infectious disease

A malaria vaccine and a strange tree

Photo by Olga Stalska on Unsplash

On October 6, 2021 the World Health Organization made a historic announcement. They had approved the world’s first malaria vaccine, which had been in development for more than thirty years. Of course, this amount of time is trivial compared to the history of malaria itself. The disease is one of humanity’s oldest scourges. There are tombs along the Nile that hold mummies who died of malaria. As Rome collapsed in the late fourth and fifth century malaria ravaged Italy, and depopulated entire regions. When a Spanish conquistador descended the Amazon river from Peru to the Atlantic, the friar Carvajal reported that the river bank was so densely settled that each town lay only a crossbow shot from the next one. A hundred years later these communities had vanished. And even today in Africa and southeast Asia every year hundreds of thousands of children either die or are left with life long disabilities (such as epilepsy) from the disease. In many regions, it’s almost impossible to avoid, although the WHO has put great effort into promoting sleeping nets and insecticides.

I recently did a podcast interview with Dr. Marylynn Steckley, who talked about her experience researching in Haiti, while both she and her family suffered from frequent illness. Malaria makes some parts of the world difficult to live and work in for everyone, including outsiders. Although I have not had malaria, I have known many people who have, and for whom it had an enduring impact on their health. Indeed, for many of my Africanist colleagues it was almost assumed that they would acquire the disease, and perhaps live with it’s long term effects. Some of my African colleagues -such as one archaeologist- have many stories about their bouts with the disease.

It’s ironic that during this terrible COVID-19 pandemic we finally have some positive news. This is not only the first vaccine against malaria, but -as many observers note- the first against any parasitic disease. As such, it’s a proof of principle. Some people have wondered if it might prove to be impossible to develop vaccines against these class of diseases, since parasites have evolved to overcome the human immune system for long periods of time. Now we have seen that it can be done.

The vaccine is known as RTS,S/AS01, and it has its limitations. It’s only effective around 40% of the time. It also requires four doses. Even so, given that more 200 million people a year are infected with malaria, this can prevent an immense amount of suffering. More vaccines are in the development process.

There is something remarkable about this new vaccine. It relies on an ingredient from an evergreen tree (the quillay tree) that grows in only one place in the world, Chile on the Pacific coast of South America. This rare ingredient is an adjuvant, which is an ingredient in a vaccine that helps to create an immune response in the human body. The first useful medication for malaria was quinine, which comes from a tree grown in the Amazonian region. Now, once again, Indigenous knowledge and a South American plant, is proving vital in the struggle against malaria. It also places intense pressure upon the stocks of the quillay trees, especially as this ingredient is also being used to develop at least one COVID-19 vaccine and a shingles vaccination. There is currently a technological race on to understand how to extract this ingredient from seeds and immature Quillay trees, because currently the supply replies upon mature trees of at least thirty years of age.

Humanity still has a long way to go in this fight against a killer that even affected pharaohs. But -with help from an usual Latin American tree- the world has its first vaccine, and that is an immense step forward.

Shawn Smallman, 2021

Why was the 1918 flu pandemic more frightening than COVID-19?

The Spanish Influenza. Chart showing mortality from the 1918 influenza pandemic in the US and Europe. Wikipedia commons.

According to the CDC, as of September 10, 2021, 652,480 Americans had died of COVID-19. This is nearly as many as the perhaps 675,000 Americans who died in the 1918 flu pandemic. But there seems to be much less fear of COVID-19 now than there was of the influenza pandemic then, at least in some parts of the United States. Why?

Of course, the first point to make is that there was certainly denial and minimizing in the United States in 1918, which people used to justify holding everything from war-bond rallies to weddings. Still, after the terrible month of November 1918 this declined. Is the difference between then and now in part that we live in social media bubbles? I think that there is some truth to this, but there are a few factors that explain the different attitude that many people had towards influenza then.

In 1918, there was a “W” shaped mortality curve, as most people who died were infants, young adults and the elderly. Before the arrival of the delta variant, there was a perception that those people most at risk of COVID-19 were over 65, and perhaps their deaths were less shocking. In contrast, younger people felt relatively safe. In 1918 it was people in the prime of their life who were dying, as well as their children. This made people feel more vulnerable.

