Professional Documents
Culture Documents
Table of Contents
Contents
Table of Contents ............................................................................................................................................... 1
The SIR Model in Relation to TB in the Context of the Mozambican Population .............................................. 2
Rationale ........................................................................................................................................................ 2
Estimating the Dynamics of TB in the Mozambican Population for the Years of 2020, 2021, and 2022 ...... 2
Introduction and Aim ................................................................................................................................. 2
The SIR Model for Infectious Diseases and its Necessary Assumptions .................................................... 3
The Variables in This Investigation ............................................................................................................ 4
Initial Equations for Changes in the Values of , , and .................................................................... 5
Obtaining the Values of , , and .................................................................................................... 7
Preparation for Solving the Equations Using the Forward Euler Method ................................................. 8
Does the SIR Model Predict that the Targets From the Global Plan to End TB Will be Achieved in
Mozambique? ............................................................................................................................................ 9
Evaluation and Conclusion ....................................................................................................................... 13
Works Cited ...................................................................................................................................................... 15
Appendices....................................................................................................................................................... 19
Appendix 1: SIR TB Proportions of the Mozambican Population for 2020, 2021, and 2022 ....................... 19
2
These overwhelming and worrying numbers have, for a long time, been a priority to the
Mozambican health ministry. As far as I remember, from a very young age I have always witnessed
campaigns that had the objective of alerting the population about the dangers of TB and there were
always posters and pamphlets spread throughout the cities. However, all of this has recently been
replaced by material regarding the outbreak of COVID-19. Thus, the impression created is that
tuberculosis is no longer a danger to society, which evidently does not portray reality. It is
important that people realize that tuberculosis still exists and, like COVID-19, it ―is a global
pandemic, killing someone approximately every 21 seconds (TB Alliance). It was for all these
reasons that I decided to investigate the incidence of tuberculosis in Mozambique for the present
year and the two years after it.
to End TB is very appealing to me. And this plan is of great importance as it is part of an even
bigger project, the END TB Strategy, also created by the WHO, which ends in 2035 and aims to end
the tuberculosis epidemic (World Health Organization, ―The End TB Startegy‖). However, even
though this plan has made use of mathematical modeling such as the TB Impact and Model
Estimates (TIME) (47) to establish its goals and expect realistic scenarios, the calculations involved
in the process are not explicitly presented or explained in the official document that has been
published.
Using a simpler mathematical model for infectious diseases – the SIR model, the present
investigation aims to study the incidence of tuberculosis (TB) in Mozambique from 2020, the
present year, to 2022, when every country involved in the End TB Partnership is expected to have
achieved the ―90-(90)-90‖ targets. However, because of the limitations of this model, it will only be
possible to do this in relation to the first and third targets.
The SIR Model for Infectious Diseases and its Necessary Assumptions
The Susceptible-Infectives-Recovered (SIR) model is one of the simplest models for analyzing the
behavior of an infectious disease among a given population for a given time. Its initial version was
originally presented by Kermack and McKendrick in 1927 in the publication of ―A Contribution to
the Mathematical Theory of Epidemics‖. As Philipps et al. explain, ―in the SIR model, individuals
begin their lives in the susceptible (S) class, enter the infectious (I) class as they contract the
disease, and finally move to the recovered (R) class‖ (3). So, the total population is divided into
these three categories where the suceptibles are those who have not gotten the disease and have the
biological potential to do so, the infectives are those who have the disease and can pass it to others,
and the recovered are the ones who have been through treatment therapies and no longer have the
disease. Other mathematicians like Tom Crawford, also state that the ―R‖ letter is not only
applicable to the recovered group but that it also includes the people who have died from the
disease and therefore, they also refer to it as the ―removed population‖. It is presumable that in the
case where a disease has vaccination available or any other form of effective preventive method,
like TB does, the ones who have had access to these treatments will also be part of the removed
population, as they would neither be susceptible nor infective.
For the purpose of simplifying the model from a real-life context into the hypothetical context of an
investigation, it is necessary that assumptions are made. Dr. Tom Crawford, from the Oxford
University, clearly explains these assumptions and why they are necessary. According to him, the
first assumption that has to be done is that the population will remain constant for the time period
being studied. This means that there will be no additions to the population size, and as a result, the
time-frame for the investigation must not be too large, otherwise results might be excessively
different from reality. A constant population means that there will be no births and no immigration.
