The Code Breaker, page 40
As with CRISPR therapies, a difficult part of the vaccine development was creating the delivery mechanism into the cell. Moderna had been working for ten years to perfect lipid nanoparticles, the tiny synthetic capsules that can carry molecules into a human cell. This gave it one advantage over BioNTech/Pfizer: its particles were more stable and did not have to be stored at extremely low temperatures. Moderna is also using this technology to deliver CRISPR into human cells.8
Our biohacker steps in
At this point Josiah Zayner, the garage scientist who injected himself with CRISPR, came back onstage to play Puck again. As others were eagerly awaiting results for the genetic vaccines that went into clinical trials in the summer of 2020, Zayner brought his wise-fool spirit to the battle, enlisting a couple of like-minded biohackers in the cause. His plan was to produce and then inject himself with one of the many potential coronavirus vaccines that were being developed. Then he would see whether (a) he survived and (b) he developed antibodies to protect against COVID. “You can call it a stunt if you want, but it’s really about people taking control of science and moving it fucking faster,” he told me.9
Specifically, he decided to make and test a potential vaccine that had been described that May in a Science paper by researchers at Harvard. The vaccine was just beginning human trials.10 It was a DNA vaccine that included the genetic code for the spike of the coronavirus. The paper described precisely how to make it. With the recipe in hand, Zayner ordered the ingredients and went to work.
From his garage lab in Oakland, just seven miles south of Doudna’s at Berkeley, Zayner launched a YouTube streaming course—named Project McAfee, after the anti-virus software—so that others could follow along and perform the experiments on themselves. “Biohackers can be like the test pilots of the modern world by doing the slightly crazy shit that needs to be done,” he declared.
He had two copilots. David Ishee is a ponytailed rural Mississippi dog breeder who uses CRISPR to edit the genes of Dalmatians and mastiffs to try to make them healthier, stronger, and in one offbeat experiment glow in the dark. He joined by Skype from a wooden shed in his backyard crammed with lab equipment. When Zayner said that they would be streaming their experiments for the next two months, Ishee took a sip of a Monster energy drink and interjected in his languid honeysuckle-scented drawl, “Or at least until the authorities come for us.” Also Skyping in was Dariia Dantseva, a student in Dnipro, Ukraine, who created her country’s first biohacking lab. “Ukraine is pretty easy about regulating biohacking, because the state literally does not exist,” she says. “I believe that knowledge is not just for the elites, it’s for all of us. That’s why we do this.”
The experiments that Zayner performed through the summer of 2020 were not just a showy stunt, like when he injected CRISPR into his arm at the San Francisco conference. “We could just inject this shit,” he said of the DNA vaccine described by the Harvard researchers. “But I don’t think anyone would get anything out of that. We want to add a lot more value.” Instead, he and his copilots carefully, week after week, did a livestream demonstration to teach people how to make the code for the spike proteins of the coronavirus. That way they could get dozens, perhaps hundreds, of people to test it, thus gathering useful data about its effectiveness. “If a bunch of scrubs like us can do this, hundreds of people could be doing it and moving science forward more quickly,” he says. “We want everyone to have the opportunity to create this DNA vaccine and test if it creates antibodies in human cells.”
I asked him why he thought a DNA vaccine would work with just a simple injection rather than the electroporation shocks and other techniques that some researchers said were needed to assure that the DNA got into the nucleus of human cells. “We wanted to follow the Harvard paper as closely as possible, and they did not use any special techniques like electroporation,” he replied. “DNA is easy to produce, so if some delivery method doubles the efficiency you can get the same results just by doubling or so the amount of DNA you inject.”
On Sunday, August 9, the three biohackers appeared together—from California, Mississippi, and Ukraine—in a live video-stream to inject into their arms the vaccines they had been concocting over the past two months. “We three tried to push science forward by showing what people are capable of doing in a do-it-yourself environment,” Zayner explained as the video began. “So anyway, here we go! We’re doing it!” Then Zayner, wearing a Michael Jordan red tank-top jersey, plunged a long needle into his arm as Dantseva and Ishee followed suit. He offered a bit of reassurance to his audience: “For all of you who signed in to see us die, it’s not going to happen.”
