A Pox on Us All

Written by David Kushner, Wired

Monday March 25th, 2019

Synthetic Biology is making it easier than ever to produce life-saving vaccines - and life-taking viruses that humanity is not prepared to fight.

At around 11:30 am on July 1, 2014, a scientist from the Food and Drug Administration went inside Room 3C16, a cold-storage area at the National Institutes of Health Labs in Bethesda, Maryland.

The FDA had been using the space since the early 1990s to store samples for biological research but had been cleaning it out in preparation for a move to a nearby campus in Silver Spring.

The scientist who entered saw 12 mysterious cardboard boxes on a crowded shelf in the far left corner of the storage space and pried one open to see what it contained. Inside, dozens of long vials were packed in rolls of white cotton and sealed with melted glass; many of the labels were worn to the point of illegibility. The scientist noticed one vessel that held some loose, freeze-dried material. Its label bore a single decipherable word: “variola,” another word for smallpox—a disease that the 19th-century British historian Thomas Babington Macaulay deemed “the most terrible of all the ministers of death.”

The highly contagious virus spreads through close contact, bodily fluids, or contaminated objects. It starts like chicken pox: The victim runs a high fever and is prone to vomiting. A rash develops in the mouth and spreads quickly over the entire body, like tiny marbles pushing up from under the skin. Some 30 percent of people who contract the virus die within two weeks. Those who survive are often scarred, blinded, or disfigured.

Smallpox ravaged the world for centuries. It wasn’t until 1796 that English physician Edward Jenner famously discovered how to turn the immune system against the disease. Even so, it took centuries for the vaccine he created to be fully deployed. Smallpox killed an estimated 500 million people in the 19th and 20th centuries before it was finally eradicated worldwide in 1980. Yet here in this cluttered Maryland lab were six forgotten vials of the dreaded poxvirus, including at least two live samples still capable of growing and infecting untold masses.

During a two-year investigation into the origin of the vials, the FDA determined that they dated to February 10, 1954. But the agency couldn’t figure out how or why they ended up in a cold-storage room at the NIH. The incident triggered a government-wide search for other dangerous materials that may have been overlooked and led to revisions in the FDA’s policies on the storage of infectious agents. The 60-year-old smallpox strains were destroyed under the watch of World Health Organization officials.

The existence of the vials raised another chilling possibility: Could smallpox make a comeback? If these samples were left behind, who knows how many others could remain. The US maintains enough of the smallpox vaccine to protect all 328 million Americans. But in the decades since the disease was eradicated, scientists have discovered that several groups of people—those with HIV, pregnant women, newborns, and cancer survivors among them—are at risk for complications from the vaccine, such as heart inflammation and brain infections. It’s likely that most of these people would be advised to avoid taking the remedy, as would anyone sharing a home with them. Given those significant limitations, many health officials and researchers believe there’s a pressing need for a better smallpox vaccine.

It’s this mission that possesses David Evans, a veteran virologist at the University of Alberta in Canada. The son of a medical health officer in what was the British colony Northern Rhodesia (now Zambia), Evans has been studying poxviruses for more than 30 years.

As one of the world’s foremost experts on smallpox, Evans believes it’s only a matter of time before the disease—or one of its ugly cousins in the pox family—could resurface, brought to life by a hostile government, a terrorist, or an amateur biohacker using gene editing and commercially available DNA fragments.

If that occurs, he says, the world needs to be ready with the safest, most efficient vaccine possible. The best way to improve upon a vaccine is to make one derived from the virus itself.

The Frankensteinian act stirred outrage among the international scientific community, which cast Evans as the Walter White of synthetic biology. Despite the fury he provoked, Evans has no regrets. Better he be the first to resurrect these deadly specters, the virologist maintains, than someone with nefarious intentions. “Nothing will stop the state actor or technically sophisticated country that decides to want to do this,” Evans adds, so better to be prepared.

When smallpox was eliminated nearly 40 years ago, after millions of people were given the vaccine in Africa, Asia, and South America, it was hailed as one of the greatest achievements in human history. In a grim act of Cold War diplomacy, the last two smallpox samples were stored for future study at the Centers for Disease Control and Prevention in Atlanta and at the State Research Center of Virology and Biotechnology in Siberia. Ever since, the World Health Organization has kept tabs on the samples to ensure they are safe.In 2001, Evans joined the WHO’s scientific advisory committee on smallpox. The aim for many in the group was for Russia and the US to destroy those final samples of smallpox for good. “The hope and expectation,” Evans says, “was that the committee would say, ‘Yep, we’re all done, they’ve dealt with all these research goals. You can close it down and autoclave the viruses.’?”