The second assumption he points out is that the rate of increase in the group of the infectives must
4
be considered the same as the rate of contact between the suceptibles and the infectives, and this
contact ratio must always be constant and is called the transmission rate. A major limitation of this
assumption, however, is that it may either over amplify or under amplify the consequences of this
interaction, as different infected individuals will carry out different interactions through a day or
even through a year, and the same happens with the susceptible population. Lastly, the third and
final assumption Crawford defines is that the removal rate should also be considered constant,
being that recovery, or death (or prevention), and recovery means total immunity so, this is a
unidirectional model.
Hence, in order to develop the SIR model in a specific hypothetical scenario it is important to note
that (i) susceptibles (S) either remain aseptic or get infected, (ii) that infected (I) individuals become
immediately infectious and remain infectious until they are convalesced, and that (iii) a removed
(R) person will never be susceptible to getting the disease again, they become immune.
The independent variable for this study will be time, because the SIR model explains the
development of infectious diseases as a function of a period of time. Time, in this investigation will
be represented by t.
The dependent variables will be the values of S, I, and R as a matter of time (t):
, the number of individuals that have been infected by TB and are infectious;
, the number of individuals that have permanently recovered from a TB infection and are
considered immune.
For simplification purposes, , , and will often be simply referred to as S, I, and R, but these
dependent variables will always be a function of the independent variable, time (t).
In the context of TB in Mozambique, the susceptible individuals will be all people living in this
country during the selected time periods (2020–2022) that will not have had tuberculosis and that
will never have had it.
5
The category of infected people will be of those in Mozambique that will have TB during the time
periods that this investigation covers.
In this study, the R group will only include recovered individuals, excluding people who will have
died from TB, will have gone through some form of preventive therapy, or will have taken the BCG
(Bacillus Calmette–Guérin) vaccine, which prevents from some forms of TB (MISAU, Manual para
o Manejo da Tuberculose na Criança, no Adolescente e na Mulher Grávida 130). ―BCG is the only
Vaccine against tuberculosis‖ (Okafor, Rewane, and Momodu) and it is expected to be given to
children at birth (MISAU, Manual de Tuberculose infantil em Moçambique 33) or until they are 23
months old, as part of Mozambique’s Extended Vaccination Program (Programa Alargado de
Vacinação – PAV) (MISAU, Manual para o Manejo da Tuberculose na Criança, no Adolescente e
na Mulher Grávida 130). This means that at least for the three years this investigation will study,
almost every new born is expected to have received the BCG vaccine.
These three categories of individuals (death from TB, preventive-therapy, and BCG-vaccinated)
will be excluded from the removed group because first, no statistical information could be found
regarding the yearly predictions of deaths caused by TB in Mozambique until 2022; secondly,
because preventive therapy in Mozambique is usually only given to people who have been in close
contact with an infected person (Manual de Diagnóstico e Tratamento de Tuberculose Resistente e
Multi-Droga Resistente, 43; MISAU, Manual para o Manejo da Tuberculose na Criança, no
Adolescente e na Mulher Grávida 119) and these numbers have still not been well quantified even
in population projections; and thirdly, because the BCG vaccine, like the other aspects, also does
not seem to have statistical population coverage estimates and it yet only provides protection to a
limited amount of TB forms and to a 60-80% degree (MISAU, Manual para o Manejo da
Tuberculose na Criança, no Adolescente e na Mulher Grávida 130).
Unlike new diseases that keep emerging around the world, where at the beginning of the outbreak
there is no clear perception about it, and consequently there is still no treatment, in the case of TB
there is already a large number of people who have recovered from the disease, just like there are
people who will be in the susceptible group and in the infectious. These values from the beginning
of the investigation will be represented as , , and . In these cases, 0 indicates the initial time
(t) of the investigation, and so is the initial number of susceptibles, is the initial number of
infectives, and is the initial value of recovered people. These are the naught values.
