Lee2018 - Avian human half-saturated incidence (HSI) model

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Short description
Related Publication
  • Transmission dynamics and control strategies assessment of avian influenza A (H5N6) in the Philippines
  • Hanl Lee, Angelyn Lao
  • Elsevier BV , 3/ 2018 , Volume 3 , pages: 35-59 , DOI: 10.1016/j.idm.2018.03.004
  • Mathematics & Statistics Department, De La Salle University , 2401 Taft Avenue, 0922 Manila, Philippines Mathematical & Statistical Modeling Research Unit, Center for Natural Sciences and Environmental Research, 2401 Taft Avenue, 0922Manila, Philippines
  • Due to the outbreaks of Highly Pathogenic Avian Influenza A (HPAI) H5N6 in the Philippines (particularly in Pampanga and Nueva Ecija) in August 2017, there has been an increase in the need to cull the domestic birds to control the spread of the infection. However, this control method poses a negative impact on the poultry industry. In addition, the pathogenicity and transmissibility of the H5N6 in both the birds and the humans remain largely unknown which call for the necessity to develop more strategic control methods for the virus. In this study, we constructed a mathematical model for the bilinear and half-saturated incidence to compare their corresponding effect on transmission dynamics of H5N6. The simulations of half-saturated incidence model were similar to what occurred during the H5N6 outbreak (2017) in the Philippines. Instead of culling the birds, we implemented other control strategies such as non-medicinal (personal protection and poultry isolation) and medicinal (poultry vaccination) ways to prevent, reduce, and control the rate of the H5N6 virus transmission. Among the proposed control strategies, we have shown that the poultry isolation strategy is still the most effective in reducing the infected birds.
Submitter of the first revision: Sarubini Kananathan
Submitter of this revision: Sarubini Kananathan
Modellers: Sarubini Kananathan

Metadata information

is (2 statements)
BioModels Database MODEL1808280010
BioModels Database BIOMD0000000717

hasTaxon (3 statements)
Taxonomy Homo sapiens
Taxonomy Aves
Taxonomy H5N6 subtype

isDescribedBy (1 statement)
hasProperty (3 statements)
Mathematical Modelling Ontology Ordinary differential equation model
Experimental Factor Ontology avian influenza
NCIt Viral Infection

Curation status


Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files

HSI reactions.xml SBML L2V4 representation of Lee2018 - Avian human half-saturated incidence (HSI) model 50.21 KB Preview | Download

Additional files

HSI reactions.cps Copasi file for the model. 80.25 KB Preview | Download

  • Model originally submitted by : Sarubini Kananathan
  • Submitted: Aug 28, 2018 3:46:26 PM
  • Last Modified: Oct 18, 2018 11:20:35 AM
  • Version: 7 public model Download this version
    • Submitted on: Oct 18, 2018 11:20:35 AM
    • Submitted by: Sarubini Kananathan
    • With comment: Automatically added model identifier BIOMD0000000717
  • Version: 4 public model Download this version
    • Submitted on: Aug 28, 2018 3:46:26 PM
    • Submitted by: Sarubini Kananathan
    • With comment: Edited model metadata online.

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

: Variable used inside SBML models

Species Initial Concentration/Amount
S h

0000514 ; Homo sapiens
171977.0 mmol
S b

0000514 ; Aves
244956.0 mmol
I b

0000511 ; Aves
36485.0 mmol
I a

0000511 ; Homo sapiens
0.0 mmol
Reactions Rate Parameters
=> S_h compartment*LAMBDA_h LAMBDA_h = 11.1667257534247
=> S_b compartment*LAMBDA_b LAMBDA_b = 5.64383561643836
I_b => compartment*delta_b*I_b delta_b = 0.00346708500589333
S_h => I_a; I_b compartment*beta_bh*S_h*I_b/(H_bh+I_b) beta_bh = 1.62354134956875E-10; H_bh = 120000.0
I_a => compartment*d*I_a d = 6.0882800608828E-11
S_b => compartment*mu_b*S_b mu_b = 0.00136986301369863
S_b => I_b; I_b compartment*beta_b*S_b*I_b/(H_b+I_b) beta_b = 0.00346731269415168; H_b = 180000.0
Curator's comment:
(added: 18 Oct 2018, 11:18:58, updated: 18 Oct 2018, 11:18:58)
2nd column of Figure 2 from the reference publication has been reproduced. The model shows the half-saturated incidence of avian influence being transmitted. Initial conditions were taken from the publication. The model was simulated using Copasi 4.22 and the figure was generated using Python 2.7.