Covid’s scientific silver lining: A chance to watch the human immune system respond in real time

While an increasingly anxious world watched a new coronavirus spread across the globe in early 2020, veteran immunologist Rafi Ahmed quickly grasped that his field was about to experience something truly extraordinary. His former student Ali Ellebedy was gnawed by frustration as Covid shutdowns stalled his influenza research; it took until the summer, when mass vaccination planning hit his radar, before the same realization kicked in.

For scientists who study the human immune system, the penny dropped at different points in the early frenetic months of the Covid-19 pandemic. Looking back now, many marvel at the realization that they witnessed and were able to chronicle something no other scientists had ever actually seen.

The Covid pandemic marked the first time people armed with powerful scientific tools could study how the immune system awakens to and develops defenses against a new threat, in real time, in the global population. Think about it: At the start of 2020, the immune systems of nearly 8 billion people were effectively blank slates as pertains to this new coronavirus.

That immunological homogeneity produced some amazing observations. Paul Bieniasz, a virology professor at Rockefeller University, described seeing nearly identical antibodies develop in a variety of people, “which blew me away.”

“Some of the antibodies that you made and I made are probably identical, and theoretically that shouldn’t happen, because of the theoretical size of antibody repertoires,” he told STAT.

Since then, scientists have been able to chart how immune systems respond to a single infection, a first dose of Covid vaccine in a naive person, a first infection in a previously vaccinated person, and a first vaccination in a previously infected person — seeing clearly what each encounter activated and how those responses broadened and built on each other.

“You could see B cell responses. T cell responses. Interferon type 1 responses. You see textbook immunology happening in real time,” said Marc Veldhoen, a professor of immunology at the University of Lisbon.

“We really got beautiful insight into antibody responses during a primary infection, and also vaccination,” said Ahmed, who is the director of the Emory University Vaccine Center.

Bieniasz’s face broke into a grin when he was asked how often scientists get an opportunity like this. “You don’t,” he said. “You absolutely don’t.”

There is a tenor of awe in the voices of some scientists as they describe how — for a window of time that has since closed — they were able to see the world’s population develop immunity to SARS-CoV-2, at a cellular level. “As a 50-year-old researcher, I’ve never had the ability to access samples where I could track the evolution of an immune response from what we call naive cells that have never been activated before to multiple boosts that were timed,” said Marion Pepper, chair of the department of immunology at the University of Washington School of Medicine. “We could actually watch an immune system develop in a way that we have never been able to do before.”

“This was the silver lining of the pandemic for us as immunologists.”

Quick! Collect samples!

Steven Deeks, an HIV researcher at the University of California, San Francisco, admitted he hadn’t yet recognized the blank slate possibilities when his university shut down research programs in March 2020 as the country went into lockdown mode. But based on their work on HIV, he and colleagues felt certain that there would be lingering consequences of Covid infections in some survivors. To fully understand those consequences, they’d need to start banking specimens fast. What has since become the LIINC study — Long-term Impact of Infection with Novel Coronavirus — was born.

“We knew something was going to happen. We had no idea what it was going to be. And we figured, well, let’s just start doing what we do best, which is collecting data, collecting samples, and observing people,” Deeks said.

A number of other groups also put together biobanks from the earliest days of the pandemic, realizing that as the immunological picture evolved, questions would become harder to answer when some people had had seven vaccinations and one infection, others had four infections and two vaccinations, and others still had received several types of Covid vaccines and an infection or two.

John Wherry, for one, regrets that more of this biobanking wasn’t done.

“Do I lay in bed at night wishing we had done it at a 10- or a 100-fold larger scale? It pains me, because we can only ask a limited number of questions, because [a biobank is] a very expendable resource,” said Wherry, director of the Institute for Immunology and Immune Health at the University of Pennsylvania.

Deeks believes answers to questions that have plagued medicine for decades about so-called long conditions — lingering side effects of infections, like chronic Lyme disease or myalgic encephalomyelitis/chronic fatigue syndrome — will be found in the study of banked specimens from people who developed long Covid after an initial infection at the start of the pandemic.

The early Covid lockdowns — not just here, but across much of the world — not only gave Deeks a new field of study, they made the work of researchers who wanted to explore the immune system’s response to Covid infinitely easier. That’s because respiratory viruses like influenza and RSV that could have been confused for Covid — and would have triggered immune responses that would have muddied the immunological picture scientists were seeing — went quiet for the first 18 months or so of the pandemic.

“You couldn’t have designed a better experiment. All the other viruses basically disappeared,” Deeks said. “[By] 2021, everything got complicated again. But in 2020, it was an absolute ideal environment to study a new pathogen in terms of its short-term and long-term effects.”

Has this truly never been seen before?

This is hardly the first time a new pathogen has made its way from nature into humans. For instance, four coronaviruses normally described as “common cold coronaviruses” at some point in the past made the jump from bats, mice, or some other species into people. But these events were either unobserved at the time or took place before scientists had the tools to identify what was happening, let alone chart in exquisite detail their impact on immune systems.

