Covasim: An agent-based model of COVID-19 dynamics and interventions

PLoS Computational Biology, Journal Year: 2021, Volume and Issue: 17(7), P. e1009149 - e1009149

Published: July 26, 2021

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), open-source model developed to help address these questions. includes country-specific demographic information on age structure population size; realistic transmission networks in different social layers, including households, schools, workplaces, long-term care facilities, communities; age-specific disease outcomes; intrahost viral dynamics, viral-load-based transmissibility. also supports extensive set interventions, non-pharmaceutical such as physical distancing protective equipment; pharmaceutical vaccination; testing symptomatic asymptomatic testing, isolation, contact tracing, quarantine. These interventions incorporate effects delays, loss-to-follow-up, micro-targeting, other factors. Implemented pure Python, been designed with equal emphasis performance, ease use, flexibility: highly customized scenarios be run a standard laptop under minute. In collaboration local health agencies policymakers, already applied examine dynamics inform policy decisions more than dozen countries Africa, Asia-Pacific, Europe, North America.

Language: Английский

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Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control

PLoS Biology, Journal Year: 2020, Volume and Issue: 18(11), P. e3000897 - e3000897

Published: Nov. 12, 2020

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent of Disease 2019 (COVID-19) disease, has moved rapidly around globe, infecting millions and killing hundreds thousands. The basic reproduction number, which been widely used—appropriately less appropriately—to characterize transmissibility virus, hides fact that transmission is stochastic, often dominated by a small number individuals, heavily influenced superspreading events (SSEs). distinct features SARS-CoV-2, e.g., high stochasticity under low prevalence (as compared to other pathogens, such as influenza), central role played SSEs on dynamics cannot be overlooked. Many explosive have occurred in indoor settings, stoking pandemic shaping its spread, long-term care facilities, prisons, meat-packing plants, produce processing fish factories, cruise ships, family gatherings, parties, nightclubs. These demonstrate urgent need understand routes transmission, while posing an opportunity effectively contain outbreaks with targeted interventions eliminate SSEs. Here, we describe different types SSEs, how they influence empirical evidence for their COVID-19 pandemic, give recommendations control SARS-CoV-2.

Language: Английский

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Controlling COVID-19 via test-trace-quarantine

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 20, 2021

Abstract Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures. However, these interventions have had enormous societal economic costs. Here, we demonstrate feasibility of an alternative control strategy, test-trace-quarantine: routine testing primarily symptomatic individuals, tracing their known contacts, placing contacts quarantine. We perform this analysis using Covasim, open-source agent-based model, which has been calibrated to detailed demographic, epidemiological data for Seattle region from January through June 2020. With current levels mask use schools remaining closed, find that high but achievable are sufficient maintain epidemic even under a return full community mobility with low vaccine coverage. The easing restrictions 2020 subsequent scale-up programs September provided real-world validation our predictions. Although show test-trace-quarantine can both theory practice, its success is contingent rates, quarantine compliance, relatively short delays, moderate use. Thus, order transmission strong performance all aspects program required.

Language: Английский

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Predictive symptoms for COVID-19 in the community: REACT-1 study of over 1 million people

PLoS Medicine, Journal Year: 2021, Volume and Issue: 18(9), P. e1003777 - e1003777

Published: Sept. 28, 2021

Background Rapid detection, isolation, and contact tracing of community COVID-19 cases are essential measures to limit the spread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed identify a parsimonious set symptoms that jointly predict investigated whether predictive differ between B.1.1.7 (Alpha) lineage (predominating as April 2021 in US, UK, elsewhere) wild type. Methods findings obtained throat nose swabs with valid SARS-CoV-2 PCR test results from 1,147,370 volunteers aged 5 years above (6,450 positive cases) REal-time Assessment Community Transmission-1 (REACT-1) study. This study involved repeated community-based random surveys prevalence England (study rounds 8, June 2020 January 2021, response rates 22%–27%). Participants were asked about occurring week prior testing. Viral genome sequencing was carried out for PCR-positive samples N-gene cycle threshold value < 34 ( N = 1,079) round 8 (January 2021). In univariate analysis, all 26 surveyed associated positivity compared non-symptomatic people. Stability selection (1,000 penalized logistic regression models 50% subsampling) among people reporting at least 1 symptom identified 7 positively 2–7 (June December 2020): loss or change sense smell, taste, fever, new persistent cough, chills, appetite loss, muscle aches. The resulting model (rounds 2–7) predicted area under curve (AUC) 0.77. same selected infection although when comparing type, cough sore more while smell main limitations our (i) potential participation bias despite sampling named individuals National Health Service register weighting designed achieve representative sample population (ii) necessary reliance on self-reported symptoms, which may be prone recall therefore lead biased estimates England. Conclusions Where testing capacity is limited, it important use tests most efficient way possible. that, considered together, maximize detection community, including lineage.

