CCST9017

Hidden Order in Daily Life:

A Mathematical Perspective
Lecture 2
Infectious disease modeling II

Prof. Patrick Tuen Wai Ng

Department of Mathematics
Infectious disease modeling II
Content
 Review of SIR Model
 Continuous SIR model
 sir model
 Herd Immunity

Herd immunity: will the UK's

coronavirus strategy work?
(13 March 2020)
https://www.theguardian.com/world/2020/mar/13/herd-immunity-will-the-uks-
coronavirus-strategy-work
Brief review on the SIR model
 The members of the population progress
through the three classes in the following
order.

Susceptible Infective Immune/ SIR

It Removed
St
Rt
Brief review on the SIR model
St It It
Susceptible Infective Recovered /
St It immune Rt

St 1  St   St I t
I t 1  I t   St I t   I t
Rt 1  Rt   I t
 If we let S= St+1-St and similarly for I and R,
then the dynamics of the functions S,I and R are
governed by the following equations.

 S  -  St I t ,
 I   St I t   I t ,
 R   It .

 The value of the infection parameter

 depends on the mode of transmission.
 1/  : it is the average duration of infectious
period, i.e. the duration of staying in
infective class I before moving into the
removed class R .

• For example, if the period of contagion

lasts 7 days, then each day we expect
roughly or approximately 1/7 of the total
number of infectives to move from the
infective class It into the removed class Rt

Just enter 1 day 2 days 3 days 4 days 5 days 6 days

 Let’s find out when  I is zero.

I   St I t   I t  ( St   ) I t

 I =0 once It=0 (as the population is disease

free).
 Now assume It >0, then we have

If S t  , then  I  0 .


If S t  , then  I  0 .


If S t  , then  I  0 .

 Note that St+1  St for all t . Therefore,
if S 0   , then for all t, St   .
 

 Thus, if S0 is below the value , then  I
< 0 for all times, and the disease
decreases in the population.

 However, when S0  , the number of

infective will grow and an epidemic
occurs. In other words, we have an
outbreak if and only if
R0 
 S 1

0
 On the other hand, we have

1
R0  ( S 0 )  
 
 no. of new cases arising from one   average duration 
     .
 infective per unit time   of infection 
 Thus, R0 is interpreted as the average number of
secondary infections that would be produced by
an infective in a wholly susceptible population of size S0 .
 Classwork 2
Suppose we apply the SIR model to study the spread of COVID-19 in
Hong Kong.
Q1: After the Prevention and Control of Disease (Wearing
of Mask) (Public Transport) Regulation (Cap. 599I) came
into effect at 0.00am on July 15, 2020.

Which of the following should be true for the parameters 

and  ?
a) The value of  will be increased.
b) The value of  will be increased.
c) The value of  will be decreased.
d) The value of  will be decreased.
e) No changes in  and .
 Classwork 2
Q2: To combat the COVID-19 epidemic, the HKSAR Government launched the
Universal Community Testing Programme (UCTP) on September 1, 2020 to provide
a one-off free testing service of for members of the public. The UCTP aims to
identify as early as possible asymptomatic COVID-19 patients in the community
and achieve the target of early identification, isolation and treatment to cut the
community transmission.
Which of the following should be true for the parameters 
and  after the launch of UCTP ?
a) The value of  will be increased.
b) The value of  will be increased.
c) The value of  will be decreased.
d) The value of  will be decreased.
e) No changes in  and .
Please answer these questions in Moodle within 24 hours after
the lecture (i.e. before 2:30pm the next day for section A and
6:30pm for section B).
 Continuous model
 Note that so far we are using discrete time
intervals (e.g. one day). Now if we let the time
interval to be very small, say one second. Then
I is almost equal to the instinct change of I.
 Therefore, one may replace I by dI/dt, which is
the rate of change of I (also called the derivative
of I). Similarly, we may replace S and R by
dS/dt and dR/dt respectively.
 With these notations, our system of equations
can be replaced by the following system of
ordinary differential equations.
 A system of three ordinary differential
equations describes the SIR model:

dS  I (t)S (t)

dt
dI  I (t)S (t) I (t)
dt
dR  R(t)
dt

where is  the infection rate and  the removal rate of

infectives.
Graphs of S,I,R functions

Figure 1: Typical dynamics for the SIR model.

Interactive SIR model

https://maple.cloud/app/4837052487041024
The sir model
Infectious disease models are often formulated a
bit differently from we did before. Quite often,
instead of absolute numbers, proportions of the
population are used.

