Introduction

SIR model is an acronym of three concepts involved in the model: S for Susceptible, I

for infected and R for the removed. This model is fascinating for me as I was amazed by the

way how a simple model could be used to predict a deathly epidemic. In order to approach

this topic, we firstly need to understand the real life situation which is the cholera outbreak in

South Sudan and we need to understand what SIR modelling actually is. After we have

understood these two crucial areas for this investigation we can bring them into a relation and

investigate this real life case through this mathematical area which is most definitely

appropriate.

Cholera
First of all, by World Health organization cholera is defined as an acute diarrheal

disease that can kill within hours if left untreated. Researchers have estimated that each year

there are 1.3 million to 4.0 million cases of cholera, and 21 000 to 143 000 deaths worldwide

due to cholera. Most of those infected will have no or mild symptoms, and can be

successfully treated with oral rehydration solution. Severe cases will need rapid treatment

with intravenous fluids and antibiotics. Provision of safe water and sanitation is critical to

control the transmission of cholera and other waterborne diseases. Safe oral cholera vaccines

should be used in conjunction with improvements in water and sanitation to control cholera

outbreaks and for prevention in areas known to be high risk for cholera. A global strategy on

cholera control with a target to reduce cholera deaths by 90% was launched in 20171.

Cholera outbreak in South Sudan

1
World Health Organization page visited on 28.10.2018
http://www.who.int/news-room/fact-sheets/detail/cholera
 The fight against cholera in South Sudan has involved a range of agencies such as

World Health Organization, UN etc. working together to enhance surveillance, deploy rapid

response teams to investigate and respond to cases, provide clean water, promote good

hygiene practices and treat cholera patients. To enhance outbreak response efforts, the

government worked with the European Union Humanitarian Aid (ECHO), GAVI, the

Vaccine Alliance, the United States Agency for International Development (USAID) and the

World Health Organization (WHO), securing 2.2 million doses of the Oral Cholera Vaccine

(OCV) from the Gavi-funded global stockpile. In 2017 more than 885,000 people at higher

risk of cholera were immunized in the first round and nearly 500,000 people also received a

second round of the vaccine. Due to security challenges, not everyone was able to receive the

recommended two doses, which would significantly decrease their risk of being affected by

cholera. “Cholera is a virulent disease which spreads when hygiene and sanitation are

inadequate,” said Evans Liyosi, WHO Acting Representative to South Sudan. “The outbreak

was declared on 18 June 2016 and spread to many parts of the country, including the capital

Juba. By the time the last confirmed cholera case was discharged on 18 December 2017, over

20,000 suspected cholera cases and 436 deaths were reported.

The country is dealing with several complex health emergencies with 5.1 million

people in need of health assistance. Armed conflict has forced almost 4 million people to flee

their homes. Nearly 5 million people, more than 40% of the population, are severely food

insecure. These challenges place a huge burden on the country’s health system, while the

sanitation infrastructure needs further strengthening2.

SIR modelling

2
World Health Organization Regional Office for Africa page visited on 28.10.2018
https://afro.who.int/news/south-sudan-declares-end-its-longest-cholera-outbreak
 SIR model is a quantative model that explains the dynamics of epidemics. This model

takes into account the possibility of a disease-contracted patient to recover and become

immune to infection in the future.

After we have introduced our real life situation and understood what cholera is we

may proceed to investigation about SIR modelling which is the mathematical part of this

investigation. An SIR model is an epidemiological model that computes the theoretical

number of people infected with a contagious illness in a closed population over time. The

name of this class of models derives from the fact that they involve coupled equations

relating the number of susceptible people S(t), number of people infected I(t), and number of

people who have recovered R(t). One of the simplest SIR models is the Kermack-

McKendrick model. In order to put this real life example into the SIR modelling we firstly

need to get few numbers. So we need to have number of susceptible people to the cholera in

South Sudan, after a short investigation we have come to a conclusion that around 973,980

people were susceptible to cholera in South Sudan during this outbreak. Furthermore, we

have investigated as well that around 620,122 people were infected and about 413,873 people

recovered3. After knowing these stats we need to know the time which is required for

equations in order to plot the graph as precisely as possible. Cholera outbreak was officially

clamed on 18th June 2016 and it finished on 18th December 2017 making it 548 days. After

we know how many people are infected, how many recovered and how many susceptible and

we know the time in days we may proceed further.

This is an ordinary differential equation model, described by the following equation:

3
World Health Organization Regional Office for Africa page visited on 28.10.2018
https://afro.who.int/news/south-sudan-declares-end-its-longest-cholera-outbreak
After we know all of this we may proceed to plotting a graph.

