Computational Models of Swine Flu Epidemics with

Vensim PLE

Background

There are many different families of virus, influenza virus is one large virus family.
Within the influenza family there are many “strains” of virus that may differ in the type
of organism, tissue or cell that they infect, how sick they make that organism, and in how
easily they spread between individuals of a species, or between species. The swine flu
virus belongs to the influenza A family, and the h1n1 strain.

Over the years many cases have been observed in which people contracted swine flu
through contact with infected pigs or pig waste. While this fact makes the virus
dangerous to people in close contact with pigs, it is not very dangerous to the entire
human population because most of us don’t have close contact with pigs, and our level of
contact can be easily regulated. What makes the swine flu so dangerous now is that this
virus has acquired the ability to infect other people from a human host. So now people
can transmit the disease to other people, which raises the threat that a major outbreak or
epidemic could occur. While the current human transmissible form apparently arose in
Mexico, cases have been confirmed in 10 states in the U.S., Austria, Canada, Germany,
Israel, New Zealand, Spain, and the United Kingdom. Each of these cases can be traced
to people who recently traveled to Mexico.

Health organizations around the world are currently working feverishly to gather and
share information, and to try to understand how the disease is spreading and how it will
play out in individual communities, states, countries and across the globe. A vital part of
these efforts involve the use of computational models that make quantitative predictions
about how the disease will spread, based on measured data and scientific understanding
of the biological and systematic processes involved. This educational module includes
two types of models that can be used to learn about these processes and how they interact
to determine the severity of the disease outbreak.

An agent-based model has been produced using the NetLogo software. This model
represents individuals in a population as well as their movements and interactions. A
variety of factors known to be important in the transmission of disease are included in
this model, as described below. This type of model is useful in evaluating how the
behavior of individuals can affect the spread of the disease. A system dynamics model has
been produced using the Vensim Personal Learning Edition software. In this model
populations of people are represented along with the ways that people move from one
population to another, for example, from healthy to sick to recovered. This type of model
is useful for quickly exploring how various interventions can affect the overall spread of
the disease through all of the populations.
Infectiousness

Infectiousness is a property of the virus and the way it interacts with our bodies. This is
determined by the genetic features of the virus, which are passed down from earlier
generations of the virus. In addition, influenza virus is notorious for picking up pieces of
genetic material (DNA) from it’s host organism (pigs, people or a variety of other hosts
depending on the strain of the virus), and incorporating them into the genetic material of
the virus.

Infectiousness can be though of as how easily someone who is already sick can infect a
healthy person. It can depend on a number of things like: how much virus is produced
during infection, how potently each individual virus can infect cells, or how long virus
stays biologically active outside of the hosts body.

NetLogo Model
In our agent-based model individuals move around and interact much as they do in the
real world. Individuals only interact with some of the other individuals during a given
time interval. When a healthy person encounters a sick person, the infectiousness
parameter represents the chance that the healthy person will become infected. A slider
control can be used to adjust this parameter from 0 to 100%.

Vensim Model
In the system dynamics model we can use a decimal fraction between 0 and 1 for our
infectiousness parameter, so that, as in the NetLogo model it represents the chance that a
healthy person becomes sick when they interact with a sick person. However, in a system
dynamics model there are no individuals moving around and interacting. Therefore, when
we calculate the infection rate, we need to take into account that only a fraction of the
interactions between sick and healthy people that could occur are going to occur within a
particular time interval.

So if we felt that a sick person would only interact with 10 people in a day, but there are
1000 people in our model, we would say that only 10/1000 = 1/100 = 0.01 of the possible
interactions that could occur actually happen on a given day (a single time-step). Then, to
calculate the overall infection rate we would use the formula:

Infection rate = 0.01 x infectiousness

This takes into account that not all interactions between members of the population that
are possible happen in a single day, and only a fraction of those interactions that do
happen lead to infection.
Hygiene

The most significant impact that you as an individual can have on the spread of a flu
epidemic, without the help of a doctor, is to practice good hygiene. Influenza virus is
spread through mucous droplets expelled from the lungs when an infected person coughs
or sneezes. When these droplets land on a surface the virus can remain biologically active
for up to two hours.

Hygiene on the part of infected persons has the biggest impact on disease spread. Infected
persons should try to avoid contact with others (see quarantine below), however covering
coughs or sneezes with a tissue (which should be thrown away) is a very effective
approach to limiting virus expulsion.

Healthy people should try to avoid contact with infected persons. You should try to avoid
touching surfaces that may be contaminated as well. However, since just about any
surface may be contaminated, you should avoid touching your eyes and mouth, since
your hands may have contacted contaminated surfaces, and wash your hands often.
Maintaining general good health, by getting enough sleep and exercise, and eating
healthy foods, is another defensive measure that you can take without the assistance of a
doctor.

NetLogo Model
There is no implementation in NetLogo that directly relates to hygiene. However the
“avoid contact” setting could be compared to the use of a mask, avoiding touching an
infected person, or an infected person using tissues and other methods to contain the
infection.

Vensim Model
Good hygiene reduces the chance that people will become infected during an epidemic.
Some people will practice good hygiene and others will not. In a system dynamics we can
use a hygiene parameter to represent the average extent to which the hygienic practices in
the population reduce the infection rate. In this model the hygiene parameter is used as
the divisor in the equation that is used to calculate the infection rate:

Infection rate = 0.01 x infectiousness / hygiene

The hygiene parameter is limited to values between 1 and 10 so that, in this model, good
hygiene can lead to as much as a10-fold reduction in the infection rate.

