Related papers: Probabilistic HIV Recency Classification -- A Logi…

The United Nations (UN) issued official probabilistic population projections for all countries to 2100 in July 2015. This was done by simulating future levels of total fertility and life expectancy from Bayesian hierarchical models, and…

Evaluating causal effects in the presence of interference is challenging in network-based studies of hard-to-reach populations. Like many such populations, people who inject drugs (PWID) are embedded in social networks and often exert…

When modelling HIV epidemics, it is important to incorporate set-point viral load and its heritability. As set-point viral load distributions can differ significantly amongst epidemics, it is imperative to account for the observed local…

UNAIDS has embraced an ambitious global target for the implementation of treatment for people living with HIV. This 90-90-90 target would mean that, by 2020, 90% of all those living with HIV should know their status, 90% of these would be…

Stochastic compartmental models are important tools for understanding the course of infectious diseases epidemics in populations and in prospective evaluation of intervention policies. However, calculating the likelihood for discretely…

Respondent-driven sampling is a form of link-tracing network sampling, which is widely used to study hard-to-reach populations, often to estimate population proportions. Previous treatments of this process have used a with-replacement…

The OraQuick In-Home HIV self-test represents a fast, inexpensive, and convenient method for users to assess their HIV status. If integrated thoughtfully into existing testing practices, accompanied by efficient pathways to formal…

In this work we develop a stochastic model of acute HIV infection, based on the well-known standard model, that allows us to simulate the complex mutation pathways of HIV escape from multiple CTL responses. Under this model, we describe two…

This paper presents an impact assessment for the imputation of missing data. The data set used is HIV Seroprevalence data from an antenatal clinic study survey performed in 2001. Data imputation is performed through five methods: Random…

We study the influence of the rate of the attainment of herd immunity (HI), in the absence of an approved vaccine, on the vulnerable population. We essentially ask the question: how hard the evolution towards the desired herd immunity could…

An increasing amount of geo-referenced mobile phone data enables the identification of behavioral patterns, habits and movements of people. With this data, we can extract the knowledge potentially useful for many applications including the…

With the advent of effective pre-exposure prophylaxis agents, active-controlled HIV prevention trials have become a common study design. Nevertheless, estimating absolute efficacy relative to a placebo remains important. In this paper, we…

Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…

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…

Network models are increasingly used to study infectious disease spread. Exponential Random Graph models have a history in this area, with scalable inference methods now available. An alternative approach uses mechanistic network models.…

In this paper, we construct a model to describe the transmission of HIV in a homogeneous host population. By considering the specific mechanism of HIV, we derive a model structured in three successive stages: (i) primary infection, (ii)…

Dynamic models have been successfully used in producing estimates of HIV epidemics at the national level due to their epidemiological nature and their ability to estimate prevalence, incidence, and mortality rates simultaneously. Recently,…

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…

Purpose: The use of cumulative measures of exposure to raised HIV viral load (viremia copy-years) is an increasingly common in HIV prevention and treatment epidemiology due to the high biological plausibility. We sought to estimate the…

Naomi is a spatial evidence synthesis model used to produce district-level HIV epidemic indicators in sub-Saharan Africa. Multiple outcomes of policy interest, including HIV prevalence, HIV incidence, and antiretroviral therapy treatment…