*What model structure would the disease you are interested be and please start adjusting the R code to that structure.

My interested disease discussed in the previous session was Dengue Fever. The model structure that I would like to develop for my topic is SEIR (Susceptible-Exposure-Infected-Recovered). I would like to use this model to describe the transmission prediction of Dengue in Thailand.

The reason to use the SEIR model is because the virus included incubation or latency period which occur just before infection. In the case of Dengue, the exposure time is approximately 8-9 days before manifestation of the disease once It is transmitted by an infected mosquito. Therefore, take the exposured population into account reflects the realistic disease dynamic and enhances the model’s ability to predict the transmission of dengue used for work towards in reducing the burden of this mosquito-borne disease in the future.

*R Code:

# Define the SEIR dynamics function

SEIR.dyn <- function(t, var, par) {

S <- var[1]

E <- var[2]

I <- var[3]

R <- var[4]

N <- S + E + I + R

beta <- par[1]

gamma <- par[2]

sigma <- par[3]

dS <- -(beta * S * I) / N

dE <- (beta * S * I) / N – sigma * E

dI <- sigma * E – gamma * I

dR <- gamma * I

# Return the rates of change as a list

return(list(c(dS,dE, dI, dR)))

}

install.packages(“deSolve”)

library(deSolve)

# Define initial conditions, time points, and parameters

R0<-3.42 # Basic Reproduction Number (Liu et al., 2020)

gamma <- 1/7 # Infectious period of 7 days, infectious period (7days)= 1/gamma (CDC:

https://www.cdc.gov/dengue/training/cme/ccm/page47478.html)

beta <- R0*gamma # 3.42/7

sigma <- 1/7 # incubation period of dengue 5-7 days

SEIR.par <- c(beta,sigma,gamma)

SEIR.init <- c(5000,1000,50,50) # Assume total population of 5000,Exposed 1000, Infected 50, recovery 50)

SEIR.t <- seq(0,365,by=1) # 0-365 days,increase every 1 day

SEIR.sol <- lsoda(SEIR.init, SEIR.t, SEIR.dyn, SEIR.par) # Solve the SIR model using lsoda

TIME <- SEIR.sol[,1]

S <- SEIR.sol[,2]

E <- SEIR.sol[,3]

I <- SEIR.sol[,4]

R <- SEIR.sol[,5]

N <- S + E + I + R

# Plot the results

plot(TIME, S, type = “l”, col = “blue”, lwd = 2, ylim = c(0, 5000), xlab = “Time”, ylab = “Population”, main = “SEIR model for Degnue “)

lines(TIME, E, type = “l”, col = “yellow”, lwd = 2)

lines(TIME, I, type = “l”, col = “red”, lwd = 2)

lines(TIME, R, type = “l”, col = “green”, lwd = 2)

legend(“right”, legend = c(“Susceptible”, “Exposure”, “Infected”, “Recovered”), col = c(“blue”,”yellow”, “red”, “green”), lty = 1, cex = 0.8)

# I am not able to upload the Plot picture ka Ajarn, I will submit by email na ka.

• Incubation period refers to the time between exposure to a pathogen and the onset of symptoms of the disease it causes. The incubation period of the dengue virus is 3–14 days, with an average of 4–7 days.

Source: https://www.ecdc.europa.eu/en/dengue-fever/facts

• Viremic period is known as the “period of infectivity”. In sick persons, viremia typically coincides with the presence of fever. Both symptomatic and asymptomatic persons are viremic and can transmit DENV to mosquitoes that bite them during this approximately 7-day period.

Source:https://www.cdc.gov/dengue/training/cme/ccm/page45915.html#:~:text=Intrinsic%20Incubation%20Period%20(3%2D14,the%20human%20can%20become%20ill.

*Reference:

Liu, Y., Lillepold, K., Semenza, J. C., Tozan, Y., Quam, M. B. M., & Rocklov, J. (2020, Mar). Reviewing estimates of the basic reproduction number for dengue, Zika and chikungunya across global climate zones. Environ Res, 182, 109114. https://doi.org/10.1016/j.envres.2020.109114