Category Archives: Outbreak

The Speed of Spread

I have opened my presentation slides on pandemics (nearly 400 slides) to find this small subset. This is a graphic representation of how quickly the Spanish Flu spread across the US in 1918 in just a few weeks. Remember, we didn’t have air travel at the time, so long distance travel was by train and recall that the Model T Ford had only come on the market in 1908, so travel by automobile was still relatively new. This is a good illustration of how quickly things can move through the US, but when you think about how much easier and quicker transportation is today, it’s likely things will spread much more rapidly.

Why Italy is a New Level of Concern

From February 26, 2020

I will try to explain why my views of the impact of COVID-19 dramatically changed due to the cluster of cases in Italy. Of course, I’ll use a graph to try to make the concepts clearer.

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One of the terms we use in epidemiology is called the incubation period. That is the time from which a person is first exposed to a communicable disease until they start showing symptoms of the disease. They also can start spreading the disease later during this time period. I’ve represented that with three horizontal bars with gradients somewhat indicating that they get more likely to spread infection as they get closer to the time they are identified as a patient. The incubation period for this disease is thought to be 14 days, which is the lengths of the bars I used.

The first two cases (purple) were a husband and wife who were tourists from China. It is thought that he caused her illness as well as well as 12 others. There is only one other case (orange) that shows up on 2/7. No more are identified until 2/21, when over the course of five days we have seen an additional 319 cases so far. That is one of the things that is so alarming to me. There are three possibilities that I can think of:

1. There were other cases that haven’t been identified that spread the disease. This could be good or bad, depending on how much of a proportion of the population are asymptomatic spreaders.

2. These three individuals combined are somehow responsible for the next 319 cases (so far), or worse, maybe just 1 or 2 of them are. If this is the case, that means at a minimum that one person was responsible for over 100 cases, and if it’s only 1 or 2 of them causing most of the spread, a number much higher.

3. In some individuals, the incubation period may be longer than 14 days.

People like this are called super spreaders. For comparison, during SARS it is thought that the majority of the disease in Singapore was spread by five of these types of individuals, the highest causing 76 cases.

This is a concept I covered earlier called the reproductive number, or R0 of a disease. It’s the average people infected by an individual that is infected. The WHO estimate had been 1.4-2.5, but a recent analysis (link below) of various literature indicates that the value is 1.4 to 6.49 and with an average of 3.28. For comparison, the Spanish Flu of 1918 was 1.2-3.0

The reproductive number of COVID-19 is higher compared to SARS coronavirus

Combining this with what I had described earlier of the differences between how I expected this to travel in the West versus the East is very alarming. We are looking at a disease that could easily rival 1918 in scope. The mortality numbers I have calculated assuming a 30% attack rate (the percentage of the world population that get infected), which is the estimated rate from 1918, are simply shocking. However, we do not know exactly how many people will be infected, so this could be far worse or far better.

I’m sorry this one was probably a little more technical and harder to grasp but some concepts but it’s late and I don’t have the energy to wordsmith. I will try to answer any questions though as I have time.

Disclaimer: This commentary is my own interpretation and does not represent the analysis by the government or my employer. The data is from the Johns Hopkins University’s Center for Systems Science and Engineering.

Not If, But When

From February 26, 2020

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I had been hopeful that COVID-19 could be contained because of some of the differences between eastern and western philosophies and social practices.. My update on Feb 24 had a change in tone. Now that we have almost 5 days of outbreak data in Italy, I am very concerned about the ramifications of this globally.

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This mirrors what was stated by Nancy Messonnier, the director of the CDC’s National Center for Immunization and Respiratory Diseases, “It’s not a question of if but rather a question of when and how many people will have severe illness.”

In short, start preparing. What transpires in Italy will be a good indicator of what will happen in other Western countries.

Please note that while the graphs of the diseases globally and in Italy use the same methodology, they have very different scales to represent the data. Don’t try to compare them to each other for that reason.

