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List of COVID-19 simulation models

From Wikipedia, the free encyclopedia

COVID-19 simulation models are mathematical infectious disease models for the spread of COVID-19.[1] The list should not be confused with COVID-19 apps used mainly for digital contact tracing.

Note that some of the applications listed are website-only models or simulators, and some of those rely on (or use) real-time data from other sources.

Models with the most scientific backing

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The sub-list contains simulators that are based on theoretical models. Due to the high number of pre-print research created and driving by the COVID-19 pandemic,[2] especially newer models should only be considered with further scientific rigor.[3][4]

Simulations and models

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Genome databases

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Several of these models make use of genome databases, including the following:

Consortia, research clusters, other collections

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  • CDC list of Forecast Inclusion and Assumptions[54] – large list with different models, etc.
  • CORSMA – EU consortium (COVID-19-Outbreak Response combining E-health, Serolomics, Modelling, Artificial Intelligence and Implementation Research)[55]
  • COVID-19 Forecast Hub[56] – Serves as a central repository of forecasts and predictions from over 50 international research groups.[57][58]
  • Nextstrain – Open-source project to harness the scientific and public health potential of pathogen genome data[59]
    • See also Nextstrain SARS-CoV-2 resources[60]
  • SIMID[61] – Simulation Models of Infectious Diseases – Belgium research consortium
  • RAMP – Rapid Assistance in Modelling the Pandemic[62] (UK)
  • UT Austin COVID-19 Modeling Consortium[63]
  • Computational Approaches to Foster Innovation in the Treatment and Diagnosis of Infectious Diseases by Frontiers

Vaccination monitors, models or dashboards

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Note: The following (additional) resources are mostly based on actual data, not simulation. They might include predictive features, e. g. vaccination rate estimation, but in general are not based on theoretical or modeling grounds as the main list of this article. Nonetheless, forecasting remains important.[64] (See for example the COVID-19 Forecast Hub)[65]

Models with less scientific backing

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The following models are purely for educational purposes only.

  • Cellular Defense Automata model[75]
  • Overview of SARS-CoV-2 variants and mutations that are of interest[76]
  • Covid-19 Simulator[77]
  • COVID19: Top 7 - A curated list[78] posted on Medium
  • github.com/topics: covid-19[79]
  • ISEE Systems COVID-19 Simulator[80]
  • nCoV2019.live[81] - "Numbers you need at a quick glance" by Schiffmann/Conlon
    • cov19.cc- by Conlon[82]
  • Simul8 - COVID-19 Simulation Resources[83]
  • Simulating coronavirus with the SIR model[84]
  • Virus Spread Simulation[85]
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  • (American Chemical Society) CAS COVID-19 BIOINDICATOR EXPLORER[86]
  • CDC's COVID Data Tracker[87]
  • Civil Society Partners in Solidarity against COVID-19 (CSPAC): Full, live, global, COVID-19 Status Report for 251 locales & 71 Ships[88]
  • Cornell Institute for Social & Economic Research (CISER): COVID-19 Data Sources[89]
  • Eulerian–Lagrangian multiphase modeling, e. g. for transmission of COVID-19 in elevators based on CFD[90]
  • Onset of Symptoms of COVID-19 simulation (Stochastic Progression Model) by Larsen et al.[91]
  • Our World in Data's Coronavirus Source Data[92]
  • The Atlantic's COVID 19 Tracking Project[93]
  • Vadere - Open Source Framework for Pedestrian and Crowd Simulation[94]
  • WHO Coronavirus (COVID-19) Dashboard[95]