( )
6
where the derivative notation (d) indicates the change in S in relation to the change in t, and r is the
transmission rate between susceptibles and infectives. The value of r is negative because, as it is
proposed by the second assumption the model requires, it is expected that there will be a decrease in
the amount of susceptible individuals as they become infected. This of course will depend on the
amount of people who are still susceptible to getting TB and those that have already been infected,
and that is exactly what the multiplication between I and S indicates. This equation is expected to
explain how the number of susceptible individuals decreases (changes) as more people pass on to the
infected group.
The rate of change in the group of infected/infectives will be indicated by the following equation,
where the derivative notation (d) indicates a change in I in relation to the change in t, and r is the
transmission rate between susceptibles and infectives. The value of r is positive because, opposing
what happened with the susceptible population, it is expected that the infected population increases
over time, as it is also proposed by the second assumption from the SIR model. That is why the rate
of change in I is initially directly proportional to that in S, as the loss in S is the gain in I. However,
when the last portion of the equation is added (-a * I), we understand that the situation might not be
as unfortunate as it seemed. In this equation, a is the rate of recovery and it indicates the amount of
people who are permanently recuperated from a TB infection.
The rate of change in the group of the recovered will be indicated by the following equation,
where the derivative notation (d) indicates a change in R in relation to the change in t, and a is the
rate of recovery. The right side of this equation is directly proportional to the last portion of the
previous equation because the loss in I will be the gain in R. And this, of course, is the aspect that
interests us the most in this investigation, as it will indicate how much it will have been possible to
reduce TB levels in Mozambique to a minimum by 2022, following the Global Plan to End TB.
These three equations to find the rate of change in , , and have been well explained by
Crawford and Sullivan (“SIR Model For Disease Spread- 1‖). It is important to note that the values of r
and a will be constant. And because the values of , , and all add up as the total population,
that will mean that the net changes ( ) in the population that result from the three equations
explained above will add up to zero (0). So, , which means that (
) .
7
Because the present study will be calculating TB numbers in Mozambique for a period of three
years (2020, 2021, and 2022), there will be a need for one new set of the naught values for each
year. That is because when doing these calculations, the population will be held constant for one
year, as it is explained by the first assumption of the SIR model. Keeping the same population
values for a period of three years would be extremely unrealistic, and therefore, affect the results in
a negative way; more than keeping a constant population for one year only. That means that the
same calculations will have to be made three times and that the results obtained for 2020 will affect
those for 2021 and 2022, and the ones for 2021 will affect those of 2022.
for a specific year will be obtained by subtracting the people in Mozambique who are expected
to have been infected by TB in that year and the people who are expected to have recovered in the
previous year from the total population (N) projection for that year.
( ) ( ) ( ( )) ( )
( ) ( ) ( ( ) ( )) ( )
( ) ( ) ( ( ) ( )) ( )
for a specific year will be obtained directly from notifications targets estimated for Mozambique
by the Stop TB Partnership. Those will be the amount of people who are expected to have been
infected (and posteriorly successfully treated) by TB in that year.
( ) ( )
( ) ( )
( ) ( )
for a specific year will also be obtained directly from the notifications targets from the Stop TB
Partnership. Those will be the amount of people who are expected to have been successfully treated
from tuberculosis in the previous year to the one under analysis, a value that will pass on to the
following year as to be used as the naught.
( ) ( )
( ) ( )
8
( ) ( )
All the data used to establish , , and have been collected from the Stop TB Partnership (―TB
diagnosis and treatment targets‖ 4), from where information could be used to get the amount of TB
infected and recovered individuals that is expected to exist in each year, and the population
projections provided by the National Statistics Institute of Mozambique [Instituto Nacional De
Estatística] (INE) from 2007 to 2040.
As it is pointed out by Dr. Tom Crawford, the rate of change of in the susceptible population is
always negative, as it is shown in the equation used to calculate it, ―so this tells us that must
always be smaller than its initial value‖ (Crawford 00:07:34 - 00:07:41). That will mean that
* + .
It is important to note that, in this study, the initial date for each year will be January 1st always, and
consequently, the final date for each year will be December 31st.
Preparation for Solving the Equations Using the Forward Euler Method
The calculations that will be made to estimate TB numbers in Mozambique for 2020, 2021, and
2022 will be based on the solutions of the equations used for the rate of change in the independent
variables. And this will be done using the forward Euler method, as it is presented by Sullivan (―SIR
Model For Disease Spread- 2‖ 00:03:24 – 00:06:17) and Collins and Abdelal (19-20). This is ―a
method for solving ordinary differential equations‖ (Weisstein).
