H3N2 California/7 Hemagglutinin Sequence at Los Alamos
Recombinomics Commentary
February 27, 2005
The sequence of HA from cell passaged and egg passaged A/California/7/2004 is available at Los Alamos. The virus appears to have arrived in Santa Clara, California by way of Taiwan and Zhegiang Province in China. Isolates from 2003 contain some of the new polymorphisms found in California/7. Additional changes are also found in some New York isolates from 2003 also. HA is the only sequenced gene from California/7 that is publicly available. A full data set for all 8 genes would be useful.
Full sequences from a large number of New York isolates are currently on deposit at GenBank and are part of the NIAID program to develop a Genetic Blueprint for Flu. The full set of sequences on New York flu patients is a good start.
The rapid spread of A/California and the ineffectiveness of the current vaccine strategy are becoming increasingly apparent. It seems likely that by the time the A/California vaccine is available in the fall, the H3N2 will have already evolved away from California/7, isolated September 16, 2004.
Influenza A evolves via recombination, which can be used to predict emerging genomes for human H3N2, as well as H5N1 bird flu, before they emerge. These predictions are enhanced by full data sets, which should significantly improve vaccine selection.