  H1N1 influenza causes substantial seasonal illness and was the subtype of the
2009 influenza pandemic. Precise measures of antigenic distance between the
vaccine and circulating virus strains help researchers design influenza
vaccines with high vaccine effectiveness. We here introduce a sequence-based
method to predict vaccine effectiveness in humans. Historical epidemiological
data show that this sequence-based method is as predictive of vaccine
effectiveness as hemagglutination inhibition (HI) assay data from ferret animal
model studies. Interestingly, the expected vaccine effectiveness is greater
against H1N1 than H3N2, suggesting a stronger immune response against H1N1 than
H3N2. The evolution rate of hemagglutinin in H1N1 is also shown to be greater
than that in H3N2, presumably due to greater immune selection pressure.
