global health

A new COVID-19 variant

November 26, 2021 / Africa, COVID-19, global health / , , ,

Early in the pandemic I thought it likely that COVID-19 would have multiple waves, perhaps three like the 1918 influenza pandemic. So I never thought that the pandemic would end quickly. But over the last six or seven months I keep finding myself thinking that this time, finally, it must be ending. In June I had both of my COVID-19 vaccinations, cases in the US were plummeting, and I thought that by this winter it would have finally ended. Then Delta arrived, and filled the emergency rooms of the US south. This fall I was able to travel to Lisbon, where I am carrying out historical research on the 1918 influenza pandemic. When I arrived this October Portugal was the most vaccinated country in Europe, and was the subject of a front page article in the New York Times. And yet since I’ve arrived I’ve seen the case right rise dramatically. Not long ago I was looking at the New York Times country data page, and saw that cases in Portugal had increased 116% in two weeks. The country’s case rate may pass that of the US before long. Keep in mind that not only does Portugal have a high vaccination rate, but also people are very good about wearing masks here. It’s common to even see people wearing them in the street, at least if the street is crowded.

While Portugal is facing serious challenges, the situation is far better here than it is in other places, such as Austria. The COVID-19 incidence there is growing at a stunning rate. The government is implementing firm measures, but is facing mass protests. Other countries, such as the Netherlands, are in the same situation, as we have seen from the protests in Rotterdam. Still, the situation is much worse in Eastern Europe, where in some countries such as Bulgaria only a quarter of adults are vaccinated.

It’s in this context that we are receiving news about a new -as yet unnamed- variant in South Africa. There is a lot that we don’t know about this variant yet. The German news channel recently interviewed one expert who suggested that it might be 500 percent more infectious than Delta, although he stressed that we just don’t know yet. Even such qualified statements are dangerous. We will have more data soon. Still, there is a lot of speculation that this variant might partially evade vaccines, because there are so many mutations, including a number involving the virus’s spike protein.

Nations are rushing to block flights from South Africa. Britain was very slow to respond to the Delta variant, and allowed travel to continue for weeks after it was clear that Delta might lead to a new wave. But after the news of this new variant emerged Britain blocked air travel from Southern Africa. Many other nations are also imposing travel restrictions. Of course, this variant has already been found in Israel. And in Hong Kong -where it was brought by a traveler from South Africa- it managed to spread to one other person in a quarantine hotel. Blocking travel from South Africa will help to buy some time, which might be put to use gathering data on the virus. It might also give people the time to be fully vaccinated and get their boosters, if they are in countries in which vaccines are readily available. But in the end, it won’t be enough. Without a complete border and air travel shut down, a highly infectious virus will certainly spread globally.

Given that Delta is already so severe in Europe, the timing for the emergence of this variant could not be worse for this region as it heads into winter. People are exhausted from the pandemic. But it’s not over. Please, if you are not vaccinated, hurry to be vaccinated now, so that your body has time to build immunity. While all medical treatments have risks, the risks of COVID-19 are much greater, billions of people have had the vaccines, and a new variant is coming. And if you are eligible for a booster, now would also be a good moment for that too. Two months ago there was a significant debate around whether boosters were necessary. Given what’s happening now in places like Portugal, there’s no doubt that only focusing on the severity of cases, and not on transmission, is a poor public health approach.

Let’s hope that this proves to be a false alarm, and that the new variant doesn’t greatly increase severity, transmission, or vaccine evasion. We all deserve some luck.

Shawn Smallman, 2021

Before entering restaurants in Taiwan people sanitize their hands and have their temperature taken. Image courtesy of Isabella Mori.

A malaria vaccine and a strange tree

October 18, 2021 / Africa, global health / , , ,

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

The lessons of COVID-19

September 29, 2021 / COVID-19, global health / , ,

In my latest podcast episode for Dispatch 7, I talk about what we’ve learned from the COVID-19 pandemic. Why did some developed countries respond more poorly than developing nations? What lessons does history teach us about the value of quarantine? And what is a One World approach to global health?