Beginning with the equation used to calculate the rate of change in the population that will be
considered susceptible to TB ( ( ) ), to solve this equation using Euler’s method, one
must split up the derivative presented in the left side of the equation to be able to predict the change
in the nominator (small change in the suceptibles, i.e. ) according to what was the denominator
(small change in time, i.e. ). This way there can be advancements in time, which will affect the
independent variable of S. Assuming that the change in time is by one day, as it will be used in this
investigation, the derivative can be separated into two days, one being for the initial (day i) and
the second being for the following day (day i+1). The same notation for the first day (i), must be
added to the functions and that are in the right side of the equation represented as I and S just
for the matter of simplicity. Therefore, wherever there should be a t, there will be an i, as this will
be the specific day to be used. The purpose of this whole process is to obtain the number of
individuals from the given population (Mozambican) that will be susceptible in the days after the
investigation has started, starting by day i+1, then I +2, etc. So, at the end, the term that will be
on the left side should be moved to the right side of the equation. All these movements are
presented below:
9
( )
( )
( )
( )
And following the same pattern we obtain similar equations for the changes in the infectious and
recovered populations that come from their initial equations to find the rate of change:
( )
and
Does the SIR Model Predict that the Targets From the Global Plan to End TB Will
be Achieved in Mozambique?
The values of , , and have already been estimated for the beginning of each year, according
to the assumptions from the SIR model. Similarly, the equations needed to estimate the changes in
susceptible, infectious, and recovered populations for the days after the 1st of January (day 0 or day
i), have also been structured. Therefore, it will now be possible to calculate the predictions of TB
dynamics for the Mozambican population for the years of 2020, 2021, and 2022, when the Global
Plan to End TB has established that 90% of individuals with TB should have been successfully
reached and treated ((Stop TB Partnership, The Paradigm Shift 2018-2022 34-35).
As it is of greater statistical interest to know the proportion of the Mozambican population that will
be susceptible, infective or recovered at the end of each year than to simply have the number of
individuals in each category, the values of , , and have been converted into percentages. This
could be done because it is evident that ( ). If N represents
100% of Mozambicans, then the proportions of , , and will add up to it. For the matter of
simplicity, however, instead of using 100%, this investigation will use 1 (one) as a representation of
the total amount of N. To achieve this, all percentages for , , , and N have been multiplied by
1 (100/100) and divided by the total population ( , where V is any of the three
variables). The following table presents these values for the three years to be studied, based on
population projections provided by the National Statistics Institute (INS), the estimates from the
WHO and the Global Plan to End TB, and calculations made in this investigation.
10
The other important values that need to be established are the constants for all three years, and these
will be the change in time (dt), the rate of transmission (r), and the rate of recovery (a). The time
change for all three years will be of 1 day, which means that 2020 will have 366 changes in time,
for example (Table 1). The transmission rate (r) will be calculated by transforming the average
infection rate to a decimal number. Since the infection rate for TB is of 5%-10% (Center for
Disease Control and Prevention, ―TB Risk Factors‖), the transmission rate will be of 0.75
(7.5:100), which rounded up will be 0.8. The recovery rate (a) will be calculated using the formula
(Brian Sullivan, ―SIR Model for Disease Spread-3‖ 00:01:27 –
00:01:32). As it takes at least six months (180 days) to treat tuberculosis (Center for Disease
Control and Prevention, ―TB Disease‖), . Table 2 shows these three
constant parameters that are fundamental for all the calculations that have to be done.
Constant Parameters
dt 1
Transmission Rate [r] 0.08
Recovery Rate [a] 0.01
Table 2 - Constant Parameters for TB in Mozambique in this Investigation
With the variables, parameters (Table 2), and specific data for each year (Table 1), the dynamics of
TB for the years of 2020, 2021, and 2022 can now be calculated in the context of the Mozambican
population using the expressions
( ) , ( ) , and , which have been
explained in the previous section. These formulae are inserted in a spreadsheet to allow for more
efficient calculations for the three years. The complete tables with raw data that show the results for
each day of each year can be found in the appendices (Appendix 1). For better illustration, the SIR
graphs for each year are presented below.