He was right. They didn’t die. They simply winced a lot. And in the end, there was evidence that the vaccine may have worked. Because his experiment did not include any special method for getting the DNA into the nucleus of human cells, the results were not totally clear or convincing. But when he tested his blood in September, streaming it live on the internet for everyone to watch, Zayner found evidence that he had developed neutralizing antibodies to fight the coronavirus. He called it a “mild success,” but noted that biology often produces murky results. It gave him a greater appreciation for careful clinical trials.
Some of the scientific researchers I talked to were appalled by what Zayner did. But I found myself rooting for him. If his shadow has offended, think but this and all is mended: More citizen involvement in science is a good thing. Genetic coding will never become as crowdsourced and democratized as software coding, but biology should not remain the exclusive realm of a gospel-guarding priesthood. When Zayner kindly sent me a dose of his homemade vaccine, I decided not to inject it. But I admired him and his two other musketeers for doing so. It made me want to get involved in testing vaccines, though in a more authorized way.11
My clinical trial
My own involvement in citizen science was to sign up for a clinical trial of the Pfizer/BioNTech mRNA vaccine. As noted in the opening of this chapter, it was a double-blind study, meaning that neither I nor the researchers were told who got a real vaccine and who got a placebo.
When I volunteered at Ochsner Hospital in New Orleans, I was told that the study could last up to two years. That raised a few questions in my mind. What would happen, I asked the coordinator, if the vaccine got approved before then? She told me that I would then be “unblinded,” meaning that they would tell me if I had gotten the placebo and, if so, give me the real vaccine.
What would happen if some other vaccines got approved while our trial was still underway? I could drop out whenever I wanted, she said, and seek to get the approved vaccine. Then I asked a more difficult question: If I dropped out, would I then be unblinded? She paused. She called her supervisor, who paused as well. Finally I was told, “That’s not been decided.”12
So I went to the top. I posed these questions to Francis Collins at the National Institutes of Health, which was overseeing the vaccine studies. (There is an advantage to being a book writer.) “You have asked a question that is currently engaging the members of the Vaccines Working Group in serious debate,” he replied. Just a few days earlier, a “consultation report” on this issue had been prepared by the Department of Bioethics at NIH headquarters in Bethesda, Maryland.13 Even before reading the five-page report, I was impressed and comforted that the NIH had something called a Department of Bioethics.
The report was thoughtful. For a variety of scenarios, the scientific value that could come from continuing a blinded study was balanced against the health of the trial participants. In the case that the vaccine got FDA approval, the advice was: “There will be an obligation to inform participants so that they can decide whether to obtain the vaccine.”
After digesting all of this, I decided to quit asking questions and enroll. It might aid the science a little bit, and I would learn firsthand, or first arm, about RNA vaccines. Some people are very skeptical about vaccines and clinical trials. I err on the side of being trusting.
RNA victorious
In December of 2020, with COVID once again resurging throughout much of the world, the two RNA vaccines were the first to be authorized in the United States and became the vanguard of the biotech battle to beat back the pandemic. The plucky little RNA molecule, which had spawned life on our planet and then plagued us in the form of coronaviruses, rode to our rescue. Jennifer Doudna and her colleagues had employed RNA in a tool to edit our genes and then as a method to detect coronaviruses. Now scientists had found a way to enlist RNA’s most basic biological function in order to turn our cells into manufacturing plants for the spike protein that would stimulate our immunity to the coronavirus.
