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Antibodies a hot topic in COVID-19 research

Hutch scientists tap their antibody expertise for new tests, treatments, vaccines
cartoon of antibodies swarming a coronavirus
Illustration of Y-shaped immune proteins, known as antibodies, swarming a coronavirus Illustration by Getty Images

Since the unwelcome arrival of COVID-19, a class of tiny, Y-shaped proteins in our blood called antibodies has emerged as a focus of attention for researchers hoping to find a way to treat it, a vaccine to prevent it and tests to confirm whether a person has gotten over it.

One of the workhorses of the human immune system, antibodies are part of our natural defenses against infectious diseases. Their role is to recognize features of invading microbes. Swarms of antibodies can block infection by jamming a virus’s ability to enter a healthy cell or by flagging already infected cells for destruction, like a building inspector’s red tags.

Antibodies are standard tools used in medical research and a component of many cancer drugs. Most vaccines work by stimulating production of antibodies against viruses or bacteria. Antibodies can also tell us more about the spread and severity of viruses. So, when the pandemic struck, dozens of scientists at Fred Hutchinson Cancer Research Center set their existing work aside and began applying their antibody-wrangling skills. Experience with other viruses is guiding efforts to track and counter SARS-CoV-2, the cause of COVID-19.

From flu to SARS-CoV-2

Dr. Jesse Bloom is an expert on influenza and how that virus interacts with the antibodies we produce against it. The Hutch researcher and Howard Hughes Medical Institute investigator is turning this expertise to the study of SARS-CoV-2 and our immune responses to it, starting with local children.

He and Dr. Adam Dingens, a research scientist in Bloom’s lab, collaborated with Dr. Janet Englund, an infectious disease researcher at Seattle Children’s, to examine prevalence of SARS-CoV-2 infection in Seattle-area children. Although kids make up nearly a quarter of the nation’s population, less than 2% of confirmed coronavirus cases are among them.

“That sets up this question: Are kids protected from infection and not getting infected, or are they still getting infected and we’re missing them?” Dingens said.

The researchers screened blood samples from 1,076 youngsters who had visited the hospital in March and April of this year, when COVID-19 infections began picking up steam. They tested sera — the clear liquid left over when clotting factors and cells are filtered from blood — for antibodies that bind the novel coronavirus. If the screen finds them, the child is called seropositive. It means they had been exposed to COVID-19, had developed antibodies to the virus and were likely immune to it.

The team found only one seropositive child in March, but the seroprevalence increased in April, with just over 1% of those tested showing evidence of SARS-CoV-2-binding antibodies. A majority of those seropositive children had not been suspected of having COVID-19.

Dr. Jesse Bloom
Dr. Jesse Bloom has developed a way to test whether antibodies drawn from blood samples can neutralize SARS-CoV-2, the virus responsible for COVID-19. Photo by Robert Hood / Fred Hutch News Service

The researchers also tested whether the children’s antibodies could block the virus from infecting cells, a phenomenon known as neutralization. Most of the kids’ antibodies easily passed a test developed by Bloom, and one child’s sera was particularly potent. Bloom said it was too early to gauge how the potency of children’s immune responses to coronavirus compare to those of adults. “But we can say that despite the fact that kids are often asymptomatic or only have a mild sickness, they're certainly mounting quite good immune responses,” he said.

The 1% infection rate in this small group of kids aligns with infection estimates for all age groups in the Seattle area developed using epidemiological models. Most of the children who tested positive for past exposure to SARS-CoV-2 came to Seattle Children’s for other health concerns, showed few to no symptoms consistent with COVID-19, and were not suspected of being infected during their hospital stay. Consequently, the researchers said their findings also suggest that only screening children with COVID-19 symptoms will likely miss many cases, and that measures to control the spread of the coronavirus should not focus exclusively on those who are clearly sick.

Bloom said it is also difficult to compare the study’s infection rates in children with those reported in adults, because the kids’ antibody tests indicate there was a prior infection, while adults are most often tested for the presence of the virus itself using a nasal swab instead of a blood sample. Unlike the children in the hospital study, who were mostly asymptomatic, adults are typically tested because they have some symptoms, such as a fever and cough, consistent with COVID-19.

A biological record of past infections

Antibodies are released by immune cells known as B cells. We make a huge variety of antibodies to help protect against the wide array of microbes we may encounter. Prior to infection with a given pathogen, we have relatively few B cells whose antibodies can bind to it.

Infection changes this: The B cells whose antibodies recognize the infecting pathogen multiply and start churning out enormous amounts of antibodies. Even long after the pathogen has been conquered, a few lingering B cells will continue making antibodies to help stave off a second infection. These antibodies in our blood serve as a biological record, so antibody tests are an easy way to assess whether we have been infected with a specific pathogen.

Hutch researchers  (left to right) Drs. Andrew McGuire, Leo Stamatatos and Justin Taylor
Drs. Andrew McGuire, Leo Stamatatos and Justin Taylor Photos by Robert Hood / Fred Hutch News Service

Dr. Justin Taylor and colleagues are using sophisticated tools developed in his lab to gain a deeper understanding of how our B cells respond to SARS-CoV-2. Much of their focus is on pre-existing immunity that people develop early in life to four other, less harmful coronaviruses that cause common colds.

“We all have pre-existing immunity. We’ve all been exposed,” said Dr. Jim Boonyaratanakornkit, a research assistant in the Taylor Lab.

That exposure, much of it occurring in early childhood, is one reason scientists think may explain why COVID-19 occurs in very few children. Head colds come early and often, triggering a strong antibody response. But as people age, that immunity may wane, and that may influence how older people respond to the arrival of the new coronavirus.

