Operation Onesimus

After hearing that the Spanish government had named their response to the COVID-19 pandemic “Operación Balmis” after the Balmis Expedition of the early 1800s, I decided that my own personal response to the pandemic had to have its own name. The Balmis expedition was an expedition headed by Javier Balmis, the royal surgeon to the King of Spain in the early 1800s. As Jenner’s discovery of the smallpox vaccine became widely known, the King decided that his subjects in the Americas and in the Philippines were going to be free from the scourge of smallpox. He read Jenner’s papers and those of a French physician validating Jenner’s findings. So he entrusted Dr. Balmis to head the expedition and bring the vaccine to what is now Latin America and the Caribbean.

After a long deliberation on what to name my personal efforts in the Pandemic, I decided to name it Operation Onesimus. Onesimus was an African slave who was forcefully brought to the American Colonies in the early 1700s. At that time, there was no vaccine against smallpox. The disease just came around time after time and would take the lives of hundreds or even thousands of people. There was not much beyond social distancing that the people could do. By the time they realized they had an epidemic on their hands, many people had been exposed and would be sick. Many of them would die.

Onesimus was bought by Cotton Mather, a clergyman from the Massachusetts Colony. Reverend Mather, if you remember, had been involved in the Salem Witch Trials. As one epidemic of smallpox went through Boston and the countryside near it, Mather noticed that Onesimus was immune to the disease. He also notices that Onesimus was bright, seemingly education. Mather asked Onesimus about his immunity, and Onesimus pointed to his arm.

For centuries, people who wanted to be immune to smallpox would ask to be variolated. Variolation is the process by which the smallpox disease (variola) would be given to people in a controlled manner and under the supervision of a physician. The process usually included taking some of the pus from a person with smallpox and injecting it into the arm of a healthy person. The person would then develop a milder form of smallpox and then recover and be immune. Some people would get the full-blown disease, especially since there was no knowledge of how much pus with smallpox was too much. (We know now of things such as viral dose.)

Onesimus had been variolated when he lived in Africa. It is believed that the Arab traders who ventured into the sub-Saharan part of the continent brought the practice with them. When people found out that variolation prevented smallpox, they went along with it. Onesimus had been one such person, and that is why he survived so many smallpox epidemics in Massachusetts. He told all this to Mather, and Mather consulted with physician friends about it. After much deliberation, Mather and his physician friend decided to give it a try. After successfully receiving the variolation procedure, Mather and his family — and the family of the physician who went along with the plan — were spared from yet another wave of smallpox that went through the colonies.

This was not without consequences for Mather, though. What is perhaps the first anti-vaccine group formed around him and even firebombed his house. They claimed that he had given in to “African witchcraft” by taking the advice of a slave. Mather didn’t relent. He recommended the practice to other people in the colonies and in the British Empire. By the time the Americans decided to revolt, variolation proved to be key to defeating the British… But that is for some other time.

I decided to call my efforts “Operation Onesimus” because I decided to use the knowledge and wisdom of others throughout the generations to guide what I was doing. From John Snow’s crazy idea to map cases of cholera to understand its spread to my Hopkins professors’ lessons on epidemiology and public health, I was going to use everything and anything to try to make a dent in what is going on. And it would not matter to me if the naysayers were incredulous of my efforts. I was going to use all that to do well and try very hard to save my own corner of the universe, even if I didn’t do it.

As the pandemic has evolved, however, I’ve decided to change the name of my efforts to a new name… But that is for a later post at a later time. For now, it’s time for sleep, because sleep is at a premium right now.

Stay safe out there… We’ll get through this.

Your Obsession with Data

As the pandemic continues, one of the questions that I see asked by people all over the country (and the world) is very much, “Where is my data?” For example, in one county in the US, people are clamoring that data be released at the ZIP code level. They want to know where the “hot spots” of COVID-19 are so that they can… Well, they don’t really say what they will do with that information.

The state where this county is located is already under a general quarantine order. People are to stay home unless they are essential personnel in the pandemic response or they perform some sort of essential work function for the public like preparing food, fixing cars or restocking supplies. Everyone else should stay home. So what would change if the average person — who should be home — knows how many cases there are in this or that ZIP code? What changes if they know that they are in or outside of a hot spot?

Some of the same people calling for those data say that they are “high risk” and want to know if it is safe for them in their geographic area. Again, if the order is to stay inside, then what would it change if they were in a hot spot or not? I couldn’t wrap my head around this until someone explained it to me.

Human beings like to think that they have control over stuff. Stuff just happens at random sometimes. Back in October of 2019, an animal was infected with coronavirus. A few of the viruses it was carrying landed on a human being somehow. A few of those had a genetic mutation that allowed them to enter the human cells and replicate. Then thousands of those burst out from this person’s mouth and nose and infected a second person. Two became four. Four became eight… And here we are today.

