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Afrin SZ, Paul SK, Begum JA, Nasreen SA, Ahmed S, Ahmad FU, Aziz MA, Parvin R, Aung MS, Kobayashi N. Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020. New Microbes New Infect 2021; 41:100889. [PMID: 33936746 PMCID: PMC8065242 DOI: 10.1016/j.nmni.2021.100889] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
In Bangladesh, coronavirus disease 2019 (COVID-19) has been highly prevalent during late 2020, with nearly 500 000 confirmed cases. In the present study, the spike (S) protein of severe acute respiratory coronavirus 2 (SARS-CoV-2) circulating in Bangladesh was genetically investigated to elucidate the diversity of mutations and their prevalence. The nucleotide sequence of the S protein gene was determined for 15 SARS-CoV-2 samples collected from eight divisions in Bangladesh, and analysed for mutations compared with the reference strain (hCoV-19/Wuhan/WIV04/2019). All the SARS-CoV-2 S genes were assigned to B.1 lineage in G clade, and individual S proteins had 1-25 mutations causing amino acid substitution/deletion. A total of 133 mutations were detected in 15 samples, with D614G being present in all the samples; 53 were novel mutations as of January 2021. On the receptor-binding domain, 21 substitutions including ten novel mutations were identified. Other novel mutations were located on the N-terminal domain (S1 subunit) and dispersed sites in the S2 subunit, including two substitutions that remove potential N-glycosylation sites. A P681R substitution adjacent to the furin cleavage site was detected in one sample. All the mutations detected were located on positions that are functionally linked to host transition, antigenic drift, host surface receptor binding or antibody recognition sites, and viral oligomerization interfaces, which presumably related to viral transmission and pathogenic capacity.
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Affiliation(s)
- S Z Afrin
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - S K Paul
- Department of Microbiology, Netrokona Medical College, Netrokona, Bangladesh
| | - J A Begum
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - S A Nasreen
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - S Ahmed
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - F U Ahmad
- Department of Microbiology, TMSS Medical College, Bogura, Bangladesh
| | - M A Aziz
- Department of Microbiology, Rangpur Medical College, Rangpur, Bangladesh
| | - R Parvin
- Department of Pathology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - M S Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - N Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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