Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 2; 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:4f49711f07a3426ebb6d8bbed2cfcd43 2023-10-29T02:35:09+01:00 Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 2; peer review: 2 approved, 1 approved with reservations] Arup Kumar Banerjee Prem Prakash Tripathi Upasana Ray Feroza Begum Dluya Thagriki Debica Mukherjee Sandeepan Das 2023-09-01T00:00:00Z https://doi.org/10.12688/f1000research.23805.2 https://doaj.org/article/4f49711f07a3426ebb6d8bbed2cfcd43 EN eng F1000 Research Ltd https://f1000research.com/articles/9-371/v2 https://doaj.org/toc/2046-1402 2046-1402 doi:10.12688/f1000research.23805.2 https://doaj.org/article/4f49711f07a3426ebb6d8bbed2cfcd43 F1000Research, Vol 9 (2023) Spike India West Bengal Mutations eng Medicine R Science Q article 2023 ftdoajarticles https://doi.org/10.12688/f1000research.23805.2 2023-10-01T00:36:27Z 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 F1000Research 9 371 |
institution |
Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Spike India West Bengal Mutations eng Medicine R Science Q |
spellingShingle |
Spike India West Bengal Mutations eng Medicine R Science Q Arup Kumar Banerjee Prem Prakash Tripathi Upasana Ray Feroza Begum Dluya Thagriki Debica Mukherjee Sandeepan Das Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 2; peer review: 2 approved, 1 approved with reservations] |
topic_facet |
Spike India West Bengal Mutations eng 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 |
Arup Kumar Banerjee Prem Prakash Tripathi Upasana Ray Feroza Begum Dluya Thagriki Debica Mukherjee Sandeepan Das |
author_facet |
Arup Kumar Banerjee Prem Prakash Tripathi Upasana Ray Feroza Begum Dluya Thagriki Debica Mukherjee Sandeepan Das |
author_sort |
Arup Kumar Banerjee |
title |
Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India [version 2; 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 2; 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 2; 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 2; 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 2; 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 2; peer review: 2 approved, 1 approved with reservations] |
publisher |
F1000 Research Ltd |
publishDate |
2023 |
url |
https://doi.org/10.12688/f1000research.23805.2 https://doaj.org/article/4f49711f07a3426ebb6d8bbed2cfcd43 |
genre |
Avian flu |
genre_facet |
Avian flu |
op_source |
F1000Research, Vol 9 (2023) |
op_relation |
https://f1000research.com/articles/9-371/v2 https://doaj.org/toc/2046-1402 2046-1402 doi:10.12688/f1000research.23805.2 https://doaj.org/article/4f49711f07a3426ebb6d8bbed2cfcd43 |
op_doi |
https://doi.org/10.12688/f1000research.23805.2 |
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F1000Research |
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