There is absolutely nothing that any mortal could have done to prevent that genetic accident. Maybe if stronger measures against “wet markets” were in place in China and other parts of the world the “jump” or “spillover” to humans would have been prevented. Maybe. Or maybe if could have been delayed. Maybe.

Now, as was the case with the millions of constitutional scholars that popped up during the impeachment trial, we have millions of epidemiologists who think that they can somehow control their lives and their environment — or glean some insight in to the epidemic — by knowing how many cases there are in a given geographic area. Or they measure their individual risk by looking at who is getting sick and thinking that they are not “those people.” It’s all about control, none of which we really feel like we have if all we do is stay home and play on the internet all day.

So I get it. You want data and you want to analyze it and interpret it your way without really having much training in it because you feel out of control and you want to have some control. Fortunately for us, and unfortunately for you, you’re not getting more than you need to know to be safe. You’re just going to have to come to terms with that and wash your hands and stay home while those of us with years of experience in handling these things do it for you.

That’s how these things work. Your pipe freezes and breaks, so you call the plumber. You don’t stand over the shoulder of the plumber and ask them to give you the data in their heads while they do their work, do you? Do you?

You do? Then we have nothing to talk about.

You don’t? Good. Let the professionals do their work. Have a little faith once in a while.

Now, if you’ll excuse me, I’m heading back once more into the fray.

Epidemic Curves and Homicide Counts in Baltimore

One of the tools that we use in the investigation of outbreaks is the epidemic curve, or, as we say in the biz, the “epi curve.” An epidemic curve is a simple graphical representation of the number of cases per a unit of time over a span of time. For example, you could graph the number of new cases of diarrhea when you’re investigating an outbreak of cholera. You’d be able to see when the epidemic began, if it has peaked, and in which direction is it heading… Is it ending or continuing.

Epi curves are also useful in helping epidemiologists understand what kind of outbreak they’re dealing with. For example, the epidemic curve below is a point source epidemic, where the source of the infection was one single source. The cases had one exposure to the causative agent, and the agent was somehow removed from the environment and did not cause any more cases.

Image courtesy of CDC.

As you can see, the epidemic started on August 23, peaked the next day, and it was over by August 27. The size of the time categories in the x-axis (in this case it was one day) depends on what you’re looking at. If the disease takes a while to manifest itself from exposure to onset, you’d use longer intervals, like weeks (e.g. influenza) or months (e.g. tuberculosis) or even years (e.g. HIV/AIDS).

Another epi curve is the propagated source epidemic. In this type of outbreak, the initial exposure infects a group of people shown in the first peak of cases. Those cases go on to infect others, shown in the second peak. Then the secondary cases go on to infect even more people, shown in the third peak… And so on. One good example of this type of outbreak is a measles outbreak. One person with measles can infect a large number of secondary cases, and those could infect another large number themselves. (Lucky for us, the MMR vaccine has altered these dynamics to the point that measles outbreaks in the United States look more like a point-source epidemic or even an intermittent source epidemic.)

Propagated source epi curve, courtesy of CDC.

In an intermittent source epidemic, the number of cases falls back to zero before more cases pop up. This could be because the incubation period is particularly long for the infection, so one case that is infected today takes weeks to show up. Or because the source(s) of the epidemic leaves the population only to come back again.

Screenshot 2018-02-12 11.36.13
Also from that CDC place…

The final epi curve looks at the continuous source epidemic. In a continuous source epidemic, the source stays in the population and doesn’t go away. The cases don’t drop to zero. The number of cases per unit of time may go up or down a little bit, but they’re very much, well, continuous. These kinds of epidemics keep going until you remove the exposure or there are no more susceptible people left to infect.

Screenshot 2018-02-12 12.08.15
Continuous source epidemic… Can’t stop, won’t stop, until the source or the susceptibles are removed.

So now that you know what epidemic curves are, what they look like for different types of outbreaks, and what information they tell us… What does the following curve look like?

Screenshot 2018-02-12 12.12.54
HINT: It’s not a point-source epidemic.

It’s a continuous source epidemic, right? As I told you above, the epidemic continues until the exposure is removed or there are no more susceptible subjects. The source of the epidemic is pervasive in this case. It’s always there… And, here’s the kicker… The source may actually be sources, plural.

In the case of homicides in Baltimore, it’s hard to graph a proper epidemic curve. There is no set incubation period for homicide. It’s not like you get exposed to violence on day 1 and are expected to commit a homicide (or be the victim of a homicide) by day 21, like with measles. But there are surely some events that trigger homicides, like the arrest of a drug kingpin that leads to a turf war between the underlings within the kingpin’s organization and/or between organizations.

