Spike

mostly babies from poor black families. The trial went badly, really badly. Dozens of infants got a new RSV vaccine, and not only did the vaccine not protect them from the virus, it actually seemed to expose them to graver sickness. So the vaccinated babies who caught RSV fared worse than those who got no vaccine at all. Eighteen of those kids ended up in the hospital and two of them die. As far as vaccine trials go, it was a total disaster.

It's a cruel irony of vaccine development that those two kids deaths fifty years ago indirectly led to one of the greatest successes in the history of modern drugs. The COVID nineteen vaccines, the single biggest breakthrough in coronavirus vaccine research, was inspired by scientists who wanted to protect kids from RSV, and because of that work, they figured out how to make a vaccine for coronavirus two years before the first

case of COVID nineteen. In this episode, we're going to get a little technical on you, but it's necessary in order to get to the heart of how these vaccines work. From iHeartRadio and School of Humans, I'm Sean Revive and this is long shot. Yeah, people want, you know, they want to see smoking vessels of like Purvalla, but you know,

by all just for not chemists. That's Jason McClellan. He works at the University of Texas in Austin, and he's telling us that his office isn't as exciting as visitors might think. I mean, when people come to visit, we add food, gallering and things because they want to see yellow. But like everything the work of his water, it's like biological. I'm in Austin, Texas, at the University of Texas. I'm in one of the departments called a Molecular Biosciences department.

I'm a structural biologist. Structural biologists zoom a way in on large molecules or groups of molecules and figure out how their parts are put together and why they work the way they do. They spend a lot of time looking at proteins, which play a ton of roles in the body of humans and other living things. Proteins help you grow, digest food, fight disease, stay energized. They also help bind cells together and transport nutrients. Some hormones like insulin,

are proteins. Antibodies are proteins, Enzymes are proteins. Hemoglobin, which is the dominant component of our blood, is a protein. Structural biologists like Jason want to know exactly what proteins look like. Without the structures, we don't really know what these proteins look like. We draw them as ovals or squares. But once we determine their structures, we're able to like three D print the actual molecule essentially and know where every amino acids is located on the protein, how the

proteins fold The structure leads to function. So by understanding the structure, we know something about how the protein works. And if you know how proteins work and how they look. You can figure out ways to alter them, change amino acids, maybe make the protein more stable, or chop off some parts. We don't want to try to make them the best possible vaccine antigens. Understanding what specific proteins do is the key to the COVID vaccines. But it's not like Jason

went to college and majored in proteins. Oh, it was a kind of winding path, I guess. I went to college Wayne State University in Detroit, Michigan. I wanted to do pre med and be a doctor. Most I was just trying to think of things I could do to help people. But early on I realized I really liked chemistry. Was quick good at chemistry, so I went to graduate school. I've learned a technique called X ray crystallography, and that's

one of the methods for determining structures of proteins. But ultimately I wanted to do a bit more than just determine destructures. I wanted to try to have some applied research to create things that could end up going into humans and improve human health. Around two thousand and eight, Jason heard about a guy at the NIH doing a lot of cool stuff with HIV, looking closely at the

virus's structure and trying to design a vaccine. He joined the lab there, and while at the NAH he ended up working with a doctor and virologist named Barney Graham, a world expert on RSV. The RSV vaccine that failed back the sixties was made by weakening a strain of the virus by passing it through animal tissue or human cells. That's the way the great vaccine creators of the past,

like Maurice Hilleman made their vaccines. Jason and doctor Graham wanted to create a vaccine in a totally different way. They wanted to manipulate a specific protein of the RSV virus, the one the virus uses to infect human cells. It's called the f protein f as in fudge, and it comes in two forms or a scientists say two confirmations, prefusion and post fusion. Here's Jason to explain more. Proteins exist in some initial confirmation on the surface of the virus.

