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




... 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


joint project with Trevor Bedford & his lab

Emergence and dominance of VoCs

VoCs have more mutations than expected...



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


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