Images of antibodies as they neutralize the COVID-19 virus

When the COVID 19 pandemic spread across the globe in the first half of 2020, researchers around the world worked around the clock to understand and combat it.

Caltech postdoctoral researcher Christopher Barnes is one of these researchers. In the laboratory of Pamela Björkman, the David Baltimore Professor of Biology and Biological Engineering, Barnes usually studies how the human body produces immune cells and specialized proteins called antibodies that can fight the countless different HIV strains. In recent months, however, he has led the laboratory's COVID-19 research team and refocused the techniques used to study HIV on the novel coronavirus, coronavirus 2 (SARS-CoV-2) of severe acute respiratory syndrome.

Now, Barnes and his team have captured the very first images of antibodies purified from the blood plasma of people recovering from COVID-19 that attach to a key protein of the SARS-CoV-2 virus. In addition, the visualisation of an exemplary antibody that interacts with this protein has enabled the team to identify sites on the surface of the virus that are particularly susceptible to attacks by the immune system. An article describing this research was published in the journal Cell and is now available online.

A detailed portrait of antibodies and virus

The human body can produce countless types of antibodies, specialized proteins that are directed against viruses or other pathogens and neutralize them. Just as a football player can use numerous tactics to defend against an opponent, an antibody can try to block a virus in many different ways. However, some are more effective than others. When an antibody effectively renders a virus incapable of infecting cells, this is called "neutralizing".

Barnes and Björkman look for variations of antibodies that can be "largely neutralizing". In other words, they are looking for antibodies that are effective against many variations of one type of virus - or, in the case of SARS-CoV-2, which does not vary as much as HIV, very strong neutralizing antibodies.

The team worked with long-time collaborators at Rockefeller University in New York City, which was a major site of the COVID 19 outbreak in the United States. Michel Nussenzweig's laboratory, headed by researcher Davide Robbiani, took blood samples from people who had recovered from COVID-19. After receiving these plasmas, Barnes and his colleagues tried to isolate the unique mixture of antibodies in the samples from each person to determine which antibodies were best suited to fight SARS-CoV-2.

To understand where the corona virus might be susceptible, it helps to understand what the virus looks like and how it triggers infections. Each individual SARS-CoV-2 virus has large, spiky protein structures on its surface that give it a crown-like appearance, hence the name "coronavirus" ("corona" is the Latin word for crown). A virus uses its so-called spiky (S) protein like a grappling hook to attach itself to a human cell and start invading that cell. An antibody that can block the S protein would therefore be highly effective in preventing the virus from infecting cells.

Antibodies can attach themselves to many different regions or epitopes of the S protein, which leads to a more or less strong neutralisation of the virus. Similarly, if you want to prevent a poisonous snake from being bitten, you could either hold it by the tail so that the snake can still hit you, or grab it near the head, thus reducing the chance of being bitten.

To find out which epitopes were the predominant targets for antibody reactions, Barnes and his team took detailed images of the purified patient antibodies while interacting with the SARS CoV-2 S protein. The researchers found that the patient antibodies bound to two different regions of the S protein, including one region known as the receptor binding domain (RBD), which is crucial for the protein's ability to bind to the host cell.

"To our knowledge, this is the first time that a team has imaged a mixture of antibodies purified from human blood after a viral infection in order to visualize the targets of these antibodies circulating in the recovered individual," said Barnes.

Barnes then focused on a specific type of antibody that showed a strong ability to neutralise the virus. He first purified a complex consisting of the combined viral S protein and antibody, and then used a technique called single-particle cryo electron microscopy to take images of the entangled structures - a process similar to imaging an entire beach, while still being able to determine the exact position of each grain of sand.

The RBD of the S protein can assume two different orientations, the so-called "up" and "down" conformations. Barnes and his colleagues obtained the very first high-resolution images of a SARS-CoV-2 neutralizing antibody bound to the RBD in its "up" conformation.

Barnes found that the neutralizing antibody attaches to the RBD of the S protein at a position that overlaps with the part of the RBD that would attach to a host cell; in this way, the antibody effectively blocks the S protein from infecting cells and neutralizes the virus.

