Dataset Information

Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh.

ABSTRACT: The COVID-19 pandemic induced by the SARS-CoV-2 virus and its variants has ravaged most countries around the world including Bangladesh. We have analyzed publicly available genomic data to understand the current COVID-19 outbreak scenario as well as the evolutionary origin and transmission routes of SARS-CoV-2 isolates in Bangladesh. All the early isolates as well as recent B.1.1.7 and B.1.351 variants had already spread across the major divisional cities of Bangladesh. A sex biasness towards male COVID-19 patient samples sequencing has been observed over female patient samples in all age-group, that could be the trend in infection rate. Phylogenetic analysis indicated a total of 13 estimated countries, including Italy, India, United Kingdom, Saudi Arabia, United Arab Emirates, Germany, Australia, New Zealand, South Africa, Democratic Republic of the Congo, United States, Russia, and Denmark, could be the possible origin introduced SARS-CoV-2 isolates in Bangladesh because of regional and intercontinental travel. Recent, B.1.1.7 variant could be imported from a total of 7 estimated countries including UK, India, Nigeria, Spain, Ireland, Australia, and Indonesia, while South Africa and the United States are the most likely sources of B.1.351 variant in Bangladesh. Based on these findings, public health strategies could be designed and implemented to reduce the local transmission of the virus.

SUBMITTER: Al Nahid A

PROVIDER: S-EPMC8408051 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh.

Al Nahid Abdullah A Ghosh Ajit A

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 20210901

The COVID-19 pandemic induced by the SARS-CoV-2 virus and its variants has ravaged most countries around the world including Bangladesh. We have analyzed publicly available genomic data to understand the current COVID-19 outbreak scenario as well as the evolutionary origin and transmission routes of SARS-CoV-2 isolates in Bangladesh. All the early isolates as well as recent B.1.1.7 and B.1.351 variants had already spread across the major divisional cities of Bangladesh. A sex biasness towards ma ...[more]

PMID: 34481060

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Project description:With the progression of the global SARS-CoV-2 pandemic, the new variants have become more infectious and continue spreading at a higher rate than pre-existing ones. Thus, we conducted a study to explore the epidemiology of emerging variants of SARS-CoV-2 that circulated in Bangladesh from December 2020 to September 2021, representing the 2nd and 3rd waves. We collected new cases and deaths per million daily data with the reproduction rate. We retrieved 928 SARS-CoV-2 sequences from GISAID and performed phylogenetic tree construction and mutation analysis. Case counts were lower initially at the end of 2020, during January-February and April-May 2021, whereas the death toll reached the highest value of 1.587 per million on the first week of August and then started to decline. All the variants (α, β, δ, η) were prevalent in the capital city, Dhaka, with dispersion to large cities, such as Sylhet and Chattogram. The B.1.1.25 lineage was prevalent during December 2020, but the B.1.617.2/δ variant was later followed by the B.1.351/β variant. The phylogeny revealed that the various strains found in Bangladesh could be from numerous countries. The intra-cluster and inter-cluster communication began in Bangladesh soon after the virus arrived. The prominent amino acid substitution was D614G from December 2020 to July 2021 (93.5 to 100%). From February-April, one of the VOC's important mutations, N501Y substitution, was also estimated at 51.8%, 76.1%, and 65.1% for the α, β and γ variants, respectively. The γ variant's unique mutation K417T was detected only at 1.8% in February. Another frequent mutation was P681R, a salient feature of the δ variant, detected in June (88.2%) and July (100%). Furthermore, only one γ variant was detected during the entire second and third wave, whereas no η variant was observed in this period. This rapid growth in the number of variants identified across Bangladesh shows virus adaptation and a lack of strict quarantine, prompting periodic genomic surveillance to foresee the spread of new variants, if any, and to take preventive measures as soon as possible.

Dataset Information

Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh.

Publications

Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh.

Similar Datasets

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