Across the life sciences, researchers have contributed significantly to the response to COVID-19 — elucidating the pathogen, tracking the progression and consequences of infection, and uncovering many of the biological mechanisms associated with patients who display symptoms for months or longer.
While the infectious disease modality and epidemiology research is characteristic of any outbreak, one of the ways the response to this pandemic has been different is through its incorporation of synthetic biology. Advances in this field over the past two decades to make a meaningful difference for the battle against COVID-19.
Innovations in DNA and RNA synthesis technologies were particularly important. As news of the outbreak in Wuhan, China, spread quickly in January 2020, scientists around the world were eager to participate in research efforts focused on the emerging pathogen. Those efforts were greatly aided by the availability of a synthetic infectious clone of the virus with the entire genome assembled into a vector. The synthetic genome of the virus served as a stable source of the viral particles to scientists, instead of having to rely on clinical samples.
In addition to synthetic genomes that were produced to represent not just the original SARS-CoV-2 strain but also many of the variants that arose, gene synthesis and automation technologies were important for production of the mRNA-based vaccines that have made such a huge difference in the pandemic. These were the first mRNA-based vaccines authorized for widespread use in humans; their success has highlighted the utility of treatments based on mRNA and therefore the need for high-quality mRNA synthesis tools to support their rapid development cycles.
The COVID-19 pandemic is not the first outbreak for which advanced gene synthesis has been deployed. Back in 2013, an outbreak of the avian influenza virus H7N9 in China appeared to have the makings of an epidemic. Researchers immediately began to work on the problem. In the U.S., synthetic biology scientists who had already teamed up with Novartis on a project designed to speed up the development of vaccines shifted gears to focus on the H7N9 virus.
For this kind of work, they needed the genome sequence of the virus. Once it was published, they used cutting-edge techniques to synthesize the genes encoding the viral coat proteins. These gene constructs, synthesized in a manual process, became the foundation for a candidate vaccine. The initial synthesis work and subsequent confirmation of coat protein expression was completed in about a week — faster than samples of the live virus could be collected in China, shipped across the ocean, and delivered to the CDC.
That virus did not turn into a major epidemic, but lessons from it informed the synthetic biology response to the COVID-19 pandemic. At the University of Washington, for instance, scientists used the SARS-CoV-2 genome sequence and DNA synthesis technology to produce sequence-verified viral gene fragments. Those were turned into five vaccine candidates that progressed to mouse testing in less than two weeks from the start of the project.
In addition to genomic fragments, synthetic biology innovations paved the way for construction of full-length SARS-CoV-2 synthetic genomes. At a time when clinical samples of the virus were scarce and difficult to acquire, having access to a synthetic genome allowed anyone in the research community to study the virus and contribute new discoveries quickly.
Synthetic genomes accurately represent the original virus and can be used as a virtually unlimited source of the virus without having to keep replicating the clinical samples. Without synthetic genomes, scientists’ understanding of the virus responsible for COVID-19 and identifying the ways to stop the virus may not have advanced so rapidly during the pandemic.
As various countries entered their first lockdowns in the spring of 2020, a full-length synthetic genome of the SARS-CoV-2 virus was available to the research community (ref?). In the months that followed, a dozen more genomes were added to represent emerging variants. These genomes could be used for discovery and development programs aimed at creating new vaccines, small-molecule therapies and monoclonal antibody treatments. Researchers could also use the genomes as diagnostic controls for specific variants without the need for additional processing steps, making them a faster alternative to standard controls and enabling validation and verification of assays without the need for clinical virus samples.
Without a doubt, the most novel aspect of the response to the COVID-19 pandemic has come from the development of mRNA-based vaccines. While mRNA-based vaccines have been used in clinical studies before now, this modality has never been available for an emerging infectious disease epidemic that turned into a global pandemic.
