Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
Results
Showing 1 to 9 of 9 for “"Phylodynamics"”.
-
Exploring the phylodynamics, genetic reassortment and RNA secondary structure formation patterns of orthomyxoviruses by comparative sequence analysis
RNA viruses are among the most virulent microorganisms that threaten the health of humans and livestock. Among the most socio-economically important of the known RNA viruses are those found in the family Orthomyxovirus. In this era of rapid low-cost genome sequencing and advancements in …
-
Fitting Stochastic Epidemic Models to Multiple Data Types
… data. Such genetic analyses rely on the field of phylodynamics --- a set of population genetics tools that aim at reconstructing demographic history of a population based on molecular sequences of individuals sampled from the population of interest. In this thesis, we aim at designing a general …
-
Influenza Dynamics from Pre-pandemic to Post-pandemic Periods: Epidemiology and Genetic Characteristics
… These findings provide critical insights into phylodynamics of A/H3N2 viruses in the post-pandemic era in Australia. In summary, this research enhanced our understanding of influenza epidemiology and evolution in Australia across the pre- to post-pandemic periods, particularly for the …
-
MINING SARS-COV-2 PHYLOGENETIC TREES TO ESTIMATE CIRCULATING INFECTIONS AND PATTERNS OF MIGRATION
The SARS-CoV-2 pandemic led to the formation of very large databases of genomic viral data. These databases contain information on transmission dynamics, emergence and evolution of SARS-CoV-2. However, extracting this information from sequences is difficult, as most methods of analyzing viral …
-
Modelling the Epidemiological Dynamics of Seasonal Influenza Viruses at Local Scales
Seasonal influenza viruses are a substantial source of disease burden globally, causing epidemics across all climatic regions. Through error-prone RNA replication, influenza viruses can escape pre-existing humoral immunity and reinfect humans, resulting in recurrent epidemics within populations. …
-
Scalable Tools for High-throughput Viral Sequence Analysis
Viral sequence data are increasingly being used to estimate evolutionary and epidemiological parameters to understand the dynamics of viral diseases. This thesis focuses on developing novel and improved computational methods for high-throughput analysis of large viral sequence datasets. I have …
-
Global dynamics of Bordetella pertussis and implications for control
*Bordetella pertussis* is the main cause of whooping cough, a disease that still infects millions of individuals annually despite widespread vaccination. This is particularly problematic in neonates, where infection can lead to death. Endemicity, subclinical infections and circulation of multiple …
-
Characterisation of the Ugandan HIV epidemic with full-length genome sequence data from 1986 to 2016
Presented here are two large Ugandan HIV genome datasets, one from the modern period (by the MRC/UVRI & LSHTM group and PANGEA), and another generated from stored 1986 serum samples using target-capture next generation sequencing. Uganda uniquely has two HIV subtypes at similar proportions, and …
-
Population dynamics of infectious disease and pathogen evolution: modelling vaccine escape
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 …