Disclaimer: This commentary is my own interpretation and does not represent the analysis by the government or my employer. The data is from the Johns Hopkins University’s Center for Systems Science and Engineering.

Italian Alarm

From February 24, 2020

File:Flag of Italy (1946–2003).png - Wikimedia Commons

While the global picture continues to improve, I do have some concerns about COVID-19 at national levels. My biggest concern is the 215 cases in Italy.

One advantage of a strong central government in an outbreak situation is the ability to quickly enact policies to mitigate the spread of the virus. The rate at which hospitals were built in China was truly amazing as well.

Another reason I was a little less concerned about the disease in Asia is that respiratory hygiene measures such as mask use are now a part of the culture. This had started in Japan in 1918 during the Spanish Flu for obvious reasons, was reinforced by the Great Kanto Earthquake which led to a massive inferno in the city which resulted in smoke and ash that remained in the air for weeks. The influenza pandemic of 1934 further made mask use a common practice.

This was also spread by eastern medicine and philosophy, where “qi” is considered an essential element of health, which is tied to concepts of air, atmosphere, odor, etc. The use of masks quickly spread across eastern Asia for these reasons.

While eastern countries embrace the common good, in the west individualism and libertarian ideas make dealing with disease spread much more difficult. For example, think about how the antivax movement is causing a resurgence of measles in the US, which has been completely eliminated in 2000 as a result of vaccination efforts. Last year, there were 1282 cases in the US, which is a direct result of the antivax movement.

What people don’t seem to understand is that globally, measles has a case fatality rate of 15%, and about 0.2% in the US. In addition, about 25% of those infected with measles develop neurological damage.…/pubs/pinkbook/downloads/meas.pdf

The other point I will add on this topic is that herd immunity is crucial in preventing disease spread. Among those vaccinated for measles, about 10% do not develop adequate antibody protection, and thus are susceptible. Herd immunity protects both that group of the population as well as those who have true medical contraindications to the vaccine.

Hence, the West is likely less prepared to deal with a large cluster of cases in some countries because of these philosophical differences and resistance to some basic public health interventions.

Disclaimer: This commentary is my own interpretation and does not represent the analysis by the government or my employer. The data is from the Johns Hopkins University’s Center for Systems Science and Engineering.

COVID-19 Big Jump

from February 13, 2020

Don’t be alarmed at first glance.

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There appears to be a large jump in cases overnight. This is strictly due to the way that cases are being identified in Hubei province in China. Most testing has been through RNA tests, but results can take days. Hubei province decided to use CT scan to look for lung infections in order to start treatment earlier. This accounts for the large jump in cases. A similar thing occurred in the US in 1993 when the definition used for surveillance for AIDS changed, resulting in what looked like a massive jump that year.

A change in the testing methodology impacts two important variables: sensitivity and specificity. There are technical definitions for these but I’ll try to describe them in a way that makes them easier to understand.

In this case, switching to CT scan increased sensitivity. This essentially means that the test is more likely to capture cases. That’s why there is a large rise in the number of cases.

The other things that happens in this case is a decrease in specificity. A CT scan will identify any type of lung infection, not just from COVID-19. This is what is also known as a false positive test.

The takeaway is that this not something to get more concerned about. It makes sense to try to treat those at highest risk.

Disclaimer: This commentary is my own interpretation and does not represent the analysis by the government or my employer. The data is from the Johns Hopkins University’s Center for Systems Science and Engineering.

Ebola and Air Travel

Lately there is a number of questions about the efforts to screen passengers and ban air travel. Will these efforts be sufficient?

Passengers are getting screened who are coming from countries with Ebola (Guinea, Liberia, and Sierra Leone). This is being done both via laser thermometers (a good ideas since this doesn’t require touching anyone) as well as through questionnaires. There are a couple of gaps though with this approach.

First, one must remember that the incubation period for Ebola can run up to 21 days. This is the period of time which a person can be harboring a virus but not show any signs and/or symptoms. A fever is a telltale sign, but unless an individual is three weeks past an exposure to Ebola, this may not be effective in identifying cases. Using a fever alone as a screening tool would not have caught the first case that was diagnosed in the United States. He arrived here on 9/19 but didn’t have symptoms until 9/24.

