Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method

Ren, J; Ellis, J; Li, J

Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method

Ren, J Ellis, J

Li, J

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Publication Type:: Journal Article
Citation:: Journal of Bioinformatics and Computational Biology, 2014, 12 (5)
Issue Date:: 2014-01-01

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Field	Value	Language
dc.contributor.author	Ren, J	en_US
dc.contributor.author	Ellis, J https://orcid.org/0000-0001-7328-4831	en_US
dc.contributor.author	Li, J https://orcid.org/0000-0003-1833-7413	en_US
dc.date.issued	2014-01-01	en_US
dc.identifier.citation	Journal of Bioinformatics and Computational Biology, 2014, 12 (5)	en_US
dc.identifier.issn	0219-7200	en_US
dc.identifier.uri	http://hdl.handle.net/10453/35764
dc.identifier.uri	http://hdl.handle.net/10453/35658
dc.identifier.uri	http://hdl.handle.net/10453/35763
dc.description.abstract	© Imperial College Press. A conserved epitope is an epitope retained by multiple strains of influenza as the key target of a broadly neutralizing antibody. Identification of conserved epitopes is of strong interest to help design broad-spectrum vaccines against influenza. Conservation score measures the evolutionary conservation of an amino acid position in a protein based on the phylogenetic relationships observed amongst homologous sequences. Here, Average Amino Acid Conservation Score (AAACS) is proposed as a method to identify HA's conserved epitopes. Our analysis shows that there is a clear distinction between conserved epitopes and nonconserved epitopes in terms of AAACS. This method also provides an excellent classification performance on an independent dataset. In contrast, alignment-based comparison methods do not work well for this problem, because conserved epitopes to the same broadly neutralizing antibody are usually not identical or similar. Location-based methods are not successful either, because conserved epitopes are located at both the less-conserved globular head (HA1) and the more-conserved stem (HA2). As a case study, two conserved epitopes on HA are predicted for the influenza A virus H7N9: One should match the broadly neutralizing antibodies CR9114 or FI6v3, while the other is new and requires validation by wet-lab experiments.	en_US
dc.relation.ispartof	Journal of Bioinformatics and Computational Biology	en_US
dc.relation.isbasedon	10.1142/S0219720014500231	en_US
dc.subject.classification	Bioinformatics	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Influenza A virus	en_US
dc.subject.mesh	Hemagglutinin Glycoproteins, Influenza Virus	en_US
dc.subject.mesh	Antibodies, Viral	en_US
dc.subject.mesh	Antigens, Viral	en_US
dc.subject.mesh	Epitopes	en_US
dc.subject.mesh	Models, Statistical	en_US
dc.subject.mesh	Computational Biology	en_US
dc.subject.mesh	Evolution, Molecular	en_US
dc.subject.mesh	Amino Acid Sequence	en_US
dc.subject.mesh	Conserved Sequence	en_US
dc.subject.mesh	Models, Molecular	en_US
dc.subject.mesh	Databases, Protein	en_US
dc.subject.mesh	Influenza, Human	en_US
dc.subject.mesh	Antibodies, Neutralizing	en_US
dc.subject.mesh	Influenza A Virus, H7N9 Subtype	en_US
dc.title	Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method	en_US
dc.type	Journal Article
utslib.citation.volume	5	en_US
utslib.citation.volume	12	en_US
utslib.for	060112 Structural Biology (incl. Macromolecular Modelling)	en_US
utslib.for	1107 Immunology	en_US
utslib.for	0601 Biochemistry and Cell Biology	en_US
utslib.for	0801 Artificial Intelligence and Image Processing	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney/Strength - AAI - Advanced Analytics Institute Research Centre
pubs.organisational-group	/University of Technology Sydney/Strength - CHT - Health Technologies
pubs.organisational-group	/University of Technology Sydney/Students
utslib.copyright.status	closed_access
pubs.issue	5	en_US
pubs.publication-status	Published	en_US
pubs.volume	12	en_US

Abstract:

© Imperial College Press. A conserved epitope is an epitope retained by multiple strains of influenza as the key target of a broadly neutralizing antibody. Identification of conserved epitopes is of strong interest to help design broad-spectrum vaccines against influenza. Conservation score measures the evolutionary conservation of an amino acid position in a protein based on the phylogenetic relationships observed amongst homologous sequences. Here, Average Amino Acid Conservation Score (AAACS) is proposed as a method to identify HA's conserved epitopes. Our analysis shows that there is a clear distinction between conserved epitopes and nonconserved epitopes in terms of AAACS. This method also provides an excellent classification performance on an independent dataset. In contrast, alignment-based comparison methods do not work well for this problem, because conserved epitopes to the same broadly neutralizing antibody are usually not identical or similar. Location-based methods are not successful either, because conserved epitopes are located at both the less-conserved globular head (HA1) and the more-conserved stem (HA2). As a case study, two conserved epitopes on HA are predicted for the influenza A virus H7N9: One should match the broadly neutralizing antibodies CR9114 or FI6v3, while the other is new and requires validation by wet-lab experiments.

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http://hdl.handle.net/10453/35658