### Human seasonal influenza viruses

slide by Trevor Bedford
### Virus genomes change rapidly through time

**A/Brisbane/100/2014**

GGATAATTCTATTAACCATGAAGACTATCATTGCTTT...

**A/Brisbane/1000/2015**

GGATAATTCTATTAACCATGAAGACTATTATTGCTTT...

**A/Brisbane/1/2017**

GGATAATTCTATTAACCATGAAGACTATCATTGCTTT...

... hundreds of thousands of sequences...

### Genome sequences record the spread of pathogens

##### in SARS-CoV-2 a new mutation accumulates about every 2 weeks

images by Trevor Bedford
- Influenza viruses evolve to avoid human immunity
- Vaccines need frequent updates

### 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
## Real-time tracking of SARS-CoV-2

- hundreds of new sequences every day
- more than >6M sequences right now
- comprehensive analysis require hours to days to complete

##### → requires continuous analysis and easy dissemination

##### → interpretable and intuitive visualization

### Emergence and dominance of VoCs

## VoCs have more mutations than expected...

nextstrain
### Acknowledgments

- Fabio Zanini
- Jan Albert
- Johanna Brodin
- Christa Lanz
- GĂ¶ran Bratt
- Lina Thebo
- Vadim Puller

### Acknowledgments

- Emma Hodcroft
- Moira Zuber
- Inaki Comas
- Fernando Gonzales
- Tanja Stadler
- Sarah Nadeau
- Tim Vaughan
- Jesse Bloom
- David Veesler