About: The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh
Creator	Khan, Hossain, Sarkar, Akter, Shahina Banu, Tanjina Goswami, Barna Habib, Md Jahan, Iffat Mahmud, Mohmmad Murshed, Hasan Osman, Eshrar Sayeed, Abu Taznin, Tarannum Uzzaman, Mohammad
Source	BioRxiv
abstract	Genomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins, in which 9 unique locations were detected relative to the global strains, including 516E>Q in the boundary of the ACE2 binding region. The most dominated variant G614 (95%) based in spike protein is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%. Highlights We have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh. A total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected. The mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year. Nine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative to the global SARS-CoV-2 strains.
has issue date	2020-07-30(xsd:dateTime)
bibo:doi	10.1101/2020.07.29.226555
has license	biorxiv
sha1sum (hex)	975e0c09dfd8d453ee9e915d996ea8e65df16787
schema:url	https://doi.org/10.1101/2020.07.29.226555
resource representing a document's title	The genetic variant analyses of SARS-CoV-2 strains; circulating in Bangladesh
schema:publication	bioRxiv
resource representing a document's body	covid:975e0c09dfd8d453ee9e915d996ea8e65df16787#body_text
is schema:about of	named entity 'NON-' named entity 'SYNONYMOUS' named entity 'CORONAVIRUSES' named entity 'TRANSMISSION' named entity 'BASED' named entity 'SAMPLES' named entity 'HAVE' named entity 'ADAPTATION' named entity 'DATE' named entity 'SAMPLING' named entity 'GENETIC DIVERSITY' named entity 'OBJECTIVES' named entity 'GLOBAL' named entity 'TO CHARACTERIZE' covid:arg/975e0c09dfd8d453ee9e915d996ea8e65df16787 named entity 'SARS-CoV-2' named entity 'mutation rate' named entity 'Bangladesh' named entity 'mutation' named entity 'SARS-CoV-2' named entity 'mutation rate' named entity 'vaccination' named entity 'nucleotide substitutions' named entity 'Bangladesh' named entity 'Bangladesh' named entity 'epidemic' named entity 'nucleotide substitutions' named entity 'Nucleocapsid' named entity 'RBD' named entity 'amino acids' named entity 'uracil' named entity 'Wuhan' named entity 'nucleotide change' named entity 'MERS-CoV' named entity 'virus' named entity 'bat' named entity 'Leucine' named entity 'non-structural proteins' named entity 'coronavirus' named entity 'jumped to humans' named entity 'C-terminal' named entity 'SARS-CoV-2' named entity 'nucleocapsids' named entity 'nucleocapsid protein' named entity 'gene' named entity 'poly(A) tail' named entity 'membrane fusion' named entity 'viral RNA' named entity 'Nucleotides' named entity 'RNA dependent RNA polymerase' named entity 'mammals' named entity 'coronavirus' named entity 'amino acids' named entity 'Bangladesh' named entity 'mutation' named entity 'UTR' named entity 'clade' named entity 'viral load' named entity 'enzyme' named entity 'glutamic acid' named entity 'protein' named entity 'SARS-CoV-2 virus' named entity 'coronaviruses' named entity 'spike protein' named entity 'spike protein' named entity 'infection' named entity 'Bangladesh' named entity 'Phenylalanine' named entity 'host range' named entity 'nucleocapsids' named entity 'SARS-CoV-2'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software