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The Immune System’s Response to SARS-CoV-2

August 11, 2021
by Amy Anderson

The Immune System’s Response to SARS-CoV-2

When SARS-CoV-2 began to surface in early 2020, not much was known about the brand new disease—except that it was highly contagious and spreading rapidly.

As the virus raged on and was classified as a global pandemic, there were many questions about the disease. Some individuals had severe cases and were hospitalized with life-threatening symptoms and later discharged with lingering health conditions, and many died. Yet, others were asymptomatic. Why was it presenting itself in such extreme cases? And who was at risk, and why?

Laboratories quickly shifted their focus to the new coronavirus. Scientists and researchers began studying the disease.

The Yale School of Medicine (YSM) lab run by Akiko Iwasaki, PhD, Waldemar Von Zedtwitz Professor of Immunobiology and Molecular, Cellular and Developmental Biology, YSM; and Professor of Epidemiology, Microbial Diseases, Yale School of Public Health; was no different. As an immunobiologist, Iwasaki’s research is focused on the mechanisms of immune defense against viruses at the mucosal surfaces. The Iwasaki laboratory’s focus is on understanding how viruses are recognized and how that information is used to generate protective adaptive immunity.

In late April, the Department of Internal Medicine hosted a live discussion on Clubhouse to discuss the findings of the Iwasaki Lab since transitioning to research for COVID-19. Manisha Juthani, MD, associate professor of medicine (infectious diseases), Yale School of Medicine; and epidemiology (microbial diseases), Yale School of Public Health moderated the event to discuss the clinical manifestations of the disease. In addition to Iwasaki, Juthani was joined by two student researchers in Iwasaki’s lab—Alice Lu-Culligan and Julio Silva, both MD/PhD candidates at YSM.

The beginning

Over the last two decades, the Iwasaki Lab has studied a variety of different virus infections—from genital herpes, to rhinovirus, to the Zika virus.

“We've been interested in this question of host immune response against viruses, and what are protective responses versus what are immuno-pathologic responses. We were primed and had the tools to be able to tackle what might be going on in the COVID-19 patients.” said Akiko Iwasaki, PhD, Professor of Immunobiology and Molecular, Cellular and Developmental Biology and Professor of Epidemiology (Microbial Diseases); Professor of Molecular Cellular and Developmental Biology; Investigator, Howard Hughes Medical Institute.

Iwasaki remembers the first meeting in January 2020 with experts spanning several departments across Yale School of Medicine (YSM). The meeting included Ellen Foxman, MD, PhD; Nathan Grubaugh, PhD; Albert Ko, MD; Marie-Louise Landry, MD; and Saad Omer, MBBS, MPH, PhD. This led to the launch of one of the most influential bio-repositories in COVID research called IMPACT Yale (Implementing Public Health Action Against Coronavirus in Connecticut) where they met to discuss testing, surveillance and research around the new virus.

“We started collecting bio-specimen from patients and healthcare workers and analyzing their viral replication and immune response in real time, and I've never been so excited and so tired at the same time,” admitted Iwasaki. “As immunologists, we started seeing things that we weren't used to seeing happening in patients. We started analyzing patients that came through the hospital by collecting their blood and saliva to begin analyzing their immune responses in real time.


“We collected these mono-nuclear cell fractions from the blood and ran for cytometry assay which will tell us about what kinds of cells are in the blood and how activated they become in these patients.”

The process was involved with data being analyzed in several laboratories. RNA data was collected from patient saliva by the Grubaugh Lab. The Iwasaki Lab would then perform a PCR analysis on the saliva, while researchers in the Ring Lab ran ELISA on the patient sera for antibody levels.

“It was a great well-oiled machine that kept churning out data day in and day out. The outcome of this research showed that in severe COVID patients, there was a defect in clearing the virus and the sustained high levels of viral load over time. We saw inflammatory cytokines and also cytokines that belong to defense systems, usually reserved for fighting other types of pathogens like fungi and parasites. This study showed that the maladaptive responses are correlating with the severity of COVID,” explained Iwasaki.

Gender influence on COVID

Iwasaki adds that they are still learning what makes individuals succumb to disease, but notes that a key factor is an individual’s gender.