This approach is useful when the precise size of

the population may not be known.
 Such a formulation also allows us to replace the
transmission coefficient  with a new parameter
that has a more meaningful biological interpretation.
 Working with the SIR model as an example, let’s
set
S I R
s , i , r ,
N N N

and rebuild the model using proportions, s, i

and r.
Notice that

s  i  r 1
 We will continue to assume there are no births or
immigration so that the total population size N
remains constant, even though N will not appear in
our equations.
 In this setting, a similar thought process as used in
the SIR model leads to formulas for s, i, r, the
change in proportions of the three classes. The s i r
equations are:
 s    st it ,
 i   st it   it ,
 r   it ,
where  is called the contact rate.
  Before we explain the interpretation of  , we
should note that , if we use the s i r model and
want to introduce a specific total population size N,
we can recover S I R data by simply multiplying
the s i r formulas by N . For example, the net
change in number of susceptible is

 S  ( s) N    st it N  (  it )( st N )  (  it )St .
The first equality follows from
S = St+1-St = N st+1 - N st = Ns
 We would like to understand more about the
equation
 S = - ( it) St.
 By the term “contact”, we will mean an interaction
between individuals that is sufficient for disease
transmission.

 Note that -S= St -St+1 equals to the number of

susceptible infected by the infectives in a single
time step and infection occurs only when a
susceptible have contact with an infective, not with
a healthy or immune individual susceptible.
 Therefore, by our definition of “contact”, the total
number of contacts the susceptibles have with
infectives during a single time step should be equal
to -S .
 Since there are St susceptibles, the average
number of contacts a susceptible has with
infectives during a single time step should be
-S/ St
 Hence the factor  it in the equation
S = - ( it) St
must give the average number of contacts a
susceptible has with infectives during a single time
step.
  it = the average number of contacts a
susceptible has with infectives during a single
time step.

 Because it = It /N denotes the fraction of the

population in the infective class, we can interpret
 as the average number of contacts that an
individual has during a single time step.

This means  measures average number of

contacts (in a single time step) between anyone,
whether infective or not, that would have caused
an infection if one of the individuals was infective
and the other susceptible.
 Summary
 The contact rate  can be interpreted as the
average number of contacts an individual
experiences during one time step.
 Then  it represents the average number of
contacts with infectives that an individual
experiences in a single time step.
 To get the number of susceptibles that fall ill
from contact with infectives during a single time
step, we multiply by the number of susceptibles
St and obtain the expression  itSt.
 The value of  would depend on the particulars
of the disease under study.
 For example, because chickenpox is highly
contagious, it seems plausible that an elementary
school child might have contact, sufficient to
spread chickenpox, with four other children
throughout the course of a day.

 In this case, we would take  = 4 and  t = 1 day.

For a less contagious disease,  might be a small
number such as 0.02.
 Another important value is the contact
number  , the average number of contacts
of a typical infective during the entire
infectious period.
 This is a “per-infective” measurement. For
the s i r model above, we multiply the 1
contact rate  by the mean infectious period 
to find

 .

 The contact number  is closely related to the
basic reproduction number R0 .
 This is not surprising because both are measures
of the number of secondary cases of illness
produced by one infective introduced into a wholly
susceptible population.

 Exercise: Try to work out the relationship

between the basic reproduction number R0 and  ,
and see why they are essentially the same as
long as S0 is almost as big as N.
 Vaccinations
 Vaccinations, when available, are attractive way to
control disease dynamics. One goal of any
immunization program is to achieve herd immunity,
(i.e., to ensure that no epidemic can take place even
if a few cases of the disease are present).

 The sir model is useful to help

us to estimate what level of
vaccination confers herd
immunity for a particular
disease in a particular society.
 As an example, consider a large population at
risk for a disease modeled well by the s i r
equations.
 We would like to ensure that, regardless of
the size i0 of the fraction of the population that
was infective, it never increases. Thus, we want

 i   st it   it  0 .
But,  st it   it  (  st   ) it and since it  0 ,
this means we want to have

 1
 st    0 , or st   .
 