Shawn Smallman

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

September 13, 2021 / COVID-19, global health / , , , , ,
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

New light on the mystery of COVID-19’s origins

September 9, 2021 / COVID-19, global health / , ,
Photo by Vladimir Fedotov on Unsplash

Over the last year and half there has been a bitter debate over the origins of COVID-19, specifically whether it began as a spill-over event from a wild animal to humans (the natural origins hypothesis) or because of an accident at a science facility (the lab leak hypothesis). We now have some new information to shed light on this debate. We’re all familiar with Freedom of Information Requests in the United States. These often don’t lead to the release of information, because in practice individuals or the media often have to take the government to court to get this information. That’s exactly what the Intercept did, and the results were worth it. The Intercept received 900 pages of documents regarding two grants, which they discuss in an article, written by Sharon Lerner and Mara Hvistendahl, “New Details Emerge about Coronavirus research at Chinese Lab.”

One of the key issues with the lab leak hypothesis was whether work with bat coronaviruses was being done at a lab in Wuhan, including gain of function work. Yes, yes it was, although there is a significant debate about what constitutes gain of function work. And it turns out the documents that prove this come from a U.S. based health organization called Ecohealth Alliance, which used federal funds to finance this research. This has been suspected for some time, but we didn’t have much information to clarify the details of this work. Now we know that a US researcher, Peter Daszak, had a grant to screen bats for novel coronaviruses. This in and of itself might be valuable research, if undertaken under adequate safety conditions. The work was done at the Wuhan University Center for Animal Experiment, not The Wuhan Institute of Virology, which has received the most attention in the press. And there are concerns about the kind of work researchers were doing with bat coronaviruses. According to Richard Ebright, they were doing more than just infecting ordinary mice with this virus: “The viruses that they constructed were tested for their ability to infect mice that were engineered to display human type receptors on their cell(s)’.” According to this article, the grant to do this work ran from 2014 to 2019.

I was initially skeptical that the work of the Ecohealth Alliance could have contributed in any way to a lab leak. But there does seem to have been a contradiction of interests in the early investigation of COVID-19’s emergence. Peter Daszak was one of the scientists who signed a letter to the Lancet on February 19, 2020 in which scientists denounced as conspiracy theories the idea that a lab leak began the pandemic. He also was part of the WHO’s inquiry commission that went to China in January 2021 to try to uncover the origins of the virus. Since he was involved with work at question in China, his presence would seem to undermine the potential impartiality of this investigation. More recently, he has withdrawn from at least one effort to investigate the pandemic’s origins: “Dr Peter Daszak, president of the US-based EcoHealth Alliance, has “recused himself” from the inquiry by leading medical journal the Lancet after he failed to declare ties to the Wuhan Laboratory of Virology, which was conducting research into coronavirus in bats.” The point is that the early investigation of the lab leak theory may not have been fully impartial, and key evidence was missing.

Some scientists say that what these newly-revealed documents demonstrate is shocking. As Richard H. Ebright (Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University) has said, the “materials further reveal that one of the resulting novel, laboratory-generated SARS-related coronaviruses –one not been (sic.) previously disclosed publicly– was more pathogenic to humanized mice than the starting virus from which it was constructed. . .”

We need to have better information on multiple questions: did miners in southern China (specifically the Mojiang mine in Yunnan) suffer from an acute pneumonia similar to COVID-19 in 2012? Was this pneumonia caused by a coronavirus which was then brought to a laboratory in Wuhan for further research? Was gain of function work with coronaviruses done at one or more labs in Wuhan, and what -precisely- were the biosafety practices and procedures? Was there a major move at one of these labs in December 2019, and what were the safety practices at the lab during the move, particularly for bats and other animals, as well as coronavirus samples? Were any employees of these labs ill with a pneumonia-like illness in November/early December 2019? Is it true that one U.S. based scientist, Ian Lipkin of Columbia University, heard of the outbreak on December 15, 2019, well before China revealed the outbreak to the WHO? If so, does this mean that the Chinese authorities knew of the outbreak, but did not share this information in a timely fashion, so that the world could try to prevent the disease from escaping China? Increasingly, the answer to most of these questions would seem to be a plausible yes.

As Alina Chan (a postdoctoral fellow at the Broad Institute) points out, COVID-19 wouldn’t be the only example of a leak at a facility in China causing a significant disease outbreak. Elizabeth Shim’s article on this outbreak, “Brucellosis cases in China exceed 10,000 after vaccine factory accident,” is well worth reading. So we know that such accidents happen, including in China, at the same moment that COVID-19 itself emerged.

While we cannot yet know the truth, as others have said, it seems a strange coincidence that the outbreak began in the same city in China where -as these documents from the Intercept show- work was being done on bat coronaviruses. And how can we trust any denials, when much of the information that we had was not originally released by EcoHealth Alliance or the Chinese government, but rather by a small band of digital detectives scouring the web, as well as journalists, such as those at the Intercept?

