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Predicting antigenic variants of influenza A/H3N2 viruses.

ABSTRACT: Current inactivated influenza vaccines provide protection when vaccine antigens and circulating viruses share a high degree of similarity in hemagglutinin protein. Five antigenic sites in the hemagglutinin protein have been proposed, and 131 amino acid positions have been identified in the five antigenic sites. In addition, 20, 18, and 32 amino acid positions in the hemagglutinin protein have been identified as mouse monoclonal antibody-binding sites, positively selected codons, and substantially diverse codons, respectively. We investigated these amino acid positions for predicting antigenic variants of influenza A/H3N2 viruses in ferrets. Results indicate that the model based on the number of amino acid changes in the five antigenic sites is best for predicting antigenic variants (agreement = 83%). The methods described in this study could be applied to predict vaccine-induced cross-reactive antibody responses in humans, which may further improve the selection of vaccine strains.

SUBMITTER: Lee MS

PROVIDER: S-EPMC3320420 | biostudies-literature | 2004 Aug

REPOSITORIES: biostudies-literature

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Predicting antigenic variants of influenza A/H3N2 viruses.

Lee Min-Shi MS Chen Jack Si-En JS

Emerging infectious diseases 20040801 8

Current inactivated influenza vaccines provide protection when vaccine antigens and circulating viruses share a high degree of similarity in hemagglutinin protein. Five antigenic sites in the hemagglutinin protein have been proposed, and 131 amino acid positions have been identified in the five antigenic sites. In addition, 20, 18, and 32 amino acid positions in the hemagglutinin protein have been identified as mouse monoclonal antibody-binding sites, positively selected codons, and substantiall ...[more]

PMID: 15496238

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Project description:BACKGROUND: In pandemic and epidemic forms, avian and human influenza viruses often cause significant damage to human society and economics. Gradually accumulated mutations on hemagglutinin (HA) cause immunologically distinct circulating strains, which lead to the antigenic drift (named as antigenic variants). The "antigenic variants" often requires a new vaccine to be formulated before each annual epidemic. Mapping the genetic evolution to the antigenic drift of influenza viruses is an emergent issue to public health and vaccine development RESULTS: We developed a method for identifying antigenic critical amino acid positions, rules, and co-mutated positions for antigenic variants. The information gain (IG) and the entropy are used to measure the score of an amino acid position on hemagglutinin (HA) for discriminating between antigenic variants and similar viruses. A position with high IG and entropy implied that this position is highly correlated to an antigenic drift. Nineteen positions with high IG and high genetic diversity are identified as antigenic critical positions on the HA proteins. Most of these antigenic critical positions are located on five epitopes or on the surface based on the HA structure. Based on IG values and entropies of these 19 positions on the HA, the decision tree was applied to create a rule-based model and to identify rules for predicting antigenic variants of a given two HA sequences which are often a vaccine strain and a circulating strain. The predicting accuracies of this model on two sets, which consist of a training set (181 hemagglutination inhibition (HI) assays) and an independent test set (31,878 HI assays), are 91.2% and 96.2% respectively. CONCLUSION: Our method is able to identify critical positions, rules, and co-mutated positions on HA for predicting the antigenic variants. The information gains and the entropies of HA positions provide insight to the antigenic drift and co-evolution positions for influenza seasons. We believe that our method is robust and is potential useful for studying influenza virus evolution and vaccine development.

Dataset Information

Predicting antigenic variants of influenza A/H3N2 viruses.

Publications

Predicting antigenic variants of influenza A/H3N2 viruses.

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