Influenza A epidemics in humans are characterised by infrequent (typically on a decadal timescale), but nevertheless significant, genetic re-assortments that lead to pandemics of new sub-types (antigenic shift) as well as within-sub-type evolution (antigenic drift) on an annual timescale. In the antigenic shift scenario it is assumed that there is very little or no host cross-immunity with previous virus types, whereas within-sub-type drift can generate strains with varying degrees of host immune response. This difference is important in determining how variants invade host populations.