Of course the lab leak hypothesis is not proven. Most epidemics begin with a natural cross-over event from animals to humans. But the irony is that if, indeed, the virus emerged from a lab leak, it not only did so unintentionally, but also because scientists were trying to study coronaviruses to avoid and prevent epidemics. If the lab leak hypothesis is correct, I can’t help but feel empathy for the scientists and funding agencies, which must have been horrified as they realized what they might have unleashed. But it is long past time for transparency, so that everyone can understand the data and evidence regarding whether a lab-leak in Wuhan, China began this pandemic.

If you want to see the documents (two grant applications) themselves, Mara Hvistendahl (@Mara Hvistendahl) has Tweeted the links, which you can for yourself here. The first one is the key document:

“Understanding the Risk of Bat Coronavirus Emergence”
https://t.co/FrOP7tSs4D

“Understanding Risk of Zoonotic Virus Emergence in Emerging Infectious Disease Hotspots of Southeast Asia”
https://t.co/YDmfbcHcoN https://twitter.com/marahvistendahl/status/1435180983754579973?s=27

I want to thank both Sharon Lerner and Mara Hvistendahl for their careful investigative reporting, and making these documents public.

Shawn Smallman, 2021

The warning signs in Hong Kong

July 7, 2021 / Asia, China, COVID-19, global health, Pandemics / , ,

In 2017 I traveled to Hong Kong to do research for a paper about the pandemic risks posed by wet markets (marketplaces which sold and slaughtered live animals). I traveled to wet markets large and small, and took notes on their practices and clientele. I also interviewed public health experts and doctors about the territories system to control avian influenza in poultry.

Card in a Shenzhen hotel, which explains China’s internet restrictions to guests. Sorry for the bad lighting. Photo by Shawn Smallman

While in Hong Kong, I also traveled to Macau and Shenzhen. When I crossed into mainland China, I was struck by the extent to which information was restricted. It’s one thing to know that China has a separate digital ecosystem. It’s another to no longer be able to use Google Maps, and to know that there’s no point in even trying to use a VPN to connect with websites at home. When I arrived in Shenzhen, I found this card in my hotel. You couldn’t access your files in Google Drive, check Twitter, watch a YouTube video, or see your kids’ posts on Instagram. The Great Firewall of China is  both pervasive and efficient.

While I was in Hong Kong, I also had an opportunity to talk to someone whom I greatly respected. At one point in our discussion they asked me “Do people see what is happening here in Hong Kong? Are they following what is happening here?” I said that no, in my opinion most Americans did not. In the United States people were focused on the new presidency of Donald Trump. She/he seemed very disappointed by my answer, and asked the same question again with slightly different wording. I gave the same answer. In 2017, I don’t think most Americans -and perhaps most Europeans- were carefully following what was happening in Hong Kong. That would change over the next year and a half. …

The warning signs in Hong KongRead More »

Taiwan, Australia, and COVID-19

July 16, 2021 / Asia, Australia, COVID-19, global health / ,

 

Photo by Tommy on Unsplash

This year I am honored to be a Taiwan Fellow, and am planning to travel to National Taiwan University in Taipei, to work on a research project about how Taiwan used digital tools to control COVID-19. I say “planning” because Taiwan recently closed its borders. For over a year Taiwan had controlled the virus, which was ravaging the United States, Europe and South America. How did Taiwan do so well for so long, only for its public health efforts to unravel in the end?

Taiwan’s intelligence services notified the country’s leadership of an unusual outbreak in China relatively early in the COVID-19 outbreak. Taiwan quickly controlled its borders and notified other countries of the danger. It adopted digital tools to enforce quarantines and permit contact tracing. All travelers entered into quarantine hotels. This response worked, and Taiwan was free of sustained community transition for over a year.