That's what we call the prefusion confirmation. Then there's an event that causes the protein to begin refolding and rearranging, much like a transformer, going from a car to a robot. Parts of it, parts of the protein, just start moving and refolding, and it ends up forming an intermediate confirmation where it's part of the protein into our host cell membrane. That's pretty confusing, so let's try and visualize it. There's a virus cell and a human cell. We'll picture them

as tennis balls. The virus tennis ball has its protein on its surface, sort of shape like a cone or a stubby mushroom stalk. That's its f protein. So the virus tennis ball looks for human tennis balls in the body, and when it finds one, here's what happens. The mushroom stalk stretches and elongates and attaches itself to the human tennis ball. So it's like a bridge between the two tennis balls, human and virus. So it's stock between the host cell membrane and the viral membrane. The membrane of

a cell is like its skin. It separates the inside of the cell from whatever is on the outside, and then it bends back around like a hairpin to bring the two membranes together, and then it adopts this final state called the postfusion state. So after the stock on the virus tennis ball has elongated and attached itself to the human tennis ball, it folds itself in half in order to bring the two tennis balls together. That's the fusion. And so when the f protein has already elongated and

then folded, it's in its postfusion form. By then it's too late. You want to teach your body to fight the prefusion form before the mushroom stock has folded and attached to the human cell. And so, if you think of your immune system as a security guard, you want to train your immune system to recognize the form that might impact you, like the dangerous form, and that's the prefusion form. If you train it to recognize the postfusion form,

the prefusion form can still sneak by you. So in order to train the immune system to recognize the prefusion form of rsv F proteins, Jason needed to keep the proteins in their prefusion unfolded form. But that isn't easy. First of all, rsv F proteins really want to go into their post fusion form. Second, proteins are tiny. It's not like they could go in with tweezers and hold the F protein in place. The F protein has a molecular mass of fifty seven point four kilo daltons, which

means it's weight in Grahams has twenty one zeros. After the decimal point, it's really difficult to see what they look like, much less alter their behavior. And nobody could figure out how do we create a form of the prefusion molecule that will stay in the prefusion shape and allow us to purify it and inject it into evil. But in twenty thirteen they had a breakthrough. They were finally able to determine the exact structure of the prefusion

form of the rsv F protein. Plus they figured out how to keep it in that form, how to keep it from elongating, and we could start making changes like adding in little molecular staples to link two regions together so that we the one part couldn't pull away from the other. And that work. We were eventually able to make four different changes to the protein that really locked it in the prefusion confirmation and allowed its use as

a vaccine antigen. Basically, they discovered how a sort of staple the mushroom stock in place, and when Barney immunized mice and compared postfusion versus prefusion, the mice receiving the prefusion form of the F protein elicited neutralizing antibodies about ten times higher than those that received the postfusion This is huge. This was the first time structural biology had

helped discover a new way to stop a virus. Science magazine called it one of the top ten breakthroughs of twenty thirteen, and their success in stabilizing the F protein made them want to try the same process with other similar viruses. What else could we take this new approach, the structure based approach, and apply to what other pathogens are important? And that was around the time that the MIRS coronavirus had emerged in the Saudi Arabia and the

Middle East. That's Middle East respiratory syndrome, which is caused by a coronavirus called MRS Covey. The disease was first reported in Saudi Arabia in twenty twelve. It causes bad respiratory illness, fever, cough, shortness of breath, and it can eventually kill you with pneumonia and kidney failure. Even today, there are still cases that pop up on occasion. Thirty

five percent of people infected with it were dying. It's a real lethal virus, and we thought that this would be a good target to try to take everything we had just learned about RSV and apply it to not just mers, but coronaviruses in general, because we knew Stars coronavirus had emerged in China in two thousand and two and it caused an epidemic. Remember Eddie Holmes spoke about the First Stars in episode one. I realized is that

raccoon dogs. They were implicated in the First Stars I break of two thousand and two two thousand and three because they were positive. First came Stars one, then came Mrs Here's Jason again, and then ten years later we

saw Mirrors emerge. We felt like maybe we were on a ten year cycle or something where we keep having coronaviruses emerge into the human population, and so we wanted to figure out how can we do structure based vaccine design or coronaviruses to make the best possible vaccine antigens. Jason and Barney Graham wanted to use their ability to zoom in on viruses and their ability to play around

with them to make better vaccines. Since Mrs Covey was on their radar, they focus on that virus MERS has a protein very similar to the F protein of RSV. It's called the spike protein. The spike protein acts pretty similarly to the F protein, it just has this additional part. If you're thinking about the F protein as a mushroom stock, the spike protein is kind of like a full mushroom with a cap. When attacking a human cell, the cap of the spike protein binds to a certain enzyme on

the surface of the human cell. The enzyme is called the ACE two receptor. The ACE two receptor sort of pops off the spike protein's cap, and then the spike protein stalk does all the things the F protein does.

