Literature DB >> 34310589

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

Cliff C Kerr1, Robyn M Stuart2,3, Dina Mistry1, Romesh G Abeysuriya3, Katherine Rosenfeld1, Gregory R Hart1, Rafael C Núñez1, Jamie A Cohen1, Prashanth Selvaraj1, Brittany Hagedorn1, Lauren George1, Michał Jastrzębski4, Amanda S Izzo1, Greer Fowler1, Anna Palmer3, Dominic Delport3, Nick Scott3, Sherrie L Kelly3, Caroline S Bennette1, Bradley G Wagner1, Stewart T Chang1, Assaf P Oron1, Edward A Wenger1, Jasmina Panovska-Griffiths5,6, Michael Famulare1, Daniel J Klein1.   

Abstract

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

Entities:  

Year:  2021        PMID: 34310589     DOI: 10.1371/journal.pcbi.1009149

Source DB:  PubMed          Journal:  PLoS Comput Biol        ISSN: 1553-734X            Impact factor:   4.475


  67 in total

1.  A stochastic agent-based model of the SARS-CoV-2 epidemic in France.

Authors:  Nicolas Hoertel; Martin Blachier; Carlos Blanco; Mark Olfson; Marc Massetti; Marina Sánchez Rico; Frédéric Limosin; Henri Leleu
Journal:  Nat Med       Date:  2020-07-14       Impact factor: 53.440

Review 2.  Capturing the dynamics of pathogens with many strains.

Authors:  Adam J Kucharski; Viggo Andreasen; Julia R Gog
Journal:  J Math Biol       Date:  2015-03-24       Impact factor: 2.259

3.  Inferring the structure of social contacts from demographic data in the analysis of infectious diseases spread.

Authors:  Laura Fumanelli; Marco Ajelli; Piero Manfredi; Alessandro Vespignani; Stefano Merler
Journal:  PLoS Comput Biol       Date:  2012-09-13       Impact factor: 4.475

4.  SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients.

Authors:  Lirong Zou; Feng Ruan; Mingxing Huang; Lijun Liang; Huitao Huang; Zhongsi Hong; Jianxiang Yu; Min Kang; Yingchao Song; Jinyu Xia; Qianfang Guo; Tie Song; Jianfeng He; Hui-Ling Yen; Malik Peiris; Jie Wu
Journal:  N Engl J Med       Date:  2020-02-19       Impact factor: 91.245

5.  Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures.

Authors:  Rachael Pung; Calvin J Chiew; Barnaby E Young; Sarah Chin; Mark I-C Chen; Hannah E Clapham; Alex R Cook; Sebastian Maurer-Stroh; Matthias P H S Toh; Cuiqin Poh; Mabel Low; Joshua Lum; Valerie T J Koh; Tze M Mak; Lin Cui; Raymond V T P Lin; Derrick Heng; Yee-Sin Leo; David C Lye; Vernon J M Lee
Journal:  Lancet       Date:  2020-03-17       Impact factor: 79.321

6.  Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing.

Authors:  Luca Ferretti; Chris Wymant; David Bonsall; Christophe Fraser; Michelle Kendall; Lele Zhao; Anel Nurtay; Lucie Abeler-Dörner; Michael Parker
Journal:  Science       Date:  2020-03-31       Impact factor: 47.728

7.  Interventions to mitigate early spread of SARS-CoV-2 in Singapore: a modelling study.

Authors:  Joel R Koo; Alex R Cook; Minah Park; Yinxiaohe Sun; Haoyang Sun; Jue Tao Lim; Clarence Tam; Borame L Dickens
Journal:  Lancet Infect Dis       Date:  2020-03-23       Impact factor: 25.071

8.  Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts.

Authors:  Joel Hellewell; Sam Abbott; Amy Gimma; Nikos I Bosse; Christopher I Jarvis; Timothy W Russell; James D Munday; Adam J Kucharski; W John Edmunds; Sebastian Funk; Rosalind M Eggo
Journal:  Lancet Glob Health       Date:  2020-02-28       Impact factor: 26.763

9.  Tracing day-zero and forecasting the COVID-19 outbreak in Lombardy, Italy: A compartmental modelling and numerical optimization approach.

