Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This pap...

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Autores principales:	Thanh Thi Nguyen, Pubudu N. Pathirana, Thin Nguyen, Quoc Viet Hung Nguyen, Asim Bhatti, Dinh C. Nguyen, Dung Tien Nguyen, Ngoc Duy Nguyen, Douglas Creighton, Mohamed Abdelrazek
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d87e9398206a429395a066549c10cc85
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spelling	oai:doaj.org-article:d87e9398206a429395a066549c10cc852021-12-02T14:11:29ZGenomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)10.1038/s41598-021-83105-32045-2322https://doaj.org/article/d87e9398206a429395a066549c10cc852021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83105-3https://doaj.org/toc/2045-2322Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. Based on 6324 viral genome sequences, we create a spreadsheet dataset of point mutations that can facilitate the investigation of SARS-CoV-2 in many perspectives, especially in tracing the evolution and worldwide spread of the virus. Our analysis results also show that coding genes E, M, ORF6, ORF7a, ORF7b and ORF10 are most stable, potentially suitable to be targeted for vaccine and drug development.Thanh Thi NguyenPubudu N. PathiranaThin NguyenQuoc Viet Hung NguyenAsim BhattiDinh C. NguyenDung Tien NguyenNgoc Duy NguyenDouglas CreightonMohamed AbdelrazekNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Thanh Thi Nguyen Pubudu N. Pathirana Thin Nguyen Quoc Viet Hung Nguyen Asim Bhatti Dinh C. Nguyen Dung Tien Nguyen Ngoc Duy Nguyen Douglas Creighton Mohamed Abdelrazek Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
description	Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. Based on 6324 viral genome sequences, we create a spreadsheet dataset of point mutations that can facilitate the investigation of SARS-CoV-2 in many perspectives, especially in tracing the evolution and worldwide spread of the virus. Our analysis results also show that coding genes E, M, ORF6, ORF7a, ORF7b and ORF10 are most stable, potentially suitable to be targeted for vaccine and drug development.
format	article
author	Thanh Thi Nguyen Pubudu N. Pathirana Thin Nguyen Quoc Viet Hung Nguyen Asim Bhatti Dinh C. Nguyen Dung Tien Nguyen Ngoc Duy Nguyen Douglas Creighton Mohamed Abdelrazek
author_facet	Thanh Thi Nguyen Pubudu N. Pathirana Thin Nguyen Quoc Viet Hung Nguyen Asim Bhatti Dinh C. Nguyen Dung Tien Nguyen Ngoc Duy Nguyen Douglas Creighton Mohamed Abdelrazek
author_sort	Thanh Thi Nguyen
title	Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
title_short	Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
title_full	Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
title_fullStr	Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
title_full_unstemmed	Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
title_sort	genomic mutations and changes in protein secondary structure and solvent accessibility of sars-cov-2 (covid-19 virus)
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/d87e9398206a429395a066549c10cc85
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Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)

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