Based on decades of literature, for many researchers, it was clear that the spike protein is a key component of any vaccine because when humans are infected with coronaviruses, they make a large antibody response to the spike protein because it's really that that's the major protein on the surface of the of the virus. So we know we needed to use spike protein as the vaccine but we also know that the spike protein can change shapes and isn't so stable, so then you know what form do you

want to use. Our previous work, it's shown that what you really want to immunize with is a prefusion stabilized form that that can't change shape. So that way we train our immune system to recognize the shape of the spike protein as it exists on the surface of the virus. So with coronavirus, they knew they wanted to stabilize the spike protein, the key protein on its surface. They wanted to make sure it did not elongate. The spike protein

was pretty unstable. Its stock was liable to elongate and go to post fusion form on the drop of a dime, and they had trouble even seeing its structure. To make it easier, they switched to another virus, one that we've all gotten, HKU one. That's one of the four coronaviruses that we've probably all been infected with. It's one of

the many causes of the common cold. And for whatever reason, the spike protein from HK one was actually pretty stable and it was amenable to the structured determination efforts, and we brought in another group, doctor Andrew Ward's group at the Script's Research Institute. He's an expert in cryoelectron microscopy, and working together they were able to get that first structure of a human coronavirus spike protein in the prefusion shapes. Now we had our first blueprint to start making changes

tweaks to stabilize spike proteins of coronaviruses. Using this blueprint, Jason's post duc Nian Chung Wang look closely at the mirror structure here, he is, it's actually pretty boy, but it's also increasing. Why is it boring and why is it interesting? Is that we got to try okay and again most of the time it's got to feel yeah,

it's not that too easy. Nianshuang tested more than one hundred different mutations to the spike protein until finally coming across two changes that stabilized it, that kept the spike in its pre fusion form, and it was really stable. It stayed all in the pre fusion shape. What was exciting is that the region where we made these changes is very similar between different coronavirus spikes, So the same changes we could also introduce them into stars. Kobe from

two thousand and two, and that led to stabilization. So my twenty seventeen we really had this method, kind of a universal method for stabilizing data coronavirus spikes in their prefusion confirmation. But there was one problem with their success stabilizing the MERS spike protein. Nobody really cared. It flew away under the radar because by then it was evident that MERS, as dangerous as it was, didn't spread very easily. A few people were getting MERS a vaccine for it

didn't seem super important. Yeah, it's kind of painful. At that time, most coronavirus at that time was not considered a big issue because there are few our cases, so people didn't pay matt attention on that kind of coronavirus. Although their work didn't get much attention, they knew they had a vaccine technology ready to be put into action. By twenty seventeen, they were prepared to test their stabilizing spike protein method on another coronavirus. They just needed an outbreak.

And then two years later we found out in the beginning of twenty twenty that this new virus that was causing pneumonia outbreaks in Wuhan China was a coronavirus and very similar to Stars Kobe Ie. They'd finally have a chance to test out the spike protein in real life, but a big question remained, would it work in people.

Jason and his team spent years figuring out how to keep a spike protein stable and use that to make a new kind of vaccine, but they needed an outbreak to test it on real people infected by a coronavirus. Then all of a sudden, they have a real time pandemic crashing down on the world. The reports were coming

out of these pneumonia clusters in Wuhan. We could just see it following along on science, Twitter and on the news, and so people were already kind of nervous, especially in the coronavirus feel that we could be looking at the beginnings of a coronavirus outbreak. And then it was early in January when it was learned that in fact, it is a coronavirus, a beta coronavirus that's similar to the

first Stars Kobe from two thousand and two. At this point, Jason's working at the University of Texas and he's on vacation with his family. Barney Graham called me. He said he was in contact with the US CDC Chinese CDC. They were going to try and work quickly work with Maderna.

Maderna was then an upstart company based in Cambridge, Massachusetts that had never brought a vaccine to market, but they tested several vaccines for other viruses, and Barney Graham had a plan to work with them on a bat born virus called NIPA, but when the novel coronavirus came along, doctor Graham told Maderna they should focus on that instead, and he wanted to know if we were interested in continuing our collaboration to determine the structure of the stars

