A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design
Identifieur interne : 001D59 ( Main/Exploration ); précédent : 001D58; suivant : 001D60A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design
Auteurs : Refat Sharmin ; Abul Bashar Mir Md Khademul IslamSource :
- BMC Bioinformatics [ 1471-2105 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- enzymologie : Coronavirus.
- immunologie : Coronavirus, Protéines virales, RNA replicase.
- Algorithmes, Alignement de séquences, Humains, Protéines virales, RNA replicase, Séquence conservée, Séquence d'acides aminés, Vaccins antiviraux, Épitopes.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Epitopes, RNA Replicase, Viral Proteins.
- enzymology : Coronavirus.
- immunology : Coronavirus, RNA Replicase, Viral Proteins.
- Algorithms, Amino Acid Sequence, Conserved Sequence, Humans, Sequence Alignment, Viral Vaccines.
Abstract
Coronaviruses are the diverse group of RNA virus. From 1960, six strains of human coronaviruses have emerged that includes SARS-CoV and the recent infection by deadly MERS-CoV which is now going to cause another outbreak. Prevention of these viruses is urgent and a universal vaccine for all strain could be a promising solution in this circumstance. In this study we aimed to design an epitope based vaccine against all strain of human coronavirus.
Multiple sequence alignment (MSA) approach was employed among spike (S), membrane (M), enveloped (E) and nucleocapsid (N) protein and replicase polyprotein 1ab to identify which one is highly conserve in all coronaviruses strains. Next, we use various
Here we suggest
The online version of this article (doi:10.1186/1471-2105-15-161) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2105-15-161
PubMed: 24884408
PubMed Central: 4041900
Affiliations:
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Le document en format XML
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when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000258</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000258</idno><idno type="wicri:Area/Pmc/Curation">000258</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000258</idno><idno type="wicri:Area/Pmc/Checkpoint">001144</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001144</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:24884408</idno><idno type="wicri:Area/PubMed/Corpus">001950</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001950</idno><idno type="wicri:Area/PubMed/Curation">001950</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001950</idno><idno type="wicri:Area/PubMed/Checkpoint">001A15</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001A15</idno><idno type="wicri:Area/Ncbi/Merge">000D97</idno><idno type="wicri:Area/Ncbi/Curation">000D97</idno><idno type="wicri:Area/Ncbi/Checkpoint">000D97</idno><idno type="wicri:Area/Main/Merge">001D74</idno><idno type="wicri:Area/Main/Curation">001D59</idno><idno type="wicri:Area/Main/Exploration">001D59</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design</title><author><name sortKey="Sharmin, Refat" sort="Sharmin, Refat" uniqKey="Sharmin R" first="Refat" last="Sharmin">Refat Sharmin</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author><author><name sortKey="Islam, Abul Bashar Mir Md Khademul" sort="Islam, Abul Bashar Mir Md Khademul" uniqKey="Islam A" first="Abul Bashar Mir Md Khademul" last="Islam">Abul Bashar Mir Md Khademul Islam</name><affiliation><nlm:aff id="Aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Conserved Sequence</term><term>Coronavirus (enzymology)</term><term>Coronavirus (immunology)</term><term>Epitopes (chemistry)</term><term>Humans</term><term>RNA Replicase (chemistry)</term><term>RNA Replicase (immunology)</term><term>Sequence Alignment</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (immunology)</term><term>Viral Vaccines</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Coronavirus (enzymologie)</term><term>Coronavirus (immunologie)</term><term>Humains</term><term>Protéines virales ()</term><term>Protéines virales (immunologie)</term><term>RNA replicase ()</term><term>RNA replicase (immunologie)</term><term>Séquence conservée</term><term>Séquence d'acides aminés</term><term>Vaccins antiviraux</term><term>Épitopes ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Epitopes</term><term>RNA Replicase</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Coronavirus</term><term>Protéines virales</term><term>RNA