Law2020 - SIR model of COVID-19 transmission in Malyasia with time-varying parameters

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Model Identifier
BIOMD0000000982
Short description
The susceptible-infectious-removed (SIR) model offers the simplest framework to study transmission dynamics of COVID-19, however, it does not factor in its early depleting trend observed during a lockdown. We modified the SIR model to specifically simulate the early depleting transmission dynamics of COVID-19 to better predict its temporal trend in Malaysia. The classical SIR model was fitted to observed total (I total), active (I) and removed (R) cases of COVID-19 before lockdown to estimate the basic reproduction number. Next, the model was modified with a partial time-varying force of infection, given by a proportionally depleting transmission coefficient, [Formula: see text] and a fractional term, z. The modified SIR model was then fitted to observed data over 6 weeks during the lockdown. Model fitting and projection were validated using the mean absolute percent error (MAPE). The transmission dynamics of COVID-19 was interrupted immediately by the lockdown. The modified SIR model projected the depleting temporal trends with lowest MAPE for I total, followed by I, I daily and R. During lockdown, the dynamics of COVID-19 depleted at a rate of 4.7% each day with a decreased capacity of 40%. For 7-day and 14-day projections, the modified SIR model accurately predicted I total, I and R. The depleting transmission dynamics for COVID-19 during lockdown can be accurately captured by time-varying SIR model. Projection generated based on observed data is useful for future planning and control of COVID-19.
Format
SBML (L3V1)
Related Publication
  • Tracking the early depleting transmission dynamics of COVID-19 with a time-varying SIR model.
  • Law KB, Peariasamy KM, Gill BS, Singh S, Sundram BM, Rajendran K, Dass SC, Lee YL, Goh PP, Ibrahim H, Abdullah NH
  • Scientific reports , 12/ 2020 , Volume 10 , Issue 1 , pages: 21721 , PubMed ID: 33303925
  • Institute for Clinical Research, Ministry of Health Malaysia, Setia Alam, Malaysia. kblaw@crc.gov.my.
  • The susceptible-infectious-removed (SIR) model offers the simplest framework to study transmission dynamics of COVID-19, however, it does not factor in its early depleting trend observed during a lockdown. We modified the SIR model to specifically simulate the early depleting transmission dynamics of COVID-19 to better predict its temporal trend in Malaysia. The classical SIR model was fitted to observed total (I total), active (I) and removed (R) cases of COVID-19 before lockdown to estimate the basic reproduction number. Next, the model was modified with a partial time-varying force of infection, given by a proportionally depleting transmission coefficient, [Formula: see text] and a fractional term, z. The modified SIR model was then fitted to observed data over 6 weeks during the lockdown. Model fitting and projection were validated using the mean absolute percent error (MAPE). The transmission dynamics of COVID-19 was interrupted immediately by the lockdown. The modified SIR model projected the depleting temporal trends with lowest MAPE for I total, followed by I, I daily and R. During lockdown, the dynamics of COVID-19 depleted at a rate of 4.7% each day with a decreased capacity of 40%. For 7-day and 14-day projections, the modified SIR model accurately predicted I total, I and R. The depleting transmission dynamics for COVID-19 during lockdown can be accurately captured by time-varying SIR model. Projection generated based on observed data is useful for future planning and control of COVID-19.
Contributors
Kausthubh Ramachandran

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Model files

Law2020.xml SBML L3V1 file of SIR model of COVID-19 transmission in Malyasia with time-varying parameters 28.42 KB Preview | Download

Additional files

Law2020.sedml SED-ML file of SIR model of COVID-19 transmission in Malyasia with time-varying parameters 2.82 KB Preview | Download
Law2020.cps COPASI 4.29 (Build 228) file of SIR model of COVID-19 transmission in Malyasia with time-varying parameters 55.31 KB Preview | Download
Law2020.omex COMBINE archive of SIR model of COVID-19 transmission in Malyasia with time-varying parameters 11.29 KB Preview | Download

  • Model originally submitted by : Kausthubh Ramachandran
  • Submitted: Dec 24, 2020 9:20:59 PM
  • Last Modified: Dec 24, 2020 9:20:59 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: Dec 24, 2020 9:20:59 PM
    • Submitted by: Kausthubh Ramachandran
    • With comment: Automatically added model identifier BIOMD0000000982
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Curator's comment:
(added: 24 Dec 2020, 21:20:38, updated: 24 Dec 2020, 21:20:38)
Figs 5D, 5E, and 5F are reproduced here with parameters as given in the manuscript. The time is measured in days starting from 18-Mar-2020