A Sky Full of SARS

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I don’t like iced coffee and I don’t think I ever really want to try iced coffee. Wait, wait, you haven’t even tried it? No, I just don’t think- How can- no, no, no, no, you can’t sit there and like state an opinion like this and then just be like, but I’ve never tried it. Your whole thing is that you don’t like iced coffee.

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How do you know if you haven’t tried it? Like there are things that you can say you don’t like and you haven’t tried them. Really, foods and drinks aren’t like one of those. Hi, I’m Dr. Dustin Edwards.

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And I’m Faith Cox. Welcome to Germomics, where we go to, be, from, a, and the most roundabout way. In this series, we connect different aspects of modern life and society to microbes through seemingly unconnected natural events, discoveries, and inventions.

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Now, no one knows the exact origins of coffee. Coffee plants themselves are thought to have originated from Ethiopia. They’re these small trees or shrubs that have these glossy, oval, simple leaves.

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They’re like dark green. Simple leaves are leaves that have a single blade coming- a single leaf blade coming off of a node. So like coffee leaves or maple leaves as compared to compound leaves, which are leaves that have a bunch of different leaf blades coming out of a single node.

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So that’s like your pecan leaves or like a very commonly people have seen like the marijuana ones. So you have like the little five leaflets coming out of a single node in the middle. Coffee plants produce creamy white blossoms that supposedly smell like jasmine, and those blossoms develop into berries.

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These berries can be pitted and the beans are dried and then roasted to make coffee. There’s evidence of coffee drinking, cultivation, and trade in the 15th century in present-day Yemen at the southern end of the Arabian Peninsula. Coffee spread relatively quickly during the 16th century to areas along the eastern Mediterranean region.

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That includes modern-day Egypt, Syria, and Turkey, and in Persia, which is now modern-day Iran. To put this time into perspective, this is around the beginning of the Renaissance period. Leonardo da Vinci had just painted the Mona Lisa, and Michelangelo had just begun work on the Sistine Chapel.

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Copernicus claimed that the sun is the center of our solar system, and Galileo observed the movement of the planets. And Constantinople, now Istanbul, fell to the Muslim Ottoman Turks, which then forced European nations to pursue whole new trade routes, such as those that resulted in the voyages of Columbus and Magellan and the beginnings of the European colonizations. Coffee was first brought to Europe by imprisoned Turkish slaves through the island of Malta, which is off the southern coast of Italy.

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Coffee was also brought to the Republic of Venice in what is now part of northeast Italy during trade with people in North Africa. And it’s in Venice that the first coffee houses eventually opened in Europe in 1645, which is about the same time that they were at war with the Ottoman Turks. You know, the best coffee ever had was in Venice.

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So people all around the Mediterranean were having lots of intense interactions with each other. Coffee then spread northwards into the rest of Europe, and these nations then sought out live coffee bushes of their own. It was the Dutch, though, that were the first to acquire live specimens by stealing them from a plantation in the port city of Mocha in Yemen.

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They were brought by Pieter van der Broek of the Dutch East Indies Company, and the plants were kept alive and conditioned for growth inside of greenhouses at the Amsterdam Botanical Gardens. However, the plants were not suitable for large-scale cultivation outside of the surrounding country, which, of course, it gets really cold there in the winter. In a rivalry with the British East Indies Company, who actually had permission to trade from Yemen to Persia and to India, the Dutch East Indies Company sent their illegally obtained plants to Ceylon in modern-day Sri Lanka, which is an island located south of India, to establish the first coffee plantation outside of Yemen.

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Plants were then sent to Southeast Asia, to Batavia, which is now called Jakarta, and to Sumatra, which is where my favorite beans for homebrew come from. And both of these places are in Indonesia. Coffee plants were then sent to the island of Java, thus the coffee nickname.

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And then during the signing of the Treaty of Utrecht, there was a peace brokered among several countries of Europe, and the Dutch actually gifted France a coffee plant for their very own botanical gardens. Clippings from this bush would then be sent westward to the Caribbean islands of Guadeloupe, Santo Domingue, and Martinique, as well as eastward to the French colony of Vietnam. Which reminds me of something that happened in grad school.

