Dataset Information

Understanding the possible origin and genotyping of the first Bangladeshi SARS-CoV-2 strain.

ABSTRACT: The novel coronavirus, SARS-CoV-2, has caused the most unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen from Bangladesh, the first complete genome of the virus has very recently been published. Therefore, long-awaited questions regarding the possible origin and typing of the strain(s) can now be answered. Here, we endeavor to mainly discuss the published reports or online-accessed data (results) regarding those issues and present a comprehensive picture of the typing of the virus alongside the probable origin of the subclade containing the Bangladeshi strain. Our observation suggested that this strain might have originated from the United Kingdom or the other European countries epidemiologically linked to the United Kingdom. According to different genotyping classification schemes, this strain belongs to the A2a clade under the G major clade, is of B and/or L type, and is a SARS-CoV-2a substrain. In the future, randomized genomic data will certainly increase in Bangladesh, however because of globalization and immigrant movement, we urgently need a mass regional sequencing approach targeting the partial or complete genome that can link the epidemiological data and may help in further clinical intervention.

SUBMITTER: Alam ASMRU

PROVIDER: S-EPMC7300542 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Understanding the possible origin and genotyping of the first Bangladeshi SARS-CoV-2 strain.

Alam A S M Rubayet Ul ASMRU Islam M Rafiul MR Rahman M Shaminur MS Islam Ovinu Kibria OK Hossain M Anwar MA

Journal of medical virology 20200928 1

The novel coronavirus, SARS-CoV-2, has caused the most unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen from Bangladesh, the first complete genome of the virus has very recently been published. Therefore, long-awaited questions regarding the possible origin and typing of the strain(s) can now be answered. Here, we endeavor to mainly discuss the published reports or online-accessed data ( ...[more]

PMID: 32492206

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Project description:Diagnostic tests based on reverse transcription-quantitative polymerase chain reaction (RT-qPCR) are the gold standard approach to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from clinical specimens. However, unless specifically optimized, this method is usually unable to recognize the specific viral strain responsible of coronavirus disease 2019, a crucial information that is proving increasingly important in relation to virus spread and treatment effectiveness. Even if some RT-qPCR commercial assays are currently being developed for the detection of viral strains, they focus only on single/few genetic variants that may not be sufficient to uniquely identify a specific strain. Therefore, genome sequencing approaches remain the most comprehensive solution for virus genotyping and to recognize viral strains, but their application is much less widespread due to higher costs. Starting from the well-established ARTIC protocol coupled to nanopore sequencing, in this work, we developed STArS (STrain-Amplicon-Seq), a cost/time-effective sequencing-based workflow for both SARS-CoV-2 diagnostics and genotyping. A set of 10 amplicons was initially selected from the ARTIC tiling panel, to cover: (i) all the main biologically relevant genetic variants located on the Spike gene; (ii) a minimal set of variants to uniquely identify the currently circulating strains; (iii) genomic sites usually amplified by RT-qPCR method to identify SARS-CoV-2 presence. PCR-amplified clinical samples (both positive and negative for SARS-CoV-2 presence) were pooled together with a serially diluted exogenous amplicon at known concentration and sequenced on a MinION device. Thanks to a scoring rule, STArS had the capability to accurately classify positive samples in agreement with RT-qPCR results, both at the qualitative and quantitative level. Moreover, the method allowed to effectively genotype strain-specific variants and thus also return the phylogenetic classification of SARS-CoV-2-postive samples. Thanks to the reduced turnaround time and costs, the proposed approach represents a step towards simplifying the clinical application of sequencing for viral genotyping, hopefully aiding in combatting the global pandemic.

Dataset Information

Understanding the possible origin and genotyping of the first Bangladeshi SARS-CoV-2 strain.

Publications

Understanding the possible origin and genotyping of the first Bangladeshi SARS-CoV-2 strain.

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