Real-time tracking of seasonal influenza
virus evolution in humans
Video tutorial
Feature overview
The date slider allows exploration of viruses isolations through time
Color tree by epitope evolution

Epitope substitutions are based on HA structure and exposed residues. Multiple recent mutations at epitope sites have been suggested to be predictive for strains dominating future seasons.

Color tree by evolution outside epitopes

Mutations outside of the epitopes (see above) -- termed non-epitope sites --- tend to be damaging and are suggested to be predictive of clade contraction.

Color tree by evolution at the receptor binding site

Antigenic evolution has been shown to depend primarily on substitutions surrounding the receptor binding site of HA1. These seven positions (145, 155, 156, 158, 159, 189, 193 in HA1 numbering) are referred to here as receptor binding positions and changes at these positions could correspond to large changes in antigenic properties.

Color tree by the local branching index

The local branching index is the exponentially weighted tree length surrounding a node, which is associated with rapid branching and expansion of clades. A more detailed explanation is available here. Retrospective analysis has shown that LBI correlates with clade growth. For coloring, the LBI is normalized to the interval 0-1.

Color tree by sampling location
Color tree by genotype

Use the input box to specify positions to color viruses by genotype. Amino acid positions must be separated by a comma (e.g. 159,225). Only positions at which at least 10 strains have mutations are included.

Mouse-over tip

Placing the mouse over a circle corresponding to a virus strain displays the name, sampling date, and the numerical values of the different features.

Mouse-over branch

Placing the mouse a branch ancestral to a clade will display the frequency at the date specified by the date slider. For large clades, the frequency trajectory will be shown in the "mutation and genotype frequencies" plot as the curve labeled "clade".

Plotting frequencies of mutations and genotypes