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In silico modelling of parasite dynamics

Twumasi, Clement 2022. In silico modelling of parasite dynamics. PhD Thesis, Cardiff University.
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Understanding host-parasite systems are challenging if biologists employ just the experimental approaches adopted, whereas mathematical models can help uncover other in-depth knowledge about host infection dynamics. Previous experimental studies have explored the infrapopulation dynamics of Gyrodactylus turnbulli and G. bullatarudis ectoparasites on their fish host, Poecilia reticulata. However, other important and open biological questions exist concerning parasite microhabitat preference, host survival, parasite virulence, and the transmission dynamics of different Gyrodactylus strains across different host populations over time. This thesis mathematically investigates these relevant biological questions to understand the gyrodactylid-fish system’s complexity better using a sophisticated multi-state Markov model (MSM) and a novel individual-based stochastic simulation model. The infection dynamics of three different gyrodactylid strains are compared across three different host populations. A modified approximate Bayesian computation (ABC) with sequential Monte Carlo (SMC) and sequential importance sampling (SIS) is developed for calibrating the novel stochastic model based on existing empirical data and an auxiliary stochastic model. In addition, an extended local-linear regression (with L2 regularisation) for ABC post-processing analysis has been proposed. Advanced statistics and an MSM are used to assess spatial-temporal parasite dynamics. A linear birth-death process with catastrophic extinction (B-D-C process) is considered the auxiliary model for the complex simulation model to refine the modified ABC’s summary statistics, with other theoretical justifications and parameter estimation techniques of the B-D-C process provided. The B-D-C process simulation using τ -leaping also provides additional insights on accelerating the complex simulation model by proposing a reasonable error threshold based on the trade-off between simulation accuracy and computational speed. The mathematical models can be extended and adapted for other host-parasite systems, and the modified ABC methodologies can also aid in efficiently calibrating other multi-parameter models with a high-dimensional set of correlating or independent summary statistics.

Item Type: Thesis (PhD)
Date Type: Completion
Status: Unpublished
Schools: Mathematics
Date of First Compliant Deposit: 22 June 2022
Last Modified: 06 Jul 2023 02:00

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