The code breaker, p.39
The Code Breaker, page 39
Zhang named the device STOP-COVID. But the platform can be easily adapted to detect any virus. “That’s why we chose the STOP name, which can be paired with any target,” he says. “We could create a STOP-flu or a STOP-HIV or have many detection targets on the same platform. The device is agnostic about what virus it’s looking for.”7
Mammoth has the same vision of making it easy to reprogram its own tool to detect any new virus that comes along. “The beauty of CRISPR is that once you have the platform, then it’s just a matter of reconfiguring your chemistry to detect a different virus,” Chen explains. “It can be used for the next pandemic or any virus. It can also be used against any bacteria or anything that has a genetic sequence, even cancer.”8
Biology hits home
The development of home testing kits has a potential impact beyond the fight against COVID: bringing biology into the home, the way that personal computers in the 1970s brought digital products and services—and an awareness of microchips and software code—into people’s daily lives and consciousness.
Personal computers and then smartphones became platforms on which waves of innovators could build neat products. In addition, they helped make the digital revolution into something personal, which caused people to develop some understanding of the technology.
When Zhang was growing up, his parents emphasized that he should use his computer as a tool to build things on. After his attention turned from microchips to microbes, he wondered why biology did not have the same involvement in people’s daily lives as computers did. There were no simple biology devices or platforms that innovators could build things on or that people could use in their homes. “As I was doing molecular biology experiments, I thought, ‘This is so cool and it’s so robust, but why hasn’t it impacted people’s lives in ways that a software app does?’ ”
He was still asking that question when he got to graduate school. “Can you think of how we can bring molecular biology into the kitchen or into people’s homes?” he would ask his classmates. As he was working on developing his at-home CRISPR tests for viruses, he realized that they could be the way to do that. Home testing kits could become the platform, operating system, and form factor that will allow us to weave the wonders of molecular biology more into our daily lives.
Developers and entrepreneurs may someday be able to use CRISPR-based home testing kits as platforms on which to build a variety of biomedical apps: virus detection, disease diagnosis, cancer screening, nutritional analyses, microbiome assessments, and genetic tests. “We can get people in their homes to check if they have the flu or just a cold,” says Zhang. “If their kids have a sore throat, they can determine if it’s strep throat.” In the process, it might give us all a deeper appreciation for how molecular biology works. The inner workings of molecules may remain, for most people, as mysterious as those of microchips, but at least all of us will be a bit more aware of the beauty and power of both.
Dariia Dantseva, Josiah Zayner, and David Ishee injecting their own vaccine
CHAPTER 53 Vaccines
My shot
“Look me in the eyes,” the doctor ordered, staring at me from behind her plastic face guard. Her eyes were vividly blue, almost as blue as her hospital mask. Yet after a moment, I started to turn to the doctor on my left, who was jabbing a long needle deep into the muscle of my upper arm. “No!” the first doctor snapped. “Look at me!”
Then she explained. Because I was part of a double-blind clinical trial of an experimental COVID vaccine,1 they had to make sure that I didn’t get any clues about whether I was being injected with a real dose or merely a placebo made of saline solution. Would I really be able to tell just by looking at the syringe? “Probably not,” she answered, “but we want to be careful.”
It was early August of the plague year, and I had enlisted as a participant in the clinical trial for the COVID vaccine that was being developed by Pfizer with the German company BioNTech. It was a new type of vaccine that had never before been deployed. Instead of delivering deactivated components of the targeted virus, like traditional vaccines do, it injects into humans a snippet of RNA.
As you know by now, RNA is the strand that runs throughout Doudna’s career and this book. In the 1990s, while other scientists were focused on DNA, her Harvard professor Jack Szostak turned her on to its less-celebrated but harder-working sibling that oversaw the making of proteins, acted as a guide for enzymes, could replicate itself, and was probably the root of all life on earth. “I never, ever got over my fascination about how RNA can do so many things,” she says when I tell her of my participation in the RNA vaccine trial. “It’s the genetic material of the coronavirus and, in a very interesting way, could be the basis for vaccines and cures.”2
Traditional vaccines
Vaccines work by stimulating a person’s immune system. A substance that resembles a dangerous virus (or any other pathogen)I is delivered into a person’s body. That substance could be a deactivated version of the virus or a safe fragment of the virus or genetic instructions to make that fragment. This is intended to kick the person’s immune system into gear. When it works, the body produces antibodies that will, sometimes for many years, fend off any infection if the real virus ever attacks.
Vaccinations were pioneered in the 1790s by an English doctor named Edward Jenner who noticed that many milkmaids were immune to smallpox. They had all been infected by a form of pox that afflicts cows but is harmless to humans, and Jenner surmised that the cowpox had given the milkmaids immunity to smallpox. So he took some pus from a cowpox blister, rubbed it into scratches he made in the arm of his gardener’s eight-year-old son, and then (this was in the days before bioethics panels) exposed the kid to smallpox. He didn’t become ill.
