SARS-CoV-2 spike protein displays sequence similarities with paramyxovirus surface proteins; a bioinformatics study
Recent emergence of SARS-CoV-2 and associated COVID-19 pandemic have posed a great challenge for the scientific community. In this study, we performed bioinformatic analyses on SARS-CoV-2 protein sequences, trying to unravel potential molecular similarities between this newly emerged pathogen with n...
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| Veröffentlicht in: | PloS one 2021-12, Vol.16 (12), p.e0260360-e0260360 |
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| creator | Ahmadi, Ehsan Zabihi, Mohammad Reza Hosseinzadeh, Ramin Mohamed Khosroshahi, Leila Noorbakhsh, Farshid |
| description | Recent emergence of SARS-CoV-2 and associated COVID-19 pandemic have posed a great challenge for the scientific community. In this study, we performed bioinformatic analyses on SARS-CoV-2 protein sequences, trying to unravel potential molecular similarities between this newly emerged pathogen with non-coronavirus ssRNA viruses. Comparing the proteins of SARS-CoV-2 with non-coronavirus positive and negative strand ssRNA viruses revealed multiple sequence similarities between SARS-CoV-2 and non-coronaviruses, including similarities between RNA-dependent RNA-polymerases and helicases (two highly-conserved proteins). We also observed similarities between SARS-CoV-2 surface (i.e. spike) protein with paramyxovirus fusion proteins. This similarity was restricted to a segment of spike protein S2 subunit which is involved in cell fusion. We next analyzed spike proteins from SARS-CoV-2 “variants of concern” (VOCs) and “variants of interests” (VOIs) and found that some of these variants show considerably higher spike-fusion similarity with paramyxoviruses. The ‘spike-fusion’ similarity was also observed for some pathogenic coronaviruses other than SARS-CoV-2. Epitope analysis using experimentally verified data deposited in Immune Epitope Database (IEDB) revealed that several B cell epitopes as well as T cell and MHC binding epitopes map within the spike-fusion similarity region. These data indicate that there might be a degree of convergent evolution between SARS-CoV-2 and paramyxovirus surface proteins which could be of pathogenic and immunological importance. |
| doi_str_mv | 10.1371/journal.pone.0260360 |
| format | Article |
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In this study, we performed bioinformatic analyses on SARS-CoV-2 protein sequences, trying to unravel potential molecular similarities between this newly emerged pathogen with non-coronavirus ssRNA viruses. Comparing the proteins of SARS-CoV-2 with non-coronavirus positive and negative strand ssRNA viruses revealed multiple sequence similarities between SARS-CoV-2 and non-coronaviruses, including similarities between RNA-dependent RNA-polymerases and helicases (two highly-conserved proteins). We also observed similarities between SARS-CoV-2 surface (i.e. spike) protein with paramyxovirus fusion proteins. This similarity was restricted to a segment of spike protein S2 subunit which is involved in cell fusion. We next analyzed spike proteins from SARS-CoV-2 “variants of concern” (VOCs) and “variants of interests” (VOIs) and found that some of these variants show considerably higher spike-fusion similarity with paramyxoviruses. The ‘spike-fusion’ similarity was also observed for some pathogenic coronaviruses other than SARS-CoV-2. Epitope analysis using experimentally verified data deposited in Immune Epitope Database (IEDB) revealed that several B cell epitopes as well as T cell and MHC binding epitopes map within the spike-fusion similarity region. These data indicate that there might be a degree of convergent evolution between SARS-CoV-2 and paramyxovirus surface proteins which could be of pathogenic and immunological importance.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0260360</identifier><identifier>PMID: 34855795</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Amino acid sequence ; Bioinformatics ; Biology and life sciences ; Cell fusion ; Computer and Information Sciences ; Coronaviridae ; Coronaviruses ; COVID-19 ; Epitopes ; Fusion protein ; Health aspects ; Immunology ; Lymphocytes ; Lymphocytes T ; Major histocompatibility complex ; Medicine and health sciences ; Nucleotide sequence ; Pandemics ; Phylogenetics ; Proteins ; Research and Analysis Methods ; Severe acute respiratory syndrome ; Severe acute respiratory syndrome coronavirus 2 ; Similarity ; Spike protein ; T cells ; Viral diseases ; Viruses</subject><ispartof>PloS one, 2021-12, Vol.16 (12), p.e0260360-e0260360</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Ahmadi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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In this study, we performed bioinformatic analyses on SARS-CoV-2 protein sequences, trying to unravel potential molecular similarities between this newly emerged pathogen with non-coronavirus ssRNA viruses. Comparing the proteins of SARS-CoV-2 with non-coronavirus positive and negative strand ssRNA viruses revealed multiple sequence similarities between SARS-CoV-2 and non-coronaviruses, including