A virologist's revolutionary team approach to vaccine development
By Lina Zeldovich
Courtesy of Stony Brook University
Virologist Eckard Wimmer looked inside a refrigerator-size virus incubator that held several small transparent boxes that biologists call “well plates.” “This is where we grow our viruses,” explained Wimmer, a SUNY Distinguished Professor in the Department of Molecular Genetics and Microbiology at Stony Brook University’s School of Medicine. “These are live cultures.”
The plates, behind locked glass doors, contain animal cells, inside which dangerous viruses are growing and replicating, creating copies of themselves. Eventually, the multiplying viruses will destroy the cells and invade more cells, which is what they do when they infect humans. As the incubator, located in Stony Brook’s Life Sciences building, keeps the pathogens pampered at a comfortable 37 degrees Celsius, several stickers on the door detail exactly what’s germinating in there right now. Today, Wimmer’s laboratory is growing a poliovirus. Next week it may be viruses causing influenza or dengue fever.
Viruses are the most abundant organisms on the globe. Fortunately, only a tiny fraction of this huge number infects humans. But even this tiny fraction causes endless misery by infection that leads to disease. Scientists and medics have worked hard to control viruses throughout modern history, in some cases with great success (smallpox), in other cases with much frustration (AIDS).
Wimmer regularly grows viruses in his lab. Moreover, in the past, he had chemically synthesized viruses, essentially assembling them at the molecular level. “Some of my colleagues were really dismayed when I synthesized authentic polio, whose parent was the computer,” Wimmer said. “They were worried it may pave the way to bioterrorism.”
But Wimmer believed that in order to create an efficient vaccine against a virus, you first have to understand the virus’ genetic makeup. That belief led him, together with a small number of graduate students, postdoctoral fellows and faculty, to design a revolutionary new approach to vaccine development, and to the founding of a new company, Codagenix, which brought one of Wimmer’s novel vaccines to a clinical trial.
Vaccine medical successes
Vaccines are one of our most efficient weapons against infectious agents, said Stony Brook University President Samuel L. Stanley Jr., a physician and nationally prominent expert in infectious diseases. Until the past century, infectious diseases were the leading cause of death worldwide. “Even as recently as 1952, the poliovirus alone killed more than 3,000 people and left more than 21,000 paralyzed,” Stanley noted.
“During the 20th century, Americans’ life expectancy increased by more than 30 years,” he said, “and vaccinations were paramount for this medical success. Vaccines played a critical role in the eradication of smallpox; near elimination of polio; and control of measles, rubella, tetanus, diphtheria and various types of flu, among other diseases.”
“Today, vaccine development remains a pressing issue around the world. We may think that we have gotten the worst pathogens under control by decades of vaccinating against measles, mumps, diphtheria, tetanus and other infamous plagues, but the battle is far from over,” Stanley said. The World Health Organization estimated that in 2013 there were between 84,000 and 170,000 Yellow Fever cases, resulting in up to 60,000 deaths. It also has estimated that dengue fever infects 50 million to 100 million people annually, causing about 22,000 deaths, primarily among children.
“Even the much less spread viruses may cause highly dangerous maladies and death in very young children and in the elderly,” Stanley said. The Centers for Disease Control and Prevention estimates that the influenza virus has killed between 12,000 and 56,000 people in the United States annually since 2010. Over the past two decades, several novel viruses have emerged, including Severe Acute Respiratory Syndrome (SARS), swine flu and West Nile virus. And as recent outbreaks of Zika and Ebola showed, new pathogens can range from extremely damaging to very deadly.
“In the ’80s, scientists thought they were getting close to defeating infectious diseases, but we were underestimating nature,” Wimmer said. “New viruses will come up, old viruses will mutate, and we will always need new methods to control them.”
To keep ahead of the ever-evolving infectious diseases, mankind needs to be able to develop efficient vaccines quickly. Traditionally, however, vaccine development has been slow. Historically, scientists would take a human virus and adapt it to live and multiply inside mouse or primate cells. In the process, the virus would weaken its ability to afflict humans — become attenuated, as scientists call it. In this attenuated form, it could be used for vaccine development. But adapting viruses to grow in new cell types takes a long time and sometimes fails. The viruses may die or lose their ability to infect humans entirely, which doesn’t work for making vaccines. “You can spend three or four years adapting a virus, and at the end it doesn’t work,” Wimmer said. “If we want to beat infectious diseases, we need to move faster.”