Then -as in Australia- the system around quarantine hotels broke down. A local hotel by the airport wanted to find more customers. So they advertised that people could come to stay at their airport hotel, where people could watch the planes take off and land. They even advertised with financial support from local government. The people came and stayed. And then they left and went to museums, tea houses (brothels for an older clientele) and a masonic lodge meeting. Only later watching the local news did they find out that they had paid to stay at a quarantine hotel. While the people had not been hosted on the same floors as the air crews, they were in the same building. …

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COVID-19, the Delta variant and “fleeting contact” in Australia

June 21, 2021 / Australia, COVID-19, global health / ,

Few countries have done such a good job controlling COVID-19 as Australia, but now the nation is facing a significant test in Bondi. A driver (sometimes described as a bus driver, and sometimes as a “car-for-hire driver) worked shuttling air crews to quarantine hotels, as well as driving the general public. Even though he was a front-line worker, he was not vaccinated. He also seems to have had poor personal protective equipment (PPE). Unfortunately he was infected with COVID-19. While in the contagious phase he went to see a movie, visited a cafe twice, had lunch at a Japanese restaurant, and drove a large number of passengers.

What was most remarkable, however, was his visit to a mall in Bondi (Westfield Bondi Junction). In that mall, he appears to have infected people despite “fleeting contact” which was recorded on store cameras. There were a number of such cases. One woman was sitting outside at a cafe, where he was sitting indoors. Normally the risk of outdoor transmission is believed to be low. But she was infected. In another case he appears to have passed a shopper, in the briefest of interactions, which was captured on CCT cameras. But that person was infected. The old rules -fifteen minutes of contact is required for transmission; outdoor transmission is rare- don’t seem to apply in this case, which is causing some justified worry in Australia. People are lining up in their cars for testing.

Fortunately, people seem to have been isolating as asked, and wearing masks. As of today, there are still only eleven cases. Hopefully, this outbreak will be controlled. Health authorities are currently dealing with over a hundred exposure sites. One of the places people were exposed was on a bus. This incident raises this question: is the unusual pattern of spread the result of the new, more transmissible Delta variant, or was this something particular to this individual patient. Epidemiologists are discussing this question is multiple venues. Currently 3.2% of Australians are fully vaccinated.

Whatever the answer in this case, we may see more examples. As was the case with Taiwan, the critical failing was around quarantine hotels and air crews. All people who work in any respect with air crews (in nations without community transmission) need to be fully vaccinated. And the system for hotel quarantine needs to be improved. And more broadly, here in the US we are still far off our record for one day COVID-19 vaccinations, despite a slight uptick recently. People need to be vaccinated now, as the Delta variant is growing rapidly. Although it was originally thought that it would be the dominant strain of COVID-19 in the US as early as this August, it’s now looking as though that might happen as early this July. If you’re fully vaccinated, you have a good level of protection and don’t need to worry. If you’re not fully vaccinated, now is the time to do so.

Shawn Smallman, 2021

The strange trip from Chronic Fatigue to long COVID

May 12, 2021 / global health / ,

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

The odd reasons for Taiwan’s COVID-19 outbreak

May 17, 2021 / global health, Pandemics / ,

I am fortunate to be a Taiwan Fellow this fall. I plan to study Taiwan’s response to the COVID-19 outbreak at National Taiwan University starting this September, where I am being hosted by the global health program. I just received my visa to travel to Taiwan last week. Unfortunately, there is currently a growing outbreak in Taipei. I first heard of it last week, when I was talking with my conversational partner in Taiwan. At that time, she said that the outbreak was still relatively small, as it involved perhaps thirty individuals. But this morning I had an email and a text -the latter of which was sent to everyone who recently received a visa- to say that Taiwan is halting all travel to the island, except for residents. I am hopeful that Taiwan will soon have the situation back under control. But what happened?

Taiwan received human intelligence about the outbreak in China in December 2019. Taiwan acted quickly, in part because it’s political leaders remembered the SARS outbreak in 2003. Since that time, it has used digital apps for contact tracing, mandatory quarantine hotels for travelers, and an effective public health system to contain COVID. Then some odd things happened. Angelica Oung has written a fascinating story (How Taiwan Finally Fell) recounting how a Taiwanese hotel decided to offer a tourism package so that Taiwanese could stay in a hotel near the airport and watch the flights land and depart from their rooms. The local tourism board even advertised this. Although the people were housed on different floors from airplane crews, somehow infected pilots and crews spread the virus to the domestic tourists. After nine pilots tested positive the domestic tourists apparently found out that they had been staying at a quarantine hotel by watching the TV news. But by this point some infected people attended a Lion’s Club meeting, went to karaoke, and then attended “Grandpa shops/tea parlors” in which older women sexually catered to a senior clientele. Genomic testing revealed that everyone with COVID-19 had been infected by the same English variant. …

The odd reasons for Taiwan’s COVID-19 outbreakRead More »

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