Now, look at the last couple of years. There has been a significant increase in the number of homicides. (Even when adjusted by population, the rate has been epidemic.) So what is happening? If we remove the “expected” homicides from the graph, what will the epidemic curve look like? How do we determined what is expected? (You probably compare to a city of similar size, or the average number of homicides in all cities of a similar size… Taking into account the socioeconomic or demographic identity of those cities. Baltimore is definitely not like El Paso, Texas, though they are similar in size.)

My bet is that a graph that has the expected homicides removed will have something closer to a point-source epidemic occurring every few years. There was a violence epidemic in the 1990s, then another one in the early 2000s, and now this one since 2015. Or it could be a propagated outbreak if the circumstances are just so. One person getting killed by a rival gang leads to retribution (contagion of violence) that could take out two more people. Then the retribution of those two might lead to three homicides, and so on.

This is mostly an artform, though. It would require answering — or developing a way to answer — questions about what is the expected number of homicides for Baltimore, what is an “exposure” that would trigger a homicide, what the incubation period (time from exposure to symptoms) would be with regards to violence, or what a susceptible person looks like. Your answer could be different than mine, and my answer could be different than yours. After all, politicians say that one homicide is too much… And they’re right, from a certain point of view.

The 2016 Olympic Games in Rio Must Not Proceed

Here is some very thoughtful commentary from Dr. Amir Attaran published in Harvard Public Health Review.


Here’s the clincher from that opinion article:

“Which leads to a simple question: But for the Games, would anyone recommend sending an extra half a million visitors into Brazil right now? Of course not: mass migration into the heart of an outbreak is a public health no-brainer. And given the choice between accelerating a dangerous new disease or not—for it is impossible that Games will slow Zika down—the answer should be a no-brainer for the Olympic organizers too. Putting sentimentality aside, clearly the Rio 2016 Games must not proceed.”

I agree. Either Zika in South America and the Caribbean is a Public Health Emergency of International Concern, in which case the games must not proceed… Or it isn’t. It is, and the games should not be carried out because the danger is real of the virus being taken back home by athletes and visitors.

Days of a pandemic

I found these pictures in one of my hard drives today. They’re from the very early days of the 2009 influenza pandemic. I was the influenza surveillance coordinator at the state health department at the time. I decided that I was going to document as much of those days as I could. I didn’t have a good camera or good phone with a good camera. But I managed to take these candid shots. Enjoy…

What’s up with this Enterovirus virus?

The Centers for Disease Control and Prevention are reporting today on the Enterovirus D68 outbreak in the Missouri and Illinois. It appears that the outbreak was detected by astute clinicians who noticed that there was something going on:

“On August 19, 2014, CDC was notified by Children’s Mercy Hospital in Kansas City, Missouri, of an increase (relative to the same period in previous years) in patients examined and hospitalized with severe respiratory illness, including some admitted to the pediatric intensive care unit. An increase also was noted in detections of rhinovirus/enterovirus by a multiplex polymerase chain reaction assay in nasopharyngeal specimens obtained during August 5–19. On August 23, CDC was notified by the University of Chicago Medicine Comer Children’s Hospital in Illinois of an increase in patients similar to those seen in Kansas City.”

This highlights the need for infection prevention specialists at hospitals to be in constant communication with their laboratory colleagues and with the healthcare providers in their organization. Communicating on what is going on, what each provider is seeing, allows for the early detection of outbreaks. When these lines of communication are not adequate, it may be later rather than sooner before these types of things are detected.

So CDC was notified and an investigation was launched:

“To further characterize these two geographically distinct observations, nasopharyngeal specimens from most of the patients with recent onset of severe symptoms from both facilities were sequenced by the CDC Picornavirus Laboratory. Enterovirus D68* (EV-D68) was identified in 19 of 22 specimens from Kansas City and in 11 of 14 specimens from Chicago. Since these initial reports, admissions for severe respiratory illness have continued at both facilities at rates higher than expected for this time of year. Investigations into suspected clusters in other jurisdictions are ongoing.”

I can tell you from my experience at the state health department that most of the work is being done by local epidemiologists and public health nurses. A case definition has probably been determined and cases falling within the “confirmed, probable, or suspect” case definitions are being interviewed by the local health department staff. Specimens are being collected and probably processed initially at local laboratories and then sent off to CDC for further characterization.

Here is the interesting part:

“Enterovirus infections, including EV-D68, are not reportable, but laboratory detections of enterovirus and parechovirus types are reported voluntarily to the National Enterovirus Surveillance System, which is managed by CDC. Participating laboratories are encouraged to report monthly summaries of virus type, specimen type, and collection date.”

