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Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):6263-8. Epub 2002 Apr 23.

Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus.

Author information

1
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA. plotkin@ias.edu

Abstract

Continual mutations to the hemagglutinin (HA) gene of influenza A virus generate novel antigenic strains that cause annual epidemics. Using a database of 560 viral RNA sequences, we study the structure and tempo of HA evolution over the past two decades. We detect a critical length scale, in amino acid space, at which HA sequences aggregate into clusters, or swarms. We investigate the spatio-temporal distribution of viral swarms and compare it to the time series of the influenza vaccines recommended by the World Health Organization. We introduce a method for predicting future dominant HA amino acid sequences and discuss its potential relevance to vaccine choice. We also investigate the relationship between cluster structure and the primary antibody-combining regions of the HA protein.

PMID:
11972025
PMCID:
PMC122937
DOI:
10.1073/pnas.082110799
[Indexed for MEDLINE]
Free PMC Article
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