In order words, 1/ is the critical value

determining whether disease spreads.
Recall that the contact number  , the average
number of contacts of a typical infective during
the entire infectious period.
 Conclusion
If the fraction of the population that is
susceptible can be brought below 1/ then an
epidemic cannot occur.
The fraction of the population that must be
vaccinated successfully to ensure herd
immunity is thus 1-1/ .
 2021 Future Science Prize Laureate

http://www.futureprize.org/en/laureate
s/detail/53.html

https://www.thestandard.com.hk/breaking-news/section/4/179325/Mutant-virus-
shatters-%22dream%E2%80%9D-of-herd-immunity:-Yuen-Kwok-yung
Mutant virus shatters "dream” of herd immunity

In an article submitted to Ming Pao Daily, Yuen and two

other experts said that the efficacy of the BioNTech vaccine
against the Delta mutant strain is 88 percent, while the
Sinovac vaccine's efficacy is 60 percent.

It is estimated that the vaccination rate of BioNTech and

Sinovac would have to reach 97.4 percent and 142.9
percent respectively to achieve herd immunity.
https://www.thestandard.com.hk/breaking-news/section/4/179325/Mutant-virus-
shatters-%22dream%E2%80%9D-of-herd-immunity:-Yuen-Kwok-yung
Fighting AIDS with Math
 AIDS is caused by
the human
immunodeficiency
virus (HIV), which
weakens the body's
immune system.

HIV budding
HIV budding out
 Fighting AIDS with Math
Dr. David Ho (honorary director of HKU AIDS
Institute) and mathematician Alan S. Perelson
have developed a simple mathematical model to
study the dynamical nature of HIV replication.

This knowledge led David Ho to champion the 'go hard

and early' strategy to prevent HIV virus building up and
mutating drug resistance. Along with studies on mutation,
he advocated the combination antiviral therapy that has
effectively treated HIV since 1996.
 HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span,
and Viral Generation Time, Alan S. Perelson, Avidan U. Neumann, Martin
Markowitz, John M. Leonard, and David D. Ho, 1996, Science , 271, 1582-
1586.
Fighting AIDS with Math
 Despite continued increases in HIV rates across the world,
the progression of the disease to AIDS has reduced
worldwide, and deaths have decreased. In richer nations
with access to drugs, AIDS mortality has declined 6-fold
since combination therapy became widespread in 1996.
 The basic model of in-host infection
consists of a set of a system of ordinary
differential equations that describes the
interactions between susceptible cells,
x, infected cells, y, and infectious
virions v.
dx    dx(t)  x(t)v(t)
 Susceptible cells are produced at a dt
constant rate with mean  from a pool
of precursor cells and die with rate d. dy  x(t)v(t)  ay(t)
dt
 Virions are budded with rate k and have dv
probability Q of being infectious.  Qky(t)  x(t)v(t) uv(t)
dt
 Infectious virions can infect healthy
cells via mass action dynamics where 
describes the efficacy of this process.
 Infected cells die with rate a and
virions are cleared at rate u.
Assignment Two
Due date: 1:00pm, 19 Sep, 2022

You should upload your assignment to Moodle

according to your tutorial group number before
1:00pm on the following Monday.
Each assignment will be counted for 1.5 marks.
You need to answer both questions but due to the
class size, only one question will be marked.
Assignment Two: Question one
Both R0 (the basic reproduction number) for the SIR
model and σ for the sir model are interpreted as
measures of the number of secondary cases of illness
produced by one infective introduced into a wholly
susceptible population. To understand their relationship
better:
1) Express σ in terms of the SIR parameters ,  and N.
2) From your answer to part 1), compute a simple
expression for R0 / σ.
3) If a population is mostly susceptible initially, so that
S0 ≈ N, what will be the value of R0 / σ ?
4) Which one is larger: R0 or σ ?
 Assignment Two: Question two
In the following questions, suppose we model the spread of
the Delta variant of COVID-19 by the sir-model. Assume the
basic reproductive number (R0) for the Delta variant of
SARS-CoV-2 is 6.8 (while that of the original strain is 2.5).

1) Using the result from part 3) of Question 1, estimate the

contact numberσof the Delta variant of SARS-CoV-2 (here
you may assume that S0 ≈ N).
2) Assume the efficacy of the BioNTech vaccine against the
Delta mutant strain is 88%. Using the BioNTech vaccine
only, what percentage of the population should be
immunized to achieve herd immunity ?
3) Now replace the BioNTech vaccine by the Sinovac
vaccine and assume the Sinovac vaccine's efficacy against
the Delta mutant strain is 60%, is it possible to achieve herd
immunity in this case? Explain your answer.