By “not reportable,” CDC is telling us that there is no requirement for these infections to be reported to public health by healthcare providers. However, as you can see, reporting clusters and increased rates of cases is not a bad idea, especially in light of the sheer numbers of sick kids and the strain that this situation is likely to put on the pediatric healthcare system. Opening those lines of communication with the local and federal public health agencies allows for shared information and for the best situational awareness.

We’ll see how this progresses.

Ebola continues to spread just slightly slower than fear

The outbreak of Ebola in West Africa continues to spread. With over 3,000 cases and 1,552 reported deaths (as of August 31, 2014), the seriousness of the outbreak cannot be ignored. While Ebola Zaire is the one causing this outbreak, additional cases of Ebola in the Democratic Republic of Congo are raising fears that the contagion is spreading, even as scientists have told us that the Ebola in DRC is different than the one in West Africa. Those fears are the worst enemy to the people in Africa, even more than the virus itself.

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Ebola is in the United States, now what?


No, seriously. The answer to “now what?” is “nothing”. There’s nothing for us to worry about. As I wrote in the previous post on the subject, the common person in America should not be worried about Ebola. That’s not to say that we’re not. The media are doing a heck of a job at stirring everyone into a frenzy about it. And that’s just the “mainstream media.”

Social media is also chock-full of misinformation and outright lies about the patients being brought back for treatment in the United States. Plenty of people seem to believe that the patients would not receive better care here than in the hospitals in Western Africa. Or they believe that a “pandemic” will be triggered if Ebola starts spreading here. Among them are the usual suspects:

Yes, people who give up their privileged lives in the US of A should “suffer the consequences.” They should suffer the consequences of not being millionaire loudmouths like Donald Trump, writing these things from the comfort of his home, having more than likely never physically lifted a finger to help a human being. (Is he even a millionaire anymore?) Others think that the patient that came back yesterday (August 2), Dr. Kent Brantly, should be ashamed of himself: Screen Shot 2014-08-03 at 11.09.42 AM

That tweet was sent to me by someone who claims to have once served in the Marine Corps and is now a “federal agent” of some kind. You would think that he knows about service about and self-sacrifice and about how we, in America, don’t leave anyone behind. I countered by telling him that Dr. Brantly is a hero, and to get off my case about it. (Then I blocked him.)

There are plenty of examples of others on social media just losing their minds about two patients with Ebola coming to the United States, while completely forgetting or ignoring or not knowing about the other cases of hemorrhagic fevers that have come here. Look, no pandemic! We’re fine. We survived.

So what are they going to do for Dr. Brantly and the other patient here that would be different than what would be done for them in West Africa?

Probably a lot. For starters, Emory University Hospital is a nationally ranked hospital that has very close ties to the Centers for Disease Control and Prevention (CDC). They will probably designate a special team of infectious disease providers, nurses and techs to work exclusively on Dr. Brantly. They will have nothing else on their minds, be in an air-conditioned suite, and have a team of infection prevention specialists overseeing their efforts and making sure that they follow the protocols necessary to care for their patient and not be infected themselves or pass it on to other patients. Also, looking at the images of Dr. Brantly walking into the hospital on his own two legs is very encouraging. It tells me that he’s probably not spewing blood and other body fluids left and right, so the chance of him contaminating others is minimal.

Basically, Emory University Hospital is not this clinic as described by Doctors Without Borders:


The supportive care that Dr. Brantly will receive will be much, much better than what the typical patient in West Africa will get. I write that with mixed feelings because I’m glad for him but sad that such an easily preventable disease will take out all those people, many of them dying because they won’t get the supportive care available in our facilities over here. But, by an accident of history and geography, that’s the hand they were dealt, and we must do all we can to help them “over there”.

Support Doctors Without Borders

If you’re reading this and you’re one of the many people who think that bringing Americans back to be taken care of here is a bad idea, I want you to do a couple of things for me. First, check your privilege, meaning that you’re not in a position to opine about these things because you’re neither the person who is sick nor the person taking care of them in the West African setting. You’re privileged enough to be able to sit in front of a computer and read conspiracy theory sites about how Ebola is airborne or will become airborne or will kill us all or something. Unless you’re sick with Ebola or taking care of a person with Ebola, I need you to shut up.

Second, just shut up. We have bigger fish to fry than to tend to your paranoia.

Finally, this:

Where’s Donal Trump’s outrage at the anti-vaccine groups that scare people away from the influenza vaccine?

If you really want to scare the public, you need to be aware of the relative risk of things. As you can see, Americans are far more likely to die from the flu each year than from Ebola. So check your numbers.