Related papers: Inferring HIV Transmission Patterns from Viral Dee…
Pathogen deep-sequencing is an increasingly routinely used technology in infectious disease surveillance. We present a semi-parametric Bayesian Poisson model to exploit these emerging data for inferring infectious disease transmission flows…
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…
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…
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…
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…
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…
This paper describes a novel approach to modeling homphily, i.e. the tendency of nodes that share (or differ in) certain attributes to be linked; we consider dynamic networks in which nodes can be added over time but not removed. Our…
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…
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…
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,…
Background. Several studies have used phylogenetics to investigate Human Immunodeficiency Virus (HIV) transmission among Men who have Sex with Men (MSMs) in Montreal, Quebec, Canada, revealing many transmission clusters. The Quebec HIV…
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…
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…
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…
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.…
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…
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…
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 origin of the unusual incubation period distribution in the development of AIDS is largely unresolved. A key factor in understanding the observed distribution of latency periods, as well as the occurrence of infected individuals not…
Causal inference across multiple data sources offers a promising avenue to enhance the generalizability and replicability of scientific findings. However, data integration methods for time-to-event outcomes, common in biomedical research,…