Kobe to spike protein and use that information to create the vaccine antigens. Jason texted his graduate student Daniel Rapp and told him they were going to be busy the next few days. Based on this information, we were sort of ready to go. That's Daniel, because we've been studying

these spike proteins for such a long time. We knew how to effectively stabilize spike in the pre fusion confirmation and that acts as a really good vaccine candidate, and so during that time we were kind of just like sitting on our hands, like really anxiously waiting for that information to become available to everybody, because that was the thing that was holding us back from getting started back to Jason, and then we just kind of had to wait a couple of these because nothing we could really

do until the genome sequence became available so we could see what the sequence of this spike protein was. On January eleventh, a scientist in China made it available for all. That was John jen Jang who sent the sequence to Eddie Holmes in Australia, who then posted it online. Jason got the sequence and started working on a vaccine with his team the next day. So what does it actually mean to get a virus's genetic sequence. The sequence is

kind of like it's barcode. You're scanning the letters in its genome to figure out actually what it is and how it works. It's essentially a file like somebody can just you know, it's an attachment, the text file that somebody can send us containing the sequence, just a bunch of letters, so like computer code. And then we have to figure out what changes we want to make very quickly just by taking that sequence and aligning it to

the other spike sequences. We knew right where to put the two changes that we had identified earlier, so that was probably done within a couple of hours. Just the design of these constructs. Remember, Jason's team is looking for a way to alter the proteins on the surface of the virus so they won't go into that post fusion confirmation. The change that Niche Wong and the team had discovered working with mers is called the two P mutation. The P stands for prolene, one of twenty amino acids that

are the building blocks of all living things. Proleins are special because they're the most rigid amino acid and because they are rigid. Swapping out two other amino acids for two proteins at a certain joint of the spike protein keeps the mushroom stock in place, meaning it keeps it in pre fusion form. But Jason and his team couldn't just do the two P mutation on the laptop. They

had to do it in real life. There are companies out there that can take a modified genetic sequence like the one they designed at UT and turn it into something physical. And you need to turn it into a biological substance. Like actual DNA. And so that's where we need to work with the companies, where we send them the file and they're able to synthesize DNA and send it send it back to us, and then we have to stitch some of it together and do some other things.

And so in the lab we were working with the DNA. When Jason says he's working with DNA, he essentially means that they're making changes to genes in order to program human cells to produce the stable spike proteins. Remember this is the key to the whole vaccine. Our own cells will be the factories that produce the stable spike proteins, and the DNA is the thing sending those instructions via

messenger RNA. So that way the cells realized the instructions have changed, the recipe has changed, if you will, and they just make a protein containing proteins at those positions instead of the original amino acids at those positions. I think within ten days, maybe a bit more, Nianchwang had had cloned like ten different plasmids. Plasmids are like small snippets of DNA molecules, ending Chwang was working around the clock to stitch them together. Into a full DNA strand

that could encode for the spike proteins. Meanwhile, Barney Graham's lab was talking to MODERNA telling them how to stabilize the spike protein with a two P mutations, like what spike protein to encode in the mRNA, where to put the stabilizing prolein mutations. Then came January thirtieth, twenty twenty. It was an exciting day. We Daniel was harvesting. He's talking about his grad student, Daniel Repp, the purified spike proteins that were produced by the cells we had growing

in the lab. So we was able to harvest the spike, purify it and start freezing cryoEM grids. cryoEM stands for cryoelectron microscopy, a method for seeing proteins at atomic resolution. First, Daniel would flash freeze the proteins in ice on a tiny mesh disc. Then he'd use an electron microscope to take thousands of two dimensional images of the proteins. A computer program then use those pictures to create a three

D image showing the structure of the proteins. That allowed us to start the data collection that night, and we could see the individual spike proteins for the first time, and within twenty four hours we had collected a complete data set and we got the first looks at the molecular shape of the coronavirus spike protein. Within about thirty days we had determined in a manuscript submitted that paper has been sighted close to four thousand times now we have.

We were sharing the coordinates of the structure, the blueprint of the structure to people all over the world. We were shipping the plasmids that we had made two hundred groups or so. Is that way they could make the spike protein in their labs for diagnostics, for antibody isolation or additional structural studies. So it is a really crazy time early last year. Now they knew exactly how to stabilize the spike protein the mushroom shape on the surface

of the coronavirus. They'd actually created stabilized spikes in the lab, and the pharmaceutical company Baderna would use these stabilize spikes as building blocks for the vaccine. They are just directly synthesizing the mRNA, but it's still at the instructions level, such that when the RNA is injected into a person that person sells read the recipe and make a protein that contains two proteins at these positions rather than the

other amino acids that the virus normally uses. RNA is the sort of middleman between DNA and the spike proteins. We'll learn more about this in the next episode, but the saying amongst scientists is that DNA makes RNA, makes proteins makes life. Maderna's vaccine sort of skips the DNA step and sends the mRNA or messenger RNA directly into the body. Maderna encapsulates the mRNA in a fatty sphere called a lipid nanoparticle. Another thing we'll talk about in

an upcoming episode. That bubble helps the mRNA get to ourselves without falling apart, and when it does, our selves get the recipe from making two p mutated spike proteins. They make them, and the immune system sees these coronavirus proteins in their prefusion form, and the immune system learns that they are a threat. It learns that a spike protein in the folded hairpin shape is an enemy and the body has to fight it and stop it from spreading.

