12688/f1000research.23805.1 https://doaj.org/article/abd01f784fdc4247b0a897633e019844 |
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 |
F1000Research, Vol 9 (2020) |
op_relation |
https://f1000research.com/articles/9-371/v1 https://doaj.org/toc/2046-1402 2046-1402 doi:10.12688/f1000research.23805.1 https://doaj.org/article/abd01f784fdc4247b0a897633e019844 |
op_doi |
https://doi.org/10.12688/f1000research.23805.1 |
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F1000Research |
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