“Takahiro looked at the correlation between immune responses and sex, and found that the analysis from the first sampling in patients who were not treated with immuno modulatory agents revealed some key differences between male and female patients. One of the striking findings was that while many, many factors were similar between the sexes, male patients had elevated interleukin 8 and IL-18, and these are really inflammatory cytokines that trigger further inflammation,” said Iwasaki.

In contrast, female patients had more activated T-cells than male patients, and very interestingly, we found that there is an age-dependent decline in T-cell activation only in male patients, but not in female patients. So this study emphasizes the need to develop sex disaggregated data for research, because the biological sex has such an important impact on the immune system and other organ systems that this is a real key aspect to be studying in infectious disease.”

Pregnancy and fetal outcomes

When the pandemic hit, not much was known about how COVID can impact people, let alone pregnant women.

Alice Lu-Culligan’s research interests prior to the pandemic were focused on the impact of viruses on the immune system, antiviral responses during pregnancy and the way that pregnancy is executed, and also on how the fetal immune response can impact the development of the neural system.

“An early focus of work in the field was trying to figure out, does COVID actually infect the placenta? Can it cross the placenta, and can it infect babies in utero? And we had the opportunity in the Iwasaki Lab to contribute to a very early study on the pandemic on a woman who was diagnosed with a very severe SARS-CoV-2 infection in the second trimester of pregnancy, and very sadly, the case ultimately ended in fetal loss.

As researchers were brought in to kind of study this case, and we were able to acquire the placenta and find out that the SARS-CoV-2 virus is capable of invading the placenta, which was at the time very concerning because the next question that comes after that is can it cross and infect the child in utero. In our early studies we were analyzing how common this was, when it does happen, what is the impact on the fetus.”

They worked with clinical colleagues in the Department of Obstetrics, Gynecology & Reproductive Sciences, as well as Yale New Haven Hospital’s labor and delivery floor to collect placental specimens from women who were admitted to labor and delivery and had a positive SARS-CoV-2 nasal swab.

As mothers delivered full-term third trimester babies in the ward, the lab collected the placentas to analyze how common a placental infection was, and what the risk of transplacental infection was.

“Women who are infected during pregnancy with SARS-CoV-2 are at higher risk for poor outcomes. They typically are a high risk for severe COVID-19 for hospitalization, intubation, and unfortunately, poor outcomes to the fetus. In most of these cases, the placenta isn't directly infected, and further studies by not only our group, but other groups have shown that most of the time babies are not actually infected in utero with this virus, which is great news in general,” said Lu-Culligan.

From there, they were interested in how the immune system can actually impact pregnancy outcomes and fetal outcomes and began studying the placentas from women who had a respiratory SARS-CoV-2 infection.

What we found is that even when the virus does not directly attack the placenta, the placenta mounts a very robust in the immune response and actually shows signs of physiological stress and damage, including oxidative damage and metabolic stress, and we think that this actually has a lot to do with why pregnant women are so at risk for severe COVID.

Since the placenta is a very specialized organ that exists exclusively during pregnancy, as we know, and there is feedback between the systemic immune system and this localized immune organ, which a placenta really is, and we were really interested to find that the placenta can actually mount an immune response even without the virus reaching the placenta, and we think this gives us a hypothesis or framework with which to think about why women are so at risk when they're pregnant.”

The connection between the brain and nervous system

Throughout the progression of the pandemic, it was reported that patients were experiencing a widespread of symptoms beyond the respiratory system.

Juthani treated many COVID+ patients at Yale New Haven Hospital and added, “What has been interesting as an infectious disease physician is the spectrum of this virus and how it has been able to impact such a broad spectrum of systems within the human body, and one in particular is the impact on the nervous system, and the brain in particular. And for respiratory viruses in particular, it is a little bit unusual.”

This leads to another notable discovery out of Iwasaki Lab—the connection between the brain and the immune system. They investigated the possibility of whether COVID can infect cells in the brain with three separate approaches. The first system was human brain organoids, miniature brains that grow in tissue culture, where they were able to infect the tissue culture to study neuroinvasiveness. The second model used a mouse model of COVID to study tissue-specific infection in the mouse model, and the third approach used human autopsies from COVID patients who died of this infection. In all three cases, they found there was a clear infection of neurons by the virus in the organoid. They saw that neurons around the infected cells actually died of lack of oxygen


“It's kind of eerie to think that within the organ, the infected cells are soaking up the oxygen that they need to replicate the virus, while other cells around them are being deprived of oxygen and dying of hypoxia. We examined three patients' autopsy samples, and one of them had clear evidence of infection in the brain, and particularly the cortical neurons were infected, and that was accompanied also by close to the microinfarctions that were happening in the brain,” said Iwasaki.

