Worldwide, researchers are racing to develop a vaccine against SARS-CoV-2, the virus that causes COVID-19, which has brought the world to a social and economic standstill. There are 42 vaccine candidates currently being clinically evaluated,1 with more in preclinical testing,2 including vaccines based on inactivated virus, protein subunits, mRNA, plasmid DNA and non-replicating virus vector, which are using a diverse range of delivery systems.1,2 Many different parties within the scientific community are working to develop a vaccine – from scientists who have dedicated their careers to the study of coronaviruses, to specialists in vaccine design from both academia and industry, to those in other disciplines who have redirected their efforts to combat this global health threat. In this article, we meet some of the teams who are at the forefront of this endeavor.
In the McLellan Lab at the University of Texas at Austin, researchers have been quietly working on coronaviruses since the earlier severe acute respiratory syndrome (SARS and Middle East respiratory syndrome (MERS epidemics that occurred in 2003 and 2012. Now, the outputs of that work are forming the basis of at least three COVID-19 vaccine candidates in clinical trials. Their groundwork enabled the fastest development of a vaccine in history – just 66 days from when the virus’ genome was first published.
The team’s research focuses on the structure of the glycoprotein spike that COVID-19 uses to enter human cells – the target of many of the vaccines in development. The spike exists in a pre-fusion and post-fusion conformation, and a successful vaccine needs to target the pre-fusion form before it becomes internalized into cells.
“People have been working on these proteins for years,” explained Daniel Wrapp, graduate student in McLellan’s lab. “Until the advent of high-resolution cryo-electron microscopy (cryo-EM), you could really only look at individual domains, and it didn’t tell us how these proteins functioned as machines in their true biological context on the surface of a virus.”
Armed with the precision structure of the full spike proteins from SARS-CoV-1 (responsible for SARS) and MERS-CoV (responsible for MERS), a postdoc in the lab called Dr Nianshuang Wang tested mutations he’d previously designed (using another virus called HKU1 as a template) on the spikes of the viruses, and found he could successfully “staple” the SARS and MERS coronavirus spikes into their pre-fusion forms.
“As soon as the sequence of the COVID-19 virus was released on January 14, I got to work translating those stabilizing mutations (called S2P) into the new spike sequence,” said Wrapp. “Because we had worked on similar spike proteins in the past we were able to go from protein purification to cryo-EM structure in a day.”
The results were published in Science,3 and the stabilized antigen is now being trialed in various vaccine delivery constructs: from mRNA and DNA vaccines that make the body manufacture the stabilized spike protein itself, to others that deliver the synthesized antigen ready-made. Now, the team has developed a more potent antigen.4 “One thing we noticed early on is that even though the two key mutations were capable of stabilizing the SARS-CoV-2 spike, we didn’t really see the dramatically increased protein expression we saw with SARS-CoV-1 and MERS-CoV,” said Wrapp. “So, we engineered some additional stabilizing mutations more specific to the SARS-CoV-2 spike protein to produce an antigen called HexaPro. This gave a tenfold boost in expression and enhanced stability compared to the S2P antigen.” There is already interest in using the new antigen as a vaccine candidate and the team is also using it to develop neutralizing antibodies as potential therapeutics for people who have contracted SARS-CoV-2. “We’ve been researching these proteins for years on a daily basis,” said Wrapp, “but now there’s a real heightened sense of urgency. We all feel that if we are able to contribute to a vaccine or treatment, then now is the time to act and help in any way we can.”
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As COVID-19 cases began to spiral, labs around the world had to shut down. But many research groups saw an opportunity to pivot their research towards beating the virus. Dr Mark Yarmarkovich was one of them. His team’s research at the Children’s Hospital of Philadelphia (CHOP) focuses on using computational tools to discover tumor-specific molecules in cancer cells that are typically invisible to the immune system.5
“We’ve built a set of tools that have been very useful in identifying tumor-specific targets, and we saw an opportunity to redeploy these for identifying targets in coronavirus,” said Yarmarkovich. “Most of the current viruses target the spike protein but we wanted to look a little more broadly at highly conserved regions of the virus involved in its replicative lifecycle. These are genes that really don’t tolerate any mutations from one coronavirus to another, so we expect that future coronavirus outbreaks would also have these genes intact.”
The team has also developed tools that identify targets with two other key parameters: ones that will stimulate both arms of the immune system (activating antibody and T-cell responses) and ones that had limited cross-reactivity with human healthy tissue.
