smallpox martyr bio-terrorism modeling in python joe fetsch computer systems lab 2010

Smallpox Martyr Bio-terrorism Modeling in Python

Joe Fetsch

Computer Systems Lab 2010

Purpose

What is the danger now? Isn't smallpox gone forever?

Explanation of Purpose

Ok, so what are you doing to help?

Scenario

How are the terrorists going to attack?

Scenario, Cont'd

How will people react to that?

Why is that such a danger?

Scenario Cont'd

But that can't cause too many problems, right?

How could that possibly get worse?

Scenario Cont'd

But it's not over yet...

Scenario Cont'd

And it still gets worse.

Other Projects

Government simulations involving smallpox exist, and government simulations involving quarantines and vaccination exist, but not

both at the same time.

NetLogo Use

NetLogo was used to develop a basic understanding of the disease modeling system, but will not be used to create the smallpox model

NetLogo Virus Model

Smallpox

Much research was done to fully understand the Variola virus in all forms and its effects on a population

Child suffering from Smallpox

Each dot represents an Agent

Project Structure The infection, after

Prodrome phase, will then progress into a more mature phase:

Ordinary Modified Malignant Hemorrhaging Confluent

Agent Movement

Agent Movement Ignorance and randomness

World Structure

• Social Model • Effects on rate of infection

• Agents with few others near them

Visual Representation

Green agents are healthy

Yellow agents are in early stage where not contagious or visible

Orange agents are in the prodromal phase, exhibiting flu symptoms

Red agents are infected, contagious and visible

Blue agents are immune

Sugarscape-based model

Timeline

Research Smallpox to understand disease in order to better implement in program

Using NetLogo, obtained a basic understanding of the model of infection

Using Python, created basic model

Timeline

• Developed a model for infection, hoping to clarify my values and prove them accurate with past data

• Modeled fatality rates

• Implemented quarantine and vaccination possibilities

Testing

Simulation has begun, average fatality rate in a city around 35-40%

Man suffering from hemorrhagic smallpox also known as black pox – 100% fatal

Still unknown:• Vaccination is unlikely

• The chaos in the city would negate military assistance for some time

• Speculation

Simulations

• Several different times of initiation for vaccine and quarantine are used to account for several different possible scenarios.

Testing

• Fatality rates are between 35 and 40%

• All agents become infected within 6 or 7 months

• 90% of agents become infected within 4 and a half months

• The graph on the next page shows the results of many unhampered tests, showing the population statuses over time

Quarantine

• The quarantine simulation shows a world in which a military quarantine has isolated everyone from each other.

Quarantine

• The visual representation stops moving, yet diseased agents continue to progress.

• The line graph shows a red line at the time at which the quarantine begins.

Description of the graph

In the graph above, the population of the city has gone from 5000, the initial value, to 4052; a fatality rate of 20%. However, the population in this situation has been quarantined after two months of the simulation, while the rate of infection was still increasing, which would lead to many more cases of smallpox and many more fatalities. Throughout the simulation, about half of the agents became infected, which raises the relative fatality rate to slightly less than 40%.

Quarantine Results

In the following slides, the results from calculating several possible outcome times (30 days, 45 days, 60 days, and 75 days) ran 6 times to prevent outliers from significantly affecting the results are shown.

The results before show the world immediately before the quarantine, and the results after show the world 40 days after, long enough to ensure that the remaining infected agents will survive for the remainder of the simulation.

Therefore, the infected agents will be labeled immune.

Before the Quarantine

30 45 60 750%

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deadimmuneinfectedprodromecarriershealthy

Time (days) after attack

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40 Days After Quarantine

30 45 60 750%

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deadimmunehealthy

Beginning of Quarantine: Days after attack

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Fatality/Infection Rates

The fatality rates for quarantine simulations:

30 days: 102 (2%) 45 days: 350 (7%) 60 days: 643 (13%) 75 days: 992 (20%)

The infection rates for the simulations:


Vaccine

The vaccine simulation shows a mass distribution of immunizations to the smallpox virus.

Vaccine

The visual representation continues moving, and diseased agents continue to progress.

The line graph shows a green line at the time at which the vaccine is distributed.

Vaccine Results

In the following slides, the results from calculating several possible outcome times (60 days, 75 days, 90 days, and 105 days) ran 6 times to prevent outliers from significantly affecting the results are shown.

The results before show the world immediately before the vaccination, and the results after show the world 40 days after, long enough to ensure that the remaining infected agents will survive for the remainder of the simulation.

Therefore, the infected agents will be labeled immune.

Ring VaccinationWhile ring vaccination has been successfully used

before to prevent the spread of smallpox, a mass vaccination method is required because of the nature of the first infection:

Because starting points for the infection are

1) spread out over a large area inside one city

and

2) at major transit locations (airports, etc)

The possibility to confine the infectious people before they spread it further is very low.

Before Vaccination

60 75 90 1050%

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deadimmuneinfectedprodromecarriershealthy

Time (days) after attack

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After Vaccination

60 75 90 1050%

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deadimmune

Beginning of Vaccination: Days after attack

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Fatality Rates

The fatality rates for the vaccine simulations:


The infection rates for the simulations:


Conclusions

Obviously, the earlier a vaccine is developed or the earlier a quarantine is implemented, the more lives can be saved.

However, this possibility for saving lives must be weighed against the moral considerations of confining people who may or may not want to be confined.

We all know that there are going to be the outliers who complain about being held against their will... that's why I simulated the vaccine.

To Be Continued...

If further work was to be done, more data could be gathered to create a more accurate and less choppy graph of the expected results of the experiment

Without taking real-life data (about five kinds of illegal), very little information exists as to how the disease actually spreads, and in order to create a more specific scenario (school, etc), much more understanding is required.

smallpox martyr bio-terrorism modeling in python joe fetsch computer systems lab 2010

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