Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus

MOTIVATION Continual and accumulated mutations in hemagglutinin (HA) protein of influenza A virus generate novel antigenic strains that cause annual epidemics. RESULTS We propose a model by incorporating scoring and regression methods to predict antigenic variants. Based on collected sequences of influenza A/H3N2 viruses isolated between 1971 and 2002, our model can be used to accurately predict the antigenic variants in 1999-2004 (agreement rate = 91.67%). Twenty amino acid positions identified in our model contribute significantly to antigenic difference and are potential immunodominant positions.

[1]  Michael W. Shaw,et al.  Influenza A (H3N2) Outbreak, Nepal , 2005, Emerging infectious diseases.

[2]  A. Lapedes,et al.  Mapping the Antigenic and Genetic Evolution of Influenza Virus , 2004, Science.

[3]  J. McAnerney,et al.  Antigenic and molecular analysis of influenza A (H3N2) virus strains isolated from a localised influenza outbreak in South Africa in 2003 , 2004, Journal of medical virology.

[4]  J. Skehel,et al.  Variation and infectivity neutralization in influenza , 2006, Immunology.

[5]  Alex S. Morton,et al.  Modelling antigenic drift in weekly flu incidence , 2005, Statistics in medicine.

[6]  Michael W Deem,et al.  Quantifying influenza vaccine efficacy and antigenic distance. , 2005, Vaccine.

[7]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[8]  W. Fitch,et al.  Predicting the evolution of human influenza A. , 1999, Science.

[9]  T H Jukes,et al.  Rates of transition and transversion in coding sequences since the human-rodent divergence. , 1994, Genomics.

[10]  R. Grantham.  Amino Acid Difference Formula to Help Explain Protein Evolution , 1974, Science.

[11]  Jonathan Dushoff,et al.  Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Min-Shi Lee,et al.  Predicting Antigenic Variants of Influenza A/H3N2 Viruses , 2004, Emerging infectious diseases.

[13]  M. Zambon,et al.  Analysis of influenza A H3N2 strains isolated in England during 1995–1996 using polymerase chain reaction restriction , 1997, Journal of medical virology.

[14]  Baldomero Oliva,et al.  Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships , 2005, Bioinform..

[15]  E. D. Kilbourne,et al.  Independent and disparate evolution in nature of influenza A virus hemagglutinin and neuraminidase glycoproteins. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J Goodman,et al.  The value of a database in surveillance and vaccine selection , 2001 .

[17]  S. Miyazawa,et al.  Two types of amino acid substitutions in protein evolution , 1979, Journal of Molecular Evolution.

[18]  W. Fitch,et al.  Positive selection on the H3 hemagglutinin gene of human influenza virus A. , 1999, Molecular biology and evolution.

[19]  Marc Lipsitch,et al.  Patterns of antigenic diversity and the mechanisms that maintain them , 2007, Journal of The Royal Society Interface.

[20]  Chung-Yen Lin,et al.  POWER: PhylOgenetic WEb Repeater—an integrated and user-optimized framework for biomolecular phylogenetic analysis , 2005, Nucleic Acids Res..

[21]  Hong Jin,et al.  Two residues in the hemagglutinin of A/Fujian/411/02-like influenza viruses are responsible for antigenic drift from A/Panama/2007/99. , 2005, Virology.

[22]  Yu-Chieh Liao,et al.  Identifying potential immunodominant positions and predicting antigenic variants of influenza A/H3N2 viruses. , 2007, Vaccine.