Predicting COVID-19 Dynamics Using SEIR-PADC Model

Ahmad Sedaghat 1*, Amir Mosavi 2,3*

1
School of Engineering, Australian College of Kuwait, Safat 13015, Kuwait; [email protected];
2
School of Economics and Business, Norwegian University of Life Sciences, 1430 Ås, Norway
3
John von Neumann Faculty of Informatics, Obuda University, 1034 Budapest, Hungary;
[email protected]

Abstract

There are a number of derivates of SIR type models developed in mathematics community with

5 to 8 ordinary differential equations to include detailed mechanisms. These models have

included exposed, deceased, super-spreader, symptomatic and asymptomatic infected and

hospitalized populations; but are mathematically complex and cumbersome. These methods

rarely used actual clinical data in details and usually fitted with one or maximum two major

clinical data. In this paper, we introduce SEIR-PADC model to include exposed, deceased,

super-spreader and critical populations and divide infected population to symptomatic and

asymptomatic. SEIR-PADC model is a set of 8 ordinary differential equations with 12

unknown coefficients. Along with, we used an optimization algorithm in MATLAB to find

best fit coefficients to 5 set of COVID-19 data in Kuwait. Our focus is to track trends of

COVID-19 in coming days. Initial conditions for 8 populations and initial guess values for 12

unknown coefficients are found in a way to best fit COVID-19 data. We used 136 days of

COVID-19 data in Kuwait and obtained solutions to cumulative populations rather than daily

population. Predictions for 5 different population of COVID-19 in Kuwait using SEIR-PADC

model are promising and are discussed here.

Keywords: SARS-CoV-2; Coronavirus disease; COVID-19; Dynamics; Kuwait; SIR model;

prediction
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Introduction

In 2012, the Middle Eastern respiratory syndrome coronavirus (MERS-CoV) was reported with

largest impact in Saudi Arabia, United Arab Emirates, and South Korea which caused more

than 35% mortality rate among infected people with fever, cough, and shortness of breath [1,

2].

This raised concerns in the largest gathering event (Hajj) due to super-spreaders population

from the locals infected by MERS-CoV. Alasmawi et al. [3] studied MERS-CoV by an

extended SIR model with 5 set of ordinary differential equations for two main subcategories:

local population and non-local pilgrims. The 5 set of population include susceptible (S),

infected (I), super-spreaders (P), recovered (R), and hospitalized (H). Their study focused on

finding mathematically the re-production number (R0) and they model coefficients merely

found from literature.

Kim et al. [4] studied MERS-CoV which caused the major outbreak in South Korea in 2015.

They used a similar extended SIR model as [3] except with 6 set of ordinary differential

equations adding asymptomatic infected population (A) with emphasis in determining

transmission rates using estimation or literature. Only one set of clinical data on cumulative

incidence numbers were used for model validation suggesting that the super spreader

population caused initial large reproduction number. They concluded preventive measures such

as intensive lockdown and quarantine hospitalized cases had major impact on stopping spread

of the MERS-CoV outbreak.

Ndaïrou et al. [5] have recently applied the same extended SIR type model introduced in [3, 4]

for studying outbreak of COVID-19 in Wuhan, China with emphasis in stability of their model

with 8 set of ordinary differential equations including mortality rates. They fitted their model

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with only two set of clinical data including confirmed daily cases and confirmed daily death

cases in Wuhan, China. They estimated model coefficients with values so that a reproduction

number below the value of one is obtained. The SIR type models are usually designed for fitting

with cumulative clinical data than daily data.

More recently, Xue et al. [6] developed a 7 set of equations SIR type model using a

transmission network to fit COVID-19 clinical data in Wuhan (China), Toronto (Canada), and

the Italy. They used an optimization algorithm (MCMC) to fit coefficients of 7 set of ODE

equations. They only their model with two set of clinical data, confirmed total infected cases

and confirmed active infected cases.

Observing the above studied literature, it is not clear why 5 to 8 set of ordinary differential

equations are used to only fit with one or maximum two clinical data. From recent COVID-19

data, it can be easily seen that at least 5 set of different clinical data including susceptible,

infected, recovery, critical and deceased populations can be used for validation of extended

SIR type models. In this paper, we introduce SEIR-PADC which is SIR type model with 8 set

of ODE equations. The aim of the paper is to computationally study the 5 set of clinical data

on COVID-19 in Kuwait [7] simultaneously to be fitted by SEIR-PADC model using

optimization technique in MATLAB (fminsearch tool) and measure clinical significance on

development of COVID-19 in Kuwait.

Methodology

SEIR-PADC Model

We introduce here SEIR-PADC model consist of susceptible (S), exposed (E), symptomatic

infected (I), recovered (R), super spreaders (P), asymptomatic infected (A), deceased (D), and

critical (C) populations. The model consist of 8 different cumulative populations and

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transmission from each population starts similar to original SIS and SIR model reported by

Kermack andMcKendrick [8]. A flow chart of SEIR-PADC model is shown in Figure 1.

Figure 1: Flow chart of SEIR-PADC dynamic model.