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I had a friend there that asked me if I’ve ever had Vietnamese coffee before. I, of course, told him no. So we went to a Vietnamese restaurant in Houston and had these Vietnamese sandwiches, and then we ended up ordering coffee afterwards.

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I tried the coffee and I told him it tasted just like burnt French roast coffee with that overdone taste. And it took me, you know, a few minutes to try to remember that Vietnam had a considerable French influence. Anyway, within a short time, coffee was being grown throughout the Americas, including Brazil, Colombia, Venezuela, Guatemala, and Nicaragua.

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Today coffee beans are sourced from around the world and brewed in coffee houses across the U.S. Something I did not know until recently is that McDonald’s and Dunkin’ Donuts actually sells the most coffee in the U.S. I had guessed like Starbucks, but it’s a distant third. 7-Eleven, which are mostly gas stations here, was in fourth place. I think the unique one-of-a-kind places are some of my favorites to be in just for that thoughtful atmosphere.

I think the most interesting one we have been to recently was off of the Strand in Galveston. It had this wonderful hanging flower garden out over the sidewalk. However, just nothing beats Starbucks for letting you just hang out and waiter all day.

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Yeah, so I actually really liked that one at the Strand in Galveston. There were these like beautiful like honeysuckles that were hanging down over where you could sit outside to drink your coffee. And they had these fairy lights everywhere.

It was very, very beautiful. Yeah, we go to Starbucks a lot. We wrote a lot of our notes for this in a Starbucks.

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Whenever we go to conferences, we meet up at Starbucks to hang out because it’s kind of weird to hang out in a hotel lobby sometimes. We’ll go to like a local Starbucks and just like drink coffee, review our work for the next day, stuff like that. The earliest coffeehouses called Cava Cana were similar to popular coffeehouses today in that they were gathering places to chat with friends, play games, catch up on the news, listen to music, and just relax.

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So because of these exchanges of just like general information, coffeehouses became known as schools of the wise. Right. In England, coffee was used as an experimental therapy by Sir Francis Bacon and others for treatment of diseases such as gout, scurvy, and even smallpox.

By the 1650s, though, coffee was seen as more than a medicinal option, and the first English coffeehouses were started in the university town of Oxford. A penny was charged for admission to these coffeehouses, and so they earned the nickname Penny Universities. What I really liked about early coffeehouses is that it didn’t matter who you were.

They were all-inclusive. It didn’t matter what class you were or what your education was. It was basically an open academy.

Although each coffeehouse did have their own little niche, they catered to different professions or ideas such as poets, politicians, you name it. Kind of like subreddits, many of these seemed like a place of enlightenment, but there were other more not-safe-for-work groups that focused on prostitution or just simply criminal meetups. Regardless of the focus of the coffeehouse, again like subreddits, they had a huge broad set of rules that were followed to try to encourage civility.

What’s your favorite subreddit, Faith? My favorite subreddit is Cursed Images. I do this thing where when I see something horrible, I like to subject my friends to that too. I like to think it makes them stronger.

On Cursed Images, there’s a lot of weird photos. I saw one of some really explosive diarrhea, so I saved it and sent it to my best friend to make her stronger. Hold on, I want to back up real quick.

You say niche? Niche. Niche. Niche.

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I say niche, yeah. Who’s right? I don’t know. Niche.

That just sounds weird. Like it reminds me of lice for some reason. Niche.

Why are you looking at me like that? Oh wait, no. Actually, there was one time. There was one time I saw this horrible, horrible image on Cursed Images of this like ragingly bad lice or yeah, lice infection.

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There were so many eggs. They like, oh, it was just like combing and so many eggs. It was genuinely horrible.

A true cursed image. Speaking of horrible, Lloyd’s of London insurance market actually started off in Lloyd’s Coffee House. It was a popular spot for merchants, sailors, and ship owners to stop by for a cup of coffee and discuss foreign trade.

In response, Edward Lloyd, who was the owner, would post shipping news that was both current and reliable and before long became known as the place to get marine insurance. So were they like insuring their own lives too? I don’t know. I know they would like insure like a ship or they would insure the content of the ship.

All right. So interestingly enough, Lloyd’s of London is the company that insures Troy Polamalu’s hair. So that’s the football player that does Head & Shoulders commercials.

