Figure 2.

Simulation results showing epidemiological, antigenic, and genealogical dynamics. (A) Weekly time series of incidence of viral infection in north and tropics regions. (B) Two-dimensional antigenic phenotypes of 5,943 viruses sampled over the course of the simulation. Each discrete virus phenotype is shown as a bubble, with the bubble area proportional to the number of times this phenotype was sampled. (C) Genealogical tree depicting the infection history of 376 samples from the virus population. Parent/offspring relationships were tracked over the course of the simulation, giving a direct observation of the genealogy rather than a phylogenetic inference. (D) Antigenic map depicting phenotypes of 5,943 viruses sampled over the course of the simulation. To approximate experimental noise present in the observed antigenic map of H3N2 influenza, noise was added to each sample, and the resulting observations were grouped into 11 clusters and colored accordingly. Grid lines show single units of antigenic distance.