While it seemed as though these vaccines were created in the nick of time, in reality, mRNA-based vaccines have been in development more than two decades. Much of the framework that was used for the COVID-19 vaccines came from efforts to create a coronavirus vaccine modeled on the original SARS virus. When SARS-CoV-2 emerged, scientists were able to take the vaccine design, specifically, the target for the new vaccine, from the older virus and quickly adapt it to the new one. It was a truly remarkable feat that proved the concept and saved potentially millions of lives in the process.
This work would not have been possible without years of research devoted to making mRNA molecules — notoriously unstable and easily degraded — robust enough to serve as the basis for a vaccine or therapy. Now that mRNA has been clearly demonstrated as an effective foundation, mRNA synthesis will be an essential capability for any pharmaceutical or biotech researcher involved in discovering and developing other mRNA-based treatment and prophylactic options. Indeed, mRNA-based vaccine candidates for other infectious diseases and cancer are already the subject of preclinical and clinical studies.
Currently, custom mRNA constructs can be ordered from conventional gene synthesis vendors. However, with demand for mRNA soaring based on the success of the COVID-19 vaccines, drug developers may need a faster, higher-quality, in-house solution to avoid long delays in the progression of new candidates along the discovery pipeline.
For example, while studying a vaccine or a therapeutic candidate, studies require a reliable source of the different versions of the mRNA of interest, particularly as scientists test several variations of the target mRNA molecule. Each variation/modification may be tested with in vitro assays or cell-based assays to check for the desired response. After those assays are run, scientists typically iterate, fine-tuning the mRNA and testing it again and again until they know exactly which mRNA variation works best. Because each cycle of the process depends on the results of the previous cycle, any delay in synthesizing mRNA would be compounded and significantly lengthen the development timeline.
The Need for Automation
Not long ago, the practice of synthetic biology consisted entirely of laborious, manual processes. But as the field matures — and particularly as it continues to show how much value it has to offer to biological research and drug development through the COVID-19 pandemic — it is clear that automation must replace these old techniques for more reliable, robust, and high-throughput use.
The same scientists who originally contributed genomic constructs for the H7N9 virus in 2013 worked closely with engineers to automate their novel synthesis approaches. Today, researchers have access to a benchtop instrument that performs DNA synthesis for libraries, fragments, and clones and mRNA synthesis in a completely automated fashion — including assembly, cloning, amplification, and synthesis of as many as 32 complex constructs — in a simple overnight run. This BioXp system, which has been deployed in hundreds of labs around the world, has enabled many of the synthetic biology contributions in the fight against COVID-19, including mRNA vaccine development.
The mRNA synthesis capability is a recent addition to that automated platform (press release ref?). Now, scientists can design and build mRNA in their own labs. This significantly reduces turnaround time compared to ordering from vendors — from weeks or months to just hours or days — to accelerate the iterative process required for developing mRNA-based treatments.
Continued innovation will be needed, though. Automated mRNA synthesis, for instance, can be improved through increased mRNA length, fidelity, and higher yields. On the DNA front, the synthesis process could be made better by increasing the number of constructs created in a single run or by extending the maximum construct length and complexity to reduce the number of cycles needed to build a full-length genome.
Clearly, synthetic biology has emerged from an artisanal academic pursuit to a robust, semi-industrialized approach. Never have the biomedical opportunities afforded by synthetic biology been more obvious than during the COVID-19 pandemic: from expanding research to enabling faster vaccine, therapeutic, and diagnostic development, this field has made enormous contributions during a global crisis.
Automation of the many steps involved in synthetic biology — including DNA and RNA synthesis — has been essential to the maturation of this important discipline. Enhancing the current automation platforms and continuing to automate steps that remain manual will be important for building on the momentum of synthetic biology and expanding its benefits to areas beyond infectious disease such as cancer, metabolic and genetic disorders.
Krishna Kannan is the Director of R&D at Codex DNA, where he helped construct the first full-length synthetic genome for the SARS-CoV-2 virus.