Comparative genomic study for revealing the complete scenario of COVID-19 pandemic in Bangladesh

Abstract

As the COVID-19 pandemic continues to ravage across the globe and take millions of lives, worldwide efforts to understand its causative agent, SARS-CoV-2 at the genomic level are also running in full swing. Such studies are providing precious insights about the pathogenesis, evolution, strengths and weaknesses of the virus. As of October 1st, 2020, 323 SARS-CoV-2 genomes have been sequenced across Bangladesh. The current study is aimed at answering some vital questions about these sequences. From our analyses, it was discovered that the majority of the SARS-CoV-2 found in Bangladesh belonged to the lineage B 1.1.25 of GR clade. Dhaka and Chittagong division were the most diverse in terms of SARS-CoV-2 clades while Mymensing was the least. There are more variety of clades in southern parts of Bangladesh than the northern parts. The most commonly found SARS-CoV-2 mutations found in the country were Spike_D614G, NSP12_P323L, N_G204R and N_R203K. Even though no significant pattern of distribution could be drawn between mutations found in Bangladesh and the countries with similar mortality rates and the countries with large Bangladeshi diaspora, to a certain degree they match with those in the UK, Oman, Italy, Greece, South Africa and Russia. Therefore, careful eye should be kept on the performance of vaccines in those countries in the near future as they are likely to work well in Bangladesh if they work well there. Mutational events in Bangladesh were found to increase between April and July, 2020 and decrease since August, 2020. The number of mutations per SARS-CoV-2 virus sample in Bangladesh was calculated to be 6.88 which is lower than the global average of 7.23. The decrease and the lower rate of mutation raise the possibility of a vaccine or drug working sustainably to protect the people. Based on these insights, a clear picture about the ongoing pandemic can be drawn in the context of Bangladesh which will help the country take appropriate measures to combat the virus.

Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic

“…These three types of B.1 sublineages seem to be spread in the city during independent transmission events. The B.1.36 is global lineage with lots of representation of sequences from the India, Saudi Arabia, and UK (Ishtiaque et al, 2020;Joshi et al, 2020). The B.1.160 lineage is the most recently split from B.1.36 lineage and has mostly been reported from the European countries with major representation in the UK followed by Denmark, France and Switzerland (Rambaut et al, 2020).…”

Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh

“…A mutation in P681 might affect the viral transmission and infectivity ( 11 , 12 ). This lineage was predominant during the peak of the first wave in Bangladesh ( 13 ); however, in the later stages, its spike glycoprotein (S) gained new mutations ( Fig. 1 ), which, with further changes, might help the virus escape humoral immunity in the near future and raise another surge of B.1.1.25-mediated COVID-19 cases.…”

Whole genome sequencing for revealing the point mutations of SARS-CoV-2 genome in Bangladeshi isolates and their structural effects on viral proteins

“…Besides, to understand the origin of the strains, the exploration of the whole-genome sequencing (WGS) data of SARS-CoV-2 strains is highly necessary. 73 Insights into the mutations of SARS-CoV-2 is an important factor in developing therapeutics against the virus. 74 In this study, we investigated the variation, insertion, and deletion of the Bangladeshi SARS-CoV-2 strains.…”