The vaccine match failures in this season's trivalent vaccine are creating health concerns. Last Friday the CDC held a media conference in advance of the weekly CDC influenza report. Influenza activity nationwide had taken a sudden jump, which was linked to poor vaccine matches with circulating influenza strains. Moreover there had been reports out of Europe on increased Tamiflu resistant which has "startled" influenza "experts."

The conference last Friday was followed by an MMWR report this Friday, along with another press conference. The poor batting average of 1 for 3 for vaccine matches had really fallen to 0 for 3 because the H1N1 circulation was shifting from Solomon Island-like, to Brisbane/59-like and the Brisbane strain was not a good match for the Solomon Island vaccine. Consequently, next year's vaccine will change all three components.

Moreover, recent data indicates the Tamiflu resistance is also appearing on the Brisbane strain. The sequence of the Brisbane strain was recently released and it is closely related to Tamiflu resistant isolates from Hawaii. Moreover, recent data from Europe on cross reactivity data between recent isolates indicates the two Tamiflu resistant strains (from France and Norway) were also Brisbane-like. However, all of the above is on isolates from 2007. The levels of resistance in 2008 isolates may be higher.

The Department of Health in Illinois just issued an alert because 10 Tamiflu resistant isolates were identified in Chicago, and eight of the ten were from the same health care facility. It is not clear if the high number was linked to Tamiflu treatment at the facility, but patients in Europe with Tamiflu-resistant H1N1 had not been taking Tamiflu, indicating H1N1 with H274Y is evolutionarily fit.

These match failures are due in part to the rapid evolution of influenza, which may be linked to increasing genetic diversity in seasonal and pandemic flu. A high percentage of swine isolates in the United States also have human genes, which leads to an increase in productive recombination and faster evolution.

The current vaccine failures highlight shortcomings in vaccine target selection, which will continue to deteriorate as influenza evolution is driven by vaccine mismatches and productive homologous recombination.