### Sequences record the spread of pathogens

##### The resolution is limited by the number of mutations!

images by Trevor Bedford
### Human seasonal influenza viruses

slide by Trevor Bedford
- Influenza virus evolves to avoid human immunity
- Vaccines need frequent updates

## Beyond tracking: can we predict?

### Competition between different viral variants

RN, Annual Reviews, 2013; Desai & Fisher; Brunet & Derride; Kessler & Levine
### Predicting evolution

### Given the branching pattern:

- can we predict fitness?
- pick the closest relative of the future?

RN, Russell, Shraiman, eLife, 2014
### Fitness inference from trees

$$P(\mathbf{x}|T) = \frac{1}{Z(T)} p_0(x_0) \prod_{i=0}^{n_{int}} g(x_{i_1}, t_{i_1}| x_i, t_i)g(x_{i_2}, t_{i_2}| x_i, t_i)$$

RN, Russell, Shraiman, eLife, 2014
### Prediction of the dominating H3N2 influenza strain

- no influenza specific input
- how can the model be improved? (see model by Luksza & Laessig)
- what other context might this apply?

RN, Russell, Shraiman, eLife, 2014
## nextstrain.org

- integrate data from many different sources
- analyze those data in near real time
- disseminate results in an intuitive yet informative way
- provide actionable insights

### Influenza and Theory acknowledgments

- Boris Shraiman
- Colin Russell
- Trevor Bedford
- Oskar Hallatschek

### nextstrain.org

- Trevor Bedford
- Colin Megill
- Pavel Sagulenko
- Sidney Bell
- James Hadfield
- Wei Ding