Related papers: Quantifying the recency of HIV infection using mul…
Longitudinal cohorts to determine the incidence of HIV infection are logistically challenging, so researchers have sought alternative strategies. Recency test methods use biomarker profiles of HIV-infected subjects in a cross-sectional…
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…
Cross-sectional HIV incidence estimation leverages recency test results to determine the HIV incidence of a population of interest, where recency test uses biomarker profiles to infer whether an HIV-positive individual was "recently"…
The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the…
Cross-sectional incidence estimation based on recency testing has become a widely used tool in HIV research. Recently, this method has gained prominence in HIV prevention trials to estimate the "placebo" incidence that participants might…
Estimating HIV-1 incidence using biomarker assays in cross-sectional surveys is important for understanding the HIV pandemic. However, the utility of these estimates has been limited by uncertainty about what input parameters to use for…
We present a new joint longitudinal and survival model aimed at estimating the association between the risk of an event and the change in and history of a biomarker that is repeatedly measured over time. We use cubic B-splines models for…
During primary HIV infection, the kinetics of plasma virus concentrations and CD4+ cell counts is very complex. Parametric and nonparametric models have been suggested for fitting repeated measurements of these markers. Alternatively,…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
Incidence estimation of HIV infection can be performed using recent infection testing algorithm (RITA) results from a cross-sectional sample. This allows practitioners to understand population trends in the HIV epidemic without having to…
Accurate HIV incidence estimation based on individual recent infection status (recent vs long-term infection) is important for monitoring the epidemic, targeting interventions to those at greatest risk of new infection, and evaluating…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
The objective is to model longitudinal and survival data jointly taking into account the dependence between the two responses in a real HIV/AIDS dataset using a shared parameter approach inside a Bayesian framework. We propose a linear…
Ending the HIV/AIDS pandemic is among the Sustainable Development Goals for the next decade. In order to overcome the gap between the need for care and the available resources, better understanding of HIV epidemics is needed to guide policy…
With the launch of second line anti-retroviral therapy for HIV infected individuals, there has been an increased expectation on surviving period of people with HIV. We consider previously well-known models in HIV epidemiology where the…
One way in which the human immunodeficiency virus (HIV-1) replicates within a host is by infecting activated CD4+ T-cells, which then produce additional copies of the virus. Even with the introduction of antiretroviral drug therapy, which…
In this work we introduce a differential equation model with time-delay that describes the three-stage dynamics and the two time scales observed in HIV infection. Assuming that the virus has high mutation and rapid reproduction rates that…
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are…
Evaluation of HIV large scale interventions programme is becoming increasingly important, but impact estimates frequently hinge on knowledge of changes in behaviour such as the frequency of condom use (CU) over time, or other self-reported…
Reliable estimation of spatio-temporal trends in population-level HIV incidence is becoming an increasingly critical component of HIV prevention policy-making. However, direct measurement is nearly impossible. Current, widely used models…