The questionnaire is meant to identify other risks that may indicate that someone has had Ebola exposure. Like all screening measures, this has some holes as well.

When conducting surveys, there is a common problem with something called recall bias. This is simply because human memory fades both with physiological age but also as events become more distant in time. For example, could you remember what you had for lunch and portion sizes five days ago? What about 21 days ago? These are simply errors that are introduced through poor recollection.

Another problem with screening questionnaires though which is even a bigger issue for this problem is response bias. This is the instance where people will lie in order to achieve their desired outcome, in this case passage on an airline or into a country. This could simply be motivated by the desire to see friends or family or for wanting to conduct business. However, it is not outside of the realm of possibility that someone might knowingly want to bring a disease that they are harboring into another country as sort of a crude human biological weapon.

These screening measures are good, but there are clear gaps. They will be implemented at the five airports (New York JFK, Washington Dulles, Newark, Chicago O’Hare, and Atlanta) with the majority of travelers coming from affected countries. Roughly 150 people enter the US each day from the affected countries and ALMOST all of them enter through these airports.

What about those who come in through other airports? That is a distinct gap. Some people have suggested that we should ban all flights from affected countries. However, that approach has problems as well.

First, airlines are not the only means by which to exit a country. There are land and sea routes as well. Someone who was set on getting to a destination would simply find the path of least resistance into a bordering country and then begin air travel from that location. We’ve already seen something similar happening when some Liberian men were trying to illegally enter the US through Costa Rica. General John Kelly, the commander for South American operations for the Pentagon, raises a very big concern about the problems that will arise if Ebola gets established in South America. People will begin fleeing north to seek medical care in the US. That creates a massive illegal border crossing situation along the Mexican border.

There are even bigger problems with banning air travel. How do aid workers get in and out of a country to help stop the problem at its source? This is one of the big questions I’m asking as I make my decision about whether to go help. I want to know with very little uncertainty that I will be able to leave once my time in field is over. I do not want to get trapped like I’ve entered some massive diseases black hole.

Worse, banning air travel could destabilize already shaky governments in those regions. If that happens, Ebola could spread much more quickly in those areas and be even more difficult to contain, leading to a possible pandemic. That is something we DEFINITELY do not want to see.

There is also a bigger problem emerging now that Ebola has shown up in Lagos, Nigeria. It is the biggest city in Africa with an estimated population of 21 million. It is also an obvious air travel hub due to it’s size. If Ebola gains a foothold in Lagos, we might be too late because of the volume of air traffic through that city.

Air travel from areas hardest hit by Ebola from Gomes MFC, Pastore y Piontti A, Rossi L, Chao D, Longini I, Halloran ME, Vespignani A. Assessing the International Spreading Risk Associated with the 2014 West African Ebola Outbreak. PLOS Currents Outbreaks. 2014 Sep 2. Edition 1. doi: 10.1371/currents.outbreaks.cd818f63d40e24aef769dda7df9e0da5.

Clearly, we have much more to do.

10/15/2014 Addendum:

Back in August, I had started reading Linked: How Everything Is Connected to Everything Else and What It Means for Business, Science, and Everyday Life by  Albert-Laszlo Barabasi on network science and theory because I thought it would give me some insights into how outbreaks behave. Little did I know that this would be useful so soon.

Without going into the technical details, airports are scale-free networks. Essentially, in the real world this looks like larger airports with major airline hubs, significantly more medium size airports with much less commercial air traffic, and finally many small municipal airports with very little major air carrier activity at all. It’s a classic example of this type of network.

I’m going to quote from the book because what he says is important.
“The accidental removal of a single hub will not be fatal either, since the continuous hierarchy of several large hubs will maintain the network’s integrity…Amazingly, most networks of interest, ranging from the Internet to the cell, are scale-free and have a degree exponent smaller than three. Therefore, these networks break apart only after all nodes have been removed–or, for all practical purposes, never.”

