Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogens

Author:

Yan Le1ORCID,Neher Richard A2ORCID,Shraiman Boris I1ORCID

Affiliation:

1. Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, United States

2. Biozentrum, University of Basel, Swiss Institute for Bioinformatics, Basel, Switzerland

Abstract

Rapidly evolving pathogens like influenza viruses can persist by changing their antigenic properties fast enough to evade the adaptive immunity, yet they rarely split into diverging lineages. By mapping the multi-strain Susceptible-Infected-Recovered model onto the traveling wave model of adapting populations, we demonstrate that persistence of a rapidly evolving, Red-Queen-like state of the pathogen population requires long-ranged cross-immunity and sufficiently large population sizes. This state is unstable and the population goes extinct or ‘speciates’ into two pathogen strains with antigenic divergence beyond the range of cross-inhibition. However, in a certain range of evolutionary parameters, a single cross-inhibiting population can exist for times long compared to the time to the most recent common ancestor (TMRCA) and gives rise to phylogenetic patterns typical of influenza virus. We demonstrate that the rate of speciation is related to fluctuations ofTMRCAand construct a ‘phase diagram’ identifying different phylodynamic regimes as a function of evolutionary parameters.

Funder

Simons Foundation

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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