Viruses
tobacco mosaic virus
bacteria phage
influenza virus
human immunodeficiency virus
- rely on host to replicate
- little more than genome + capsid
- genomes typically 5-200k bases (+exceptions)
- many infectious diseases are caused by viruses
- very important function in microbial eco-systems
- most abundant organisms on earth $\sim 10^{31}$
Evolution of HIV
- Chimp → human transmission around 1768 gave rise to HIV-1 group M
- ~100 million infected people since
- subtypes differ at 10-20% of their genome
- HIV-1 evolves ~0.1% per year
image: Sharp and Hahn, CSH Persp. Med.
HIV infection
- $10^8$ cells are infected every day
- the virus repeatedly escapes immune recognition
- integrates into T-cells as latent provirus
image: wikipedia
HIV-1 evolution within one individual
silouhette: clipartfest.com, Zanini at al, 2015. Collaboration with Jan Albert and his group
Population genetic models of rapid evolution
RN, Annual Reviews, 2013; Desai & Fisher; Brunet & Derride; Kessler & Levine
Neutral/Kingman coalescent
strong selection
Bolthausen-Sznitman Coalescent
RN, Hallatschek, PNAS, 2013; see also Brunet and Derrida, PRE, 2007
Zanini et al, eLife, 2015
Bursts in a tree ↔ high fitness genotypes
Can we read fitness of a tree?
Human seasonal influenza viruses
slide by Trevor Bedford
- Influenza virus evolves 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
HIV acknowledgments
- Fabio Zanini
- Jan Albert
- Johanna Brodin
- Christa Lanz
- Göran Bratt
- Lina Thebo
- Vadim Puller
Influenza and Theory acknowledgments
- Boris Shraiman
- Colin Russell
- Trevor Bedford
- Oskar Hallatschek
nextstrain.org
- Trevor Bedford
- Colin Megill
- Pavel Sagulenko
- Wei Ding
- Sidney Bell
- James Hadfield