Today, people typically die in the hospital. In 1918, if you lived in a rural area -as did most of the population- a trip to the hospital would take time and might not be easy. More people were cared for –and died– at home. I think that this meant that people saw the results of outbreak much more directly. Today, the ill vanish into hospitals. Their suffering leaves nurses and doctors traumatized, but isn’t visible in the same way that the 1918 pandemic was, when family members and neighbors would see the bodies taken out the front door.

There were three distinct waves to the 1918 influenza pandemic. But the fall 1918 wave had a much higher peak in the death rate. Of course, the spring 1918 influenza outbreak was terrible in some places such as the military camps in Kansas. But by November 1918 the number of deaths was so crushing that denial was no longer an option in many communities. People were too busy taking care of their neighbors; everyone could watch the gravediggers. COVID-19 has been more spread out, which has changed how people have talked about it.

The US population was much smaller in 1918 than now, at just over 103 million people, versus 328.2 million. So although the total numbers of deaths are similar, the death rate was roughly three times higher a century ago. People saw much more death during the 1918 pandemic.

I also wonder if people didn’t have a different attitude towards medicine. The 1918 pandemic took place before most childhood vaccines, antibiotics, and modern therapies. People had more limited expectations for what a doctor might do. Now, it might be that many people expect that if they go to the hospital they will be saved, because they have often seen sick family members or friends healed in a hospital. I can’t prove this, but I suspect some COVID-19 patients are shocked when they find out that they will die. In 1918, people respected and valued doctors, but the life expectancy for men was 36.6 years, and 42.2 for women. People didn’t feel as invulnerable -and didn’t assume that the hospital would save them- because they were more familiar with death. In 1917 -the year before the pandemic- the second most common cause of death in the US was pneumonia and influenza.

Of course, in 1918 people relied heavily on newspapers and the government for information, whereas now people turn to social media. But I think that people were more familiar with infectious illness in 1918, and experienced the pandemic in a different way than with COVID-19. This difference perhaps helps to explain why in many states people seem to be much less afraid of COVID-19 than their great-grandparents were during the 1918 pandemic.

Shawn Smallman

Historical photo of the 1918 Spanish influenza ward at Camp Funston, Kansas, showing the many patients ill with the flu- U.S. Army photographer

Did a strange lab leak cause the COVID-19 pandemic?

Photo by KOBU Agency on Unsplash

In November and December 2019 a novel corona virus began circulating in China. The world -and China’s citizens- first learned of this thanks to a group of Chinese whistle blowers , including Opthamologist Dr Li Wenliang, who would ultimately die of the virus. These whistle blowers were denounced by their administrators and some of them -such as Dr. Wenliang- received a police warning. After he died from COVID-19 on February 7, 2020 there was a wave of popular outrage, and sympathy for his pregnant widow, which caused authorities to censor Chinese social media platforms. So the Chinese state sought to conceal the COVID-19 outbreak in its early stages, much as it once did with SARS. But where did the virus come from? And what do we know about its origins?

Wet markets have often been associated with the start of earlier outbreaks of infectious diseases, such as avian influenza and SARS. This makes sense because these environments bring together a diversity of wild animals that may carry unknown pathogens. Packed into cages in poorly ventilated areas, viruses can passage across the species barrier in a way that would be difficult to achieve in the wild. When the outbreak first appeared in China, many people first looked at cases that appeared to be associated with a local wet market. But as earlier cases became known, the tie to the wet market lacked strong support in the data, although a recent study perhaps strengthens this case.

Attention turned to the Wuhan Institute of Virology (WIV), which reportedly had collected novel bat viruses, including some from a cave in Yunnan. Lab leaks have caused pandemics before. For example, in 1977 an influenza pandemic swept the world. Because the virus was nearly identical to historical samples from an earlier outbreak, there have been suspicions that it began as a result of a lab leak in the Soviet Union. Gain of function experiments -in which scientists deliberately increase either the transmissibility or infectiousness of an infectious agent have been controversial for many years for this reason. Accidents have happened.