He has like the massive black curly hair and it’s got like tons of body. Supposedly, Daniel Craig also took out a $9.5 million insurance policy on his body while filming the James Bond movie since he does a lot of his own stunts and you can’t like afford to break a leg when you’re James Bond. Yeah, I hear like if the star goes down, you actually have to shut down all of production.

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So those are like… Yeah, yeah. Like I said a movie back like months, if not a year or more. Yeah, a lot of people depend on like that paycheck too.

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It was rumored that Ian Fleming, who was the creator of James Bond, lived on Goat Island, which is an island along Trinidad and Tobago. However, his family said that that was just a rumor and that all of the James Bond novels were actually written at Ian Fleming’s house, which was named Goldeneye, like the movie, near Ocho Rios in Jamaica, which Jamaica has their own certified coffee called Blue Mountain, which I did actually have some of that once we were at a conference at the Haffman Resort in Montego Bay. It was delicious.

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Yeah, what was nice about it? It was just a very smooth flavor. It was free too. Do you know what kind of roast it was? Because like I personally like medium to light.

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I’m not a big fan of dark. I would say it was kind of in the medium range because I don’t really like the dark roasted coffees because they’re a little bit bitter tasting to me. I like the more sweet ones.

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Yeah, yeah. Well, I know that one that you buy the… Sumatra coffee. Sumatra.

Yeah, that’s a medium, which is like still a little dark for like my taste. I’ll tolerate it because normally when I’m drinking it’s because you gave me like free coffee. So I’m not going to turn it down.

But it’s like if it was a less burnt tasting than that, it was probably like a nice medium light, light medium. Yeah, it’s one of those types of coffees you can drink without adding a bunch of cream or sugar to it. Speaking of goats and coffee, one of the main anecdotal origin stories that people hear in regards to the origins of coffee follows a young nomadic goat herder in Ethiopia named Kaldi, who’s said to have discovered coffee when he noticed goats eating the coffee cherries and then becoming energized and dancing around.

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Yeah, whenever I hear that story, it’s kind of picture that cute dance that Snoopy does. I don’t know. Anyway, like any good scientist of his day, he, of course, experimented and chewed on some of those berries too.

I’m guessing he probably also did that happy dance. And then he brought those cherries to an Islamic monk who, of course, disapproved of the happy berries, promptly threw them into the fire. And then, of course, they smelled amazing, which the story is considered to be a legend.

However, it does give some indication that the coffee plant does originally come from Africa. So I know that that was actually the first like anecdotal coffee origin story that I heard. In high school, my economics teacher absolutely loved coffee, like loved it.

He had this grinder that he had like on his own. He’d like buy whole beans from like imported out of the country, grind them himself. And he had like a pour over way to do it and a couple others.

I don’t remember. It’s been a few years. But we had this whole week in school devoted to him just like making us a different type of coffee each day in his different methods.

And it was actually really, really nice. Yeah, there’s a whole bunch of different ways. I think the most interesting way for me was I had a friend that was from Turkey, and she brought over this set that they use in Turkey.

So it’s this little copper pot, like about the size of a coffee cup. And I had like hammered metal all the way around and a little thin stick that was used for your handle. And you would put the hot water in, I think she put the hot water in first, and then you added in a very fine ground.

And then you let the beans, or I guess the ground beans seep in and they would drift down towards the bottom. And then you would let the whole thing just kind of settle. Then you had to very, very carefully pour from the copper pot into these very small cups.

And of course, some of the grounds would come along with it. And then you had to let that settle a little bit. And then you could finally have some coffee.

And the fun part was after you finished drinking your coffee, there would be the grounds all on the bottom. And they supposedly did some sort of like tea leaf reading, except it was with coffee grounds to kind of see what your future had in store for you. Yeah, don’t you have like a little set? Somewhere, somewhere.

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Yeah, my ex had a pour over method. I couldn’t like taste the difference between like, what he would make and like the Keurig. I’m not nearly like culture enough with my taste buds to really taste it.

And also he bought dark roast. So that’s gross to me. I know that I like cold brew though, that’s the only kind that I can stomach without creamer or sugar or anything.

Supposedly it’s because by not heating the beans you get they’re less like acidic and less bitter. I don’t. I still don’t know if I’m going to drink it.

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You currently drink cold brew. I know it’s not iced coffee, but it’s not hot coffee either. You currently do drink cold brew coffee.

