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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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2023-09-01
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| Online Access: | https://f1000research.com/articles/9-371/v2 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-11T21:26:46Z |
| format | Article |
| id | doaj.art-4f49711f07a3426ebb6d8bbed2cfcd43 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-03-11T21:26:46Z |
| publishDate | 2023-09-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-4f49711f07a3426ebb6d8bbed2cfcd432023-09-28T00:00:00ZengF1000 Research LtdF1000Research2046-14022023-09-019156601Analyses 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 Banerjee0Prem Prakash Tripathi1Upasana Ray2https://orcid.org/0000-0003-4783-9295Feroza Begum3Dluya Thagriki4Debica Mukherjee5Sandeepan Das6Department of Biochemistry, North Bengal Medical College and Hospital, Sushrutanagar, West Bengal, 734012, IndiaCSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, 730032, IndiaCSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, 730032, IndiaCSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, 730032, IndiaCSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, 730032, IndiaCSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, 730032, IndiaCSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, 730032, IndiaIndia 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.https://f1000research.com/articles/9-371/v2Spike India West Bengal Mutationseng |
| spellingShingle | 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] F1000Research Spike India West Bengal Mutations eng |
| 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_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_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_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 |
| topic | Spike India West Bengal Mutations eng |
| url | https://f1000research.com/articles/9-371/v2 |
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