AWARDEES: Jason McLellan and Daniel Wrapp

FEDERAL FUNDING AGENCIES: National Institutes of Health, Department of Energy

A Llama Named Winter: An Unlikely Partner in the Fight Against COVID-19

Winter the llama currently spends her days grazing in peaceful retirement on a research farm in Ghent, Belgium, with about 130 of her llama and alpaca friends. But although you wouldn’t know it to look at her, this cocoa-colored, long-legged camelid is already playing a pivotal role in the hunt for effective treatments for COVID-19.

In partnership with researchers at Ghent University, Dr. Jason McLellan, a structural virologist at the University of Texas at Austin, and Daniel Wrapp, a doctoral student in McLellan’s lab, linked a special antibody produced by Winter to a human antibody to create a new antibody that binds to a protein on the coronavirus that causes COVID-19, thus inhibiting the virus from infecting human cells.

The Spike of the Virus

To fully grasp Winter’s unlikely contribution to the battle against COVID-19, it helps to understand the way coronaviruses spread throughout the body.

Scientists have identified hundreds of unique coronaviruses, although most of them circulate in non-human mammals and birds. Seven coronaviruses are known to cause sickness in humans; of these, four cause only mild-to-moderate illness, including some variations of the common cold. The other three have been the cause of more serious diseases: SARS, MERS, and COVID-19.

Coronaviruses get their name from a group of specialized proteins, called spike proteins, which dot the surface of each viral envelope and give the virus the appearance of a crown-like ring, similar to a solar corona. These proteins are what allow coronaviruses to break into human cells, after which they begin to use the machinery of those cells to start replicating. If this break-in is interrupted, the virus can’t infect the host.

Here’s Where the Llama Comes In

Scientists in the 1990s discovered something special about the antibodies produced by camelids, the family of animals that includes llamas, alpacas, and camels, among others. While humans only make one kind of antibody, made up of heavy and light protein chains arranged in a Y shape, camelids produce two. One of these is very similar to a human antibody. The other, called a single-domain antibody, VHH, or nanobody, does not have any light-chain proteins. This makes it much smaller, which is a boon to researchers.

One of the ways an antibody can disrupt a coronavirus is by binding to key areas on the spike protein. Because they are smaller, the nanobodies produced by camelids can sneak into nooks and crannies on the spike protein while larger antibodies are blocked. These nanobodies also have the advantage of being stable and easy to manipulate. They can be linked with other antibodies, including human antibodies, to increase their effectiveness. Furthermore, nanobodies can be nebulized and used in an inhaler, which is good news for a respiratory illness such as COVID-19.

Camelids are not the only animals that produce nanobodies: sharks produce them, as well, although biologists suspect that those nanobodies evolved through different processes.

Since the discovery of nanobodies, scientists have worked with camelids (and even some sharks) to develop promising therapies to treat various diseases. McLellan and Wrapp are among those scientists.

Building Relationships

A first-generation college student from a suburb outside of Detroit, McLellan fell in love with structural biology in college before training in the field in graduate school. “In structural biology, we’re trying to determine the first structures of proteins and molecules,” he says. “We’re answering basic science questions about molecules, their structure, their function, but then also trying to take some shots on goal and actually generate some products—some vaccines, some antibodies—that could have an impact on human health.”

As a post-doc, he joined a lab run by Dr. Peter Kwong, who was working on the possibility of a structure-based vaccine for HIV. A quirk of fate led to another fruitful partnership. According to McLellan, there was no room for him on Dr. Kwong’s lab on the fourth floor, so he moved to the second floor. It was there that he met Dr. Barney Graham—another 2020 Golden Goose honoree—who would become a close friend and collaborator.

“He’s a really generous, warm person,” McLellan says about Graham. “He’s just one of the really good people in science.”

McLellan recalls describing his frustrations with structure-based vaccine design for HIV to Graham, who suggested that he try out his ideas on respiratory syncytial virus (RSV), a respiratory illness that can be serious in infants and older adults. McLellan’s work on the structure of the RSV F protein (a very similar protein to coronavirus spikes) caught the attention of a group of researchers in Ghent led by Dr. Xavier Saelens. They reached out about a potential collaboration. Their goal? Identifying and isolating camelid nanobodies that could neutralize RSV.

Along with Graham, McLellan and Saelens signed an agreement to work together on RSV in July 2013. Over the next couple years, the labs traded material. McLellan’s lab sent over stabilized RSV F proteins, which Saelens’ group then used to immunize a llama from their herd (Winter wasn’t born yet). When that llama produced antibodies, Saelens’ lab sent those back to McLellan’s group, where a first-year graduate student named Daniel Wrapp helped to map their structures.