replicase</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Coronavirus</term><term>RNA Replicase</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Conserved Sequence</term><term>Humans</term><term>Sequence Alignment</term><term>Viral Vaccines</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Alignement de séquences</term><term>Humains</term><term>Protéines virales</term><term>RNA replicase</term><term>Séquence conservée</term><term>Séquence d'acides aminés</term><term>Vaccins antiviraux</term><term>Épitopes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Coronaviruses are the diverse group of RNA virus. From 1960, six strains of human coronaviruses have emerged that includes SARS-CoV and the recent infection by deadly MERS-CoV which is now going to cause another outbreak. Prevention of these viruses is urgent and a universal vaccine for all strain could be a promising solution in this circumstance. In this study we aimed to design an epitope based vaccine against all strain of human coronavirus.</p></sec><sec><title>Results</title><p>Multiple sequence alignment (MSA) approach was employed among spike (S), membrane (M), enveloped (E) and nucleocapsid (N) protein and replicase polyprotein 1ab to identify which one is highly conserve in all coronaviruses strains. Next, we use various <italic>in silico</italic> tools to predict consensus immunogenic and conserved peptide. We found that conserved region is present only in the RNA directed RNA polymerase protein. In this protein we identified one epitope WDYPKCDRA is highly immunogenic and 100% conserved among all available human coronavirus strains.</p></sec><sec><title>Conclusions</title><p>Here we suggest <italic>in vivo</italic> study of our identified novel peptide antigen in RNA directed RNA polymerase protein for universal vaccine – which may be the way to prevent all human coronavirus disease.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2105-15-161) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Luis, E" uniqKey="Luis E">E Luis</name></author><author><name sortKey="Isabel, S" uniqKey="Isabel S">S Isabel</name></author><author><name sortKey="Sonia, Z" uniqKey="Sonia Z">Z Sonia</name></author><author><name sortKey="Fernando, A" uniqKey="Fernando A">A 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sortKey="Roberts, A" uniqKey="Roberts A">A Roberts</name></author><author><name sortKey="Murphy, Br" uniqKey="Murphy B">BR Murphy</name></author><author><name sortKey="Subbarao, K" uniqKey="Subbarao K">K Subbarao</name></author><author><name sortKey="Nabel, Gj" uniqKey="Nabel G">GJ Nabel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sudhakar, A" uniqKey="Sudhakar A">A Sudhakar</name></author><author><name sortKey="Robin, G" uniqKey="Robin G">G Robin</name></author><author><name sortKey="Boyd, L" uniqKey="Boyd L">L Boyd</name></author><author><name sortKey="Agnihothram, S" uniqKey="Agnihothram S">S Agnihothram</name></author><author><name sortKey="Gopal, R" uniqKey="Gopal R">R Gopal</name></author><author><name sortKey="Yount, Bl" uniqKey="Yount B">BL Yount</name></author><author><name sortKey="Donaldson, Ef" uniqKey="Donaldson E">EF Donaldson</name></author><author><name sortKey="Menachery, Vd" uniqKey="Menachery V">VD 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sortKey="Olesen, Of" uniqKey="Olesen O">OF Olesen</name></author><author><name sortKey="Lonnoroth, A" uniqKey="Lonnoroth A">A Lonnoroth</name></author><author><name sortKey="Mulligan, B" uniqKey="Mulligan B">B Mulligan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benson, Da" uniqKey="Benson D">DA Benson</name></author><author><name sortKey="Cavanaugh, M" uniqKey="Cavanaugh M">M Cavanaugh</name></author><author><name sortKey="Clark, K" uniqKey="Clark K">K Clark</name></author><author><name sortKey="Karsch Mizrachi, I" uniqKey="Karsch Mizrachi I">I Karsch-Mizrachi</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author><author><name sortKey="Ostell, J" uniqKey="Ostell J">J Ostell</name></author><author><name sortKey="Sayers, Ew" uniqKey="Sayers E">EW Sayers</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Islam, Abul Bashar Mir Md Khademul" sort="Islam, Abul Bashar Mir Md Khademul" uniqKey="Islam A" first="Abul Bashar Mir Md Khademul" last="Islam">Abul Bashar Mir Md Khademul Islam</name><name sortKey="Sharmin, Refat" sort="Sharmin, Refat" uniqKey="Sharmin R" first="Refat" last="Sharmin">Refat Sharmin</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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