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

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Nguyen, Thanh Thi
Pathirana, Pubudu N
Nguyen, Thin
Nguyen, Quoc Viet Hung
Bhatti, Asim
Nguyen, Dinh C
Nguyen, Dung Tien
Nguyen, Ngoc Duy
Creighton, Douglas
Abdelrazek, Mohamed
Griffith University Author(s)
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2021
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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.

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Scientific Reports

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11

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1

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© The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

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Genetics

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Nguyen, TT; Pathirana, PN; Nguyen, T; Nguyen, QVH; Bhatti, A; Nguyen, DC; Nguyen, DT; Nguyen, ND; Creighton, D; Abdelrazek, M, Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus), Scientific Reports, 2021, 11 (1), pp. 3487

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