Nearly a decade ago I was attending an influenza conference in Oxford, and happened to have breakfast with three well-known figures in the field of influenza virology. One of the people at the table was an outspoken advocate for gain of function research. This person’s work had attracted international controversy on this issue. He/she was an outspoken, confident person, who was more than willing to talk about the gain of function debate, and appeared to enjoy both the attention and the controversy. I thought that this person was eloquent, informed and generous in sharing their thoughts with a complete nobody like me. I was enjoying the conversation immensely. But as the discussion went on, another person at the table -a legend in influenza virology- became increasingly glum looking as he or she picked at their eggs. I felt increasingly awkward, and noticed that my charming colleague didn’t seem to be noticing their colleagues’ withdrawal from the conversation.

Finally, the gain of function researcher turned to another person -a German colleague- and said words to the effect: “You understand how these constraints are maddening.” And this German researcher said (as best as I can recall): “Yes, but I don’t do anything nearly as dangerous as you do.” One thing that I loved when I used to lecture in Germany (actually, I loved everything about Germany) was how frank my students were in giving feedback, and this response was true to form. What I took from the debate was the extent to which gain of function research worried even those people with the best practical knowledge of laboratory work with influenza viruses. As time has passed, there has been increasingly skepticism that gain of function research will produce knowledge at all worthy of the risks. But did the Wuhan Institute of Virology in fact have novel corona virus sequences, and -if so- what kind of research was being done with these strains? …

The strange trip from Chronic Fatigue to long COVID

Every pandemic leaves in its wake people who survived, but were changed by their infection. The most famous example of this is likely encephalitis lethargica, which famously reduced some people to living in a near coma after they survived the 1918 influenza pandemic. For decades some people have been arguing that Chronic Fatigue Syndrome (and perhaps chronic Lyme disease) are also caused by viruses and bacteria, which cause immense but hidden damage in the body. These sequelae endure after the initial infection subsides. Over the last several months many people who were infected by COVID-19 have developed long COVID, a syndrome that remains a medical mystery. One of my favorite new podcasts is Unexplainable, which looks at scientific mysteries. Their recent episode, “The Viral Ghosts of Long COVID” paints an unsettling picture of this disorder. The podcast begins with someone describing the long term effects of their Ebola infection, which closely resemble the symptoms reported by COVID survivors. Many people now wonder whether more research on Chronic Fatigue Syndrome earlier might not have made us better prepared to face this new challenge now.

Shawn Smallman

Two pandemics: Ghosts of the 1918 outbreak

Recently I’ve been reading a book (published in 2004) by Betty O’Keefe and Ian McDonald titled, Dr Fred and the Spanish Lady. The work examines the experience of Dr. Fred Underhill, who was the senior public health officer in Vancouver during the 1918 pandemic. While there had been a host of influenza pandemics through history, the 1918 pandemic killed perhaps 100 million people globally.

What struck me while reading the work was the manifold similarities between our experience of COVID-19 and that of almost exactly a century before. During our current pandemic some countries, such as Australia, New Zealand and Taiwan, acted quickly to enact travel restrictions. But that was the exception rather than the norm. Similarly, in 1918 troop ships brought influenza to Canada, even though during the crossings the ships would have to repeatedly stop for the burial of sea for returning soldiers (O-Keefe and MacDonald, 30-31). In 1918, travel restrictions were not implemented because everyone in Canada wanted to bring the troops home. While understandable, this was also tragic. During COVID-19 there were no effective limits on returning citizens in the United States, likely because there just was not enough public support for this measure. Of course, there were limits on non-citizens’ travel. But since the SARS-Cov2 virus does not discriminate based on citizenship, those countries that did not limit their citizen’s movement, and quarantine them on arrival, have paid a heavy price. …

HIV/AIDS, an “Introduction to International Studies” class lecture

Mercator Map of the Congo, 1595, from the Northwestern University Library Maps of Africa collection, accessed through Wikipedia.

