Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

Abstract

As the COVID-19 pandemic continues to ravage across the globe and take millions of lives and like many parts of the world, the second wave of the pandemic hit Bangladesh, this study aimed at understanding its causative agent, SARS-CoV-2 at the genomic and proteomic level and provide precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of Mid-June 2021, over 1500 SARS-CoV-2 genomesequences have been deposited in the GISAID database from Bangladesh which were extracted and categorized into two waves. By analyzing these genome sequences, it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%). Wave-2 samples also had a higher frequency of deletion, and transversion events. During the first wave, the GR clade was the most predominant but it was replaced by the GH clade in the latter wave. The B.1.1.25 variant showed the highest frequency in wave-1 while in case of wave-2, the B.1.351.3 variant, was the most common one. A notable presence of the delta variant, which is currently at the center of concern, was also observed. Comparison of the Spike protein found in the reference and the 3 most common lineages found in Bangladesh namely, B.1.1.7, B.1.351, B.1.617 in terms of their ability to form stable complexes with ACE2 receptor revealed that B.1.617 had the potential to be more transmissible than others. Importantly, no indigenous variants have been detected so far which implies that the successful prevention of import of foreign variants can diminish the outbreak in the country.

A Bioinformatics Tool for Predicting Future COVID-19 Waves Based on a Retrospective Analysis of the Second Wave in India: Model Development Study

“…Current prediction models in the COVID-19 pandemic are dominated by purely epidemiological analyses, from which hardly anyone could accurately predict an impending COVID-19 wave [23][24][25][26][27]. The importance of studying viral genomic sequences for the epidemiological surveillance of new SARS-CoV-2 variants is well recognized [31,[35][36][37][38][39][40]. However, its application in developing a predictive model to forecast upcoming virus waves has received little appreciation in the existing literature [41].…”

Experiences of the physicians in the largest COVID-19 dedicated hospital of Bangladesh about COVID-19 and its aftermath

“…The first, second, and third waves extend from April 2020 to December 2020, February 2021 to May 2021, and June 2021 to September 2021, respectively [25]. The first wave peaked in July 2020, the second wave peaked in April 2021, and the third peaked in august 2021 [24,25], and the predominant SARS CoV-2 variants isolated during these waves were alpha, beta, and delta, respectively [24]. But in the Dhaka Medical College Hospital, we observed four surges.…”

“…Officially, there are three waves of COVID-19 infections among the general population in Bangladesh after analyzing the total reported cases [24,25,26]. The first, second, and third waves extend from April 2020 to December 2020, February 2021 to May 2021, and June 2021 to September 2021, respectively [25].…”

“…Officially, there are three waves of COVID-19 infections among the general population in Bangladesh after analyzing the total reported cases [24,25,26]. The first, second, and third waves extend from April 2020 to December 2020, February 2021 to May 2021, and June 2021 to September 2021, respectively [25]. The first wave peaked in July 2020, the second wave peaked in April 2021, and the third peaked in august 2021 [24,25], and the predominant SARS CoV-2 variants isolated during these waves were alpha, beta, and delta, respectively [24].…”

“…The span of the official second and third COVID-19 waves was concordant with the third and fourth surges of Dhaka Medical College. The official first surge was long, and there was a small peak in October-November 2020 [24,25]. Officially that was not considered as a separate wave.…”