# Adapting an Agent-Based Model of Infectious Disease Spread in an Irish County to COVID-19

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## Abstract

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## 1. Introduction

#### 1.1. COVID-19 Pandemic

#### 1.2. COVID-19 Models

## 2. Materials and Methods

#### 2.1. Environment Component

#### 2.2. Society Component

#### 2.3. Transportation Component

#### 2.4. Disease Component

#### 2.5. Adapting from Measles to COVID-19

#### 2.6. Experiments

## 3. Results

#### 3.1. COVID-19 Model Results vs. Measles Model Results

#### 3.2. Modelling COVID-19 Dynamics

#### 3.3. Interventions and Their Influence on the Outbreaks

#### 3.4. COVID-19 in Leitrim: Real Interventions and Timings

## 4. Discussion

## 5. Conclusions

## Author Contributions

## Funding

## Institutional Review Board Statement

## Informed Consent Statement

## Data Availability Statement

## Conflicts of Interest

## References

- Sanyaolu, A.; Okorie, C.; Marinkovic, A.; Patidar, R.; Younis, K.; Desai, P.; Hosein, Z.; Padda, I.; Mangat, J.; Altaf, M. Comorbidity and its Impact on Patients with COVID-19. SN Compr. Clin. Med. Vol.
**2020**, 2, 1069–1076. [Google Scholar] [CrossRef] - Charaudeau, S.; Pakdaman, K.; Boëlle, P.Y. Commuter Mobility and the Spread of Infectious Diseases: Application to Influenza in France. PLoS ONE
**2014**, 9, e83002. [Google Scholar] [CrossRef] [PubMed] [Green Version] - Dalziel, B.D.; Pourbohloul, B.; Ellner, S.P. Human mobility patterns predict divergent epidemic dynamics among cities. Proc. R. Soc. B
**2013**, 280, 20130763. [Google Scholar] [CrossRef] [PubMed] - Hunter, E.; Mac Namee, B.; Kelleher, J. An open-data-driven agent-based model to simulate infectious disease outbreaks. PLoS ONE
**2018**, 13, e0208775. [Google Scholar] [CrossRef] - Simpson, C.R.; Beever, D.; Challen, K.; Angelis, D.D.; Fragaszy, E.; Goodacre, S.; Hayward, A.; Lim, W.S.; Rubin, G.J.; Semple, M.G.; et al. The UK’s pandemic influenza research portfolio: A model for future research on emergin infections. Lancet Infect. Dis.
**2019**, 19, e295–e300. [Google Scholar] [CrossRef] [Green Version] - Anderson, R.M.; Heesterbeek, H.; Klinkenberg, D.; Hollingsworth, T.D. How will country-based mitigation measures influence the course of the COVID-19 epidemic? Lancet
**2020**, 395, 931–934. [Google Scholar] [CrossRef] - ECDC. Disease Background of COVID-19; European Centre for Disease Prevention and Control: Solna, Sweden, 2020. [Google Scholar]
- WHO. Coronavirus (COVID-19) Outbreak Situation Dashboard; World Health Organization: Geneva, Switzerland, 2020. [Google Scholar]
- BBC. First Case of Coronavirus In Republic of Ireland. BBC News, 29 February 2020. Available online: https://www.bbc.com/news/world-europe-51693160 (accessed on 13 April 2020).
- DOH. Statement from the National Public Health Emergency Team—Monday 13 April. Gov.ie, 13 April 2020. [Google Scholar]
- Wang, H.; Wang, Z.; Dong, Y.; Chang, R.; Xu, C.; Yu, X.; Zhang, S.; Tsamlag, L.; Shang, M.; Huang, J.; et al. Phase-adjusted estimation of the number of Coronavirus Disease 2019 cases in Wuhan, China. Cell Discov.
**2020**, 6, 1–8. [Google Scholar] [CrossRef] [Green Version] - Quilty, B.J.; Clifford, S.; Liu, Y.; Diamond, C.; Edmunds, W.J.; Funk, S.; Gimma, A.; Munday, J.D.; Gibbs, H.; Bosse, N.I.; et al. Effectiveness of Airport Screening at Detecting Travellers Infected with Novel Coronavirus (2019-nCoV). Eurosurveillance
**2020**, 25, 2000080. [Google Scholar] [CrossRef] - Hellewell, J.; Abbott, S.; Gimma, A.; Bosse, N.I.; Jarvid, C.I.; Russell, T.W.; Munday, J.D.; Edmunds, W.J.; Funk, S.; Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group; et al. Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. Lancet Glob. Health
**2020**, 8, E488–E496. [Google Scholar] [CrossRef] [Green Version] - Keeling, M.J.; Rohani, P. Modelling Infectious Diseases in Humans and Animals; Princeton University Press: Princeton, NJ, USA, 2008. [Google Scholar]
- Danon, L.; Brooks-Pollock, E.; Bailey, M.; Keeling, M.J. A spatial model of COVID-19 transmission in England and Wales: Early spread and peak timing. medRxiv
