Population dynamics of infectious disease and pathogen evolution: modelling vaccine escape
type: CreativeWork
description: This thesis investigates how the risk that an infectious pathogen evolves antigenically (leading to pathogen strains that evade existing immunity) depends on the vaccination coverage of its host population. Deterministic compartmental models are coupled with a parsimonious approach to pathogen evolution, focussing on the selection pressure for immune escape. We study the qualitative patterns of this escape pressure — as a function of the vaccination coverage — and the epidemiological impact thereof, taking analytical approaches wherever possible. Chapter 2 varies the balance of the contributions to the escape pressure from infections in unvaccinated and vaccinated hosts. We use SIR-type models, for endemic disease and a transient epidemic wave. If within-host adaptation is substantially stronger in vaccinees, we find that the escape pressure follows a unimodal pattern: intermediate vaccination levels pose the greatest risk of escape. Otherwise, vaccination reduces the escape pressure. Chapter 3 extends the approach of Chapter 2 to heterogeneous populations. We account for differences in the pathogen adaptation rate within host types, such as immunocompromised individuals. We find that this novel form of heterogeneity may qualitatively change how the escape pressure depends on the vaccination coverage. In particular, for some parameters, the escape pressure has a bimodal pattern. We also analyse strategies for vaccine prioritisation. Chapter 4 extends the approach of Chapter 2 to account for a different pathogen adaptation rate during reinfections. We derive the final size of an epidemic in which infections induce partial protection against reinfection. If vaccines induce stronger protection than past infections, we find a new pattern: vaccination always reduces the escape pressure, regardless of the adaptation rate in hosts with prior immunity (acquired from infection, vaccination, or both). Chapter 5 extends the deterministic escape pressure of Chapter 2 to conside…
abstract: This thesis investigates how the risk that an infectious pathogen evolves antigenically (leading to pathogen strains that evade existing immunity) depends on the vaccination coverage of its host population. Deterministic compartmental models are coupled with a parsimonious approach to pathogen evolution, focussing on the selection pressure for immune escape. We study the qualitative patterns of this escape pressure — as a function of the vaccination coverage — and the epidemiological impact thereof, taking analytical approaches wherever possible. Chapter 2 varies the balance of the contributions to the escape pressure from infections in unvaccinated and vaccinated hosts. We use SIR-type models, for endemic disease and a transient epidemic wave. If within-host adaptation is substantially stronger in vaccinees, we find that the escape pressure follows a unimodal pattern: intermediate vaccination levels pose the greatest risk of escape. Otherwise, vaccination reduces the escape pressure. Chapter 3 extends the approach of Chapter 2 to heterogeneous populations. We account for differences in the pathogen adaptation rate within host types, such as immunocompromised individuals. We find that this novel form of heterogeneity may qualitatively change how the escape pressure depends on the vaccination coverage. In particular, for some parameters, the escape pressure has a bimodal pattern. We also analyse strategies for vaccine prioritisation. Chapter 4 extends the approach of Chapter 2 to account for a different pathogen adaptation rate during reinfections. We derive the final size of an epidemic in which infections induce partial protection against reinfection. If vaccines induce stronger protection than past infections, we find a new pattern: vaccination always reduces the escape pressure, regardless of the adaptation rate in hosts with prior immunity (acquired from infection, vaccination, or both). Chapter 5 extends the deterministic escape pressure of Chapter 2 to conside…
author: Gutierrez, Maria A
language: eng
keywords: phylodynamics, pathogen evolution, immune evasion, vaccine escape, SARS-CoV-2, infectious disease modelling, Influenza, vaccination strategies, antigenic phenotype, evolutionary epidemiology, compartmental models, stochastic establishment
license: https://www.repository.cam.ac.uk/bitstreams/5e20e358-f747-44f3-85b5-032c9585d524/download
license: http://purl.org/NET/rdflicense/allrightsreserved
date published: 2025-04-30
date modified: 2026-07-22T22:24:11Z
provider: Cambridge University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Cambridge

PropertyValue
property ID: DOI
value: 10.17863/CAM.121778