Trainings and other resources

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See also

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References

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  1. ^ Adam D (April 2020). "Special report: The simulations driving the world's response to COVID-19". Nature. 580 (7803): 316–318. Bibcode:2020Natur.580..316A. doi:10.1038/d41586-020-01003-6. PMID 32242115. S2CID 256820433.
  2. ^ Brierley L. "The role of research preprints in the academic response to the COVID-19 epidemic". Authorea Preprints. doi:10.22541/au.158516578.89167184.
  3. ^ "Another 178,000 deaths? Scientists' latest virus projection is a warning". NBC News. 24 September 2020. Retrieved 2021-02-22.
  4. ^ Tufekci Z (2020-04-02). "Don't Believe the COVID-19 Models". The Atlantic. Retrieved 2021-02-22.
  5. ^ Chen TM, Rui J, Wang QP, Zhao ZY, Cui JA, Yin L (February 2020). "A mathematical model for simulating the phase-based transmissibility of a novel coronavirus". Infectious Diseases of Poverty. 9 (1): 24. doi:10.1186/s40249-020-00640-3. PMC 7047374. PMID 32111262.
  6. ^ "CoSim Online". shiny.covid-simulator.com. Retrieved 14 December 2023.
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  20. ^ "CovRadar". covradar.net. Retrieved 14 December 2023.
  21. ^ Wittig A, Miranda F, Hölzer M, Altenburg T, Bartoszewicz JM, Dieckmann MA, et al. (2021-04-06). "CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance". bioRxiv 10.1101/2021.02.03.429146v2.
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  24. ^ De-Leon H, Pederiva F (July 2021). "Statistical mechanics study of the introduction of a vaccine against COVID-19 disease". Physical Review E. 104 (1): 014132. arXiv:2012.07306. Bibcode:2021PhRvE.104a4132D. doi:10.1103/PhysRevE.104.014132. PMID 34412259. S2CID 229155979.
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  27. ^ "COVID-19 simulation model creates scenarios". www.vtnews.vt.edu. Archived from the original on 2021-03-06. Retrieved 2021-02-21.
  28. ^ "Event Horizon - COVID-19". rocs.hu-berlin.de. Retrieved 14 December 2023.
  29. ^ Maier BF, Brockmann D (May 2020). "Effective containment explains subexponential growth in recent confirmed COVID-19 cases in China". Science. 368 (6492): 742–746. arXiv:2002.07572. Bibcode:2020Sci...368..742M. doi:10.1126/science.abb4557. PMC 7164388. PMID 32269067.
  30. ^ "Evolutionary AI". evolution.ml. Retrieved 14 December 2023.
  31. ^ "Evolutionary AI". evolution.ml. Retrieved 2021-04-26.
  32. ^ Miikkulainen R, Francon O, Meyerson E, Qiu X, Sargent D, Canzani E, Hodjat B (2020-08-01). "From Prediction to Prescription: Evolutionary Optimization of Non-Pharmaceutical Interventions in the COVID-19 Pandemic". arXiv:2005.13766 [cs.NE].
  33. ^ a b "Can Computer Models Select the Best Public Health Interventions for COVID-19?". IEEE Spectrum: Technology, Engineering, and Science News. 5 January 2021. Retrieved 2021-04-26.
  34. ^ Siwiak M, Szczesny P, Siwiak M (2020-07-10). "From the index case to global spread: the global mobility based modelling of the COVID-19 pandemic implies higher infection rate and lower detection ratio than current estimates". PeerJ. 8: e9548. doi:10.7717/peerj.9548. ISSN 2167-8359. PMC 7357567. PMID 32728498.
  35. ^ Abele D, Kühn MJ, Koslow W, Rack K, Siggel M, Kleinert J, et al. (2022-01-01). "MEmilio - a high performance Modular EpideMIcs simuLatIOn software". GitHub.
  36. ^ Kühn MJ, Abele D, Mitra T, Koslow W, Abedi M, Rack K, et al. (September 2021). "Assessment of effective mitigation and prediction of the spread of SARS-CoV-2 in Germany using demographic information and spatial resolution". Mathematical Biosciences. 339: 108648. doi:10.1016/j.mbs.2021.108648. PMC 8243656. PMID 34216635.