11
1.000
0.800
0.600 Susceptible
0.400 Infective
0.200 Removed
0.000
113
225
127
141
155
169
183
197
211
239
253
267
281
295
309
323
337
351
365
1
15
29
43
57
71
85
99 Days
Days
1.000
0.800
0.600 Susceptible
0.400 Infective
0.200 Removed
0.000
222
105
118
131
144
157
170
183
196
209
235
248
261
274
287
300
313
326
339
352
365
1
14
27
40
53
66
79
92
Days
1.000
0.800
0.600 Susceptible
0.400 Infective
0.200 Removed
0.000
Days
248
105
118
131
144
157
170
183
196
209
222
235
261
274
287
300
313
326
339
352
365
1
14
27
40
53
66
79
92
Even though Figures 1, 2, and 3 may look identical to the naked eye, their actual values are quite
distinct, which results from their also different initial values of , , , and N. (See Appendix 1
for raw and more detailed data). However, there is one similarity that cannot be ignored, and that is
the time of the year at which there is the peak (the maximum amount) on the number of infectious
individuals, which occurs when the slope of the susceptibles and of the removed become the same
after their lines intersect. As it can be seen in all three graphs, this will usually happen between days
99 and 113, which fall under the second to fourth weeks of April, every year. This could be an
important indicator for health organizations, as in the days leading to this peak, more people in the
population would be in need of treatment. Therefore, provisions at this time of the year should be
higher. Likewise, it can be noticed that in all three graphs, the lines for the susceptible and the
infective will mostly be opposite to each other in terms of trend, which is a visual representation of
their initial, negative direct proportion (from the equations
( ) and ) which will only be altered when the removed start to
increase rapidly (after days 99 and 113), as it is indicated by the last portion of the equation used to
calculate the rate of change in the infectives ( ).
The final proportions of the Mozambican population that are estimated for each group of the SIR
model at the end of each year can be seen in Table 3:
The proportions presented in Table 3 are the final indicators that reveal if the SIR model predicts
that the targets established for Mozambique as part of the Global Plan to End TB will be achieved.
In addition, these estimates can be of great value in epidemiology and the medical field in general,
as they can aid in planning for vaccination programs and preparation of treatment material for TB,
as it has already been mentioned. However, it is important to be aware that due to its assumptions
and simplicity, the SIR model does not present the exact numbers that are expected to occur, but an
approximate value. This is also one of the reasons why it might be better to use the proportions of
the population instead of the exact number of individuals that are expected to be in each category.
Taking into consideration the final proportion of the Mozambican population that the SIR model
predicts to be in the removed group by day 365 of 2022 (Table 3), we see that the target of having a
90% rate of successful treatment established by the WHO is not achieved, since only 79.3% of the
previous infected individuals are estimated to have been permanently cured, and therefore removed.
And this is not good, as Mozambique is already at a critical stage in terms TB numbers when
compared to other countries (World Health Organization, ―Tuberculosis Profile in Mozambique‖;
13
Global Tuberculosis Control). This is even made worse when we see that instead of increasing over
the years, the proportion of recovered people is expected to decrease from 79.5% in 2020 to 79.3%
in 2022 (Table 3). By looking at these values in the form of percentages, one may think there will
not me much difference, however every decimal in a percentage will have a huge significance when
transformed into exact numbers of individuals in millions, and even more when we consider that the
total population in 2022 is expected to have 1,512,078 more people than that of 2020 (Table 1).
Similarly, the overall increase in the infective people over the years (Table 3) is also a bad indicator
in terms of the non-reduction of TB incidence in Mozambique, meaning that not enough people are
being reached. But when this is compared to the overall decrease in the susceptibes, one might be
conducted into the illusionary thought that even though the infectives are increasing, less people
will be in danger of getting tuberculosis. However, as it has been said, this is an illusion because
this investigation did not take into consideration natural immunity, preventive therapies, and the
BCG vaccination numbers (because they are not available in a usable way), meaning that all
individuals who are no longer susceptible will immediately be in the I group before they are
removed.