Vaccines use a variety of methods to try to stimulate the human immune system. One traditional approach is to inject a weakened and safe (attenuated) version of the virus. These can be good teachers, because they look very much like the real thing. The body responds by making antibodies for fighting them, and the immunity can last a lifetime. Albert Sabin used this approach for the oral polio vaccine in the 1950s, and that’s the way we now fend off measles, mumps, rubella, and chicken pox. It takes a long time to develop and cultivate these vaccines (the viruses have to be incubated in chicken eggs), but some companies in 2020 were using this method as a long-term option for attacking COVID.
When Sabin was trying to develop a weakened polio virus for a vaccination, Jonas Salk succeeded with an approach that seemed somewhat safer: using a killed virus. This type of vaccine can still teach a person’s immune system how to fight off the live virus. The Beijing-based company Sinovac used this approach to devise an early COVID vaccine.
Another traditional approach is to inject a subunit of the virus, such as one of the proteins that are on the virus’s coat. The immune system will then remember these, allowing the body to mount a quick and robust response when it encounters the actual virus. The vaccine against the hepatitis B virus, for example, works this way. Using only a fragment of the virus means that they are safer to inject into a patient and easier to produce, but they are usually not as good at producing long-term immunity. Many companies pursued this approach in the 2020 race for a COVID vaccine by developing ways to introduce into human cells the spike protein that is on the surface of the coronavirus.
Genetic vaccines
The plague year of 2020 is likely to be remembered as the time when these traditional vaccines began to be supplanted by genetic vaccines. Instead of injecting a weakened or partial version of the dangerous virus into humans, these new vaccines deliver a gene or piece of genetic coding that will guide human cells to produce, on their own, components of the virus. The goal is for these components to stimulate the patient’s immune system.
One method for doing this is by taking a harmless virus and engineering into it a gene that will make the desired component. As we all now know, viruses are very good at worming their way into human cells. That is why safe viruses can be used as a delivery system, or vector, to transport material into the cells of patients.
This approach led to one of the earliest COVID vaccine candidates, which was developed at the aptly named Jenner Institute of Oxford University. Scientists there genetically reengineered a safe virus—an adenovirus that causes flu in chimpanzees—by editing into it the gene to make the spike protein of the coronavirus. Similar vaccines developed by other companies in 2020 used a human version of the adenovirus. The vaccine created by Johnson & Johnson, for example, used a human adenovirus as the delivery mechanism to carry a gene that codes for making part of the spike protein. But the Oxford team decided that using one from a chimpanzee was better, because patients who previously had cold infections might have an immunity to the human version.
The idea behind both the Oxford and the Johnson & Johnson vaccines was that the reengineered adenovirus would make its way into human cells, where it would cause the cells to make lots of these spike proteins. That in turn would stimulate the person’s immune system to make antibodies. As a result, the person’s immune system would be primed to respond rapidly if the real coronavirus struck.
The lead researcher at Oxford was Sarah Gilbert.3 In 1998, when she had triplets who were born prematurely, her husband took time off from his job so that she could return to her lab. In 2014, she worked on developing a vaccine for Middle East respiratory syndrome (MERS), using a chimp adenovirus edited to contain the gene for a spike protein. That epidemic died away before her vaccine could be deployed, but it gave her a head start when COVID struck. She already knew that the chimp adenovirus had successfully delivered into humans the gene for the spike protein of MERS. As soon as the Chinese published the genetic sequence of the new coronavirus in January 2020, she began engineering its spike protein gene into the chimp virus, waking each day at 4 a.m.
By then her triplets were twenty-one, and all were studying biochemistry. They volunteered to be early testers, getting the vaccine and seeing if they developed antibodies. (They did.) Trials in monkeys conducted at a Montana primate center in March also produced promising results.
The Bill and Melinda Gates Foundation provided early funding. Bill Gates also pushed Oxford to team up with a major company that could manufacture and distribute the vaccine if it worked. So Oxford forged a partnership with AstraZeneca, the British-Swedish pharmaceutical company.
DNA vaccines
There is another way to get genetic material into a human cell and cause it to produce the components of a virus that can stimulate the immune system. Instead of engineering the gene for the component into a virus, you can just deliver the genetic code for the component—as DNA or RNA—into human cells. The cells thus become a vaccine-manufacturing facility.
Let’s start with DNA vaccines. Although no DNA vaccine had ever been approved before the COVID plague, the concept seemed promising. Researchers at Inovio Pharmaceuticals and a handful of other companies in 2020 created a little circle of DNA that coded for parts of the coronavirus spike protein. The idea was that if it could get inside the nucleus of a cell, the DNA could very efficiently churn out many strands of messenger RNA to go forth and oversee the production of the spike protein parts, which serve to stimulate the immune system. DNA is cheap to produce and do not require dealing with live viruses and incubating them in chicken eggs.
The big challenge facing a DNA vaccine is delivery. How can you get the little ring of engineered DNA not only into a human cell but into the nucleus of the cell? Injecting a lot of the DNA vaccine into a patient’s arm will cause some of the DNA to get into cells, but it’s not very efficient.