I wrote a book, the AIDS Pandemic in Latin America, and have studied public policy and infectious disease for nearly twenty years. Here is a lecture that I wrote (around 2010?) for an “Introduction to International Studies” class. It would need to be updated now; it may also some references to my own experiences, which would need to be removed. But my hope is that it might prove a useful starting place for someone who wants to do a lecture on this topic in a similar class.

Shawn Smallman









Character of the Virus:

  • HIV is not one virus but many
  • The result of more than one introduction into humanity
  • Two main forms: HIV-1; HIV-2
  • Great diversity
  • Difficult to create vaccine
  • 10 year latency
  • initial infection- blood/sex/mother daughter
  • flu-like symptoms
  • body holds the virus in check
  • over time, the virus gradually erodes the immune system’s ability to defend the body
  • the person dies of opportunistic infections
  • there are different latency periods for different people: my Cuban experience
  • medicines don’t work with everyone: my experience in the support group in Sao Paulo
  • most people, the medications are effective
  • recently realized: in a discordant couple medications prevent transmission in 98% of cases
  • means that treatment is prevention
  • heart-breaking: long argued that treatment was too expensive
  • the only economical way to treat the virus was prevention
  • proves to have been a flawed paradigm

COVID-19 in Latin America

Flyer for our upcoming presentation

Next Tuesday my department will be having a presentation on Zoom  about COVID-19  in Latin America. During this discussion I’ll be talking about Bolsonaro’s leadership in Brazil, and the current pandemic trends in that country. Dr. Rodriguez will be talking about Argentina’s response, while Dr. Young will be discussing the experience of both Cuba and Mexico. Since I know little about the COVID-19 situation outside of Brazil in Latin America, I am particularly interested to hear what my co-presenters will say. The talk will be 2pm West Coast (US) time. Please RSVP if you are interested in participating.

Shawn Smallman

Fear, Fact and Fiction: COVID-19’s Origins and Spread


Photo by Isabella Mori, who provides this context: In traditional Taiwanese night markets, since people / food stands are in close contacts, most people / vendors wear masks now, in order to protect themselves and others.

I gave a talk yesterday for WorldOregon on COVID-19, and what we know about it’s origins and spread, as compared to conspiracy theories. What you might not know when you watch this is that I wrote a talk before asking how long it should be. So I wound up having a fifty minute talk for a twenty minute delivery. Throughout the whole talk I was trying to summarize. My bad. But I had a good time and enjoyed hearing the questions. Thanks WorldOregon! …

Health care and Cyber-attacks

An Opte Project visualization of routing paths through a portion of the Internet. ( via Wikimedia Commons.

Sadly, one of the most common cyberattacks is upon health care centers, particularly ransom-ware attacks upon hospitals. While digital records and telemedicine are proving essential during the COVID-19 pandemic, hospitals’ reliance upon digital resources also make our health care systems vulnerable to attack. As this article by Jocelinn Kang and Tom Uren says, cyber-defense efforts now need to prioritize our health care systems.

If you are interested in hearing more about global topics, please listen to my podcast, Dispatch 7. You can find it on Spotify here, or by searching whichever podcast platform you prefer.

Shawn Smallman, 2020

Cyber tools for predicting COVID-19’s spread


The Spanish Influenza. Chart showing mortality from the 1918 influenza pandemic in the US and Europe. Wikipedia commons.

The New York Times had a remarkable story yesterday morning by Donald G. McNeil Jr. , which talked about a company (Kinsa) that markets smart thermometers. The company can use the data on fevers from these devices to foretell where the outbreak will grow, before that data shows up in other sources.  You can see the company’s map here. As the NYT article says, there is so much interesting data here.

As someone who has spent a lot of time in Florida (my mother was a mystery writer, who set her novels in the bars of West Florida) I am deeply worried by the data on southeast Florida, as well as around Tampa. And even some of northern Florida, such as Duval county, has high levels of atypical fevers. But what is happening in Michigan? The map around Detroit has not lit up as red as Miami, but there is a swath in the south of the state where the levels of atypical fevers have raised. The swatch stretches as far west in the state as Kent county. I wouldn’t have expected what appears to be happening in Utah county, and Salt Lake county, Utah. But these counties still do not light up as much as Broward, Palm Beach, and Miami-Dade do in Florida. …

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