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Inferring Multi-Type Birth-Death Parameters for a Structured Host Population with Application to HIV Epidemic in Africa

Hassan W. Kayondo, Samuel Mwalili, John M. Mango
Computational Molecular Bioscience , Volume 9, pp 108-131; doi:10.4236/cmb.2019.94009

Abstract: Human Immunodeficiency Virus (HIV) dynamics in Africa are purely characterised by sparse sampling of DNA sequences for individuals who are infected. There are some sub-groups that are more at risk than the general population. These sub-groups have higher infectivity rates. We came up with a likelihood inference model of multi-type birth-death process that can be used to make inference for HIV epidemic in an African setting. We employ a likelihood inference that incorporates a probability of removal from infectious pool in the model. We have simulated trees and made parameter inference on the simulated trees as well as investigating whether the model distinguishes between heterogeneous and homogeneous dynamics. The model makes fairly good parameter inference. It distinguishes between heterogeneous and homogeneous dynamics well. Parameter estimation was also performed under sparse sampling scenario. We investigated whether trees obtained from a structured population are more balanced than those from a non-structured host population using tree statistics that measure tree balance and imbalance. Trees from non-structured population were more balanced basing on Colless and Sackin indices.
Keywords: HIV / Likelihood Inference / structured population / Multi-Type Birth-Death Process / Probability of Removal

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