Accurate classification and hemagglutinin amino acid signatures for influenza A virus host-origin association and subtyping

Abstract Host-origin classification and signatures of influenza A viruses were investigated based on the HA protein for tracking of the HA host of origin. Hidden Markov models (HMMs), decision trees and associative classification for each influenza A virus subtype and its major hosts (human, avian,...

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Bibliographic Details
Published in:Virology (New York, N.Y.) N.Y.), 2014-01, Vol.449, p.328-338
Main Authors: ElHefnawi, Mahmoud, Sherif, Fayroz F
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Amino Acid Sequence
Animals
Birds
HA protein
Hemagglutinin Glycoproteins, Influenza Virus - chemistry
Hemagglutinin Glycoproteins, Influenza Virus - genetics
Hemagglutinin subtyping
Humans
Infectious Disease
Influenza
Influenza A virus
Influenza A virus - classification
Influenza A virus - genetics
Influenza A virus - isolation & purification
Influenza in Birds - virology
Influenza, Human - virology
Molecular Sequence Data
Mutation, Missense
Orthomyxoviridae Infections - veterinary
Orthomyxoviridae Infections - virology
Species Specificity
Swine
Swine Diseases - virology
Virus signature
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Summary:Abstract Host-origin classification and signatures of influenza A viruses were investigated based on the HA protein for tracking of the HA host of origin. Hidden Markov models (HMMs), decision trees and associative classification for each influenza A virus subtype and its major hosts (human, avian, swine) were generated. Features of the HA protein signatures that were host-and subtype-specific were sought. Host-associated signatures that occurred in different subtypes of the virus were identified. Evaluation of the classification models based on ROC curves and support and confidence ratings for the amino acid class-association rules was performed. Host classification based on the HA subtype achieved accuracies between 91.2% and 100% using decision trees after feature selection. Host-specific class association rules for avian-host origins gave better support and confidence ratings, followed by human and finally swine origin. This finding indicated the lower specificity of the swine host, perhaps pointing to its ability to mix different strains.
ISSN:0042-6822
1096-0341
DOI:10.1016/j.virol.2013.11.010