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

Ghosh, Ajit

doi:10.1016/j.meegid.2021.105057

Cited by 2 publications

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“…Epidemiological information from the Mexican Health Ministry in the early stages of the pandemic in Mexico, together with the results from this study, suggest that the pandemic in Mexico was maintained by community transmission, following the importation of variants mainly from the United States, Europe, and South America. This same phenomenon has been reported in other countries in Europe, Asia, Africa and South America ( Al Nahid and Ghosh, 2021 ; Al-Mahruqi et al, 2021 ; Elizondo et al, 2021 ; Engelbrecht et al, 2021 ; Giovanetti et al, 2021 ; Kostaki et al, 2021 ; Richter et al, 2021 ).…”

Section: Discussionsupporting

confidence: 87%

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

et al. 2022

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BackgroundThe advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs).ObjectiveThis study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs.Methods30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed.Results148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes.ConclusionThe COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.

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Section: Discussionsupporting

confidence: 87%

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

et al. 2022

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“…All the clustering of the Bangladeshi sequences indicates the virus's transmission from expatriates to the community, which might be due to an improperly structured quarantine facility for travelers in Bangladesh. Multiple introductions have been recorded from Italy, India, and the UK [58]. The clustering of α and β variants of SARS-CoV-2 in Bangladesh illustrated that the virus reached the community transmission level, and only one Eta variant indicates the lack of community transmission of the emerging Eta variants.…”

Section: Transmission Dynamics and Phylogeny Of Emerging Variants In ...mentioning

confidence: 99%

Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh

et al. 2022

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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.

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

Cited by 2 publications

References 44 publications

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern

Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh

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