Dynamics of SARS-CoV-2 variants of concern (VOC) in Bangladesh during the first half of 2021

Afrin, Sultana Zahura; Islam, Taohidul; Paul, Shyamal Kumar; Kobayashi, Nobumichi; Parvin, Rokshana

doi:10.1016/j.virol.2021.10.005

Cited by 9 publications

(17 citation statements)

References 34 publications

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“…The 20I clade was found to be predominantly circulating in January (13.51%), February (30.16%), and March (13.40%) of 2021, and with a relatively lower prevalence (<10.0%) during rest of the months (Figure 2B). The Beta variant (20H), emerged in South Africa in May 2020, was first detected on November 2020 in Bangladesh 35 . The 20H clade or South African variant was found to be circulating widely in Bangladesh from November 2020 to July 2021 (Figure 2A).…”

Section: Resultsmentioning

confidence: 99%

“…The Alpha variant of concern that emerged in the United Kingdom in September 2020, was first identified in Bangladesh on December 31, 2020. 35 The Alpha 20I was found to be predominating in Bangladesh in early 2021 (January to March) with a decreasing trend of prevalence until July 2021. Our results corroborate with the reports India, one of the neighboring countries of Bangladesh, where the e Alpha (B.1.1.7) variant dominated in March 2021, and was rapidly replaced by the Delta (B.1.617.2) variant in April and May 2021.…”

Section: Discussionmentioning

confidence: 98%

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Temporal dynamics and fatality of SARS‐CoV‐2 variants in Bangladesh

Rahman¹,

Hoque

Chowdhury³

et al. 2023

Health Science Reports

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Background and Aims: Since the beginning of the SARS-CoV-2 pandemic, multiple new variants have emerged posing an increased risk to global public health. This study aimed to investigate SARS-CoV-2 variants, their temporal dynamics, infection rate (IFR) and case fatality rate (CFR) in Bangladesh by analyzing the published genomes. Methods: We retrieved 6610 complete whole genome sequences of the SARS-CoV-2 from the GISAID (Global Initiative on Sharing all Influenza Data) platform from March 2020 to October 2022, and performed different in-silico bioinformatics analyses. The clade and Pango lineages were assigned by using Nextclade v2.8.1. SARS-CoV-2 infections and fatality data were collected from the Institute of Epidemiology Disease Control and Research (IEDCR), Bangladesh. The average IFR was calculated from the monthly COVID-19 cases and population size while average CFR was calculated from the number of monthly deaths and number of confirmed COVID-19 cases.Results: SARS-CoV-2 first emerged in Bangladesh on March 3, 2020 and created three pandemic waves so far. The phylogenetic analysis revealed multiple introductions of SARS-CoV-2 variant(s) into Bangladesh with at least 22 Nextstrain clades and 107 Pangolin lineages with respect to the SARS-CoV-2 reference genome of Wuhan/Hu-1/2019. The Delta variant was detected as the most predominant (48.06%) variant followed by Omicron (27.88%), Beta (7.65%), Alpha (1.56%), Eta (0.33%) and Gamma (0.03%) variant. The overall IFR and CFR from circulating variants were 13.59% and 1.45%, respectively. A time-dependent monthly analysis showed significant variations in the IFR (p = 0.012, Kruskal-Wallis test) and CFR (p = 0.032, Kruskal-Wallis test) throughout the study period. We found the highest IFR (14.35%) in 2020 while Delta (20A) and Beta (20H) variants were circulating in

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 98%

Temporal dynamics and fatality of SARS‐CoV‐2 variants in Bangladesh

Rahman¹,

Hoque

Chowdhury³

et al. 2023

Health Science Reports

View full text Add to dashboard Cite

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“…Researchers worldwide are surveying the differences in the virus that cause COVID-19 ( https://www.jagranjosh.com/general-knowledge/variants-of-sars-cov-2-in-the-world-covid-19-variants-1623846555-1 ). Contemporary research is helping scientists to better understand how COVID-19 mutations might affect human health if some spread faster than the others [ 47 ].…”

Section: Components Related To Covid-19 Treatmentmentioning

confidence: 99%

A Statistical Synopsis of COVID-19 Components and Descriptive Analysis of Their Socio-Economic and Healthcare Aspects in Bangladesh Perspective

