Related papers: Inferring the sources of HIV infection in Africa f…
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…
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…
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…
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…
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…
One of the cornerstones in combating the HIV pandemic is being able to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status,…
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…
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…
Missing data is a recurrent issue in epidemiology where the infection process may be partially observed. Approximate Bayesian Computation, an alternative to data imputation methods such as Markov Chain Monte Carlo integration, is proposed…
Random mixing in host populations has been a convenient simplifying assumption in the study of epidemics, but neglects important differences in contact rates within and between population groups. For HIV/AIDS, the assumption of random…
Key populations at high risk of HIV infection are critical for understanding and monitoring HIV epidemics, but global estimation is hampered by sparse, uneven data. We analyze data from 199 countries for female sex workers (FSW), men who…
HIV is a deadly virus transmitted either through having of unprotected sex, mother to child transmission, sharing of unsterilized objects that is capable of making cut or wounds on the body, through blood or bodily fluid transmission. AIDS…
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…
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…
We extend the classical Susceptible-Infected-Recovered (SIR) model to a network-based framework where the degree distribution of nodes follows a Poisson distribution. This extension incorporates an additional parameter representing the mean…
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…
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…
Recent work has focused attention on statistical inference for the population distribution of the number of sexual partners based on survey data. The characteristics of these distributions are of interest as components of mathematical…
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"…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…