similarities between RNA-dependent RNA-polymerases and helicases (two highly-conserved proteins). We also observed similarities between SARS-CoV-2 surface (i.e. spike) protein with paramyxovirus fusion proteins. This similarity was restricted to a segment of spike protein S2 subunit which is involved in cell fusion. We next analyzed spike proteins from SARS-CoV-2 “variants of concern” (VOCs) and “variants of interests” (VOIs) and found that some of these variants show considerably higher spike-fusion similarity with paramyxoviruses. The ‘spike-fusion’ similarity was also observed for some pathogenic coronaviruses other than SARS-CoV-2. Epitope analysis using experimentally verified data deposited in Immune Epitope Database (IEDB) revealed that several B cell epitopes as well as T cell and MHC binding epitopes map within the spike-fusion similarity region. These data indicate that there might be a degree of convergent evolution between SARS-CoV-2 and paramyxovirus surface proteins which could be of pathogenic and immunological importance.</description><subject>Amino acid sequence</subject><subject>Bioinformatics</subject><subject>Biology and life sciences</subject><subject>Cell fusion</subject><subject>Computer and Information Sciences</subject><subject>Coronaviridae</subject><subject>Coronaviruses</subject><subject>COVID-19</subject><subject>Epitopes</subject><subject>Fusion protein</subject><subject>Health aspects</subject><subject>Immunology</subject><subject>Lymphocytes</subject><subject>Lymphocytes T</subject><subject>Major histocompatibility complex</subject><subject>Medicine and health sciences</subject><subject>Nucleotide sequence</subject><subject>Pandemics</subject><subject>Phylogenetics</subject><subject>Proteins</subject><subject>Research and Analysis Methods</subject><subject>Severe acute respiratory 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sciences</topic><topic>Nucleotide sequence</topic><topic>Pandemics</topic><topic>Phylogenetics</topic><topic>Proteins</topic><topic>Research and Analysis Methods</topic><topic>Severe acute respiratory syndrome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Similarity</topic><topic>Spike protein</topic><topic>T cells</topic><topic>Viral diseases</topic><topic>Viruses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ahmadi, Ehsan</creatorcontrib><creatorcontrib>Zabihi, Mohammad Reza</creatorcontrib><creatorcontrib>Hosseinzadeh, Ramin</creatorcontrib><creatorcontrib>Mohamed Khosroshahi, Leila</creatorcontrib><creatorcontrib>Noorbakhsh, Farshid</creatorcontrib><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior 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of SARS-CoV-2 and associated COVID-19 pandemic have posed a great challenge for the scientific community. In this study, we performed bioinformatic analyses on SARS-CoV-2 protein sequences, trying to unravel potential molecular similarities between this newly emerged pathogen with non-coronavirus ssRNA viruses. Comparing the proteins of SARS-CoV-2 with non-coronavirus positive and negative strand ssRNA viruses revealed multiple sequence similarities between SARS-CoV-2 and non-coronaviruses, including similarities between RNA-dependent RNA-polymerases and helicases (two highly-conserved proteins). We also observed similarities between SARS-CoV-2 surface (i.e. spike) protein with paramyxovirus fusion proteins. This similarity was restricted to a segment of spike protein S2 subunit which is involved in cell fusion. We next analyzed spike proteins from SARS-CoV-2 “variants of concern” (VOCs) and “variants of interests” (VOIs) and found that some of these variants show considerably higher spike-fusion similarity with paramyxoviruses. The ‘spike-fusion’ similarity was also observed for some pathogenic coronaviruses other than SARS-CoV-2. Epitope analysis using experimentally verified data deposited in Immune Epitope Database (IEDB) revealed that several B cell epitopes as well as T cell and MHC binding epitopes map within the spike-fusion similarity region. These data indicate that there might be a degree of convergent evolution between SARS-CoV-2 and paramyxovirus surface proteins which could be of pathogenic and immunological importance.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34855795</pmid><doi>10.1371/journal.pone.0260360</doi><tpages>e0260360</tpages><orcidid>https://orcid.org/0000-0003-4304-0048</orcidid><oa>free_for_read</oa></addata></record> |
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| source | DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Amino acid sequence Bioinformatics Biology and life sciences Cell fusion Computer and Information Sciences Coronaviridae Coronaviruses COVID-19 Epitopes Fusion protein Health aspects Immunology Lymphocytes Lymphocytes T Major histocompatibility complex Medicine and health sciences Nucleotide sequence Pandemics Phylogenetics Proteins Research and Analysis Methods Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Similarity Spike protein T cells Viral diseases Viruses |
| title | SARS-CoV-2 spike protein displays sequence similarities with paramyxovirus surface proteins; a bioinformatics study |
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