Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes

Abstract

Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. Nearly 0.4 million mutations were identified so far in ∼60,000 SARS-CoV-2 genomic sequences. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Phylogenetic analyses indicates that in Bangladesh, SARS-CoV-2 viruses might arrived through infected travelers from European countries, and the GR clade was found as predominant in this region. We found 2602 mutations including 1602 missense mutations, 612 synonymous mutations, 36 insertions and deletions with 352 other mutations types. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (95.6%) in Bangladeshi isolates. Interestingly, we found the average number of mutations in ORF1ab, S, ORF3a, M and N of genomes, having nucleotide shift at G614 (n=459), were significantly higher (p≤0.001) than those having mutation at D614 (n=215). Previously reported frequent mutations such as P4715L, D614G, R203K, G204R and I300F were also prevalent in Bangladeshi isolates. Additionally, 87 unique amino acid changes were revealed and were categorized as originating from different cities of Bangladesh. The analyses would increase our understanding of variations in virus genomes circulating in Bangladesh and elsewhere and help develop novel therapeutic targets against SARS-CoV-2.

Designing potential siRNA molecule for the nucleocapsid(N) gene silencing of different SARS-CoV-2 strains of Bangladesh: Computational approach

“…On the other hand, 12 sequences that did not belong to any clusters were found to be similar with sequences from Europe, including United Kingdom, Germany, France, Italy, and Russia, while one of these sequences was close to the sequence reported from the USA ( Shishir et al, 2021 ; Hasan et al, 2020 ). The underlying link of Bangladeshi SARS-CoV-2 isolates with part of a haplotype observed high in Europe ( Shishir et al, 2021 ; Mahmud et al, 2020 ).…”

Emerging SARS-CoV-2 Genetic Variations and Mutations in the COVID-19 genomic sequence: A Systematic and Meta-analysis review

“…It is reported that D to G mutation at position 614 (D614G) in the spike glycoprotein which is originated from Europe or China is a signi cant variation in changes of the secondary structure of protein [39] [8]. D614G mutation started in all affected regions such as Bangladesh (with 95.6% D614G mutation), Italy, Spain, North America and European countries [40] [41]. , amino-acid substitution 1109 (F→L) and 76th (S_T76I) position at spike protein found in Bangladeshi and Indonesian strain respectively [37].…”

A Review on D 614G Mutation with Bangladesh Scenario

“…Additionally, 87 unique amino acid changes were revealed and were categorized as originating from different cities of Bangladesh. The analyses would increase our understanding of variations in virus genomes circulating in Bangladesh and elsewhere and help develop novel therapeutic targets against SARS-CoV-2 [16]. This correlation indicates that the genomes containing D 614G mutation are more prone to bear other mutations which may facilitate the notion that the link of this mutation with the transmission and pathogenesis of SARS-CoV-2 [14].…”