This is interesting - it's a paper from Kristian G.called Tracking Virus Outbreaks in the Twenty-First Century. There's talk about how the world was caught unprepared but it seems like some organizations were ready:

Here, we describe how many of the key questions in infectious disease epidemiology, from the initial detection and characterization of outbreak viruses, to transmission chain tracking and outbreak mapping, can now be much more accurately addressed using recent advances in virus sequencing and phylogenetics. We highlight the utility of this approach with the hypothetical outbreak of an unknown pathogen, 'Disease X', suggested by the World Health Organization to be a potential cause of a future major epidemic.

Phylogenetics is concerned with:
1. Evolutionary relationships or histories among my species/individuals/genes of interest
2. How sequences evolve
3. Describing processes of sequence evolution with a mathematical model

Number 2 is the interesting one. This is where you get into 'gain-of-function' experiments - the idea being to take a look at evolution from the inside - give it a helping hand - see what happens - so you can better anticipate it - all for our own good etc