So, the researchers are studying the B-cell responses to SARS-CoV-2 in the blood of people of various ages. Using selected snippets of the virus, they want to see if they prompt a direct defense against it, or possibly cause the body to attack its own tissues. They want to see if SARS-CoV-2 stirs up antibodies against the old cold viruses, potentially stopping it as it appears to happen in kids; or if the immune systems of adults are fooled into mounting an ineffective defense against the old viruses, leaving them vulnerable to this new and deadlier strain.

“We’re asking whether this pre-existing immunity guides or misguides our immune response. Do they help us fight off the infection, cause damage or do nothing at all?” Boonyaratanakornkit said.

The answers to those questions are needed as researchers develop vaccines or antibody therapeutics against COVID-19. The behavior of our immune system, never simple, may be more important than the virus itself in determining whether a vaccine will work, or whether an infected person becomes only mildly ill or will end up in critical care, on a ventilator or dead.

A deeper understanding of how antibodies to SARS-CoV-2 can bind and neutralize the virus is critical to building an effective vaccine and antibody-based therapies for infected patients.

Dr. Jim Boonyaratanakornkit
Fred Hutch researcher Dr. Jim Boonyaratanakornkit Photo by Robert Hood / Fred Hutch News Service

Hutch researchers led by Bloom have developed an experimental assay that allows researchers who don’t have access to the highest biosafety-level laboratories to safely measure antibody neutralization of SARS-CoV-2. The test measures how well the antibodies perform against a harmless virus that has been genetically engineered to carry SARS-CoV-2 spikes, so it mimics the real virus. This “pseudovirus” can be used to test COVID-19 vaccines or antibody therapies in a lab setting without having to use the dangerous wild virus, which can only be tested in highly secure facilities.

That test was crucial for another Hutch team, led by immunologist Dr. Leo Stamatatos, in their studies of antibodies that bind to the distinctive spike on the coronavirus surface, a likely target of vaccines and therapies.

In the journal Immunity, Stamatatos and colleagues describe how they identified from the blood of a COVID-19 survivor an extremely potent neutralizing antibody that can block the ability of the virus to lock onto vulnerable cells thought to be its primary target inside the human lung.

The antibody fit so snugly to a spot on top of the SARS-CoV-2 spike that it stopped infection 100% of the time using Bloom’s laboratory tests.

“Because it neutralized every viral particle in our assay, it is theoretically a good candidate for a COVID-19 therapy or a vaccine,” Stamatatos said.

His team embarked with University of Washington researchers in early March on the effort to identify natural antibody defenses against SARS-CoV-2 shortly after obtaining the precious blood sample from a patient who had recovered from COVID-19.

They developed a test to isolate antibodies that this one patient had naturally developed against the coronavirus and identified 45 different varieties that latched onto one site or another on the knobbly protein surface of the spike. Of these, only three had any ability to block infection.

A top performer

The one antibody that seemed to have hit the bullseye was measured to be 530 times more potent than its nearest competitors: two others that homed in on different parts of the coronavirus spike but only weakly blocked infection.

The top performer, labeled CV30, was extraordinarily good at stopping infection, likely because it locked so securely onto a region at the tip of the spike called the receptor binding domain. That is the same site that has been so problematic for humans, because it connects the top of that spike, like a key fitting into a lock, with a receptor called ACE2 found of the surface of cells that line the deepest recesses of the human lung.

ACE2 acts like a trap door that allows the coronavirus to break into those cells and use its internal genetic machinery to make thousands of new copies of SARS-CoV-2, eventually killing those cells.

Could this antibody, by itself, be key to stopping the pandemic? Stamatatos said very likely no, because the virus would eventually escape through mutation of that closely matched site on its spike. Consequently, researchers are hoping to develop a cocktail of many different neutralizing antibodies.

“Ideally, a cocktail would presumably be better, because the virus has less chance to escape,” said study co-author Dr. Andrew McGuire, whose lab performed the genetic sequencing of the antibodies and carried out the neutralization studies using Bloom’s pseudovirus test.

Stamatatos and colleagues are now exploring whether the neutralizing antibodies isolated using these techniques could be formulated into a therapeutic infusion that could protect frontline workers from infection, or as a treatment to limit viral replication in an already infected patient.

The structure of the most successful antibodies can also inform research on a vaccine, which would be designed to teach a healthy individual’s immune system to generate similar protective proteins if exposed to SARS-CoV-2, blocking infection.

Meanwhile, McGuire has been working on neutralizing antibodies against coronaviruses for several years in a collaboration with biochemist Dr. David Veesler of the University of Washington. Predating COVID-19, the work was initially aimed at SARS and MERS, two deadly epidemics — discovered in 2003 and 2012, respectively — caused by coronavirus cousins of SARS-CoV-2.

That gave the researchers a jump start on describing the structure of the SARS-CoV-2 spike, and Veesler and McGuire were co-authors of one of the first papers to describe it.

The team hopes to identify an antibody that neutralizes all three types of the deadly coronavirus, which could be developed into an antibody-based therapeutic to treat infection by any one of these coronavirus threats.

Sabrina Richards, a staff writer at Fred Hutchinson Cancer Research Center, has written about scientific research and the environment for The Scientist and OnEarth Magazine. She has a Ph.D. in immunology from the University of Washington, an M.A. in journalism and an advanced certificate from the Science, Health and Environmental Reporting Program at New York University. Reach her at srichar2@fredhutch.org.

Sabin Russell is a staff writer at Fred Hutchinson Cancer Research Center. For two decades he covered medical science, global health and health care economics for the San Francisco Chronicle, and wrote extensively about infectious diseases, including HIV/AIDS. He was a Knight Science Journalism Fellow at MIT, and a freelance writer for the New York Times and Health Affairs. Reach him at srussell@fredhutch.org.

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Last Modified, June 24, 2020