Uddin

Shawpnil

Mugdha

et al. 2023

Journal of Environmental and Public Health

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The aim of the work is to analyze the socio-economic and healthcare aspects that arise in the contemporary COVID-19 situation from Bangladesh perspective. We elaborately discuss the successive COVID-19 occurrences in Bangladesh with consequential information. The components associated with the COVID-19 commencement and treatment policy with corresponding features and their consequences are patently delineated. The effect of troublesome issues related to the treatment is detailed with supporting real-time data. We elucidate the applications of modern technologies advancement in epidemiological aspects and their existent compatibility in Bangladesh. We statistically analyze the real-time data through figurative and tabular approaches. Some relevant measures of central tendency and dispersion are utilized to explore the data structure and its observable specifications. For a clear manifestation, Z − scores of the COVID-19 components are analyzed through the Box-Whisker plot. We have discovered that the gathered data exhibit features that are unsatisfactory for the normal distribution, are highly positively skewed, and are predominated by the earliest occurrences. Infections and deaths were initially lower than the global average, but they drastically rose in the first quarter of 2021 and persisted for the remainder of the year. Substantial preventive results were produced by the region-wisetime-worthy moves. In the fourth quarter of 2021, the infections and deaths noticeably decreased, and the number of recoveries was highly significant. In the middle of 2022, a lethal rise in infections was observed in Bangladesh and that was quickly stabilized, and the pandemic ingredients were under control. According to our assessment, some concluding remarks are made at the end of this work.

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“…55 Several in silico SARS-CoV-2 research presented the structure and functional perspective of the novel virus focusing its virulence transmission in human genome. [56][57][58] The present study explored theoretical modeling, sequence, and structure-based functional characterization of 6 accessory proteins. Phylogenetic analysis of these proteins exposed a close evolutionary relationship with the proteins of distant origins.…”

Section: Microbiology Insightsmentioning

confidence: 99%

Characterization and Structural Prediction of Proteins in SARS-CoV-2 Bangladeshi Variant Through Bioinformatics

Debnath

Khan

2022

Microbiol�Insights

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The renowned respiratory disease induced by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The most devastating thing is that the infection rate is continuously uprising and resulting in significant mortality especially among the older age population and those with health co-morbidities. This enveloped, positive-sense RNA virus is chiefly responsible for the infection of the upper respiratory system. The virulence of the SARS-CoV-2 is mostly regulated by its proteins such as entry to the host cell through fusion mechanism, fusion of infected cells with neighboring uninfected cells to spread virus, inhibition of host gene expression, cellular differentiation, apoptosis, mitochondrial biogenesis, etc. But very little is known about the protein structures and functionalities. Therefore, the main purpose of this study is to learn more about these proteins through bioinformatics approaches. In this study, ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein have been selected from a Bangladeshi Corona-virus strain G039392 and a number of bioinformatics tools (MEGA-X-V10.1.7, PONDR, ProtScale, ProtParam, SCRIBER, NetSurfP v2.0, IntFOLD, UCSF Chimera, and PyMol) and strategies were implemented for multiple sequence alignment and phylogeny analysis with 9 different variants, predicting hydropathicity, amino acid compositions, protein-binding propensity, protein disorders, and 2D and 3D protein modeling. Selected proteins were characterized as highly flexible, structurally and electrostatically extremely stable, ordered, biologically active, hydrophobic, and closely related to proteins of different variants. This detailed information regarding the characterization and structure of proteins of SARS-CoV-2 Bangladeshi variant was performed for the first time ever to unveil the deep mechanism behind the virulence features. And this robust appraisal also paves the future way for molecular docking, vaccine development targeting these characterized proteins.

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Dynamics of SARS-CoV-2 variants of concern (VOC) in Bangladesh during the first half of 2021

Cited by 9 publications

References 34 publications

Temporal dynamics and fatality of SARS‐CoV‐2 variants in Bangladesh

Temporal dynamics and fatality of SARS‐CoV‐2 variants in Bangladesh

A Statistical Synopsis of COVID-19 Components and Descriptive Analysis of Their Socio-Economic and Healthcare Aspects in Bangladesh Perspective

Characterization and Structural Prediction of Proteins in SARS-CoV-2 Bangladeshi Variant Through Bioinformatics

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