Influenza virus was first isolated in 1933. Since then, new strains of flu have assailed the human race in the pandemics of 1957, 1968, and 2009. But flu viruses share some genetic features, even those with surface proteins — the Hs and the Ns in their names — that humans haven’t yet encountered. Our immunological white boards for flu are full of impossible-to-decipher scrawls that vary enormously from person to person. Studying the immunological impact of the 2009 H1N1 pandemic, for instance, was complicated by the fact that for about 70 of the previous 90 years, a distantly related H1N1 virus had been circulating.

“For people who study the flu, this has been a frustration forever. Because you don’t know what the history of exposure or vaccination, or any of these things, really, has been,” Pepper said.

HIV, on the other hand, was a wholly new virus, one that started transmitting among people sometime in the late 1800s, it is now believed. But because of its mode of transmission, it has never spread to the degree that a respiratory pathogen, like SARS-2, can. Wherry called the emergence of HIV “a slow burn, rather than an explosion.”

For many scientists, the significance of Covid — the blank slatedness of it all — was initially obscured by the fact that this extraordinary opportunity came wrapped in a global health crisis. “So we are developing [immunity] de novo. The virus comes in and immunity goes from there. That’s the first opportunity where you can actually [study] that at a very large scale,” said Kristian Andersen, an evolutionary biologist and a professor of immunology and microbiology at Scripps Research. “Did we do that at a very large scale? Not really. But that’s because it’s not simple.… And everybody was overwhelmed.”

“We were worried about keeping people alive,” Wherry concurred.

It should be noted that the immune responses people develop to common cold coronaviruses did interact a little with those that materialized when immune systems encountered SARS-2. Alessandro Sette, a professor at the La Jolla Institute for Immunology, said there is good evidence that people who had had a recent exposure to one of the common cold coronaviruses fared better when they contracted Covid. But immunity to the common cold coronaviruses is fleeting — which is why we can be infected with them so frequently.

And those responses did not obscure the picture scientists were seeing as immune systems the world over encountered SARS-2 for the first time.

“Our control samples taken prior to the pandemic and vaccination look VERY different for most parameters,” Pepper said in an email. She acknowledged there was some cross-reaction — responses triggered both by the old coronaviruses and the new one, “but if you looked carefully you could find the novel ones as well and obviously the cross-reactive responses were not ‘close enough’ to provide significant protection against disease in most people.”

Maturing B cells, a virologic arms race, and imprinting

So what were scientists able to see when a new virus spread by coughs and sneezes dove into a pool of 8 billion immunologically naive people?

For starters, Covid research fundamentally changed scientists’ understanding of how long antibodies induced by Covid vaccination continue to mature and broaden.

Ellebedy, an immunologist at Washington University in St. Louis, was studying the response to flu vaccination when the pandemic hit. With the rollout of the messenger RNA vaccines for Covid, he started using the same approach to chart the length of the immune response following vaccination — taking tiny biopsies from the lymph nodes of volunteers to study the activation of B cells, the part of the immune system that generate antibodies.

He thought the activation process would stop after about a month. So his team took the biopsies over eight weeks, only to discover that the process continued out to eight weeks and beyond. Eventually the researchers discovered that the B cell maturation process lasted as long as six months in some people. In others, it ends at around three months.

“It’s really opened our eyes to these kinds of questions: how long, really, a response in humans can [persist],” Ellebedy said. “We knew that these questions were important before the pandemic. SARS-CoV-2 fortunately and unfortunately made the opportunity for us. Brought the resources, brought the interest, and made these questions central. It’s not an academic exercise anymore.”

Bieniasz was also surprised by how long the maturation process lasted. “I don’t think we understood, at least not on the scale that we now do, that over a period of months the antibodies get broader and broader, and that makes it more and more difficult for the virus to escape those antibodies. But, in this case at least, escape it does.”

That is another thing that has amazed researchers — the degree to which development of population immunity and the evolution of the virus have progressed in lockstep. At the start of the pandemic, the scientific community confidently opined that coronaviruses evolved slowly. SARS-2 has long since dislodged that dogma.

“To me the main thing that really stands out is that I think we have gotten a much, much, much, much better understanding of the sort of tight connection between population immunity and viral evolution,” said Andersen.

Marion Koopmans, head of the department of viroscience at Erasmus Medical Center in the Dutch city of Rotterdam, agreed. “I think the almost synchronized nature of some of these waves in a weird sense also provided an opportunity where you could actually disentangle the impact of different aspects of immunity on transmission,” said Koopmans. She remains frustrated, though, by the scientific community’s inability to predict whether new variants and subvariants will trigger more severe disease, based on study of their genetic changes. “I think that’s going to be a field where I do expect that we will have some success.”

