Evolution and spread of Influenza, HIV, and SARS-CoV-2

Richard Neher
Biozentrum, University of Basel

slides at neherlab.org/202112_CBB.html

Human seasonal influenza viruses

slide by Trevor Bedford

Positive tests for influenza in the USA by week

Data by the US CDC

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

nextstrain.org

joint project with Trevor Bedford & his lab

Emergence and dominance of VoCs

VoCs have more mutations than expected...

nextstrain

Acknowledgments

Fabio Zanini
Jan Albert
Johanna Brodin
Christa Lanz
Göran Bratt
Lina Thebo
Vadim Puller

Acknowledgments

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