The advent of extremely high throughput
DNA sequencing ensures that genomic
data from microbial organisms can be
acquired in unprecedented quantities and
with remarkable rapidity. Although this
genomic revolution will affect all microbes
alike, our focus here is on RNA viruses, as
the rapidity of their evolution, which is
observable over the time scale of human
observation, allows phylodynamic inferences
to be made with great precision. In
the foreseeable future it is likely that
complete genome sequencing will become
the standard method of viral characterization,
providing the highest possible resolution
for phylogenetic studies. The rapidity
with which genome sequence data were
generated from the ongoing epidemic of
swine-origin H1N1 influenza A virus [1] is
testament to the power of this technology