Methods of SIR
The SIR model is the following system of quadratic ODEs:

 dS = −β S I (1) dt

 dI =βSI−νI (2) dt

 dR = ν I, (3) dt
where the disease transmission rate β > 0 and the recovery rate ν > 0 (or in other words, the

duration of infection D = 1/ν).

The bi-linear incidence term β S I for the number of new infected indi- viduals per unit time

corresponds to homogeneous mixing of the infected and susceptible classes. The total

population size should remain constant, and this easily follows from the SIR system: that the

sum of the left hand sides of the three equations is the derivative of the total population size

and the sum of the right hand sides is zero. We denote the total population size by N. Since

R(t) = N − S(t) − I(t), the system can be reduced to a system of two ODEs: (1) and (2).

Suppose that each infected individual has κ contacts (each sufficient for transmission) per

unit time and κ is independent of the population size. Then κ S/N of these contacts are with

susceptible individuals. If the fraction τ of adequate contacts result in transmission, then each

infected individual infects κ τ S/N susceptible individuals per unit time. Thus β = b/N where

b = κ τ . The parameter τ is called the transmissibility of the infectious disease.

Analysis of the SIR Model

Since the right hand side of (1) is negative and the right hand side of (3) is positive,

this implies that dS/dt ≤ 0 and dR/dt ≥ 0. Since 0 ≤ S(t) ≤ S(0) ≤ N and 0 ≤ R(0) ≤ R(t) ≤ N,

this implies that the limits S(∞) = limt→∞ S(t), R(∞) = limt→∞ R(t), and thus I(∞) =

limt→∞ I(t) = N − S(∞) − R(∞) exist.

The disease always dies out

It is also easy to prove that the disease always dies out, I(∞) = 0 for all initial conditions,

without having a formula for I(t). If not, (3) implies that for t sufficiently large, dR/dt >

νI(∞)/2 > 0, and this implies that R(∞) = ∞, a contradiction.

Epidemic threshold theorem

We define the effective reproductive number Re = (S(0)/N)b/ν and the basic reproductive

number R0 = b/ν. If the entire population is initially suscep- tible, i.e., S(0) = N − 1, I(0) = 1,

R(0) = 0, and large (recall this is a model assumption), then Re = ((N − 1)/N ) b/ν is

approximately equal to R0. Henceforth, to beautify formulas involving R0, we will assume

that the quantity (N − 1)/N is equal to 1.

We now show that Re is the threshold value or tipping point that deter- mines whether an

infectious disease will quickly die out or whether it will invade the population and cause an

epidemic.

Theorem 2.1. 1. If Re ≤ 1, then I(t) decreases monotonically to zero as t → ∞.

2. If Re > 1, then I(t) starts increasing, reaches its maximum, and then decreases to zero as t

→ ∞. We call this scenario of increasing numbers of infected individuals an epidemic.

It follows that an infection can invade and cause an epidemic in an entirely susceptible

population if R0 > 1 or b > ν.

Proof. Equation (2) and the discussion in Section 2.2.1 imply that dI/dt = (β S − ν) I ≤ (β S(0)

− ν) I = ν (Re − 1) I ≤ 0 for Re < 1. This observation together with I(∞) = 0 (see Section

2.2.2) proves the first statement.

Equation (2) implies (dI/dt)(0) = ν (Re − 1) I(0) > 0 for Re > 1. Thus I(t) is increasing at t = 0.

Equation (2) also implies that I(t) has only one non-zero critical point. These observations,

together with I(∞) = 0 imply the second statement.

Figure 1 contains solutions of the SIR system simulating a highly virulent (Re = 3.5) flu

epidemic in a town of 50, 000 people.

Figure 1: Solutions of SIR system of ODEs with β = 0.7/50000,ν = 1/5,S(0) = 49955, I(0)
= 5, R(0) = 0

We stress that the existence of a threshold for infection is far from obvious and was missed

by many public health and infectious disease experts. The reason is that such a threshold can

not be discerned from data; it requires a mathematical model to illuminate.

Above we observed that (dI/dt)(0) = ν (Re − 1) I(0), which implies that the number of

infected individuals initially starts growing/decreasing expo- nentially at rate ν (Re − 1). The

next section will provide strong intuition for the exponential growth.
Conclusion
To conclude we may see that mathematics may help us in different aspects of life. For

example, thanks to the SIR model we are able to understand more efficiently cholera

outbreak in South Sudan. We are able to plot it, predict it etc.