Wimmer was originally trained as a chemist. He became interested in viruses in the 1960s, partly because they straddle the line between chemicals and living creatures. Outside a living host, viruses such as poliovirus are like tiny balls harboring a string of genetic material, which can’t replicate on their own. But inside cells, viruses come alive and start procreating, eventually destroying that cell. Attenuated viruses replicate poorly and slowly, giving the immune system enough time to kill them. So if we understood exactly what genetic kinks weaken a virus’ ability to sicken humans, we could then quickly genetically modify that virus and use the “wimpy” strain to make vaccines. This thinking led Wimmer to his revolutionary new approach in vaccine development.
Wimmer came to study viruses at Stony Brook University in 1974. Only seven years later, long before genome sequencing became ubiquitous, he had revealed the genome structure of the poliovirus. In the early 2000s, he managed to assemble the poliovirus genome by stringing together thousands of nucleotides — the building blocks of life. Then he “booted” this synthesized polio fragment to life inside cells, and made headlines all over the world, sending off waves of bioterrorism concerns through the scientific universe and drawing harsh criticism from some of his colleagues at other institutions.
Wimmer persevered, and in 2006, he synthesized a different polio version by inserting some rare nucleotides into the genome. To his surprise, he noticed that this insertion weakened the polio’s ability to replicate. It was as if some of these new genetic fragments gummed up the virus’ reproductive gears. After peering into the polio’s genome long enough, Wimmer zeroed in on what caused the weakness. The answer, it turned out, was hiding in a specific arrangement of trinucleotides, called the codons.
Codon love and hate pairs
A codon is a triplet of nucleotides. A string of codons harbors the most important information of the genome of all living things. Following reports in the literature, Wimmer noticed that certain codon pairs were present more often in the polio’s genome than other codon pairs. It looked as if some codons liked to be hooked up side by side while others avoided being together. Wimmer informally called the former “love pairs” and the latter “hate pairs.” He noticed that recoding (re-synthesizing) a viral genome with hate pairs seemed to weaken the virus. This was an important finding. If he managed to come up with the right combination of love and hate pairs, Wimmer could create a live virus that would elicit an immune response in humans, while still being weak enough to not cause any harm. “We called it a de-optimized virus,” Wimmer said of his team’s approach.
Together with his doctoral student John Robert Coleman and former student and then Stony Brook postdoctoral assistant Steffen Mueller, Wimmer set off to create such a de-optimized virus. But even relatively short viral genomes still offer millions of genetic variations that would be impossible to design manually. The task required a computational approach, so in 2004, the team partnered with Steven Skiena in the Department of Computer Science, College of Engineering and Applied Sciences, whose training was in computer algorithms design.
“It was a productive collaboration, because when one side delivers something that the other can’t do, it leads to good results,” Wimmer said of the effort. “I was just an old virologist with a bunch of ideas, and Steven was a pure computer person; virology was new to him.”
Translated biological concepts through computerization
To facilitate the handshake between two scientific disciplines, the team recruited another Stony Brook scientist, microbiologist and geneticist Bruce Futcher of the Department of Molecular Genetics and Microbiology, who had dabbled in both fields and could help turn biological concepts into algorithm development. “Biologists don’t speak computer science and computer scientists don’t speak biology,” said Futcher. “So in the beginning I was almost a translator.”
At first glance, the problem was tremendously complex. The team needed to design the weakest possible virus that would elicit the strongest immune response. “Depending on how long your virus is, the number of possible virus designs we could make is a huge number — more than there are atoms in the universe,” said Skiena.
But once Skiena understood the biological underpinnings of what had to be done, the task started to look doable and somewhat familiar. “When you use GPS, Google can find the best possible route in the many routes that exist,” Skiena explained. “This is a similar phenomenon.”
In 2008, the first computational virologist team, together with the knowledge of virus synthesis, was able to fully test their new approach. Skiena created a clever algorithm to design a de-optimized virus. The algorithm generated a string of polio’s genetic code with one-third of hate pairs in it. That assemblage was expected to weaken the pathogen. When Wimmer and his team assembled the modified virus, booted it to life inside cells, and tested its strength, the result looked good — the virus was alive but couldn’t procreate. “The virus was so weak it couldn’t make enough of its own particles to survive in a cell,” Wimmer said.