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You sit here on your high horse. And pretend you’re like, I’m so cool. I only drink hot coffee.

I’m so cool. I microwave my coffee. But you won’t drink iced coffee and then you’re going to sit here and pretend you don’t even drink cold coffee.

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Do you think goats would would eat iced coffee cherries? I think they would on a hot day. Kind of like how people give their dogs like those ice cubes with like cheese in them. They might.

Is there anything else that eats coffee cherries that you know of? Yeah. So goats really aren’t the only animal that eats coffee cherries. Oh wait, somebody told us about elephants.

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That was like your whole coffee. It was black. I know.

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Black ivory maybe? I don’t remember the name. I do know exactly what you’re talking about though. And there’s also the civet.

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Yeah. So super important are the civets though. Civets are these small mammals native to tropical Asia and Africa.

So if the average house cat is 18 inches long, like without a tail, so picture a nice little friendly cat. Civets are about 21 inches long. So just a couple inches longer than a cat.

About the same size. I think of them as having like a cat body with a baby bear face, but with like a little less fluff than a bear would have. So a cup of kopi luwak, the world’s most expensive coffee can sell for over a hundred dollars.

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The word kopi comes from the Indonesian word for coffee and luwak is a regional name that refers to the civets. So our friend Matt has tried kopi luwak in the Philippines. He said it was super smooth and had a nice kick, but he couldn’t really think of any other way to describe it.

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So what exactly is kopi luwak? Well, it’s the feces of the Asian palm civet. The feces. Yeah.

Their poop looks a lot like a payday bar. So like with all the little peanuts, but coffee beans. So the bacteria and digestive enzymes during the digestive process change the structure of the proteins in the coffee beans, which remove some of the acidity to make a smoother cup of coffee.

At first production of kopi luwak was a really positive thing for the Asian palm civets in that it encouraged people to protect them instead of treating them like pests. However, people then got greedy and they’d go and capture them and put them in cages. And so during that, the civets would stop selecting the cherries the way they do in the wild with their senses to which cherry would be the best.

And so it was that animal instinct that was causing these wonderful poop to make these cups of coffee. The fragrant poop. The fragrant poop to make these wonderful cups of coffee.

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And so when they were no longer able to be selective about the cherries they were eating, it caused the quality to dramatically decrease. Right. Because it was just people picking whatever cherries they could off the ground and just forcing it onto the civets and the civets didn’t have a choice.

Yeah. So we as humans don’t have the same ability to sit there and smell a coffee cherry and know if it’s going to produce these really nice coffee grounds after the digestive process. But the civets did have that ability.

So like I said, people started to get greedy with the civets and they would put them in cages to try to like force this Kopi Luwak production. And so they just started capturing civets and they put them in these cages and they started trading them in markets too, which is something we can come back to later. So they’re being traded in these markets in Indonesia and also like in China and surrounding countries.

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In November 2002 in Guangdong province in China near Hong Kong, a farmer at a hospital in Foshan presented symptoms of a mysterious atypical pneumonia, which means a type of pneumonia not caused by one of the pathogens that are most commonly associated with the disease. Usually the culprit of pneumonia is a bacteria. However, viruses such as influenza or measles can cause atypical pneumonia.

The symptoms of the mysterious illness included having a high fever and difficulty breathing. And in this case, the farmer died within a very short amount of time. Within about three months, there will be over 800 cases of this mysterious atypical pneumonia and over 30 deaths throughout the hospitals in Guangdong.

The illness then spread to Hong Kong in February of 2003, which is just a few months after the first outbreak, when a physician named Lu Xianlun, who had previously treated cases in Guangdong, attended a family gathering. Even though he felt sick, he still visited with his family and traveled around Hong Kong. He was what we would call a super spreader and several people at the hotel he was staying at called the Metropole eventually fell ill with this new and dangerous infectious agent.

Then just a couple of weeks on March 1st, he was admitted into a hospital and died within 20 days. Ultimately, around 80% of the eventual 1,755 cases in Hong Kong can be attributed to this traveling physician. The cases in Hong Kong would result in around 300 deaths at a 17% fatality rate.

