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SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with computational models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including both manual and digital contact tracing, and vaccination programmes. It can simulate a population of 1 million people in seconds per day, allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 are its Python and R interfaces, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic., Author summary Throughout the COVID-19 pandemic, computational modelling has been used to inform key uncertainties facing policymakers such as the number of cases and deaths, hospital capacity, tests and contact tracers. Models need to be: sufficiently complex to yield realistic predictions; computationally efficient to allow calibrations; and easy to use so that various policy mixes can be evaluated. OpenABM-Covid19 is a detailed epidemic model of the spread of COVID-19, simulating every individual in a population. Our model enables scientists and policymakers to quickly compare the effectiveness of non-pharmaceutical interventions like lockdowns, testing, quarantine, and digital and manual contact tracing. The model considers a hypothetical city with a default population of 1 million people whose ages and contact patterns are parameterised according to UK demographics. All of the parameters are openly documented and modifiable so that they can be adapted to fit other countries’ data, and refined to match our understanding of COVID-19 as the epidemic progresses. The computer model simulates people’s movement between their homes, workplaces, schools, and social interactions. OpenABM-Covid19 is open source and has been developed collaboratively by teams from academia and industry. Its modularity, documentation, testing framework, and accessibility via Python and R have provided validation, invited contributions, and encouraged wide adoption.

Contact tracing is increasingly used to combat COVID-19, and digital implementations are now being deployed, many based on Apple and Google’s Exposure Notification System. These systems utilize non-traditional smartphone-based technology, presenting challenges in understanding possible outcomes. In this work, we create individual-based models of three Washington state counties to explore how digital exposure notifications combined with other non-pharmaceutical interventions influence COVID-19 disease spread under various adoption, compliance, and mobility scenarios. In a model with 15% participation, we found that exposure notification could reduce infections and deaths by approximately 8% and 6% and could effectively complement traditional contact tracing. We believe this can provide health authorities in Washington state and beyond with guidance on how exposure notification can complement traditional interventions to suppress the spread of COVID-19.

We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. We study, by means of a mathematical model and bifurcation analysis, conditions under which the wild-type and mutant viruses, which compete for the same host cells, can coexist. The coexistence conditions are formulated in terms of the basic reproductive numbers of the strains, a maximum value of the mutation rate and the virulence of the pathogens. The analysis reveals that parameter space can be divided into five regions, each with distinct dynamics, that are organized around degenerate Bogdanov–Takens and zero-Hopf bifurcations, the latter of which gives rise to a curve of transcritical bifurcations of periodic orbits. These results provide new insights into the conditions by which viral populations may contain multiple coexisting strains in a stable manner., The research leading to these results has received funding from ‘la Caixa’ Foundation. This work has been also partially funded by the ‘María de Maeztu’ Programme for Units of Excellence in R&D (MDM-2014-0445), as well as from projects MTM2014-52209-C2-1-P and MTM2017-86795-C3-1-P from the Spanish MINECO, and from the CERCA Programme of the Generalitat de Catalunya. M.H. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 707658. Work in València was supported by Spain’s Agencia Estatal de Investigación - FEDER grant no. BFU2015-65037-P to S.F.E. J.S. has been also funded by a ‘Ramón y Cajal’ Fellowship (RYC-2017-22243).

Instantaneous contact tracing New analyses indicate that severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) is more infectious and less virulent than the earlier SARS-CoV-1, which emerged in China in 2002. Unfortunately, the current virus has greater epidemic potential because it is difficult to trace mild or presymptomatic infections. As no treatment is currently available, the only tools that we can currently deploy to stop the epidemic are contact tracing, social distancing, and quarantine, all of which are slow to implement. However imperfect the data, the current global emergency requires more timely interventions. Ferretti et al. explored the feasibility of protecting the population (that is, achieving transmission below the basic reproduction number) using isolation coupled with classical contact tracing by questionnaires versus algorithmic instantaneous contact tracing assisted by a mobile phone application. For prevention, the crucial information is understanding the relative contributions of different routes of transmission. A phone app could show how finite resources must be divided between different intervention strategies for the most effective control. Science , this issue p. eabb6936