**2020**. [Google Scholar] [CrossRef] [Green Version] - Hunter, E.; Mac Namee, B.; Kelleher, J.D. A Taxonomy for Agent-Based Models in Human Infectious Disease Epidemiology. J. Artif. Soc. Soc. Simul.
**2017**, 20, 2. [Google Scholar] [CrossRef] [Green Version] - Marini, M.; Chokani, N.; Abhari, R.S. COVID-19 Epidemic in Switzerland: Growth Prediction and Containment Strategy Using Artifical Intelligence and Big Data. medRxiv
**2020**. [Google Scholar] [CrossRef] [Green Version] - Chang, S.L.; Harding, N.; Zachreson, C.; Cliff, O.M.; Prokopenko, M. Modelling transmission and control of the COVID-19 pandemic in Australia. Nat. Commun.
**2020**, 11, 5710. [Google Scholar] [CrossRef] [PubMed] - Ferguson, N.M.; Cummings, D.A.T.; Fraser, C.; Cajka, J.C.; Cooley, P.C.; Burke, D.S. Strategies for Mitigating an Influenza Pandemic. Nature
**2006**, 7101, 448–452. [Google Scholar] [CrossRef] - Hunter, E.; Mac Namee, B.; Kelleher, J.D. A Model for the Spread of Infectious Diseases in a Region. Int. J. Environ. Res. Public Health
**2020**, 17, 3119. [Google Scholar] [CrossRef] [PubMed] - Hunter, E.; Kelleher, J. Using a Hybrid Agent-Based and equation-based Model to Test School Closure Policies. BMC Public Health
**2020**, 21. [Google Scholar] [CrossRef] [Green Version] - Hunter, E.; Mac Namee, B.; Kelleher, J.D. Hybrid Agent-Based and Equation-Based Model for Infectious Disease Spread (Version 1.0.0). CoMSES Computational Model Library. Available online: https://www.comses.net/codebases/e30e36f0-5471-46b5-9c78-27b3f2185ff9/releases/1.0.0/ (accessed on 19 April 2020).
- CSO. Census 2011 Boundary Files. 2014. Available online: https://www.cso.ie/en/census/census2011boundaryfiles/ (accessed on 26 May 2016).
- CSO. Census 2016 Place of Work, School or College—Census of Anonymised Records (POWSCAR); Central Statistics Office: Dublin, Ireland, 2017. [Google Scholar]
- Rodrigue, J.P.; Comtois, C.; Slack, B. The Geography of Transport Systems; Routledge, Taylor and Francis Group: London, UK, 2006. [Google Scholar]
- WHO. Report of the WHO-China Joint Mission on Coronavrius Disease 2019 (COVID-19); World Health Organization: Geneva, Switzerland, 2020. [Google Scholar]
- Liu, Y.; Gayle, A.A.; Wilder-SMith, A.; Rocklov, J. The reproductive number of COVID-19 is higher compared to SARS coronavirus. J. Travel Med.
**2020**, 27. [Google Scholar] [CrossRef] [PubMed] [Green Version] - Wu, Z.; McGoogan, J.M. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention. JAMA
**2020**, 323, 1239–1242. [Google Scholar] [CrossRef] [PubMed] - He, X.; Lau, E.H.; Wu, P.; Deng, X.; Wang, J.; Hao, X.; Lau, Y.C.; Wong, J.Y.; Guan, Y.; Tan, X.; et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat. Med.
**2020**, 26, 672–675. [Google Scholar] [CrossRef] [Green Version] - Hunter, E.; Kelleher, J.D. A Framework for Validating and Testing Agent-Based Models: A Case Study from Infectious Diseases Modelling. In Proceedings of the 34th annual European Simulation and Modelling Conference, Toulouse, France, 21–23 October 2020. [Google Scholar] [CrossRef]
- Fine, P.; Eames, K.; Heymann, D.L. “Herd Immunity”: A Rough Guide. Clin. Infect. Dis.
**2011**, 52, 911–916. [Google Scholar] [CrossRef] - Redmond, P.; McGuinness, S. Essential Employees During the COVID-19 Crisis. ESRI Surv. Stat. Rep. Ser.
**2020**. [Google Scholar] [CrossRef] - Health Protection Surveillance Centre. Preliminary Report of the Results of the Study to Investigate COVID-19 Infection in People Living in Ireland (SCOPI): A National Seroprevalence Study, June–July 2020; Health Service Executive: Dublin, Ireland, 2020. [Google Scholar]
- Amárach Public Opinion Survey. Available online: https://www.gov.ie/en/collection/6b4401-view-the-amarach-public-opinion-survey/ (accessed on 7 September 2020).

**Figure 1.**Infection curves for all model runs for a measles outbreak (${R}_{0}$ = 12) and a COVID-19 outbreak (${R}_{0}$ = 3.28).