“Every person has a different set of six human leukocyte antigen (HLA) genes that dictate which parts of the virus (or tumor) are visible to the immune system,” explained Yarmarkovich, “and this complicates the ability to create a vaccine that induces a T-cell response across a broad swathe of the population. One of our algorithms basically incorporates all of the most common HLA alleles that cover most of the human population, and interrogates different regions of a viral genome to see which would be most visible to the immune system in as many people as possible.”
The final computational tool assesses the similarity of viral genes to human genes that might be presented by HLA: “We adapted a tool we developed for cancer research to identify regions of the virus that are highly dissimilar to human genes, and we found that some regions of the COVID-19 genome are highly similar to human genes presented by HLA.” This is important for two reasons, said Yarmarkovich. “First, the danger is that if you induce an immune response against those regions, it could cause an autoimmune response in other tissues. Second, T cells are “educated” in the thymus to be non-reactive to self, so there is a higher likelihood of inducing an immune response to regions of the virus that are highly dissimilar to self.”
The tools have been used to identify portions of the virus for inclusion in vaccine constructs that are optimized for maximum immune presentation across the human population and drive a memory immune response.6 “With vaccines comprised of 12–16 of these 33-amino acid regions, we’re able to cover what’s predicted to be over 99% of the population in presentation for killer T cells and about 90% of the population for helper T cells,” said Yarmarkowitz. “We recently got our first set of data from mouse immunization which showed a robust induction of T cells and neutralizing antibodies. Now we plan to expand this to strains that have other HLA genes. Ultimately, we’re building a dataset that we hope will enable an investigational new drug for human clinical trials.”
While others are racing to the finish line to develop the first COVID-19 vaccine, Dr Jay Evans and his team are already working on the next generation. Evans’ team has more than 20 years’ experience in developing vaccines, having moved from GlaxoSmithKline in 2016 to establish the Center for Translational Medicine at the University of Montana. They focus on making existing vaccines better – specializing in adjuvants and delivery systems that lead to more durable responses and better population coverage.
“We’re under the assumption that, like most viruses, there’ll be opportunities either because immunity wanes or you need greater breadth of protection that adjuvants can provide,” explained Evans. “So, we’re taking the SARS-CoV-2 antigens – both the spike and the receptor-binding domain – and we’re testing them with different adjuvants and vaccine delivery systems.”
The team is using tried-and-tested systems they have been working with since the 1980s. “We have libraries of adjuvants and unique delivery systems that drive different immune responses that are preset and ready to go,” said Evans, “so we moved immediately into mouse models of vaccination, measuring antibody and T-cell responses to find the best combinations.
The leading combinations are now being evaluated further in challenge models in Dr Florian Kramer’s lab at Icahn School of Medicine at Mount Sinai in New York, which also provided the SARS-CoV-2 antigens being tested. “The challenge models will evaluate vaccine efficacy and safety in animal models following exposure to SARS-CoV-2,” explained Evans.
Once the data from the challenge models is in hand, the team will share this with the National Institutes of Health, which is funding their research, to make decisions on which vaccine to take further into clinical trials. “By early next year, we’ll get an initial read on how effective the current vaccines in Phase 3 trials are, and we’ll know what needs to be improved,” said Evans. “Some of our adjuvants are being tested in collaboration with Dr Ofer Levy at Boston Children’s Hospital who focuses on vaccines for the “edges of life” – immunocompromised people who are very young or very old.” Evans plans to tailor their adjuvant approach to where the need exists (the very young and elderly). “Hopefully, the first-generation vaccine works exceptionally well and gives long-lasting lifelong immunity,” he said, “but in case that doesn’t happen, we’re going to be ready.”
1. Draft landscape of COVID-19 candidate vaccines. World Health Organization. https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines Published 2020
2. Jeyanathan M, Afkhami S, Smaill F, et al. Immunological considerations for COVID-19 vaccine strategies. Nat Rev Immunol. 2020;20:615–632. doi:10.1038/s41577-020-00434-6
3. Wrapp D, Wang N, Corbett KS, et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 2020;367:1260–1263. doi:10.1126/science.abb2507pmid:32075877
4. Hsieh CL, Goldsmith JA, Schaub JM, et al. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 2020;369:1501–1505. doi:10.1126/science.abd0826
5. Yarmarkovich M, Farrel A, Sison A, et al. Immunogenicity and immune silence in human cancer. Front Immunol. 2020;11:69 doi:10.3389/fimmu.2020.00069
6. Yarmarkovich M, Warrington JM, Farrel A, et al. Identification of SARS-CoV-2 vaccine epitopes predicted to induce long-term population-scale immunity. Cell Reports Medicine 2020;1(3):100036. doi:10.1016/j.xcrm.2020.100036
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