This is why closing air travel to a particular country having an outbreak would not likely make much of a difference. Our travel networks are robust. Between land, sea, and air, there are many alternate routes for people to travel with whatever microorganisms they may harbor. I think the way that this applies in this case is that the only way to stop spread via transportation hubs would be to stop ALL transportation hubs in a much broader scale than to that of a few countries. That is simply not economically and possibly ethically feasible.

It’s easy to want to say that we should do that in all of the affected countries. However, I think people would have a hard time making that kind of statement when it affects their own, as it has now in the US.

Ebola in the US – Background

Ebola SEM

I’ve been having a number of friends contact me wanting to know both my thoughts about the emerging Ebola epidemic as well as asking questions about it. It finally reached a point where I realized it would be easier to write about it openly and maybe give people my views on this situation, which are strictly that, MY views. It doesn’t mean they are correct and don’t represent those of any organizations with which I’m affiliated. I’ll give a brief overview of the history of the first case in the US and then will likely post separate items as different questions get asked or other notable stories and/or ideas come to mind.

This interest began when a Liberian man was diagnosed with Ebola at Texas Health Presbyterian Hospital in Dallas. I think that was when the public finally understood just how serious a problem has been emerging in West Africa. People have come to realize that air travel no longer makes the Atlantic Ocean that big anymore. The concept of a global village became very real in a number of people’s minds as a result.

Ebola Distribution Map

Ebola Distribution Map

The timeline is pretty interesting and shows some of the gaps in our system:

9/15 The patient tried to bring a friend to a hospital in Liberia for care who had Ebola. They took a cab and he carried her when she was too weak to walk. Obviously that would qualify as very close contact. They tried multiple hospitals but were turned away. They eventually returned home where she eventually died.

9/19 The patient flies from Monrovia, Liberia to Brussels, Belgium. From there he continues the next leg of his trip to Dulles airport in Washington, DC.

9/20 He continues from Washington to Dallas, TX.

9/24 (Wednesday) He becomes symptomatic. This is a crucial piece of information because Ebola does not spread when a person is symptom free. That means that nobody aboard the flights or might have passed him in the various airports has anything to worry about. (At this point, Ebola is only spread through direct contact. This is technically referred to as contact transmission and if you pay attention in hospitals you will see signs that say “Contact Precautions” or “Contact Isolation” in some rooms. It should be noted that this doesn’t indicate an Ebola patient is in the room, there are other conditions that are only spread through direct contact. A common one in hospitals is MRSA).

9/26 (Friday) He has become sick enough to seek medical care at Texas Health Presbyterian Hospital. Somehow there was a breakdown in communication and the vital information that he had just come from Liberia didn’t make it to the right people. This was a major failure in communications given that there had been guidance to hospitals on identifying potential Ebola victims. I would assume that the hospital is conducting a root cause analysis to determine where there gaps were that allowed this breakdown and that there will be some remediation steps taken to prevent those kinds of errors from being made again. It would even be better if they are transparent with their findings so other hospitals can learn from the problem and analyze their systems for any similar gaps.

9/28 (Sunday) Dallas Fire and Rescue brings the patient back to the hospital via ambulance. I once worked in an ambulance with a patient with active tuberculosis that had not been diagnosed and remember the trepidation I had after I found that out. I can’t even imagine what is going through the minds of this crew.

9/30 (Tuesday) The patient tests positive for Ebola. The CDC holds a press conference that afternoon. I’m pretty certain that a number of people in public health and health care roles uttered a collective “Oh S***.”

At this point public health kicks it into full gear and starts its investigation, a core component of which is called contact tracing. This is trying to identify everyone that might have had contact with the patient. The disease has an incubation period of 2-21 days, which is the time it can take from being exposed to developing symptoms. It should be noted here again that until someone is symptomatic, they will not spread the disease to others. Currently there about 100 contacts identified.

That’s the basic story. Watch for subsequent posts for additional thoughts and analysis.