Coding-Complete Genome Sequence of SARS-CoV-2 Isolate from Bangladesh by Sanger Sequencing

Moniruzzaman, Md.; Hossain, Mohammad Uzzal; Islam, MM; Rahman, Md. Hadisur; Ahmed, Irfan; Rahman, Tahia Anan; Bhattacharjee, Arittra; Amin, Md. Ruhul; Rashed, Asif; Keya, Chaman Ara; Das, Keshob Chandra; Salimullah, Md.

doi:10.1128/mra.00626-20

Cited by 21 publications

(21 citation statements)

References 7 publications

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“…However, we also explored other well studied betacoronavirus Since the report of reference genome SARS-CoV-2 from Wuhan in December 2019, the deadly pathogen has spread throughout the world and produced numerous genetic variants with six predominant clades (www.gisaid.org). The GISAID CoVsurver analysis revealed that our previously reported isolate 'SARS-CoV-2 NIB-1' is a member of GR clade which has been mutated 10 times in the coding regions [12]. The NCBI BLASTN unveiled another mutation in 5' UTR region.…”

Section: Discussionmentioning

confidence: 88%

“…Hence, there is a higher possibility that a suitable NSP1 mutant of SARS-CoV-2 would work as an attenuated vaccine for COVID-19. Through computational analysis, we have observed that V121D and L122I mutant might destabilize the structure of NSP1 (Table 2 & Supplementary: 2) yet with these two mutations, the virus caused mild fever, cough and throat congestion in a young female patient [12]. Therefore, V121D and L122I mutations along with 93 th C → T in 5' UTR did not change the pathogenicity of SARS-CoV-2 significantly.…”

Section: Discussionmentioning

confidence: 94%

“…According to our report, the viral isolate shares a common ancestor with three North American SARS-CoV-2 isolates that were collected from Washington, United States of America (USA). Additionally, our isolate showed longer branch length or more genomic mutations than its closely related members [12]. When we aligned the genome with the reference genome (Accession: NC_045512.2), we found 11 mutations of which 4 of them were new.…”

Section: Coronaviruses (Covs) Are Enveloped Viruses That Belong To Thmentioning

confidence: 89%

“…MT509958, GISAID Accession ID: EPI_ISL_447904) from a young female COVID-19 patient of Bangladesh [12]. According to our report, the viral isolate shares a common ancestor with three North American SARS-CoV-2 isolates that were collected from Washington, United States of America (USA).…”

Section: Coronaviruses (Covs) Are Enveloped Viruses That Belong To Thmentioning

confidence: 90%

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Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics

Hossain¹,

Bhattacharjee

Emon

et al. 2020

Preprint

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Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the etiologic agent of Coronavirus Disease- 2019 (COVID-19), is rapidly accumulating new mutations. Analysis of these mutations is necessary for gaining knowledge regarding different aspects of therapeutic development. Recently, we have reported a Sanger method based genome sequence of a viral isolate named SARS-CoV-2 NIB-1, circulating in Bangladesh. The genome has four novel mutations in V121D, V843F, A889V and G1691C positions. V121D substitution has the potential to destabilize the Non-Structural Protein (NSP-1) which inactivates the type-1 Interferon-induced antiviral system hence this mutant could be the basis of attenuated vaccines against SARS-CoV-2. V843F, A889V and G1691C are all located in NSP3. G1691C can decrease the flexibility of the protein while V843F and A889V changed the binding pattern of SARS-CoV-2 Papain-Like protease (PLPro) inhibitor GRL0617. V843F PLPro showed reduced affinity for Interferon Stimulating Gene-15 (ISG-15) protein whereas V843F+A889V double mutants exhibited the same binding affinity as wild type PLPro. Here, V843F is a conserved position of PLPro that damaged the structure but A889V, a less conserved residue, most probably neutralized that damage. Mutants of NSP1 could provide attenuated vaccines against coronavirus. Also, these mutations of PLPro could be targeted to develop anti-SARS therapeutics.

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 94%

Section: Coronaviruses (Covs) Are Enveloped Viruses That Belong To Thmentioning

confidence: 89%

Section: Coronaviruses (Covs) Are Enveloped Viruses That Belong To Thmentioning

confidence: 90%

See 2 more Smart Citations

Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics

Hossain¹,

Bhattacharjee

Emon

et al. 2020

Preprint

Self Cite

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“…[34] The first complete genome sequencing of SARS-CoV-2 in Bangladesh was announced by Child Health Research Foundation on 12 th May, 2020. [35] Soon after, National Institute of Biotechnology announced the sequencing of SARS-CoV-2 genome by Sanger sequencing method [36]. The SARS-CoV-2 genome sequencing effort in Bangladesh flourished afterwards and as a result, 323 genomes have been sequenced by October 1 st , 2020.…”

Section: Introductionmentioning

confidence: 99%

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

Ahammad

Hossain

Bhattacharjee

et al. 2020

Preprint

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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.

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COVID-19, the firestone in 21st century: a review on coronavirus disease and its clinical perspectives

Karthika

Krishna

Rahman

et al. 2021

Environ Sci Pollut Res

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Graphical abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak began in late 2019 in Wuhan, China, and have since spread globally. Deep sequencing analysis identified the disease within a few weeks, and on February 11, the World Health Organization (WHO) named it “COVID-19 caused by SARS-CoV-2.” SARS-CoV-2 was declared a global pandemic by the WHO in March 2020. Coronavirus disease has become a global challenge for researchers and health care workers, affecting over 174 million people and causing over 3 million deaths. Because of the widespread nature, extensive measures are being taken to reduce person-to-person contact, and special precautions are being taken to prevent the transmission of this infection to vulnerable populations such as geriatrics, pediatrics, and health care professionals. We summarized the genesis of COVID-19 spread, its pathology, clinical perspectives, and the use of natural ingredients as a possible cure for COVID-19 in this review. This article has highlighted information about current vaccines approved for emergency use as well as those in various stages of clinical trials. Vaccine availability around the world is a promising development in the fight against the SARS-CoV-2 virus. We conducted a narrative review to present the current state and research on this situation, specific diagnosis, clinical manifestation, emergency approaches, herbal-based remedies, and COVID vaccines.

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Coding-Complete Genome Sequence of SARS-CoV-2 Isolate from Bangladesh by Sanger Sequencing

Abstract: ABSTRACT A coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate was revealed. The sample for the virus was isolated from a female patient from Dhaka, Bangladesh, suffering from coronavirus disease-2019 (COVID-19).

Cited by 21 publications

References 7 publications

Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics

Novel Mutations in NSP1 and PLPro of SARS-CoV-2 NIB-1 Genome Mount for Effective Therapeutics

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

COVID-19, the firestone in 21st century: a review on coronavirus disease and its clinical perspectives

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