Look at the halo of letters—GCACGUAGUGU…—on the cover of this book. It is a snippet of the RNA that creates the part of the spike protein that binds to human cells, and these letters became part of the code used in the new vaccines. Never before had an RNA vaccine been approved for use. But a year after the novel coronavirus was first identified, both Pfizer/BioNTech and Moderna had devised these new genetic vaccines and tested them in large clinical trials, involving people like me, where they proved more than 90 percent effective. When the CEO of Pfizer, Albert Bourla, was informed of the results on a conference call, even he was stunned. “Repeat it,” he asked. “Did you say 19 or 90?”14
Throughout human history, we have been subjected to wave after wave of viral and bacterial plagues. The first known one was the Babylon flu epidemic around 1200 BC. The plague of Athens in 429 BC killed close to 100,000 people, the Antonine plague in the second century killed ten million, the plague of Justinian in the sixth century killed fifty million, and the Black Death of the fourteenth century took almost 200 million lives, close to half of Europe’s population.
The COVID pandemic that killed more than 1.5 million people in 2020 will not be the final plague. However, thanks to the new RNA vaccine technology, our defenses against most future viruses are likely to be immensely faster and more effective. “It was a bad day for viruses,” Moderna’s chair Afeyan says about the Sunday in November 2020 when he got the first word of the clinical trial results. “There was a sudden shift in the evolutionary balance between what human technology can do and what viruses can do. We may never have a pandemic again.”
The invention of easily reprogrammable RNA vaccines was a lightning-fast triumph of human ingenuity, but it was based on decades of curiosity-driven research into one of the most fundamental aspects of life on planet earth: how genes encoded by DNA are transcribed into snippets of RNA that tell cells what proteins to assemble. Likewise, CRISPR gene-editing technology came from understanding the way that bacteria use snippets of RNA to guide enzymes to chop up dangerous viruses. Great inventions come from understanding basic science. Nature is beautiful that way.
I. A “pathogen,” commonly referred to as a “germ,” is any microorganism that causes disease or infection. The most common are viruses, bacteria, fungi, and protozoa.
Stanley Qi
Nathan and Cameron Myhrvold
CHAPTER 54 CRISPR Cures
The development of vaccines—both the conventional sort and those employing RNA—would eventually help to beat back the coronavirus pandemic. But they are not a perfect solution. They rely on stimulating a person’s immune system, always a risky thing to do. (Most deaths from COVID-19 came from organ inflammation due to unwanted immune-system responses.)1 As vaccine makers have repeatedly discovered, the multilayered human immune system is very tricky to control. In it lurk mysteries. It contains no simple on-off switches, but instead works through the interaction of complicated molecules that are not easy to calibrate.2
The use of antibodies from the blood plasma of recovering patients or made synthetically also helped fight the COVID plague. But these treatments are, likewise, not a perfect long-term solution for each new wave of virus. Convalescent plasma is difficult to harvest from donors in large quantities, and lab-made monoclonal antibodies are hard to manufacture.
The long-range solution to our fight against viruses is the same as the one bacteria found: using CRISPR to guide a scissors-like enzyme to chop up the genetic material of a virus, without having to enlist the patient’s immune system. Once again, the circles of scientists around Doudna and Zhang found themselves in competition as they raced to adapt CRISPR to this urgent mission.
Cameron Myhrvold and CARVER
Cameron Myhrvold straddles the world of digital coding and genetic coding, which is not surprising given his heritage and breeding. The lookalike son of Nathan Myhrvold (pronounced MEER-vold), who was the longtime chief technology officer and sparky genius at Microsoft, he has his father’s gleeful eyes, chipmunk-cheeked round face, effervescent laugh, and free-range curiosity. People of my generation were awed by his father’s brilliance not only in the digital realm but also in fields ranging from food science to asteroid tracking to the speed at which dinosaurs could whip their tails. Cameron shares his father’s facility with computer coding, but like many in his generation he focused more on genetic coding and the wonders of biology.
