4 research outputs found
Spatiotemporal patterns and trends of community transmission of the pandemic COVID-19 in South Asia: Bangladesh as a case study
Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh
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
Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics
Transmission Pathways and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in the Environment
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread to the environment through several routes and persist for a more extended period. Therefore, we reviewed pertinent literature to understand the transmission dynamics of SARS-CoV-2 and genomic epidemiology of emerging variants of concern (VOCs) in the environment, their inactivation strategies, and the impact of COVID-19 on the ecosystem. The fallouts of the reviewed studies indicate that SARS-CoV-2 transmits through air and fomite, contaminated surfaces, biomedical wastes, and stool, which contaminates the environment through wastewater. As a result, multiple VOCs of SARS-CoV-2 were circulating in the environment. Genomic epidemiology revealed that the most prevalent VOC was Delta (B.1.617.2; 44.24%), followed by Omicron (B.1.1.529; 43.33%), in the environment. Phylogenetic analysis showed that environmental strains are clustered with a likeness of the human strains of the same or nearby countries, emphasizing the significance of continued environmental surveillance to track the emergence of the new variant. Thus, we should reduce viral dispersion in the environment through rapid and appropriate disinfection strategies. Moreover, the increased production and use of macro and microfiber plastic products should be brought under strict legislation with integrated waste management to control the unrelenting propagation of viral RNA. Finally, a comprehensive understanding of the environmental transmission pathways of SARS-CoV-2 is crucial for forecasting outbreak severity in the community, allowing us to prepare with the correct tools to control any impending pandemic. We recommend wastewater-based SARS-CoV-2 surveillance and air particulates to track the emerging VOCs of SARS-CoV-2 spread in the environment