  37. ^ Kühn MJ, Abele D, Binder S, Rack K, Klitz M, Kleinert J, Gilg J, Spataro L, Koslow W, Siggel M, Meyer-Hermann M, Basermann A (2022). "Regional opening strategies with commuter testing and containment of new SARS-CoV-2 variants in Germany". BMC Infectious Diseases. 22 (1): 333. doi:10.1186/s12879-022-07302-9. ISSN 1471-2334. medRxiv 10.1101/2021.04.23.21255995. PMC 8978163. PMID 35379190.
  38. ^ Koslow W, Kühn MJ, Binder S, Klitz M, Abele D, Basermann A, Meyer-Hermann M (2022-05-16). "Appropriate relaxation of non-pharmaceutical interventions minimizes the risk of a resurgence in SARS-CoV-2 infections in spite of the Delta variant". PLOS Computational Biology. 18 (5): e1010054. Bibcode:2022PLSCB..18E0054K. doi:10.1371/journal.pcbi.1010054. ISSN 1553-7358. medRxiv 10.1101/2021.07.09.21260257. PMC 9135349. PMID 35576211.
  39. ^ Shattock AJ, Le Rutte EA, Dünner RP, Sen S, Kelly SL, Chitnis N, Penny MA (March 2022). "Impact of vaccination and non-pharmaceutical interventions on SARS-CoV-2 dynamics in Switzerland". Epidemics. 38 (7): 100535. Bibcode:2021PLSCB..17E9146H. doi:10.1016/j.epidem.2021.100535. PMC 8669952. PMID 34923396.
  40. ^ "Git-repository with open access source-code for OpenCOVID". GitHub. Swiss TPH. 2022-01-31. Retrieved 2022-02-15.
  41. ^ "COVID-19 Government Response Tracker". www.bsg.ox.ac.uk. 18 March 2020. Retrieved 14 December 2023.
  42. ^ "COVID-19 Government Response Tracker". www.bsg.ox.ac.uk. 18 March 2020. Retrieved 2021-04-26.
  43. ^ "sc-cosmo – Stanford-CIDE COronavirus Simulation MOdel". Retrieved 14 December 2023.
  44. ^ "SDL PAND - Mapa global". pand.sdlps.com. Retrieved 2023-05-20.
  45. ^ Khailaie S, Mitra T, Bandyopadhyay A, Schips M, Mascheroni P, Vanella P, Lange B, Binder SC, Meyer-Hermann M (2021). "Development of the reproduction number from coronavirus SARS-CoV-2 case data in Germany and implications for political measures". BMC Medicine. 19 (1): 32. doi:10.1186/s12916-020-01884-4. ISSN 1741-7015. medRxiv 10.1101/2020.04.04.20053637. PMC 7840427. PMID 33504336.
  46. ^ "simm / covid19 / SECIR". GitLab. Retrieved 2021-07-05.
  47. ^ "Report · Wiki · simm / covid19 / SECIR". GitLab. Retrieved 2021-07-05.
  48. ^ "Our research". Helmholtz Centre for Infection Research. Retrieved 2021-07-05.
  49. ^ Syga S, David-Rus D, Schälte Y, Hatzikirou H, Deutsch A (November 2021). "Inferring the effect of interventions on COVID-19 transmission networks". Scientific Reports. 11 (1): 21913. arXiv:2012.03846. Bibcode:2021NatSR..1121913S. doi:10.1038/s41598-021-01407-y. PMC 8578219. PMID 34754025.
  50. ^ "Epidemiology Collection". epubs.siam.org.
  51. ^ Kastalskiy IA, Pankratova EV, Mirkes EM, Kazantsev VB, Gorban AN (November 2021). "Social stress drives the multi-wave dynamics of COVID-19 outbreaks". Scientific Reports. 11 (1): 22497. arXiv:2106.08966. Bibcode:2021NatSR..1122497K. doi:10.1038/s41598-021-01317-z. PMC 8602246. PMID 34795311.
  52. ^ "COVID-19 Simulation Tool". corona-lab.ch. Retrieved 28 April 2021.
  53. ^ Gorji H, Arnoldini M, Jenny DF, Hardt WD, Jenny P (2021-05-04). "Dynamic modelling to identify mitigation strategies for the COVID-19 pandemic". Swiss Medical Weekly. 151 (1718): w20487. doi:10.4414/smw.2021.20487. hdl:20.500.11850/484250. ISSN 1424-3997. medRxiv 10.1101/2020.11.30.20239566. PMID 33945149.
  54. ^ "CDC list of Forecast Inclusion and Assumptions". www.cdc.gov/coronavirus.
  55. ^ "CORESMA". CORESMA. Retrieved 2021-07-05.
  56. ^ "Home - COVID 19 forecast hub". covid19forecasthub.org. Retrieved 14 December 2023.
  57. ^ Best R, Boice J (2020-05-01). "Where The Latest COVID-19 Models Think We're Headed — And Why They Disagree". FiveThirtyEight. Retrieved 2021-02-21.
  58. ^ "Home - COVID 19 forecast hub". covid19forecasthub.org. Retrieved 2021-02-21.
  59. ^ "Nextstrain". nextstrain.org. Retrieved 2021-04-26.
  60. ^ "Nextstrain". nextstrain.org. Retrieved 14 December 2023.