The virus then appeared in Vietnam when a traveler named Johnny Chin, he was an American Chinese businessman who had stayed on the same floor of the Metropole Hotel as Lu, traveled to Hanoi in Vietnam. He was admitted to the French Hospital of Hanoi and eventually 40 staff members become infected with this mysterious disease. He was then evacuated to Hong Kong, but died about two weeks later after first presenting symptoms.

It is in Hanoi that Dr. Carlo Ubrani, an Italian doctor and World Health Organization infectious disease specialist first examined Chin. He was one of the first to realize that this new outbreak was new and highly contagious. So an outbreak can be defined as an occurrence of disease cases and excess of normal expectancy.

So with a brand new disease, like right away, it starts out as an outbreak because it previously wasn’t exhibiting in humans. Dr. Urbani immediately called the World Health Organization and convinced the health ministry to begin isolating patients and screening travelers as they came into various countries there in Southeast Asia. On March 11th, Dr. Urbani flew from Hanoi, Vietnam to Bangkok, Thailand to present at a conference.

It was on the plane ride that he began to feel ill and as soon as the plane landed, his colleagues brought him directly to a hospital in Bangkok and he died 18 days later. The disease that Dr. Urbani alerted the world to was called SARS, Severe Acute Respiratory Syndrome. An additional outbreak occurred starting on March 1st when 26-year-old Esther Mok traveled from Hong Kong to Singapore.

Although she survived, the country experienced around 340 cases of SARS and 33 related deaths. So seeing that this was a disease that hadn’t been seen in humans yet, in the days following Dr. Urbani’s report, the WHO issued global health alerts. In impacted areas, quarantines were established and schools and universities were closed.

Because this hadn’t been seen in humans before, the WHO and really the world needed to take every protective measure we could to prevent transmission because we didn’t have any idea what we were dealing with at this point. We just knew that it was spreading very rapidly and that people were dying. By the end of March, the massive Amoy Gardens complex recorded 300 cases of SARS and the residents were quarantined.

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A patient that had been released from a hospital that was treating SARS patients actually infected a family member that lived in that complex. Some of the apartments shared the same sewage line and it’s possible that the virus was spread through this shared drainage. So at the beginning of April, the U.S. and WHO issued travel warnings to Hong Kong and Guangdong.

An alert to the virus could be spread to other countries by air travel. The 2003 FIFA Women’s World Cup was moved from China to the U.S. Tourism and entertainment industries began to close venues in cities across China to slow the spread of the virus. Within just a few months, more than 8,200 people were infected in 17 different countries with around 800 total deaths.

The fatality rate was around 10 percent. In North America, there was a cluster of infected persons that happened around Toronto, Canada, which ended up resulting in the quarantine of over 5,000 people. Although the WHO requested information about the disease outbreak back in December, so remember the initial outbreak was in November 2002, and they requested information in December 2002, Chinese authorities did not provide information about the outbreak until several months into it.

This certainly led to the death of at least 500 people and thousands of new infections. However, by the end of April, the number of new cases plummeted and by May, several of the affected locations were actually removed from the World Health Organization list of infected areas. So the SARS outbreak was largely contained through aggressive public health measures.

There’s not really a treatment for SARS beyond supportive treatment. Supportive treatment is when a physician tries to manage the symptoms of a disease, although they don’t treat the actual cause of the disease. One of the things that the U.S. did to stop or prevent SARS from spreading was to place an embargo on the import of civets as a whole to prevent an outbreak in the U.S. SARS was linked back to the masked palm civet, which is in the same family as the Asian palm civet, so closely related but not the same, similar to how humans are related to other great apes.

But as a fun fact, the masked palm civet also does eat coffee beans, but we just don’t like harvest kopi luwak from them. Civets were found to carry viruses that were genetically similar to the virus that caused SARS and in the year following the embargo, civets were hypothesized to be the animal origin of the virus. It was later found that the strains circulating in civets did evolve to infect humans.

After that though, it was later found that the SARS- like viruses circulating in civets didn’t have the genetic diversity necessary to evolve to infect humans without the civets acquiring the virus from another animal. Cave-dwelling bats were found to have a richer diversity of the SARS-like viruses, which led to the current hypothesis that SARS originated in bats, with civets acting as an intermediary amplifying host before transmitting the SARS-associated coronavirus to humans. So in humans, SARS presented with high fevers, so fevers over 100.4 degrees Fahrenheit or 38 degrees Celsius.