Vaccination
A vaccine is a mixture that is introduced into a persons body (usually by injection) and
includes some of the molecular pieces of a bacteria or virus. These molecular pieces
trigger the persons immune system to find and destroy those molecules. If they are
attached to the actual virus or bacteria then those infectious agents are destroyed as well.
Unfortunately, there is currently no vaccine for swine flu. It is still a good idea to get a flu
vaccine, however, since all influenza infections compromise your resistance to illness and
are usually associated with increased mortality (see below).

NetLogo Model
If you turn on the “vaccination” option in the NetLogo model, you will also need to add
doctors who will administer the vaccine. The doctors will vaccinate any susceptible
(green) individuals they encounter. Vaccinated agents turn blue to indicate that they are
immune, and they have a yellow shield on the right to show that they are vaccinated.

Vensim Model
Vaccination in the Vensim model is represented as a flow that removes people from the
Healthy (susceptible) population, and moves them into the Immunized population.
Although, in the real world there may still be some slight chance that vaccinated people
can become infected, in the model these people cannot be infected.

Duration

The duration of a disease is how long the disease keeps you sick. The longer you stay
sick, the more chance there is for the disease to be spread to other people. Some strains
of virus can keep a person sick longer than others. Also, many factors such as age or
health of the infected person can affect the amount of time it takes to fight off infection.
Finally, the environment a person is in (sanitation, medical care, good nutrition) can
affect the duration of the disease. In these models, the duration is represented as a single
number rather than taking into account all the individual variations

NetLogo Model
In the agent-based model the duration of infection is implemented as a “days-to-recover”
slider. When agents become infected, they begin counting the days they have been sick,
and then recover on the day indicated by the slider. A “day” in this model is 2 ticks.

Vensim Model
In the system dynamics model there are no individuals whose duration of illness can be
tracked. However, if on average it takes 20 days for a person to get better, then in one day
we would expect 1/20th of the sick people to recover. In this model the duration parameter
represents the average number of days until sick people recover. This parameter is then
used as the divisor in a formula to calculate the daily recovery rate:

Recovery rate = 1 / duration

Medication

Antiviral medications are available that are effective in keeping flu viruses from
reproducing in your body. The Centers for Disease Control recommends oseltamivir and
zanamivir for treatment of swine flu. These medications are sold as prescriptions
(Tamiflu is the brand name of one of these medications) and are most effective if taken
within two days of observing symptoms. These medications can reduce the severity of
symptoms, the duration of illness, and the quantity of virus produced (and possibly
expelled).

NetLogo Model
If you turn on the “Tamiflu” option in the NetLogo model, you will also need to add
doctors who will administer the medication. The doctors will treat any infected (red)
individuals they encounter. Medicated agents turn blue to indicate that they are immune,
and they have a little pill bottle on the left to show that they are medicated.

Vensim Model
Medication is represented as decimal fraction (between 0 and 1) that is multiplied by a
factor of 20 when calculating the recovery rate. Using this implementation, medication
can speed up recovery up to a maximum of 20-fold. Speeding up recovery is the only
effect of medication that is represented with this approach. Can you think of a better way
to represent medication in the model?

recovery rate = (20*medication)/duration

Quarantine

Quarantine is the isolation of an infected group to try to prevent the spread of disease to
the susceptible population. The practice of quarantining infected individuals goes far
back into history. Isolating those infected can be an effective way to contain a disease, if
done successfully. Also, simply making people stay home and avoid interpersonal
interactions can help. Often times if there is a threat of disease, schools will be closed to
try to keep students and teachers from becoming infected. Whole countries may take
measures to control travel more tightly, particularly travel to and from a country known
to have a threat of disease.
NetLogo Model
There is no quarantine in the NetLogo model. However, there are different measures that
can be taken to contain the disease. One is the use of borders, which can represent
different countries, towns, or even schools. The borders can be closed off (no crossings)
or can allow limited travel between sections of the model. The more isolated the disease
is, the less people it will be able to infect.

The other factor in the model that keeps susceptible and infected populations away from
each other is the parameter called “avoid contact.” When this setting is on, infected
people will turn around if they see a healthy person in front of them. Healthy people will
do the same if they see an infected person. This means that they essentially avoid contact
with each other. This could be compared to the use of masks or simply “keeping your
distance” from an infected individual.

Vensim Model
In the Vensim model quarantine is represented as a population of sick people that do not
come in contact with susceptible people. They can still recover, but this population only
grows based on the fraction of sick people that are isolated from healthy people.

Mortality

The mortality of a disease the proportion of infected people that die as a result of
infection. Whether or not a person dies from a disease is affected by the condition of the
infected person and the environment they are in. However, when studying factors of a
disease, the mortality rate is the percent of infected people who die from the disease,
regardless of individual factors.

NetLogo Model
The mortality rate in the NetLogo model is represented using a percentage slider. When a
person becomes infected, they will have that given percent chance of dying from the
disease.

Vensim Model
In the Vensim model infection mortality is implemented as a rate that is added to the
normal death rate (even healthy people die at some rate) before multiplying by infected
population size:

(death rate + flu fatality rate) * sick population = deaths of sick people
Additional Resources
WHO Swine Flu page
CDC Swine Flu page
Epidemic and pandemic spread section of the Wikipedia entry on Influenza
The Flu Wiki