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

Abstract

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.

Impact of Climate on the Expansion of Dengue Fever in an Endemic Urban Area

“…Well established knowledge since pioneering work of May & Andersen [32], and widely demonstrated along the COVID-19 pandemic, transmissibility is not related, or even is inversely related, to virulence. Contrasting 2003 SARS epidemic to the most recent SARS-CoV-2 pandemic, it is clear that a virulent variant/genotype will decrease its incidence in the host population, while those genotypes which are less virulent may evolve towards forms which are more transmissible, thus, becoming highly incident, even though more difficult to detect due to low hospitalization [33][34][35][36][37] Even though virulence of dengue is expected to be preserved along time due to the insect vector phase, especially considering vertical transmission [38], a newly arriving serotype must cause more severe disease but not further dissemination. On the contrary, the fast hospitalization removes a host to the transmission cycle.…”

The COVID-19 Mortality Rate Is Associated with Illiteracy, Age, and Air Pollution in Urban Neighborhoods: A Spatiotemporal Cross-Sectional Analysis

“…Despite the fact that numerous COVID-19 vaccines are available, the virus continues to mutate [ 6 , 7 ] and spread as new variants, such as Omicron [ 8 ]. In addition, the association between COVID-19 incidence rates and biological, socioeconomic, and environmental determinants, such as air pollution, is established in the literature [ 9 ].…”

“…In addition, the association between COVID-19 incidence rates and biological, socioeconomic, and environmental determinants, such as air pollution, is established in the literature [ 9 ]. However, cities with large populations are economic growth centres with high levels of aggregation and mobility, making it difficult to control the rate of COVID-19 spread [ 6 , 9 , 10 , 11 , 12 , 13 ]. Moreover, social factors that might cause poor health increase the population’s vulnerability during pandemics [ 14 ].…”

COVID-19: Current Status and Future Prospects

“…Our knowledge has expanded on the pathogenesis and treatment of COVID-19 and experience gained within different countries, and this is reflected in the enormous number of scientific papers generated, including those in this Special Issue. There have been 24 papers published upon peer review acceptance in this Special Issue, including 17 research papers [ 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ], 2 review papers [ 20 , 21 ], 1 opinion piece [ 22 ], 1 commentary [ 23 ], and 3 systematic reviews [ 24 , 25 , 26 ]. Each paper in this Special Issue contributes to our understanding of COVID-19.…”

“…The eighth of these explored the epidemiology of emerging variants of SARS-CoV-2 that circulated in Bangladesh from December 2020 to September 2021, representing the second and third waves. A rapid growth in the number of variants identified across Bangladesh showed 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 [ 10 ]. The ninth was a document review of the health operations and technical expertise (HOTE) pillar coordination meetings’ minutes, reports, policy, and strategy documents of the activities and outcomes and feedback on updates on the HOTE pillar given at regular intervals to the regional incident management support team of the World Health Organization regional office for Africa.…”