Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh.
As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insight...
Guardado en:
| Autores principales: | , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/65af944635644acb974c64483e8e3a01 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:65af944635644acb974c64483e8e3a01 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:65af944635644acb974c64483e8e3a012021-12-02T20:17:26ZWave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh.1932-620310.1371/journal.pone.0258019https://doaj.org/article/65af944635644acb974c64483e8e3a012021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0258019https://doaj.org/toc/1932-6203As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.Ishtiaque AhammadMohammad Uzzal HossainAnisur RahmanZeshan Mahmud ChowdhuryArittra BhattacharjeeKeshob Chandra DasChaman Ara KeyaMd SalimullahPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0258019 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Ishtiaque Ahammad Mohammad Uzzal Hossain Anisur Rahman Zeshan Mahmud Chowdhury Arittra Bhattacharjee Keshob Chandra Das Chaman Ara Keya Md Salimullah Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh. |
| description |
As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country. |
| format |
article |
| author |
Ishtiaque Ahammad Mohammad Uzzal Hossain Anisur Rahman Zeshan Mahmud Chowdhury Arittra Bhattacharjee Keshob Chandra Das Chaman Ara Keya Md Salimullah |
| author_facet |
Ishtiaque Ahammad Mohammad Uzzal Hossain Anisur Rahman Zeshan Mahmud Chowdhury Arittra Bhattacharjee Keshob Chandra Das Chaman Ara Keya Md Salimullah |
| author_sort |
Ishtiaque Ahammad |
| title |
Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh. |
| title_short |
Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh. |
| title_full |
Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh. |
| title_fullStr |
Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh. |
| title_full_unstemmed |
Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh. |
| title_sort |
wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of covid-19 pandemic in bangladesh. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/65af944635644acb974c64483e8e3a01 |
| work_keys_str_mv |
AT ishtiaqueahammad wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh AT mohammaduzzalhossain wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh AT anisurrahman wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh AT zeshanmahmudchowdhury wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh AT arittrabhattacharjee wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh AT keshobchandradas wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh AT chamanarakeya wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh AT mdsalimullah wavewisecomparativegenomicstudyforrevealingthecompletescenarioanddynamicnatureofcovid19pandemicinbangladesh |
| _version_ |
1718374347624677376 |