As a Princeton undergraduate, he studied molecular and computational biology, then he got his doctorate from Harvard’s Systems, Synthetic, and Quantitative Biology Program, which combines biology and computer science. He loved the intellectual challenge but worried that his work on nano-engineering of organisms was so cutting-edge that it would have little practical impact in the foreseeable future.3
So after he got his PhD, he took time off to hike the Colorado Trail. “I was really trying to figure out where to go scientifically,” he says. On one leg of his hike, he met a guy who asked him a lot of earnest questions about science. “During that conversation,” Myhrvold says, “it became apparent to me that I liked working on problems that were directly relevant to human health.”
That led him to decide to become a postdoc in the lab of Pardis Sabeti, a Harvard biologist who uses computer algorithms to explain the evolution of disease. She was born in Tehran and as a child fled with her family to America during the Iranian Revolution. A member of the Broad Institute, she collaborates closely with Feng Zhang. “Joining Pardis’s lab and working with Feng Zhang seemed like a really great way to take on the problem of fighting viruses,” Myhrvold says. As a result, Myhrvold became part of the Boston-area orbit around Zhang and eventually a player in its CRISPR star wars with the Berkeley-area orbit of Jennifer Doudna.
* * *
While studying for his doctorate at Harvard, Myhrvold became friends with Jonathan Gootenberg and Omar Abudayyeh, the two grad students who worked with Zhang on CRISPR-Cas13. Myhrvold would often kick around ideas with them when he visited Zhang’s lab to use its gene-sequencing machine. “That’s when I realized, wow, like those two guys were a really special pair,” Myhrvold says. “We came up with ways to use Cas13 to detect different RNA sequences, and I thought it would be a really cool opportunity.”
When Myhrvold suggested to Sabeti that they should collaborate with Zhang’s lab, she was enthusiastic because there was a lot of synergy between the two teams. It resulted in a made-for-the-movies diverse American platoon: Gootenberg, Abudayyeh, Zhang, Myhrvold, Sabeti.
They worked together on Zhang’s 2017 paper describing the SHERLOCK system for detecting RNA viruses.4 The following year, they collaborated on a paper showing how to make the SHERLOCK process even simpler.5 It appeared in the same issue of Science as the paper from Doudna’s lab describing the virus-detection tool developed by Chen and Harrington.
* * *
In addition to using CRISPR-Cas13 to detect viruses, Myhrvold became interested in turning it into a therapeutic treatment, one that could get rid of viruses. “There are hundreds of viruses that can infect people, but there’s only a handful that have available drugs,” he says. “That’s in part because viruses are so different from each other. What if we could come up with a system that we could program to treat different viruses?”6
Most of the viruses that cause human problems, including the coronavirus, have RNA as their genetic material. “They are precisely the type of virus for which you would want a CRISPR enzyme that targets RNA, such as Cas13,” he says. So he came up with a way to use CRISPR-Cas13 to do for humans what it does for bacteria: target a dangerous virus and chop it up. Continuing the tradition of reverse-engineering clever acronyms for CRISPR-based inventions, he dubbed the proposed system CARVER, for “Cas13-assisted restriction of viral expression and readout.”
In December 2016, shortly after he joined Sabeti’s lab as a postdoc, Myhrvold sent her an email reporting on some initial experiments using CARVER to target a virus that causes the symptoms of meningitis or encephalitis. His data showed that it reduced the levels of the virus significantly.7
Sabeti was able to get a DARPA grant to study the CARVER system as a way to destroy viruses in humans.8 Myhrvold and others in her lab did a computer analysis of more than 350 genomes from RNA viruses that infected humans and identified what are known as “conserved sequences,” meaning those that are the same in many viruses. These sequences have been preserved unchanged by evolution, and thus are not likely to mutate away anytime soon. His team engineered an arsenal of guide RNAs designed to target these sequences. He then tested Cas13’s ability to stop three viruses, including the type that causes severe flu. In cell cultures in a lab, the CARVER system was able too significantly reduce the level of viruses.9