Some patients experienced headaches, overall discomfort, body aches, and mild respiratory symptoms during the onset and diarrhea. So these are just your general flu-like symptoms that many different things present with in the beginning, including just your general colds and flus. After two to seven days, the patients may have developed a dry cough and then many of the patients eventually develop pneumonia.

Pneumonia is just defined as having liquid in the lungs, so like Dr. Edwards talked about, many different diseases can cause it, many different bacteriums and viruses. So it’s not a good symptom to have, but it’s not at all unique to SARS. SARS was found to be spread through close contact, so that’s kind of your aerosolized droplets through coughing and sneezing or touching like a contaminated object and then touching a mucus membrane, so like a doorknob, and then, I don’t know, eating without washing your hands, kissing and hugging, so very intimate interaction, sharing utensils, and direct touching.

It wasn’t spread through anything as minute as just like walking by a person who wasn’t talking or anything. It was rather intimate contact. The WHO was able to find that isolating patients before the fifth day after symptoms began dramatically decreased viral transmission, and the days before the fifth day was primarily when patients were only exhibiting those general flu-like symptoms.

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The problem with this and the fifth day was that patients often couldn’t differentiate SARS and a bad cold, so they would continue to do what they had planned to do. So if they were going to go on a plane ride to a different country, they would do just that. Doctors and nurses went to work while sick, creating super spreader events like Dr. Edwards talked about, and patients who began getting sick would still fly home.

These general symptoms, longer incubation periods, and a prodromal period, and airfare, and a lack of transparency between governments allowed SARS to spread very rapidly across oceans in a way that diseases previously never could without air travel. So these patients would like get in an airplane and travel across oceans like from China to the US and Toronto. This wasn’t previously something we were having when we were like migrating by ship because you had these months of travel, whereas now you can like hop on a plane and be in Australia in 16 hours.

So a sky full of SARS. Yeah, a sky full of SARS. So can you tell me what the prodromal period was? So the prodromal period is just after the incubation period.

It’s the time that you’re exhibiting those general flu-like symptoms. SARS is caused by a coronavirus. Coronaviruses are called that because they have this spike protein that sticks out from the virus and it looks sort of like either like a crown or a halo around the virion.

Faith, what is a virion? So a virion is like the individual unit of a virus, just one little dude that’ll go and infect a cell, not the whole disease, just one unit. The spike protein is the key that connects with a lock that allows entry of the virus into the cell. So for SARS to infect a cell, the spike protein binds to the cellular receptor called ACE2, which is short for angiotensin-converting enzyme 2, which is expressed on epithelial cells.

These are a cell type that forms barriers, such as for skin or blood vessels. And ACE2 receptor functions to help regulate the blood pressure and other heart-related functions. So treatment for hypertension, which is high blood pressure, often includes using ACE inhibitors.

SARS is an enveloped virus, meaning it has a lipid bilayer, just like our cells do. Many viruses that spread by aerosol happen to be enveloped viruses. Coronaviruses cause a significant portion of cases of the common cold.

SARS and other coronaviruses are able to infect epithelial cells that are in the respiratory tract. Coronaviruses have a genome made of single-strand RNA. The genome is composed of things like the A’s, G’s, C’s, and T’s, and in this case, U’s because it’s RNA.

And we call these nucleotides or bases. For SARS, its genome is close to 30,000 bases in length. For comparison, people have 3 billion bases in their genome.

SARS-associated coronavirus has a moderate mutation rate, which is the frequency of changing the base that it’s supposed to be to a different base. This can change the shape of the protein, the size of the protein, or even what the protein can bind to. So like I said earlier, the current theories that the virus originated in bats, strains were found of SARS-associated coronavirus circulating in bats that were extremely genetically similar to the early civet and human strains.

That strain then mutated to infect civets before mutating a second time to infect humans.

Written and performed by Dr. Dustin Edwards and Faith Cox

Music from https://filmmusic.io
“George Street Shuffle” by Kevin MacLeod (https://incompetech.com);
license CC BY 4.0

Images from
Coronavirus © Fred Murphy, CDC; public domain
Asian palm civet  © unknown; license CC BY-SA 2.0