Another limitation that was specific to this study was the lack of information on vaccination
programs, preventive treatment, and death rates from TB in Mozambique. Not having enough and
usable data on these aspects may also cause the SIR results to be very different from what they will
actually be in the future. As a Mozambican citizen, I am personally worried about the lack of such
information and I think that obtaining more statistics related to TB should be a government priority
for the following years. Without them, it will be harder to work towards the goals that have been
established for and by the country
In conclusion, this study has shown that, according to the SIR model, the TB targets for
Mozambique will not be achieved by 2022, and nor will there be much improvement in reducing
the incidence of the disease, as over the years, more of the susceptible individuals become infected.
14
This investigation is a clear example of how mathematics can be of huge importance for analyzing
real-life phenomena and it helped me explore my inquiries in a complex and interesting way.
15
Works Cited
Crawford, Tom. ―Oxford Mathematician Explains SIR Disease Model for COVID-19
(Coronavirus).‖ YouTube, uploaded by Tom Rocks Maths, 18 Mar. 2020,
www.youtube.com/watch?v=NKMHhm2Zbkw.
Collins, Julia, and Nadia Abdelal. ―Spread of Disease.‖ ASMI CALCULATE, Australian
Mathematical Sciences Institute, 2018, calculate.org.au/wp-
content/uploads/sites/15/2018/10/spread-of-disease.pdf.
Global Tuberculosis Control. ―Country Profile: Mozambique.‖ WHO Report 2008, p. 121-124, Stop
TB Partnership, 2008,
http://www.stoptb.org/assets/documents/countries/acsm/Mozambique.pdf.
Okafor, Chika N., Ayesan Rewane, and Ifeanyi I. Momodu. ―Bacillus Calmette Guerin
(BCG).‖ StatPearls, StatPearls Publishing, 8 July 2020,
https://pubmed.ncbi.nlm.nih.gov/30844212/.
16
Ramirez, Vanessa Bates. ―What Is R0? Gauging Contagious Infections.‖ Healthline, Healthline, 20
Apr. 2020, www.healthline.com/health/r-nought-reproduction-number.
Stop TB Partnership. ―Challenge Facility for Civil Society Round 8: Gratee Profile – ADPP
Mozambique. Stop TB Partnership, Executive Director: Birgit Holm, Stop TB Partnership,
2018,
www.stoptb.org/assets/documents/global/awards/cfcs/R8/ROUND8_MOZAMBIQUE.pdf.
Stop TB Partnership. ―TB diagnosis and treatment targets‖. Stop TB Partnership, Stop TB
Partnership, 26 Nov. 2019,
www.stoptb.org/assets/documents/global/advocacy/unhlm/TB_NotificationTargets_Novembe
r_2019.pdf
17
Stop TB Partnership. ―The Paradigm Shift 2018-2022‖. Stop TB Partnership, Stop TB Partnership,
Global Helath Campus, 2019,
http://www.stoptb.org/assets/documents/global/plan/GPR_2018-2022_Digital.pdf
Sullivan, Brian. ―SIR Model For Disease Spread- 1. Introduction.‖ YouTube, uploaded by Brian
Sullivan, 25 Mar. 2020, www.youtube.com/watch?v=vL6NfB7BKeY.
Sullivan, Brian. ―SIR Model For Disease Spread- 2. Preparation for Solving.‖ YouTube, uploaded
by Brian Sullivan, 31 Mar. 2020, https://www.youtube.com/watch?v=2K3FupgfBx4&t=95s
―TB Disease | Questions and Answers | Pamphlets, Brochures, Booklets | Publications & Products |
TB | CDC.‖ Center for Disease Control and Prevention, Center for Disease Control and
Prevention,
www.cdc.gov/tb/publications/faqs/qa_tbdisease.htm#:%7E:text=TB%20bacteria%20die%2
0very%20slowly,a%20few%20weeks%20of%20treatment. Accessed 2 Oct. 2020.
―TB Risk Factors | Basic TB Facts | TB | CDC.‖ Center for Disease Control and Prevention, Center
2020.
Willige, Andrea. ―Here Are 4 Other Infectious Diseases That Should Not Be Forgotten during
COVID-19.‖ World Economic Forum, World Economic Forum, 26 May 2020,
www.weforum.org/agenda/2020/05/coronavirus-infectious-diseases-tb-malaria-cholera-
measles/.
World Health Organization. ―The End TB Strategy.‖ World Health Organization, World Health
Appendices