Feeding the program with genetic specs
Once perfected, the process worked significantly faster than the existing methods of vaccine development. “Our algorithm runs in minutes to hours,” said Skiena, adding that it can de-optimize any other viruses the same way — whether Ebola or swine flu. “More complex viruses with longer genomes might take longer than simpler ones, but it’s still minutes to hours.”
Plus, the algorithm’s code did not have to be altered to de-optimize a new virus — the same program just had to be fed the new virus’ genetic specs. “It would not really require reprogramming so much as setting it up with the genome sequence of the desired pathogen we seek a vaccine for,” Skiena explained. Synthesizing the de-optimized virus took several weeks and testing it took several months, but it was still significantly faster than any of the existing methods.
After publishing their de-optimized virus findings in 2008, the team was excited and hoped to attract immediate interest from the pharmaceutical industry, but to their surprise, that’s not what happened.
“When we published the papers, we expected the pharmaceutical companies to come to us, but none did,” Wimmer said. “We received a few phone calls from their reps, but when they heard that no clinical trials were even pending and we had no money for clinical trials, they would lose interest.”
For the next three years, the technology essentially sat on the shelf unused, until Wimmer and his former students Coleman and Mueller decided that the only way to bring the new technology to people was to form their own enterprise.
A company emerges
In 2011, the year Wimmer celebrated his 75th birthday, Codagenix was founded. With “coda” stemming from coding and “genix” from gene, the name was meant to represent the concept of re-coding a genome.
The next step was funding the vaccine development efforts. Unlike other technologies that don’t directly affect human health — mobile technology, for example — medical and biological advances are significantly more complicated and expensive to bring to market and generate profit.
“In mobile technology, if you create a $2 app and a million people download it, you’ve made $2 million,” said Mueller, now president and chief science officer of Codagenix. But to get a medicine approved by the Food and Drug Administration, you must first test it in animals, and then follow up with multiple phases of robust human trials — to prove the substance is effective and has no side effects.
It’s a long road that “takes years and costs millions of dollars,” added Coleman, now the company’s chief operating officer.
To assure Codagenix had funds necessary to succeed, the founders sought a combination of public and private funding options. The company received its initial funding from the National Institutes of Health (NIH) through a Small Business Innovation Research grant program.
“Ultimately, vaccine development benefits public health, so as a publicly funded entity, NIH funds vaccine-development initiatives,” Coleman said, adding that the U.S. Department of Agriculture (USDA), which was interested in animal vaccinations, also contributed to the effort. “The company raised over $2 million in direct funding from NIH and USDA.”
Codagenix also received matching funding from Stony Brook’s Center for Biotechnology through a program that helps technologies developed at the school to come to market and commercialize them more efficiently. “We were lucky to raise these initial funds for Codagenix,” said Mueller, “so we could set up our own lab, pay rent and hire our first employee.”
That public funding supported Codagenix until it attracted its first private investor in 2012 — the venture capital firm Topspin Partners, which invested $4.25 million in the vaccine development.
With that money, Codagenix was able to bring its influenza vaccine to humans in Australia, at clinical trials that began in March 2017. “Right now, we’re doing a human trial only with influenza, but we have other vaccines in the pipeline, hopefully starting soon,” said Coleman. “We have already tested Zika and dengue in animal trials, so we’re now in the preclinical stage with them.”
Stanley commended Wimmer’s contribution to public health. “From his unraveling of the poliovirus to his more recent work in the field of synthetic biology, Dr. Wimmer has had a tremendous impact on the advancement of infectious disease research,” he said.
Because Wimmer’s method can help create vaccines so fast, Codagenix’s technology may enable humankind to quickly and efficiently circumvent unexpected viral pandemics — like the 2014 Ebola outbreak. Wimmer, who spent his professional career hoping to see this happen, feels that his lifelong work is finally about to bear fruit. If all goes as planned, within a few years his computer-generated vaccines may become the new norm.
“Even if I don’t get to see Codagenix’s vaccines in clinics — because I am 80 years old — I do hope that they will have a long-lasting effect on humanity,” he said.
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