**Figure 2.**The number of infected agents by time-step (each time-step represents two hours) in the simulation with different ${R}_{0}$ values.

**Figure 3.**Infection curves for model runs with and without infectious agents before they begin to show symptoms.

**Figure 5.**Infection curves for nine individual model runs for school closures in a measles outbreak.

**Figure 6.**Infection curves for all model runs for school closures in a COVID-19 outbreak (${R}_{0}$ = 3.28).

**Figure 7.**Infection curves for 9 individual model runs for school closures in a COVID-19 outbreak (${R}_{0}$ = 3.28).

**Table 1.**Key outbreak characteristics from the measles model and the COVID-19 model (${R}_{0}$ = 3.28).

Measles | COVID-19 | |
---|---|---|

Total Infected | 29,275 | 26,134 |

(27,120 31,430) | (23,870 28,367) | |

Maximum Infected | 1441 | 2144 |

(1333 1548) | (1956 2331) | |

Total Days | 113.12 | 114.86 |

(105.44 120.79) | (107.28 122.44) | |

Days to Max Infected | 74.18 | 57.11 |

(67.14 81.21) | (52.13 62.09) |

${\mathit{R}}_{0}$ | 2.00 | 3.28 | 6.49 |
---|---|---|---|

Total Infected | 25,671 | 26,134 | 28,058 |

(22,820 28,522) | (23,870 28,367) | (25,979 30,137) | |

Max Infected | 2240 | 2144 | 2766 |

(1993 2489) | (1956 2331) | (2558 2973) | |

Total Days | 114.49 | 114.86 | 105.22 |

(106.09 112.89) | (107.28 122.44) | (98.93 111.52) | |

Days to Max | 59.06 | 57.11 | 43.88 |

(53.46 64.66) | (52.13 62.09) | (40.30 47.46) |

**Table 3.**Key characteristics from the COVID-19 model with an ${R}_{0}$ of 3.28 with and without agents being infectious before symptoms begin.

Infectious before Symptoms | Yes | No |
---|---|---|

Total Infected | 27,927 | 26,134 |

(25,741 30,112) | (23,870 28,367) | |

Max Infected | 2536 | 2144 |

(2332 2740) | (1956 2331) | |

Total Days | 112.04 | 114.86 |

(105.32 118.76) | (107.28 122.44) | |

Days to Max | 48.08 | 57.11 |

(43.81 52.36) | (52.13 62.09) |

No Interventions | Vaccination | School Closures | |
---|---|---|---|

Total Infected | 29,275 | 602 | 868 |

(27,129 31,430) | (419 784) | (724 1010) | |

Max Infected | 1,441 | 110 | 208 |

(1333 1548) | (78 143) | (185 232) | |

Total Days | 113.12 | 100.88 | 149 |

(105.44 120.79) | (92.16 109.62) | (137 170) | |

Days to Max | 74.18 | 69.26 | 66 |

(67.14 81.21) | (61.99 76.53) | (49 83) |

No Interventions | Vaccination | School Closures | |
---|---|---|---|

Total Infected | 26,134 | 2339 | 1078 |

(23,870 28,367) | (2256 2422) | (953 1203) | |

Max Infected | 2144 | 753 | 373 |

(1956 2331) | (723 784) | (343 404) | |

Total Days | 114.86 | 135.38 | 141.44 |

(107.28 122.44) | (131.48 139.47) | (127.84 155.04) | |

Days to Max | 57.11 | 81.13 | 54.51 |

(52.13 62.09) | (78.15 85.10) | (46.56 62.47) |

**Table 6.**Key characteristics from the COVID-19 model with an ${R}_{0}$ of 3.28 with and without Irish Interventions.

No Intervention | Irish Interventions | |
---|---|---|

Total Infected | 26,134 | 304.41 |

(23,870 28,367) | (198.71 410.11) | |

Maximum Infected | 2144 | 48.14 |

(1956 2331) | (33.12 63.17) | |

Total Days | 114.86 | 142.13 |

(107.28 122.44) | (118.91 165.34) | |

Days to Max | 57.11 | 63.43 |

(52.13 62.09) | (48.60 78.25) |

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**MDPI and ACS Style**

Hunter, E.; Kelleher, J.D.
Adapting an Agent-Based Model of Infectious Disease Spread in an Irish County to COVID-19. *Systems* **2021**, *9*, 41.
https://doi.org/10.3390/systems9020041

**AMA Style**

Hunter E, Kelleher JD.
Adapting an Agent-Based Model of Infectious Disease Spread in an Irish County to COVID-19. *Systems*. 2021; 9(2):41.
https://doi.org/10.3390/systems9020041

**Chicago/Turabian Style**

Hunter, Elizabeth, and John D. Kelleher.
2021. "Adapting an Agent-Based Model of Infectious Disease Spread in an Irish County to COVID-19" *Systems* 9, no. 2: 41.
https://doi.org/10.3390/systems9020041