Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

Hasan, Saam; Khan, Salim; Ahsan, Gias U.; Hossain, Maqsud

doi:10.1101/2020.05.13.094441

Cited by 4 publications

(2 citation statements)

References 10 publications

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“…Another group analyzed only 14 isolates and found 42 mutations ( Parvez et al, 2020 ). A separate study identified only 9 variants where unique mutations (UMs) were found prevalent mostly in ORF1ab ( Hasan et al, 2020 ). Another study involved 64 SARS-CoV-2 whole-genome sequences and identified the presence of 180 mutations in the coding regions of the viruses, and mutations at nsp2 were the most prevalent ( Ahmed et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Global and local mutations in Bangladeshi SARS-CoV-2 genomes

et al. 2021

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Section: Introductionmentioning

confidence: 99%

Global and local mutations in Bangladeshi SARS-CoV-2 genomes

et al. 2021

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“…It contains a variable number (6)(7)(8)(9)(10)(11) of open-reading frames (ORFs). The first ORF is almost two-third of the whole genome and encodes four structural, 16 non-structural and eight accessory proteins [1,2].…”

Section: Introductionmentioning

confidence: 99%

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

Hasan

Das

Rasheduzzaman

et al. 2020

Preprint

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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.

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Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh

Saha

Shatadru

Rakhi

et al. 2020

Preprint

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Along with intrinsic evolution, adaptation to selective pressure in new environments might have resulted in the circulatory SARS-CoV-2 strains in response to the geoenvironmental conditions of a country and the demographic profile of its population. Thus the analysis of genomic mutations of these circulatory strains may give an insight into the molecular basis of SARS-CoV-2 pathogenesis and evolution favoring the development of effective treatment and containment strategies. With this target, the current study traced the evolutionary route and mutational frequency of 198 Bangladesh originated SARS-CoV-2 genomic sequences available in the GISAID platform over a period of 13 weeks as of 14 July 2020. The analyses were performed using MEGA 7, Swiss Model Repository, Virus Pathogen Resource and Jalview visualization. Our analysis identified that majority of the circulating strains in the country belong to B and/or L type among cluster A to Z and strikingly differ from both the reference genome and the first sequenced genome from Bangladesh. Mutations in Nonspecific protein 2 (NSP2), NSP3, RNA dependent RNA polymerase (RdRp), Helicase, Spike, ORF3a, and Nucleocapsid (N) protein were common in the circulating strains with varying degrees and the most unique mutations(UM) were found in NSP3 (UM-18). But no or limited changes were observed in NSP9, NSP11, E (Envelope), NSP7a, ORF 6, and ORF 7b suggesting the possible conserved functions of those proteins in SARS-CoV-2 propagation. However, along with D614G mutation, more than 20 different mutations in the Spike protein were detected basically in the S2 domain. Besides, mutations in SR-rich region of N protein and P323L in RDRP were also present. However, the mutation accumulation showed an association with sex and age of the COVID-19 positive cases. So, identification of these mutational accumulation patterns may greatly facilitate drug/ vaccine development deciphering the age and the sex dependent differential susceptibility to COVID-19.

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Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

Cited by 4 publications

References 10 publications

Global and local mutations in Bangladeshi SARS-CoV-2 genomes

Global and local mutations in Bangladeshi SARS-CoV-2 genomes

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

Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh

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