Authors:  Lucia Russo; Cleo Anastassopoulou; Athanasios Tsakris; Gennaro Nicola Bifulco; Emilio Fortunato Campana; Gerardo Toraldo; Constantinos Siettos
Journal:  PLoS One       Date:  2020-10-30       Impact factor: 3.240

10.  OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing.

Authors:  Robert Hinch; William J M Probert; Anel Nurtay; Michelle Kendall; Chris Wymant; Matthew Hall; Katrina Lythgoe; Ana Bulas Cruz; Lele Zhao; Andrea Stewart; Luca Ferretti; Daniel Montero; James Warren; Nicole Mather; Matthew Abueg; Neo Wu; Olivier Legat; Katie Bentley; Thomas Mead; Kelvin Van-Vuuren; Dylan Feldner-Busztin; Tommaso Ristori; Anthony Finkelstein; David G Bonsall; Lucie Abeler-Dörner; Christophe Fraser
Journal:  PLoS Comput Biol       Date:  2021-07-12       Impact factor: 4.475

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  67 in total

1.  Estimating the impact of interventions against COVID-19: From lockdown to vaccination.

Authors:  James Thompson; Stephen Wattam
Journal:  PLoS One       Date:  2021-12-17       Impact factor: 3.240

2.  COVID-19 forecasts using Internet search information in the United States.

Authors:  Simin Ma; Shihao Yang
Journal:  Sci Rep       Date:  2022-07-07       Impact factor: 4.996

3.  Prediction and prevention of pandemics via graphical model inference and convex programming.

Authors:  Mikhail Krechetov; Amir Mohammad Esmaieeli Sikaroudi; Alon Efrat; Valentin Polishchuk; Michael Chertkov
Journal:  Sci Rep       Date:  2022-05-09       Impact factor: 4.996

4.  Estimated Transmission Outcomes and Costs of SARS-CoV-2 Diagnostic Testing, Screening, and Surveillance Strategies Among a Simulated Population of Primary School Students.

Authors:  Alyssa Bilinski; Andrea Ciaranello; Meagan C Fitzpatrick; John Giardina; Maunank Shah; Joshua A Salomon; Emily A Kendall
Journal:  JAMA Pediatr       Date:  2022-07-01       Impact factor: 26.796

5.  An Agent-Based Digital Twin for Exploring Localized Non-pharmaceutical Interventions to Control COVID-19 Pandemic.

Authors:  Souvik Barat; Ritu Parchure; Shrinivas Darak; Vinay Kulkarni; Aditya Paranjape; Monika Gajrani; Abhishek Yadav; Vinay Kulkarni
Journal:  Trans Indian Natl Acad Eng       Date:  2021-01-29

6.  SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg.

Authors:  Paul Wilmes; Jacques Zimmer; Jasmin Schulz; Frank Glod; Lisa Veiber; Laurent Mombaerts; Bruno Rodrigues; Atte Aalto; Jessica Pastore; Chantal J Snoeck; Markus Ollert; Guy Fagherazzi; Joël Mossong; Jorge Goncalves; Alexander Skupin; Ulf Nehrbass
Journal:  Lancet Reg Health Eur       Date:  2021-02-27

7.  Estimation of local time-varying reproduction numbers in noisy surveillance data.

Authors:  Wenrui Li; Katia Bulekova; Brian Gregor; Laura F White; Eric D Kolaczyk
Journal:  medRxiv       Date:  2022-04-28

8.  Microscopic dynamics modeling unravels the role of asymptomatic virus carriers in SARS-CoV-2 epidemics at the interplay between biological and social factors.

Authors:  Bosiljka Tadić; Roderick Melnik
Journal:  Comput Biol Med       Date:  2021-04-24       Impact factor: 6.698

9.  Modelling the impact of relaxing COVID-19 control measures during a period of low viral transmission.

Authors:  Nick Scott; Anna Palmer; Dominic Delport; Romesh Abeysuriya; Robyn M Stuart; Cliff C Kerr; Dina Mistry; Daniel J Klein; Rachel Sacks-Davis; Katie Heath; Samuel W Hainsworth; Alisa Pedrana; Mark Stoove; David Wilson; Margaret E Hellard
Journal:  Med J Aust       Date:  2020-11-18       Impact factor: 12.776

10.  COUnty aggRegation mixup AuGmEntation (COURAGE) COVID-19 prediction.

Authors:  Siawpeng Er; Shihao Yang; Tuo Zhao
Journal:  Sci Rep       Date:  2021-07-12       Impact factor: 4.379

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