Software

Modelling the potential impact of mask use in schools and society on COVID-19 control in the UK

As the UK reopened after the first wave of the COVID-19 epidemic, crucial questions emerged around the role for ongoing interventions, including test-trace-isolate (TTI) strategies and mandatory masks. Here we assess the importance of masks in secondary schools by evaluating their impact over September 1–October 23, 2020. We show that, assuming TTI levels from August…
Individual and community-level benefits of PrEP in western Kenya and South Africa: Implications for population prioritization of PrEP provision

Background Pre-exposure prophylaxis (PrEP) is highly effective in preventing HIV and has the potential to significantly impact the HIV epidemic. Given limited resources for HIV prevention, identifying PrEP provision strategies that maximize impact is critical. Methods We used a stochastic individual-based network model to evaluate the direct (infections prevented among PrEP users) and indirect (infections…
Covasim: an agent-based model of COVID-19 dynamics and interventions

The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here we describe the methodology of Covasim (COVID-19 Agent-based Simulator), an open-source model developed to help address these questions. Covasim includes demographic information on age structure and population size; realistic transmission networks in…
COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support

Policymakers make decisions about COVID-19 management in the face of considerable uncertainty. We convened multiple modeling teams to evaluate reopening strategies for a mid-sized county in the United States, in a novel process designed to fully express scientific uncertainty while reducing linguistic uncertainty and cognitive biases. For the scenarios considered, the consensus from 17 distinct…
Modelling the health and economic impacts of different testing and tracing strategies for COVID-19 in the UK

Background: Coronavirus disease 2019 (COVID-19) is resurgent in the UK and health and economic costs of the epidemic continue to rise. There is a need to understand the health and economic costs of different courses of action. Methods: We combine modelling, economic analysis and a user-friendly interface to contrast the impact and costs of different…
Schools are not islands: Balancing COVID-19 risk and educational benefits using structural and temporal countermeasures

Background School closures around the world contributed to reducing the transmission of COVID-19. In the face of significant uncertainty around the epidemic impact of in-person schooling, policymakers, parents, and teachers are weighing the risks and benefits of returning to in-person education. In this context, we examined the impact of different school reopening scenarios on transmission…
The role of masks in reducing the risk of new waves of COVID-19 in low transmission settings: a modeling study

Objectives To evaluate the risk of a new wave of coronavirus disease 2019 (COVID-19) in a setting with ongoing low transmission, high mobility, and an effective test-and-trace system, under different assumptions about mask uptake. Design We used a stochastic agent-based microsimulation model to create multiple simulations of possible epidemic trajectories that could eventuate over a…
Cost-effectiveness of using environmental surveillance to target the roll-out typhoid conjugate vaccine

Highlights • Environmental surveillance is an alternative to case-based surveillance. • Vaccine targeted to high-risk populations is less expensive than national campaigns. • Surveillance-based vaccine introductions are more cost-effective than blanket decisions. • Environmental surveillance is valuable, even if costs are higher than anticipated.
Vector genetics, insecticide resistance and gene drives: an agent-based modeling approach to evaluate malaria transmission and elimination

Vector control has been a key component in the fight against malaria for decades, and chemical insecticides are critical to the success of vector control programs worldwide. However, increasing resistance to insecticides threatens to undermine these efforts. Understanding the evolution and propagation of resistance is thus imperative to mitigating loss of intervention effectiveness. Additionally, accelerated…
The effect of 90-90-90 on HIV-1 incidence and mortality in eSwatini: a mathematical modelling study

Background The rapid scale-up of antiretroviral therapy (ART) towards the UNAIDS 90-90-90 goals over the last decade has sparked considerable debate as to whether universal test and treat can end the HIV-1 epidemic in sub-Saharan Africa. We aimed to develop a network transmission model, calibrated to capture age-specific and sex-specific gaps in the scale-up of…