Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh

Saha, Senjuti; Malaker, Roly; Sajib, Mohammad Saiful Islam; Hasanuzzaman, Hasanuzzaman; Rahman, Hafizur; Ahmed, Zabed Bin; Islam, Mohammad Shahidul; Islam, Maksuda; Hooda, Yogesh; Ahyong, Vida; Vanaerschot, Manu; Batson, Joshua; Hao, Samantha; Kamm, Jack; Kistler, Amy; Tato, Cristina M.; DeRisi, Joseph L.; Saha, Samir K.

doi:10.1128/mra.00568-20

Cited by 34 publications

(32 citation statements)

References 11 publications

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“…As SARS-CoV-2 genomes spread, they leave footprints behind (mutations) allowing us to trace them. From this footprint, we have found that mutational frequency in the circulating SARS-CoV-2 genome in Bangladesh is fluctuating over time which is supported by another recent study by Saha et al, 2020c . It is feasible to complement the conventional approach with genome sequencing in an unbiased way.…”

Section: Discussionsupporting

confidence: 82%

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

Saha

Hossain

2020

Gene Reports

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new strain of beta coronavirus that has spread worldwide within a short period of time and has been responsible for the current COVID-19 pandemic. This novel virus shows high transmission and adaptability frequency into the host with rapid changes in genomic sequences. In this study, we analyzed the complete genome of 41 strains isolated in Bangladesh to understand the evolutionary route and genetic variations of this rapidly evolving virus. The phylogenetics, parsimony informative sites and mutation analyses were performed using MEGA X, Multiple sequence alignment program (MAFFT), and Virus Pathogen Resource. The phylogenetic analysis of the studied genomes along with the reference genome suggested that the viral strains found in Bangladesh might be coming from multiple countries such as France, Germany, India, the USA, and Brazil. After entering into the country, intra-cluster and inter-cluster began to circulate in the 8 individual divisions of Bangladesh. We also identified 26 parsimony-informative sites along with the 9 most important sites for virus evolution. Genome-wide annotations revealed 256 mutations, of which 10 were novel (NSP3, RdRp, Spike) in Bangladeshi strains where I120F(NSP2), P323L(RdRp), D614G (Spike), R203K, G204R(N) are the most prominent. Most importantly, numerous mutations were flourishing in the N protein gene (67) followed by S (45), RdRp (38), NSP2 (34), NSP3 (20), and ORF8 (6) gene. Moreover, nucleotide deletion analysis found nine deletions throughout the genomes including in ORF7a (8), ORF8 (1) with one insertion (G) at 265 positions in only one genome. The underlying mechanism of disease severity, molecular evolution, and epidemiology lie in genomic sequences that are not fully understood yet. Identification of the evolutionary history, parsimony-informative sites and others genetic variations of this deadly virus will facilitate the development of new strategies to control the local transmission and provide deep insight in the identification of potential therapeutic targets for controlling COVID-19.

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Section: Discussionsupporting

confidence: 82%

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

Saha

Hossain

2020

Gene Reports

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“…MN908947.3, https://github.com/czbiohub/sc2-msspe-bioinfo ). 15 , 16 Consensus sequences of the 9 SARS-CoV-2 genomes were uploaded on GISAID 17 and subsequently analyzed using NextStrain ( https://nextstrain.org/ ). 18 …”

Section: Methodsmentioning

confidence: 99%

The Direct and Indirect Impact of SARS-CoV-2 Infections on Neonates

Saha

Ahmed

Sarkar

et al. 2020

Pediatric Infectious Disease Journal

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“…(I300F), can be a destabilizing factor for nsp2 and thus modulating the strategy of host cell survival [11,20]. This mutation can lead to a reduction of conformational entropy due to the presence of the side chains that can result in charge neutralization of the phosphorylated serine residues [21].…”

Section: Prevalence Of Global Common Mutationsmentioning

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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Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh

Abstract: The complete genome sequence of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) isolate obtained from a nasopharyngeal swab from a patient with COVID-19 in Bangladesh is reported.

Cited by 34 publications

References 11 publications

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh

The Direct and Indirect Impact of SARS-CoV-2 Infections on Neonates

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

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