"Vaccines work by giving a person a piece of a pathogen, thereby causing the body to make antibodies against that pathogen so that future infections cannot take hold. A vaccine must therefore be designed to induce the human body to produce the most effective types of antibodies," explains Barnes. "Knowing which regions on the SARS CoV-2 virus are particularly susceptible to antibodies is really important for vaccine development. And knowing which classes of antibodies are most effective may help us develop better antibody therapies," he says.

"One thing that is particularly interesting about Christopher's structure is that it shows that, although the antibody has a strong neutralising effect, it has not developed to bind optimally to the SARS CoV-2 S protein," says Björkman. "This suggests that this type of antibody should not be difficult to induce in the human body by a vaccine. It also suggests that it should be possible to apply protein engineering techniques to improve such antibodies for use as therapeutics.

The intersection of science and researchers

The COVID 19 pandemic has given this research an urgency, but the work, like all scientific endeavours, does not take place in a vacuum, isolated from other events taking place in the world; nor can scientists completely detach themselves from their experiences, good and bad, in and outside the laboratory. In fact, just when the team's work was accepted for publication, many researchers, including Barnes and his colleagues, were concerned about another serious problem. On May 25, the death of George Floyd at the hands of Minneapolis police officers sparked national protests against police brutality and systemic racism. For Barnes, it was a difficult reminder of his own struggle with the racism he encountered in the world and in academia.

"At some point, I'm going to tweet about my work," Barnes wrote in his Twitter account a few days after Floyd's death. "But today I'd rather tweet about George Floyd, Ahmaud Arbery [a black man who was shot dead in February] and all the other brothers we lost for no reason. #"BlackLivesMatter."

"I am a scientist. I'm a black scientist. I have been on campus since 2004, and many times I was the only African-American scientist in my whole building. Until I arrived at Caltech, I never had a black male mentor I could go to to talk about science as well as race and culture," says Barnes. "It's a difficult room to shut yourself off as a person, to shut off your feelings," says Barnes. We can't just hire colored people and then tell them to leave their culture, their experiences and their humanity at the door. These current events are a perfect example of this duality: having to show my colleagues the joy and excitement of publishing our newspaper, while inside I am aching with pain and sadness because I am constantly reminded of the racist society we have to live in as blacks.

"The academic world, like all of America, is corrupted by the racist structure that underlies everything in our society. As black scientists, all of our experiences are affected by this, and we carry this burden along with the responsibility that is expected in our positions. To work as a black scientist at this high level, you have to be extraordinary, as Dr. Barnes' work shows," says Bil Clemons, professor of biochemistry at Caltech and, like Barnes, a structural biologist. Clemons was his mentor when Barnes arrived at Caltech. Clemons not only heads his own group, but is also chairman of the President's Diversity Council at Caltech. "Dr. Barnes' research on HIV was already enough to show that he was ready for a faculty position. The rapid progress he has made in COVID-19 research in the face of all our social problems proves that he will be a leader of the next generation of academics.

A few days after Floyd's death, the Caltech Center for Inclusion & Diversity (CCID) hosted a virtual panel discussion in which members of the African-American and black Caltech community - students, faculty and staff - shared some of their diverse experiences with an audience of nearly 1,000 members of the wider Caltech community. Clemons and Barnes both participated. The event was the first in a series of programs and talks through which the Caltech community will discuss and evaluate the climate of inclusion.

"Telling my story was an important first step in starting conversations with peers, difficult conversations that hopefully will continue over the years," said Barnes.

Cindy Weinstein, Caltech's Chief Diversity Officer, notes: "Telling my story was an important first step in starting peer-to-peer conversations: "Inclusion is the essential foundation for happiness, creativity and productivity. It is the foundation on which individuals and communities can reach their full potential; without it, they cannot. Caltech is committed to equality, inclusion and diversity and recognizes that these are the pillars on which membership is experienced, built and maintained.

In a memo to the Caltech community on July 6, the President and Caltech's academic leadership informed the Institute of the new steps it will take "to ensure that we continue to create and affirm a campus where it is clear in everything we do that black lives matter, black minds matter," including increased funding and programs to build a pipeline of students, postdoctoral students and colored faculty.

"We are striving to become an example of how a diverse and inclusive community committed to equality enables individuals to succeed in fulfilling the Institute's mission of excellence in research and education," the memo said.

A paper describing Barnes' research is entitled "Structures of human antibodies bound to SARS-CoV-2 spikes show common epitopes and recurring characteristics of antibodies".