The following year, however, an experiment by scientists at the State University of New York at Stony Brook suggested that simply destroying the samples might not be enough. On July 11, 2002, the researchers revealed that they had synthesized the polio virus, which had been wiped out in the US in 1979. It was the first time a virus had been created from scratch with synthetic DNA. The work was funded by the Pentagon in part to establish whether terrorists could pull off such a feat. The answer was yes. It took the SUNY researchers three years to cobble the virus together using mail-order DNA and genetic sequences referenced from an online public database. The experiment’s surprise success raised the possibility of a cyberpunk-style era of biowarfare, and the possibility that an exponentially deadlier disease, smallpox, could be cooked up in a lab through the science of synthetic biology.

For Evans, the study proved that no virus could truly be considered extinct. “I said, ‘Yeah, well, there’s the writing on the wall for people concerned with eradicating smallpox,’?” he recalls. After polio’s revival, he was one of the first to warn the WHO about the potential resurrection of smallpox. But his warnings fell on deaf ears. Though Evans comes across as a measured scientist, his frustrations were mounting. He felt like Chicken Little and feared that action wouldn’t be taken until it was too late. “You know the way the world works,” he tells me. “It focuses on crises, right? It wasn’t a crisis.” At least not yet.

On a crisp falls day in September in Edmonton, Evans sits behind the desk of his cluttered office at the University of Alberta wearing a blue button-down shirt and khakis. He has wispy gray hair and small, round glasses. There’s a large microscope on his windowsill and shelves weighed down by thick books about viruses. Two stickers on his computer capture his natural skepticism—one reads “Really?” and the other “WTF?” (“I’m suspicious of reporters,” he tells me within the first few minutes of our meeting.)Buying samples of synthetic DNA is surprisingly easy. The trade is overseen by the International Gene Synthesis Consortium, an industry-led group that works with government agencies to screen orders and buyers. But such oversight can’t prevent someone from purchasing hazardous DNA samples on the black market. A cursory search online brings up dozens of sources for samples from China, Germany, and beyond. China “is kind of notorious for having unregulated pharmaceutical companies, right?” Evans says. Chinese biohackers could “be quite capable of running an unregulated DNA synthesis company.”

In June 2015, thanks in part to research by Evans and his colleagues into synthetic biology, public health advisers issued a report warning of smallpox’s potential return. “With the increasing availability of DNA fragments that can be synthesized from simple chemicals, it would be possible to re-create variola virus,” the report found, “and that could be done by a skilled laboratory technician or by undergraduate students working with viruses in a relatively simple laboratory.”

The following year, the US national intelligence director at the time, James Clapper, cited bioengineered pandemics as one of his agencies’ biggest concerns; the Worldwide Threat Assessment report added genome editing to its appraisal of current weapons of mass destruction and proliferation—alongside North Korea’s nukes, Syria’s chemical weapons, and Russia’s cruise missiles. As Bill Gates warned in 2017 at the Munich Security Conference, “the next epidemic could originate on the screen of a terrorist intent on using genetic engineering to create a synthetic version of the smallpox virus.”

If that wasn’t enough, a disturbing mystery emerged out of Russia. The Siberian Times reported in early 2017 that professor Ilya Drozdov, the 63-year-old microbiologist who ran the state research facility where Russia’s sole smallpox sample is held, vanished from his hometown of Saratov in southwestern Russia. No further information has been made public. A WHO spokeswoman said it was not in the organization’s “mandate to confirm or deny the existence of an investigation.”

For years, Evans had been urging his colleagues to upgrade their smallpox defenses. But it wasn’t until he met Seth Lederman that he found a like-minded scientist with the will and resources to do something about it. The CEO and cofounder of a New York company called Tonix Pharmaceuticals, Lederman was interested in funding research to develop biodefense technologies and drugs.Lederman shared Evans’ apprehension about the potential for a smallpox epidemic. “There’s an urgent need for a new vaccine,” he says. Smallpox vaccinations ended in 1978, meaning that the roughly 5 billion people worldwide under the age of 40 have not been inoculated.