The model have 12 unknown transmission coefficients x=[x1 x2 …x12], which all are positive

or negative constants and are obtained by an optimization algorithm to fit clinical data. In

Figure 1, x’1=x1E/N is selected as introduced in [8] and flow in and out of each population is

simply expressed as follows:

𝑑𝑆 𝑥1 (1)
= − 𝑆𝐸
𝑑𝑡 𝑁
𝑑𝐸 𝑥1 (2)
= 𝑆𝐸 − 𝑥2 𝐸 − 𝑥3 𝐸 − 𝑥4 𝐸
𝑑𝑡 𝑁
𝑑𝐼 (3)
= 𝑥3 𝐸 − 𝑥5 𝐼 − 𝑥6 𝐼 − 𝑥7 𝐼
𝑑𝑡
𝑑𝑃 (4)
= 𝑥4 𝐸 − 𝑥8 𝑃 − 𝑥9 𝑃 − 𝑥10 𝑃
𝑑𝑡
𝑑𝐴 (5)
= 𝑥2 𝐸
𝑑𝑡
𝑑𝐶 (6)
= 𝑥5 𝐼 + 𝑥9 𝑃 − 𝑥11 𝐶 − 𝑥12 𝐶
𝑑𝑡
𝑑𝑅 (7)
= 𝑥6 𝐼 + 𝑥8 𝑃 + 𝑥11 𝐶
𝑑𝑡

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 𝑑𝐷 (8)
= 𝑥7 𝐼 + 𝑥10 𝑃 + 𝑥12 𝐶
𝑑𝑡

The total population N is constant and is defined by:

𝑁 = 𝑆 + 𝐸 + 𝐼 + 𝑃 + 𝐴 + 𝐶 + 𝑅 + 𝐷 = 𝑐𝑜𝑛𝑠𝑡𝑎𝑛𝑡 (9)

Kuwait has a population around 4,270,571 based on Worldometer 2020 [9]. A set of initial

conditions are applied for the 8 populations and 12 coefficients to solve the set of 8 ODE

equations (1-8) as follows:

𝑆0 = 1200,000; 𝐸0 = 5; 𝐼0 = 0; 𝑃0 = 5; 𝐴0 = 0; 𝐶0 = 0, 𝑅0 = 0 ; 𝐷0 = 0 (10)

𝑥0 = [1 1 1 0 0 1 0 0 2 0 0 1] (11)

The SEIR-PADC model outlined above are solved using ode45 in MATLAB [10]. The

optimization tool (fminsearch) [11] is used to find best fitted ODE coefficients by applying the

following convergence criteria for 5-set of available data on goodness of fit (GOF):

𝐺𝑂𝐹 = 𝑀𝑖𝑛𝑖𝑚𝑖𝑧𝑒(𝑅𝑀𝑆𝑅(𝑆) + 𝑅𝑀𝑆𝑅(𝐼) + 𝑅𝑀𝑆𝑅(𝑅) + 𝑅𝑀𝑆𝑅(𝐷) (12)

+ 𝑅𝑀𝑆𝑅(𝐶))

In equation (12), the root mean-square ratio (RMSR) of computed population versus available

COVID-19 population are calculated and the optimization algorithm (fminsearch) in

MATLAB is used to minimize the summation. This is discussed next.

Goodness of fit technique

The root mean-square ratio

The root mean-square ratio (RMSR) is defined here using the coefficient of determination

which is widely used on goodness of fit when predicted variables are compared with actual

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data particularly for situations that future outcomes are sought. The coefficient of determination

(R2) evaluates the predicted values (y) against actual data (𝑦𝑒𝑥𝑝 ) and is rewritten to provide

RMSR as follows [12,13]:

2
2 ∑(𝑦−𝑦𝑒𝑥𝑝 )
RMSR = 1 − R = 2 (13)
∑(𝑦𝑒𝑥𝑝 −𝑦
̅̅̅̅̅̅̅)
𝑒𝑥𝑝

In equation (13), 𝑦
̅̅̅̅̅̅
𝑒𝑥𝑝 is the average of COVID-19 clinical data value for certain population.

Better fitted functions provide R2 value close to unity and RMSR close to zero.

Results of SEIR-PADC model

Using the optimization algorithm (fminsearch) in MATLAB and initial conditions given in

equations (10-11), the following values are found for the model coefficients:

𝑥 = [1.9150 1.0159 0.8187 0.0014 0.0008 0.0499 − 0.0000 (14)

− 0.0003 0.4009 0.0030 0.0032 0.0403]

(a) Critical population (e) Recovered population

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 (b) Infected population (f) Susceptible population

(c) Deceased population (g) All populations in SEIR-PADC model

Figure 2: Fitting 5 set of COVID-19 data simultaneously with SEIR-PADC model for

dynamics of COVID-19 in Kuwait (8 July 2020).

Figure 2 shows that 5 set of COVID-19 data including critical, infected, deceased, recovered,

and susceptible populations are simultaneously fitted with SEIR-PADC model. Goodness of

fit value (GOF) is obtained 1.5756 for 5-set of data in equation (12).

Important dates including peak number and day of infectious, peak value and day of people in

critical condition, maximum recovered and deceased populations, and end of pandemic in

Kuwait can be feasibly obtained from the Figure 2 and computed values from SEIR-PADC

model.

Conclusions

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We have developed SEIR-PADC dynamic model for COVID-19 in Kuwait. The aim is to

computationally fit simultaneously any available set of COVID-19 data for better prediction of

trends of COVID-19 dynamics in Kuwait. From the results of this study, it can be concluded

that:

• SEIR-PADC dynamic model was successfully implemented.

• Initial conditions for 12 unknown coefficients in SEIR-PADC model were correctly

identified.

• MATLAB optimization with a convergence criterion is successfully applied to find best

fitted prediction from SEIR-PADC model to COVID-19 data in Kuwait.

• Important peaks of population sizes and dates are predicted successfully indicting that

Kuwait has passed all important peaks of critical hospitalization and peak of infectious

populations.

SEIR-PADC model is a simple and robust model to correctly pick up various well-defined

population in SIR type models. The model has successfully fitted 5-set of COVD-19 data in

Kuwait.

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*Declaration: Authors have no conflict of interests.