Related papers: Towards a phylogenetic measure to quantify HIV inc…
Understanding historical trends in the epidemic of HIV is important for assessing current and projecting future trends in prevalence, incidence and mortality and for evaluating the impact and cost-effectiveness of control measures. In…
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…
Infectious diseases are studied to understand their spreading mechanisms, to evaluate control strategies and to predict the risk and course of future outbreaks. Because people only interact with a small number of individuals, and because…
In this article, we propose a network spread model for HIV epidemics, wherein each individual is represented by a node of the transmission network and the edges are the connections between individuals along which the infection may spread.…
Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, because the higher resolution of these data compared to standard Sanger sequencing provide evidence into the direction of infectious…
As the global HIV pandemic enters its fourth decade, increasing numbers of surveillance sites have been established which allows countries to look into the epidemics at a finer scale, e.g. at sub-national levels. Currently, the epidemic…
In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account…
The rates of escape and reversion in response to selection pressure arising from the host immune system, notably the cytotoxic T-lymphocyte (CTL) response, are key factors determining the evolution of HIV. Existing methods for estimating…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
It is the main purpose of this paper to introduce a graph-valued stochastic process in order to model the spread of a communicable infectious disease. The major novelty of the SIR model we promote lies in the fact that the social network on…
Estimating new HIV infections is significant yet challenging due to the difficulty in distinguishing between recent and long-term infections. We demonstrate that HIV recency status (recent v.s. long-term) could be determined from the…
Network surveys of key populations at risk for HIV are an essential part of the effort to understand how the epidemic spreads and how it can be prevented. Estimation of population values from the sample data has been probematical, however,…
Molecular HIV Surveillance (MHS) has been described as key to enabling rapid responses to HIV outbreaks. It operates by linking individuals with genetically similar viral sequences, which forms a network. A major limitation of MHS is that…
HIV transmission within serodiscordant couples remains a significant public health challenge, particularly in sub-Saharan Africa. Estimating the rate of such infection, alongside the rates of introduction of infection from outside the…
Individual-based models of contagious processes are useful for predicting epidemic trajectories and informing intervention strategies. In such models, the incorporation of contact network information can capture the non-randomness and…
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…
The contact structure between hosts has a critical influence on disease spread. However, most networkbased models used in epidemiology tend to ignore heterogeneity in the weighting of contacts. This assumption is known to be at odds with…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent parameters, such as effective population size, offer limited…
HIV is a retrovirus that attacks the human immune system and can lead to death without proper treatment. In collaboration with the WHO and Wits University, we study how to improve the efficiency of HIV testing with the goal of eventual…