Cargando…

Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition

SARS-COV-2, Severe Acute Respiratory Syndrome (SARS), and the Middle East respiratory syndrome-related coronavirus (MERS) viruses are from the coronaviridae family; the former became a global pandemic (with low mortality rate) while the latter were confined to a limited region (with high mortality r...

Descripción completa

Detalles Bibliográficos
Autores principales: Ahsan, Reza, Tahsili, Mohammad Reza, Ebrahimi, Faezeh, Ebrahimie, Esmaeil, Ebrahimi, Mansour
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Ltd. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106241/
https://www.ncbi.nlm.nih.gov/pubmed/34004573
http://dx.doi.org/10.1016/j.compbiomed.2021.104471
_version_ 1783689746853134336
author Ahsan, Reza
Tahsili, Mohammad Reza
Ebrahimi, Faezeh
Ebrahimie, Esmaeil
Ebrahimi, Mansour
author_facet Ahsan, Reza
Tahsili, Mohammad Reza
Ebrahimi, Faezeh
Ebrahimie, Esmaeil
Ebrahimi, Mansour
author_sort Ahsan, Reza
collection PubMed
description SARS-COV-2, Severe Acute Respiratory Syndrome (SARS), and the Middle East respiratory syndrome-related coronavirus (MERS) viruses are from the coronaviridae family; the former became a global pandemic (with low mortality rate) while the latter were confined to a limited region (with high mortality rates). To investigate the possible structural differences at basic levels for the three viruses, genomic and proteomic sequences were downloaded and converted to polynomial datasets. Seven attribute weighting (feature selection) models were employed to find the key differences in their genome's nucleotide sequence. Most attribute weighting models selected the final nucleotide sequences (from 29,000(th) nucleotide positions to the end of the genome) as significantly different among the three virus classes. The genome and proteome sequences of this hot zone area (which corresponds to the 3′UTR region and encodes for nucleoprotein (N)) and Spike (S) protein sequences (as the most important viral protein) were converted into binary images and were analyzed by image processing techniques and Convolutional deep Neural Network (CNN). Although the predictive accuracy of CNN for Spike (S) proteins was low (0.48%), the machine-based learning algorithms were able to classify the three members of coronaviridae viruses with 100% accuracy based on 3′UTR region. For the first time ever, the relationship between the possible structural differences of coronaviruses at the sequential levels and their pathogenesis are being reported, which paves the road to deciphering the high pathogenicity of the SARS-COV-2 virus.
format Online
Article
Text
id pubmed-8106241
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Elsevier Ltd.
record_format MEDLINE/PubMed
spelling pubmed-81062412021-05-10 Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition Ahsan, Reza Tahsili, Mohammad Reza Ebrahimi, Faezeh Ebrahimie, Esmaeil Ebrahimi, Mansour Comput Biol Med Article SARS-COV-2, Severe Acute Respiratory Syndrome (SARS), and the Middle East respiratory syndrome-related coronavirus (MERS) viruses are from the coronaviridae family; the former became a global pandemic (with low mortality rate) while the latter were confined to a limited region (with high mortality rates). To investigate the possible structural differences at basic levels for the three viruses, genomic and proteomic sequences were downloaded and converted to polynomial datasets. Seven attribute weighting (feature selection) models were employed to find the key differences in their genome's nucleotide sequence. Most attribute weighting models selected the final nucleotide sequences (from 29,000(th) nucleotide positions to the end of the genome) as significantly different among the three virus classes. The genome and proteome sequences of this hot zone area (which corresponds to the 3′UTR region and encodes for nucleoprotein (N)) and Spike (S) protein sequences (as the most important viral protein) were converted into binary images and were analyzed by image processing techniques and Convolutional deep Neural Network (CNN). Although the predictive accuracy of CNN for Spike (S) proteins was low (0.48%), the machine-based learning algorithms were able to classify the three members of coronaviridae viruses with 100% accuracy based on 3′UTR region. For the first time ever, the relationship between the possible structural differences of coronaviruses at the sequential levels and their pathogenesis are being reported, which paves the road to deciphering the high pathogenicity of the SARS-COV-2 virus. Elsevier Ltd. 2021-07 2021-05-08 /pmc/articles/PMC8106241/ /pubmed/34004573 http://dx.doi.org/10.1016/j.compbiomed.2021.104471 Text en © 2021 Elsevier Ltd. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Ahsan, Reza
Tahsili, Mohammad Reza
Ebrahimi, Faezeh
Ebrahimie, Esmaeil
Ebrahimi, Mansour
Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition
title Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition
title_full Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition
title_fullStr Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition
title_full_unstemmed Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition
title_short Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition
title_sort image processing unravels the evolutionary pattern of sars-cov-2 against sars and mers through position-based pattern recognition
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106241/
https://www.ncbi.nlm.nih.gov/pubmed/34004573
http://dx.doi.org/10.1016/j.compbiomed.2021.104471
work_keys_str_mv AT ahsanreza imageprocessingunravelstheevolutionarypatternofsarscov2againstsarsandmersthroughpositionbasedpatternrecognition
AT tahsilimohammadreza imageprocessingunravelstheevolutionarypatternofsarscov2againstsarsandmersthroughpositionbasedpatternrecognition
AT ebrahimifaezeh imageprocessingunravelstheevolutionarypatternofsarscov2againstsarsandmersthroughpositionbasedpatternrecognition
AT ebrahimieesmaeil imageprocessingunravelstheevolutionarypatternofsarscov2againstsarsandmersthroughpositionbasedpatternrecognition
AT ebrahimimansour imageprocessingunravelstheevolutionarypatternofsarscov2againstsarsandmersthroughpositionbasedpatternrecognition