For Stanley Perlman, a microbiologist and immunologist at the University of Iowa’s Carver College of Medicine who has studied coronaviruses since long before Covid, the fleeting nature of immune protection against reinfection was unexpected. “Protection was both relatively short-lived and not complete,” he said.

Scientists have also learned about how what has become known as hybrid immunity — protective responses generated by a combination of vaccination and infection — influences the durability of immunity, Koopmans said. “It makes sense biologically.”

Even the specifics of how hybrid immunity is acquired matters, scientists have discovered. “I think we almost thought that as long as you had the same number of exposures — let’s say, you had three vaccines or two vaccines and then an infection — that maybe you would get the same end result. And that’s not what we saw,” Pepper said. “We saw that you actually ended up with different abilities of those cells. The cells could do different things. And that’s what we study now.”

For Wherry, the patterns of illness in severe Covid infection early in the pandemic — triggered by divergent immune responses — were a real eye opener. Many people had overwhelming reactions to the virus. In others, though, there was no evidence of B cell and T cell activation; their immune systems were creating antibodies that targeted cytokines, the proteins the immune system uses to send instructions to its component parts. “The fact that a viral infection could provoke de novo antibodies against the molecules your immune system uses to communicate with itself … that’s devious,” Wherry said.

The sheer numbers of people sickened by Covid quickly made visible rare events that otherwise would have taken far longer to come to light, he added, pointing to this aberrant immune response and to MIS-C, or multisystem inflammatory syndrome in children, a serious post-infection illness. “You don’t see that when you’ve got 30 people, 100 people. You see that when you’ve got 100,000 people in your city infected.”

Another phenomenon scientists have been able to study because of Covid is known as original antigenic sin or imprinting, the notion that immune systems are effectively programmed to recognize a pathogen based on the first iteration of it they encounter. The fear is that this imprinting then undermines efforts to protect an individual against evolved versions of that pathogen — that a vaccine targeting the latest variant of SARS-2 will preferentially boost antibodies to the original version of the virus, which is now long gone. This effect is believed to influence the immunity people develop to influenza viruses and reduce the impact, in some cases, of flu vaccines.

But Sette, the professor at the La Jolla Institute for Immunology, said the emergence of the Omicron variant in late 2021 showed that immunity acquired against the original strain of SARS-2 continued to broaden and adapted to target the new, heavily mutated version of the virus.

Wherry and colleagues recently published on SARS-2 and imprinting in the journal Immunity. For him, the upshot is that imprinting does happen with this virus, but the impact isn’t deleterious. “I’d say the reality is we’re all pretty well protected, and it’s not clear to me, anyway, that there’s been any negative effect of imprinting on protective immunity and lowering disease burden and all that,” he said.

Wherry’s co-senior author, Scott Hensley, a professor of microbiology at the Penn Institute of Immunology, added a caveat. Imprinting hasn’t undermined responses to SARS-2 yet. Contemporary versions of the virus share enough genetic targets with the original strain that the current vaccine evokes an effective response. Continued evolution, though, may alter that scenario. “It is possible that [future] variant vaccines might elicit a mostly non-neutralizing antibody response,” Hensley said in an email.

The window has closed

So where are we now? The magic hour is over. There is no more homogeneity. True, almost everyone on the planet has been infected at least once, but that might have been with the original virus, the Alpha variant, or one of the Omicron-era viruses. Many people will have been infected multiple times. Much of the global population has been vaccinated, but with a variety of vaccines and a variety of doses. There is too much jotted on our immunological white boards; scientists can no longer clearly see the effect of a new viral prompt.

“One would like, for example, to know in the context of booster vaccinations: How does the immune response of someone that has been immunized two or three times compare to someone who has [been immunized] four or five times,” Sette said. “And those studies are now difficult to perform exactly for the reason that it’s very difficult to find someone that was immunized only once.”

Pepper is doing less Covid work these days, in part because this window closed. “Now you have to ask, ‘How are people experiencing Covid?’ without actually knowing what their immune history is. And for me, that’s a less interesting question.” She’s back to studying immune responses in mice, where she can see clearly what happens when a naive mouse is vaccinated and then exposed to a pathogen.

Ellebedy works on a model system that allows him to see what he could see early in the pandemic, giving vaccines for rare pathogens — like rabies, for example — to volunteers who have never been infected with that pathogen and aren’t likely to encounter it. That way he knows that the immune response unfurling before his eyes is solely the result of exposure to the vaccine.

As for the opportunity presented by the pandemic, Ahmed said much of what was seen supported what was already known about the immune system, but broadened science’s understanding of how our bodies generate protection for us. “When you take the whole collection of the work that was done by many outstanding labs, I think it provided great insight. And insight that we had not had before.”

Veldhoen agreed, saying that scientists have learned an immense amount about SARS-2 in the past four years. “You see a huge body of work that is really immunology in real time, and a huge reference for whenever this may happen again,” he said.