If you get infected with coronavirus. The body now knows what to do when it comes across the spike protein in pre fusion form. It knows how to keep you from getting sick. They tested the vaccine in mice and saw that it produced an antibody response, and then they readied it for humans. By March twenty twenty, Maderna had enough vaccine to be used for a phase one clinical trial.

That material was shipped to the different sites in the US where they began immunizing the first forty five people with different doses, testing side effects, dose response, the level of antibodies being produced. Yeah, I think it's like it's like sixty three days or sixty five days something. After the genome sequence was made available online, the first people are being immunized, which is incredible. Um. Hi, my name is Nicolas Nicola in the second episode was one of

those first people. I was part of the Phase one of modernas vaccine trial for COVID. Feisser and Johnson and Johnson also used the two P mutation for their COVID vaccines. It's the driving force behind all the vaccines that Americans are getting and of some other vaccines being made around the world. The last year is difficult because there's a lot of mixed emotions because there are certain scientific successes that we would normally celebrate, but the whole time the

economy is being devastated. People are losing their jobs, hospitalizations, deaths. So it's really a range of mixed emotions where we're excited for the science and everything we've been working on for years being translated into a vaccine that was looking very promising, but at the same time also just really devastating.

We spoke with Jason in March of this year. At the time, three vaccines were already approved for emergency use by the FDA, More than thirty million Americans had already been fully vaccinated, and millions more were scrambling for appointments. Me and my producer Gabby had gotten the Maderna shot a few days earlier, but Jason still hadn't been vaccinated. He was young and healthy, not a frontline worker, happy to wait his turn. He got his first shot a

couple of weeks later. The search for an RSV vaccine after that trial went bad in the sixties inspired the technology used in today's COVID vaccines. But what about RSV that virus that still kills thousands of people every year. It's normally a virus that peaks in winter, but it's been surging in children this summer alongside of and maybe even because of the surge in the coronavirus delta variants. There's still no vaccine for RSV on the market, but

they're working on it. Last year November October of twenty twenty, prefusion f proteins have gone into phase three clinical trials, and yeah, we're really excited about that. It's taken a long time, that's sort of the normal vaccine development timelines, starting a thirteen with the antigen just entering phase three clinical trials in twenty twenty, but yeah, everything still looks

really good and we're really excited by it. Scientific failure and scientific success are unstable concepts, about as unstable as prefusion spike proteins. When a trial for an RSV vaccine failed about as badly as a vaccine trial can fail, it led to a newer and better way of making vaccines. Fifty years later in twenty seventeen, when they stabilize the spike protein, Jason and Nichuang and Daniel and everyone else they worked with. All they got was crickets, but they

did it anyway. Here's Daniel Rapagin. Yeah, it's it's a little surreal because we would be doing this work whether or not COVID nineteen became a pandemic. We would still be studying the spike protein figuring out how it worked. But it's been a little surreal to have so much attention paid to our work because, like as I've been describing to you, we do things that most people would think of is just like minutia, Like if there wasn't a pandemic, we would still be doing this and people

would wonder why. The best example of it is, for the past like five or six years, I've been telling people I studied coronaviruses, and up until like a year ago, people would say, what's a coronavirus. On the next episode of long Shot, we'll speak with the founders of Moderna, a company that started with essentially zero employees before becoming one of the biggest names in COVID nineteen vaccines. We'll also find out what role Jennifer Aniston played in that

origin story. Today's episode of long Shot was produced, written, and narrated by me Sean Revie. My co producer is Gabby Watts. Special thanks to Noel Brown and iHeartRadio and journalist Alan Dove and Ryan Cross. Executive producers are Virginia Prescott, Brandon Barr and Else Crowley. Long Shot was scored by Jason Shannon. The score was mixed by Vic Stafford. Sound design and audio mix was by Harper Harris with Tunewelder School of Humans