Lederman, a former associate professor of medicine at Columbia University, was prepared to commit his company to coming up with a solution. He was convinced that the secret to a better vaccine could be found in horsepox, a lesser-known cousin of smallpox. Horsepox isn’t known to be harmful to humans, but its genetic makeup is closely related to smallpox. In theory, the closer one can get to a virus’s origins, the more effective the vaccine that can be derived.

Evans was intrigued. But the Centers for Disease Control maintains a single sample of horsepox, extracted from an infected horse in Mongolia in 1976, and Evans said it was unlikely he would be able to use the sample for commercial purposes. There was another option for getting their hands on some horsepox, Evans told Lederman: They could re-create the virus from scratch using synthetic DNA, similar to the way researchers had synthesized polio a decade earlier. The horsepox genome sequence had been published by researchers in 2006, offering up a road map for the virus’s revival.

When I ask Evans if he had any doubts about re-creating a cousin of smallpox, he hesitates. “You do think about that,” he says, “I don’t like controversy.” He had seen what had happened when polio was synthesized and had spoken with those researchers. Evans accepted that many would not agree with his choice. But he also believed, emphatically, that people already knew how to create such a virus–it was just that no one had achieved it yet. This was his chance, then, to prove that a synthetic version of a poxvirus was not only conceivable but a looming reality. “As long as people kept debating whether it was possible,” Evans notes, “nothing was ever going to be done about it.” It was time to put those questions to rest.

In 2016, with approval from the University of Alberta’s biosafety office, Evans purchased 10 DNA fragments from GeneArt, a DNA synthesis company based in Regensburg, Germany. The synthetic DNA, which arrived by FedEx as vaporized powder, was harmless. “If you wanted to, you could eat it,” Evans says, “My guess is that it would have a fizzy tang, like Pop Rocks.”

The arduous job of assembling the horsepox genome fell to Evans’ research associate, a young microbiologist named Ryan Noyce. Noyce wears his dark hair short and favors socks that read “Get shit done.” Like Evans, he has devoted his career to studying the nuances of viruses.

Building a virus from scratch is like assembling Lego blocks. A decade ago, Evans had improved on a process that uses a “helper virus”—another form of a poxvirus—to kick-start the replication of DNA. In this case, once the helper virus started growing inside a cell, Noyce would use pipettes to introduce a solution containing the horsepox DNA. “You’re laying down a piece here, a piece here,” Evans says, “mortaring them together.” The fragments affix to each other using an enzyme called DNA ligase, which acts as a kind of glue. If the DNA fragments are introduced into a cell in the right way, under just the right conditions, they’ll join together through a natural biological process and hopefully grow into a virus.

Noyce had to get every step of the process exactly right, from the sequence of the fragments to the timing of their insertion into the cell. If any part of the chain fails, the entire process falls apart. “It takes a tremendous amount of planning and timing and design work,” Evans explains.

Every weekday morning at 7:30, Noyce crossed the University of Alberta campus to reach Evans’ dimly lit lab. He’d don his long white lab coat, then spend 10 hours moving between his computer and a microscope, stitching DNA fragments together based on horsepox’s previously published genome sequence.

One day, after 18 months of meticulous work in the lab, Noyce looked through his microscope and saw it: a clearing of cells infected with the horsepox virus. He’d successfully re-created a poxvirus. But the rush of excitement was quickly tempered by the realization of what of was to come. Noyce believed that if they could help develop better vaccines, that “would outweigh the potential negatives” of reviving a pox. But given the history of the virus, Evans says, “We knew that there was going to be controversy.”

The trio published their findings in the scientific journal PLOS One in January 2018—and the blowback was swift and brutal. Critics accused Evans and Noyce of opening a Pandora’s box that could send humanity back to the dark ages of disease. The Washington Post’s editorial board wrote that “the study could give terrorists or rogue states a recipe to reconstitute the smallpox virus.” Tom Inglesby, director of the Center for Health Security at the Johns Hopkins Bloomberg School of Public Health, denounced the research on National Public Radio: “Anything that lowers the bar for creating smallpox in the world is a dangerous path.” Gregory Koblentz, director of the biodefense program at George Mason University, warned in the journal Health Security that the synthesis of horsepox “takes the world one step closer to the reemergence of smallpox as a threat to global health security.”