Language: Английский

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An Agent-Based Modeling of COVID-19: Validation, Analysis, and Recommendations

Cognitive Computation, Journal Year: 2021, Volume and Issue: 16(4), P. 1723 - 1734

Published: Feb. 19, 2021

The coronavirus disease 2019 (COVID-19) has resulted in an ongoing pandemic worldwide. Countries have adopted non-pharmaceutical interventions (NPI) to slow down the spread. This study proposes agent-based model that simulates spread of COVID-19 among inhabitants a city. can be accommodated for any location by integrating parameters specific simulation gives number total cases. Considering each person as agent susceptible COVID-19, causes infected individuals transmit via various actions performed every hour. is validated comparing real data Ford County, KS, USA. Different interventions, including contact tracing, are applied on scaled-down version New York City, USA, and lead controlled epidemic determined. Our experiments suggest tracing smartphones with more than 60% population owning smartphone combined city-wide lockdown results effective reproduction (Rt) fall below 1 within 3 weeks intervention. For 75% or users, new infections eliminated, contained months Contact accompanied early suppress growth completely sufficient owners. In places where it difficult ensure high percentage ownership, only emergency service providers during go long way contain

Language: Английский

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Predicting the second wave of COVID-19 in Washtenaw County, MI

Journal of Theoretical Biology, Journal Year: 2020, Volume and Issue: 507, P. 110461 - 110461

Published: Aug. 29, 2020

Language: Английский

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Comparative effectiveness of contact tracing interventions in the context of the COVID-19 pandemic: a systematic review

European Journal of Epidemiology, Journal Year: 2023, Volume and Issue: 38(3), P. 243 - 266

Published: Feb. 16, 2023

Abstract Contact tracing is a non-pharmaceutical intervention (NPI) widely used in the control of COVID-19 pandemic. Its effectiveness may depend on number factors including proportion contacts traced, delays tracing, mode contact (e.g. forward, backward or bidirectional training), types who are traced index cases cases), setting where household workplace). We performed systematic review evidence regarding comparative interventions. 78 studies were included review, 12 observational (ten ecological studies, one retrospective cohort study and pre-post with two patient cohorts) 66 mathematical modelling studies. Based results from six can be effective at controlling COVID-19. Two high quality showed incremental adding digital to manual tracing. One intermediate that increases associated drop mortality, acceptable prompt case clusters / symptomatic individuals led reduction reproduction R. Within seven exploring context implementation other interventions, was found have an effect epidemic not remaining five However, limitation many these lack description extent we identified following highly policies: (1) coverage either medium-term immunity, efficacious isolation/quarantine and/ physical distancing (2) hybrid app adoption isolation/ quarantine social distancing, (3) secondary (4) eliminating delays, (5) (6) reopening educational institutions. also highlighted role enhance some interventions 2020 lockdown reopening. While limited, shows for epidemic. More empirical accounting required.

Language: Английский

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The SARS-CoV-2 test scale-up in the USA: an analysis of the number of tests produced and used over time and their modelled impact on the COVID-19 pandemic

The Lancet Public Health, Journal Year: 2025, Volume and Issue: 10(1), P. e47 - e57

Published: Jan. 1, 2025

Language: Английский

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From node to network: weaving a global perspective on efficacy and costs of non-pharmaceutical interventions

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 22, 2025

Non-pharmaceutical intervention (NPI) policies, ranging from mild measures to total isolation, were implemented worldwide during the COVID-19 pandemic. We adopt a systematic approach guide policymakers in deploying NPI policies mitigate pandemic's effects while balancing their social and economic impacts. Our results show that each has an optimal duration, beyond which its effectiveness plateaus. Stricter require longer durations, when sustained for period, earlier implementation is more effective. However, this duration unattainable, timing becomes critical, as both early late reduce efficacy. Stringent with insufficient durations may perform worse than less restrictive applied over same policy aimed at minimizing overall healthcare burden under fixed significantly intensify peak-time strains. Finally, virus transmissible lethal, gap between stringent narrows, targeted interventions vulnerable groups outperforming universal strict measures.

Language: Английский

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Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics

PLoS Computational Biology, Journal Year: 2021, Volume and Issue: 17(6), P. e1009122 - e1009122

Published: June 17, 2021

Simultaneously controlling COVID-19 epidemics and limiting economic societal impacts presents a difficult challenge, especially with limited public health budgets. Testing, contact tracing, isolating/quarantining is key strategy that has been used to reduce transmission of SARS-CoV-2, the virus causes other pathogens. However, manual tracing time-consuming process as case numbers increase smaller fraction cases’ contacts can be traced, leading additional spread. Delays between symptom onset being tested (and receiving results), low symptomatic cases traced also impact on transmission. We examined relationship increasing delays pathogen reproductive number R t , implications for infection dynamics using deterministic stochastic compartmental models SARS-CoV-2. found increased sigmoidally due decreasing efficacy. This results in accelerating because initially increases, rather than declines, infections increase. Shifting tracers from locations high burdens relative capacity intermediate maximizes their reducing (but minimizing total may more complicated). Contact efficacy decreased sharply lower tested. Finally, testing reductions sometimes greatly delay highly heterogeneous These demonstrate importance having an expandable or mobile team control surges cases. They highlight synergistic value capacity, easy access rapid turn-around results, outreach efforts encourage immediately after onset.

Language: Английский

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