“That was actually the first crystal structure I ever solved,” says Wrapp, “that first little camelid nanobody that neutralized RSV.”

Prior to this first big solve, back when he was still a senior in college, Wrapp started reading the work on RSV that McLellan was publishing. “This is the coolest thing in the world,” he recalls thinking. “He’s found a way to look at these proteins on an atomic level. He’s figured out how to manipulate them, and make them function—or not function—exactly the way that he wants, and he’s figured out how to manipulate that and leverage it to elicit a particular immune response that will be effective at neutralizing a virus. And I thought that that was incredible.” Wrapp applied to Dartmouth, where McLellan was at the time, specifically because he wanted to join his lab.

It was a charmed partnership from the start. During Wrapp’s first year of graduate school, the lab received a National Institutes of Health R01 grant to look at the structure and function of coronaviruses. He remembers the date they received the good news with absolute clarity: it was his birthday.

Though the NIH funding was critical, the team’s investigation of protein structures, including those related to SARS-CoV-2, also received a critical assist from the Department of Energy’s Argonne National Laboratory. “For structural determination, we hit the protein crystals with x-rays,” McLellan explains. Argonne allocate time to the team to use its synchrotron facilities for this purpose.

Laying the Groundwork

After the success of their work on RSV, McLellan and Graham decided to apply what they had learned about structure-based vaccine design to coronaviruses. It was a natural leap: the RSV F protein McLellan and his team had mapped out belongs to the same family of proteins as the coronavirus spike. And again, they reached out to Saelens’ lab—and herd—in Ghent.

Winter was just nine months old when she was chosen at random to participate in the coronavirus study. This was in 2016. Just as they had with another llama and RSV, scientists at Winter’s facility in Ghent injected her with stabilized spike proteins from SARS-CoV-1 and MERS-CoV. Inspired by work in the influenza field, their hope was to isolate a single antibody that could neutralize all coronaviruses.

“We wanted to get the one antibody or nanobody to rule them all,” McLellan says. That didn’t work. But the team was able to isolate some potent MERS-specific and SARS-specific nanobodies. They were writing up their findings when everything started to change in January 2020.

The Call

McLellan was on a snowboarding trip with his family in Park City, UT, when he got the call that changed everything. It was Dr. Graham, calling to tell him that he had been in contact with the CDC, and that it looked like the new pathogen that was making headlines was a coronavirus. McLellan recalled Graham wanting to know if he wanted to rush to make a vaccine together. “I said, ‘sure, let’s do it. This is what we’ve been preparing for,’” McLellan says. “I immediately messaged Daniel, told him, ‘Be ready. We’re going all-in as soon as we get the sequence.’”

Because of their past work understanding and manipulating the spike proteins of SARS-CoV and MERS-CoV, McLellan’s team, which included colleague Nianshuang Wang as well as Wrapp, was able to rapidly map the structure of the SARS-CoV-2 spike protein and develop a stabilized version of it that could be used as a COVID-19 vaccine antigen. Antigens, which are molecules or molecular structures that trigger a hoped-for immune response, are crucial elements of vaccine development. Shortly after that, the team filed a joint patent application on their stabilized spike protein along with fellow 2020 Golden Goose Award winners Graham and Kizzmekia Corbett. (For more on Graham and Corbett, read A Spike in Momentum.) Genetic information from this stabilized protein has been incorporated in the vaccines currently under development at Moderna, Pfizer/BioMTech, Novavax, and Johnson & Johnson.

At the same time, Wrapp and McLellan still had Winter’s MERS- and SARS-reactive nanobodies and decided to put together an experiment to see if either of them bound to SARS-CoV-2. They discovered that one of them, the SARS-CoV-1 nanobody, did. They then linked this to a fragment from a human antibody to produce an antibody that tightly binds to a key area of the SARS-CoV-2 spike protein, effectively blocking it from infecting human cells.

Wrapp recalls that the experiment “was kind of almost an afterthought, which sounds ridiculous now, because it ended up being so fruitful.” The hope is that Winter’s nanobodies might be used to develop prophylactic treatments. Unlike a vaccine, which must be administered before a person is infected to provide protection, antibody therapies can be used to treat someone who is already sick. The team published their findings earlier this year, and a company has formed with the hopes of shepherding the research through the testing process to a viable product. In the meantime, Wrapp plans to finish his Ph.D. Winter will continue to enjoy her retirement.

Reflecting on the discovery, McLellan stressed the importance of funding basic research. When they first immunized Winter, he pointed out, SARS no longer in the human population, and MERS was only popping up sporadically. Their funding “wasn’t in response to a pandemic: it was just good science on an important class of pathogens, and I think it’s really paid off.”

By Haylie Swenson