  61. ^ "SIMID – Simulation Models of Infectious Diseases". Retrieved 14 December 2023.
  62. ^ "Rapid Assistance in Modelling the Pandemic: RAMP | Royal Society". royalsociety.org. Retrieved 2021-03-09.
  63. ^ "UT COVID-19 Modeling Consortium". covid-19.tacc.utexas.edu. Retrieved 14 December 2023.
  64. ^ CDC (2020-02-11). "Coronavirus Disease 2019 (COVID-19) - COVID-19 Forecasting: Background Information". Centers for Disease Control and Prevention. Retrieved 2021-10-03.
  65. ^ "About the Hub - COVID 19 forecast hub". covid19forecasthub.org. Retrieved 2021-10-03.
  66. ^ "COVID-19 Map". Johns Hopkins Coronavirus Resource Center. Retrieved 14 December 2023.
  67. ^ "COVID-19 Map". Johns Hopkins Coronavirus Resource Center. Retrieved 2021-04-26.
  68. ^ Dong E, Du H, Gardner L (May 2020). "An interactive web-based dashboard to track COVID-19 in real time". The Lancet. Infectious Diseases. 20 (5): 533–534. doi:10.1016/S1473-3099(20)30120-1. PMC 7159018. PMID 32087114.
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  74. ^ "IHME | COVID-19 Projections". Institute for Health Metrics and Evaluation. Retrieved 14 December 2023.
  75. ^ "Cellular Defense Automata model". thememeticist.github.io.
  76. ^ "CoVariants (CoVariants] - Overview of SARS-CoV-2 variants and mutations that are of interest)". covariants.org. Retrieved 14 December 2023.
  77. ^ "Covid-19 Simulator". www.coronasimulator.com. Retrieved 28 April 2021.
  78. ^ Prabowo A (3 May 2020). "COVID19: Top 7 online interactive simulations, curated". Medium. Retrieved 2021-02-21.
  79. ^ "Build software better, together (topics/covid-19)". GitHub. Retrieved 14 December 2023.
  80. ^ "COVID-19 Simulator". exchange.iseesystems.com. Retrieved 14 December 2023.
  81. ^ "Coronavirus Dashboard". ncov2019.live. Retrieved 14 December 2023.
  82. ^ "cov19.cc". Retrieved 18 August 2023.
  83. ^ "COVID-19 Simulation Resources". Retrieved 2020-02-21.
  84. ^ "Simulating coronavirus with the SIR model". fatiherikli.github.io. Archived from the original on 2021-04-19. Retrieved 2021-02-21.
  85. ^ "Covid-19 Spread Simulation". c19model.com. Retrieved 14 December 2023.
  86. ^ "CAS COVID-19 Resources". CAS. Retrieved 2021-06-02.
  87. ^ "COVID Data Tracker". Centers for Disease Control and Prevention. 28 March 2020. Retrieved 14 December 2023.
  88. ^ "Full, live, global, COVID-19 Status Report for 251 locales & 71 Ships". civilsocietysolidarityagainstcovid19.com. Retrieved 2021-07-01.
  89. ^ Bohan J. "LibGuides: Cornell Institute for Social & Economic Research (CISER): COVID-19 Data Sources". guides.library.cornell.edu. Retrieved 14 December 2023.
  90. ^ Dbouk T, Drikakis D (January 2021). "On airborne virus transmission in elevators and confined spaces". Physics of Fluids. 33 (1): 011905. Bibcode:2021PhFl...33a1905D. doi:10.1063/5.0038180. PMC 7984422. PMID 33790526.
  91. ^ Larsen JR, Martin MR, Martin JD, Kuhn P, Hicks JB (2020). "Modeling the Onset of Symptoms of COVID-19". Frontiers in Public Health. 8: 473. doi:10.3389/fpubh.2020.00473. PMC 7438535. PMID 32903584.
  92. ^ Mathieu E, Ritchie H, Rodés-Guirao L, Appel C, Giattino C, Hasell J, Macdonald B, Dattani S, Beltekian D, Ortiz-Ospina E, Roser M (5 March 2020). "Coronavirus Pandemic (COVID-19)". Our World in Data. Retrieved 14 December 2023.
  93. ^ "The COVID Tracking Project". The COVID Tracking Project. Retrieved 14 December 2023.
  94. ^ "Vadere – Open Source Framework for Pedestrian and Crowd Simulation". www.vadere.org. Retrieved 14 December 2023.
  95. ^ "WHO Coronavirus (COVID-19) Dashboard". covid19.who.int. Retrieved 2021-07-01.

Further reading

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Articles

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Books

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