Some of the developers of DNA vaccines, including Inovio, tried to facilitate the delivery into human cells through a method called electroporation, which delivers electrical shock pulses to the patient at the site of the injection. That opens pores in the cell membranes and allows the DNA to get in. The electric pulse guns have lots of tiny needles and are unnerving to behold. It’s not hard to see why this technique is unpopular, especially with those on the receiving end.
* * *
One of the teams that Doudna organized at the beginning of the coronavirus crisis in March 2020 focused on these delivery challenges facing DNA vaccines. It was led by her former student Ross Wilson, who now runs his own lab down the hall from her at Berkeley, and Alex Marson of the University of California, San Francisco. At one of Doudna’s regular Zoom meetings, Wilson showed a slide of the Inovio electric zapper. “They actually shoot the patient in the muscle with one of these guns,” he said. “About the only visible advance they’ve made in ten years is now they have a little plastic thing to hide the tiny needles so they don’t frighten the patient as much.”
Marson and Wilson devised a way to address the DNA vaccine delivery problem using CRISPR-Cas9. They put together a Cas9 protein, a guide RNA, and a nuclear localization signal that helps the complex get into the nucleus. The result was a “shuttle” that could get the DNA vaccine into cells. The DNA then directs the cells to make coronavirus spike proteins and thus stimulate the immune system to fend off the real coronavirus.4 It’s a brilliant idea that could have uses for many treatments in the future, but it has been difficult to make work. By the beginning of 2021, Wilson and Marson were still trying to prove it could be effective.
RNA vaccines
That leads us back to our favorite molecule, the biochemical star of this book: RNA.
The vaccine that was tested in my clinical trial makes use of the most basic function that RNA performs in the central dogma of biology: serving as a messenger RNA (mRNA) that carries genetic instructions from DNA, which is bunkered inside a cell’s nucleus, to the manufacturing region of the cell, where it directs what protein to make. In the case of the COVID vaccine, the mRNA instructs cells to make part of the spike protein that is on the surface of a coronavirus.5
RNA vaccines deliver their payloads inside tiny oily capsules, known as lipid nanoparticles, that are injected by a long syringe into the muscles of the upper arm. My muscle hurt for days.
An RNA vaccine has certain advantages over a DNA vaccine. Most notably, the RNA does not need to get into the nucleus of the cell, where DNA is headquartered. The RNA does its work in the outer region of cells, the cytoplasm, which is where proteins are constructed. So an RNA vaccine simply needs to deliver its payload into this outer region.
* * *
In 2020, two innovative young pharmaceutical companies produced RNA vaccines for COVID: Moderna, based in Cambridge, Massachusetts, and the German company BioNTech, which formed a partnership with the American company Pfizer. My clinical trial was for BioNTech/Pfizer.
BioNTech was founded in 2008 by the husband-and-wife research team of Uğur Şahin and Özlem Türeci with the goal of creating cancer immunotherapies, which stimulate the immune system to fight cancerous cells. It soon also became a leader in devising medicines that use mRNA as vaccines against viruses. In January 2020, when Şahin read a medical journal article on the new coronavirus in China, he sent an email to the BioNTech board saying that it was wrong to believe that this virus would come and go as easily as MERS and SARS. “This time it is different,” he told them.6
BioNTech launched what they dubbed Project Lightspeed to devise a vaccine based on RNA sequences that would cause human cells to make versions of the coronavirus’s spike protein. Once it looked promising, Şahin called Kathrin Jansen, the head of vaccine research and development at Pfizer. The two companies had been working together since 2018 to develop flu vaccines using mRNA technology, and he asked her whether Pfizer would want to enter a similar partnership for a COVID vaccine. Jansen said she had been about to call and propose the same thing. The deal was signed in March.7
By then, a similar RNA vaccine was being developed by Moderna, a much-smaller company with only eight hundred employees. Its chair and cofounder, Noubar Afeyan, a Beirut-born Armenian who immigrated to the United States, became fascinated in 2005 by the prospect that mRNA could be inserted into human cells to direct the production of a desired protein. So he hired some young graduates from the Harvard lab of Jack Szostak, who had been Jennifer Doudna’s PhD adviser and turned her on to the wonders of RNA. The company mainly focused on using mRNA to try to develop personalized cancer treatments, but it also had begun experimenting with using the technique to make vaccines against viruses.
In January 2020, Afeyan was celebrating the birthday of one of his daughters at a Cambridge restaurant when he got an urgent text message from the CEO of his company, Stéphane Bancel, in Switzerland. So he stepped outside in the freezing temperature to call him back. Bancel said that he wanted to launch a project to use mRNA to attempt a vaccine against the new coronavirus. At that point, Moderna had twenty drugs in development but none had been approved or even reached the final stage of clinical trials. Afeyan instantly authorized him to start work without waiting for full board approval. Lacking Pfizer’s resources, Moderna had to depend on funding from the U.S. government. Anthony Fauci, the government’s infectious disease expert, was supportive. “Go for it,” he declared. “Whatever it costs, don’t worry about it.” It took Moderna only two days to create the desired RNA sequences that would produce the spike protein, and thirty-eight days later it shipped the first box of vials to the NIH to begin early-stage trials. Afeyan keeps a picture of that box on his cell phone.