The PLOS One paper also triggered calls for tighter regulation. Elizabeth Cameron, vice president of global biological policy and programs for the Nuclear Threat Initiative, a nonprofit that works to prevent attacks by weapons of mass destruction, issued an ominous warning that “the capability to create and modify biological agents is outpacing governmental oversight and public debate.”

Evans still bristles over the criticism, which he feels missed the point. “One of the very irritating things on the reporting on our work was the idea that somehow it was so easy,” he says. “No it’s not. Ryan busted butt to make this.” For now, synthesizing a virus, as Evans and Noyce have, requires a high level of expertise. But while such a feat may be difficult to achieve, even Evans admits that “you make it more accessible to people simply by letting them know it can be done.”

The research paper seemed to spur the federal government to shore up its defenses against the threat that someone could create and unleash a synthetic virus. In June, the US National Academies of Sciences, Engineering, and Medicine released a 231-page study warning that even existing viruses like the common flu could be tweaked in a lab to evade immune responses and resist therapeutics (see sidebar). Several efforts are now underway to better assess potential threats before it’s too late.Darpa has launched an initiative called Safe Genes to protect service members from the accidental or intentional misuse of genome-editing technologies. The agency is trying to develop military tools to both counter and reverse the effects of synthetically created bioweapons. The Office of the Director of National Intelligence has announced its own initiative to find better methods for detecting and evaluating synthetic bioweapons. The system is designed to prevent rogue actors from getting their hands on the building blocks needed to make a dangerous virus.

To make better screening tools, the government enlisted Ginkgo Bioworks, a biotech startup founded by a group of MIT PhDs. Based in an old Army warehouse along Boston Harbor, Ginkgo’s main business is making custom microbes for use in everything from sustainable agriculture to perfumes. But with its government contracts, the biotech company helped build an algorithm that can recognize any genetic sequence on the “threat list” of potentially harmful viruses and bacteria. The software—a literal antivirus program—would be voluntarily installed on the servers of every company that synthesizes DNA. It’s like a wanted list for genetic riffraff. “If somebody tries to synthesize horsepox, alarm bells go off,” says Patrick Boyle, Ginkgo’s 34-year-old head of codebase. At that point, the DNA company can ask questions of the buyer and, if warranted, deny the sale.

Of course, even these automated checks can’t prevent determined buyers from obtaining samples through less scrupulous vendors on the black market. As with computer viruses, new strains appear from the ether before society is aware they exist. The same is true for trying to keep ahead of potentially lethal synthetic DNA.

The scientists at Ginkgo never expected to be policing the DNA trade. But as tools like Crispr allow for cheaper and easier creation of new biological organisms, technology is quickly surpassing enforcement measures. In 20 years, Boyle predicts, it will be possible to synthesize smallpox from home. He likens this moment to the early days of computing, when the concept of computer viruses was still new: “If I was working for the US government, I would have wanted to fund an effort in antivirus software in 1975,” he says. “That’s exactly the thinking we’re doing now,” but with synthetic biological viruses.

At this uncertain juncture, synthetic biology is entering new territory. It’s only a matter of time before others with the skill and wherewithal follow Evans and Noyce’s lead and replicate other viruses. Although not all viruses are deadly, scientists and bioengineers are in a race to predict and defend against new threats. There’s no telling when a manufactured disease will become a reality. If that occurs, the culprit might be a lab-trained terrorist or a basement biohacker, a bumbling grad student or a Russian microbiologist on the lam.

In the meantime, Evans and Noyce’s horsepox work is now the basis of a new smallpox vaccine called TNX-801. It’s being developed by Tonix, the pharmaceutical firm that funded their research. In a study published last year, the vaccine was shown to successfully protect mice from a relative of smallpox.

Today, Evans and Noyce are using what they learned in the horsepox effort to try to use DNA fragments to engineer oncolytic viruses, which target and destroy cancer cells. Past the lab where they work, down a quiet hallway and inside a windowless room, a beige freezer hums at –79 degrees Celsius. Inside, the synthetic horsepox samples remain under lock and key.