Software

Impact along the HIV pre-exposure prophylaxis â€œcascade of preventionâ€ in western Kenya: a mathematical modelling study

Introduction Over one hundred implementation studies of HIV pre-exposure prophylaxis (PrEP) are completed, underway or planned. We synthesized evidence from these studies to inform mathematical modelling of the prevention cascade for oral and long-acting PrEP in the setting of western Kenya, one of the world’s most heavily HIV-affected regions. Methods We incorporated steps of the…
Determining the optimal strategy for reopening schools, the impact of test and trace interventions, and the risk of occurrence of a second COVID-19 epidemic wave in the UK: a modelling study

Background As lockdown measures to slow the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection begin to ease in the UK, it is important to assess the impact of any changes in policy, including school reopening and broader relaxation of physical distancing measures. We aimed to use an individual-based model to predict the…
Modelling the impact of relaxing COVID-19 control measures during a period of low viral transmission

Objectives To assess the risks associated with relaxing coronavirus disease 2019 (COVID-19)-related physical distancing restrictions and lockdown policies during a period of low viral transmission. Design Network-based viral transmission risks in households, schools, workplaces, and a variety of community spaces and activities were simulated in an agent-based model, Covasim. Setting The model was calibrated for…
Cost-effectiveness of point-of-care testing with task-shifting for HIV care in South Africa: a modelling study

Background The number of people on antiretroviral therapy (ART) requiring treatment monitoring in low-resource settings is rapidly increasing. Point-of-care (POC) testing for ART monitoring might alleviate burden on centralised laboratories and improve clinical outcomes, but its cost-effectiveness is unknown. Methods We used cost and effectiveness data from the STREAM trial in South Africa (February, 2017â€“October,…
(Preprint) Compartmental Modeling Software: a fast, discrete stochastic framework for biochemical and epidemiological simulation

The compartmental modeling software (CMS) is an open source computational framework that can simulate discrete, stochastic reaction models which are often utilized to describe complex systems from epidemiology and systems biology. In this article, we report the computational requirements, the novel input model language, the available numerical solvers, and the output file format for CMS.…
Optimization of frequency and targeting of measles supplemental immunization activities in Nigeria: A cost-effectiveness analysis

Background Measles causes significant childhood morbidity in Nigeria. Routine immunization (RI) coverage is around 40% country-wide, with very high levels of spatial heterogeneity (3–86%), with supplemental immunization activities (SIAs) at 2-year or 3-year intervals. We investigated cost savings and burden reduction that could be achieved by adjusting the inter-campaign interval by region. Methods We modeled…
Reducing malaria burden and accelerating elimination with long-lasting systemic insecticides: a modelling study of three potential use cases

Background While bed nets and insecticide spraying have had significant impact on malaria burden in many endemic regions, outdoor vector feeding and insecticide resistance may ultimately limit their contribution to elimination and control campaigns. Complementary vector control methods such as endectocides or systemic insecticides, where humans or animals are treated with drugs that kill mosquitoes…
Compartmental Modeling Software: A Fast, Discrete Stochastic Framework for Biochemical and Epidemiological Simulation

The compartmental modeling software (CMS) is an open source computational framework that can simulate discrete, stochastic reaction models which are often utilized to describe complex systems from epidemiology and systems biology. In this article, we report the computational requirements, the novel input model language, the available numerical solvers, and the output file format for CMS.…
Small contribution of gold mines to the ongoing tuberculosis epidemic in South Africa: a modeling-based study

Background Gold mines represent a potential hotspot for Mycobacterium tuberculosis (Mtb) transmission and may be exacerbating the tuberculosis (TB) epidemic in South Africa. However, the presence of multiple factors complicates estimation of the mining contribution to the TB burden in South Africa. Methods We developed two models of TB in South Africa, a static risk…
Modeling the impact of Plasmodium falciparum sexual stage immunity on the composition and dynamics of the human infectious reservoir for malaria in natural settings

Malaria transmission remains high in Sub-Saharan Africa despite large-scale implementation of malaria control interventions. A comprehensive understanding of the transmissibility of infections to mosquitoes may guide the design of more effective transmission reducing strategies. The impact of P. falciparum sexual stage immunity on the infectious reservoir for malaria has never been studied in natural settings.…