When neurons die, they cannot be replaced. This explains the reports of “brain fog” and lack of memory, described by many recovering COVID patients. “This could happen because of a direct infection of the neurons, as Eric has shown, or other inflammatory cytokines could act upon the endothelial cells in the brain, making a blood-brain barrier leaky, and that could also result in some of these brain-specific organ dysfunction.”

Autoimmune resemblance

Another peculiar symptom seen in some COVID patients is the development of symptoms that resemble arthritis or syndromes that resemble autoimmune disease.

“This is not something I'm used to seeing with the run-of-the-mill respiratory viruses,” commented Juthani.

Iwasaki agrees.”What we found was quite striking. In collaboration with Dr. Aaron Ring’s lab, we found numerous autoantibodies against autoantigens that are found in many different places in the body. The extent of these autoantibody development was comparable or even more severe than what he found in lupus patients, and so some of these were against immune proteins and immune cells, which impair the antiviral defense system altogether.

One autoantibody in particular is striking because it is against the type 1 interferons, which are the very cytokines that our body makes to block virus replication, and so, in essence, what's happening in these people is that there is this antibody that blocks the effectiveness of the antiviral cytokines that basically makes them immunocompromised, and so we found about 20% of the severe COVID patients had this autoantibodies that blocked interferon type 1.

And this also correlated with their lack of ability to control the viral load in the nasopharynx and the saliva, and curiously, many of these people turned out to be men, and so Jean-Laurent Casanova's group had already reported last year that he also found similar types of anti-interferon antibody in severe COVID patients, and in his case, it was 94% were male. So there's again an interesting sex difference here in those who are carrying interferon specific antibodies.

And in addition to these kinds of autoantibody that block immune's function, we also saw many that are against the tissue antigens.”

Researchers are still trying to understand whether they cause dysfunction in some of the organs. Iwasaki and team are interested in understanding the link between the antibodies and potential long hauler disease.

Other risk factors

In addition, there are other risk factors that play a role in severe cases of COVIDcomorbidities. Comorbidities are the presence of two or more diseases or health conditions.

“What we found was that there was an interesting correlation between the amount of risk factors that an individual had and the overall viral load that they would carry, especially, in the initial stages of the disease, and so particularly the saliva of viral load. For example, if a patient has diabetes, in addition to chronic lung disease, or maybe they have some hypertension as well, they were more likely to actually have a higher viral replication seen in their saliva,” said Julio Silva, who worked on the study.

”We can imagine that these conditions, because of their chronic state, tend to exert inflammation throughout the body chronically, and so there may be some avenue in which both the hindered immune response as well as this sort of chronic state of inflammation sort of presets you to be less able to fight the infection.”


Looking forward

One of the many remaining and perplexing questions is the “why” behind those who continue to experience long term effects of COVID. These patients—also known as “long-haulers”—have symptoms such as brain fog, shortness of breath, and more.

While there are findings of such recurring symptoms and effects, scientists are unsure of the reasons why.

“We understand a little bit better about the acute disease now because of hundreds of thousands of papers that are being published, but with respect to the long hauler disease, we know very little. We understand their symptoms, we understand their demographics, but we don't really understand the underlying cause of long hauler disease. There are a couple of different hypotheses about how long haul disease is mediated; one may be that there is a lingering virus infection or remnants of virus, that's a remnant, remaining in these people for a long period of time that may be leading to chronic inflammation.

The other possibilities that long haulers develop autoantibodies or auto-reactive T-cells, as I mentioned just now, there are already lots of evidence, of auto-antibodies that are happening during acute COVID, and that could potentially linger and cause long-term symptoms, and in March we started hearing about people with long haul disease feeling better after vaccination, and not all people feel better, but about 40% of people are reporting improvement in their symptoms, and so with that, I got very excited because it might give us a window through which we can study the long haul disease, because we know what the vaccine does. The vaccine induces immunity against the spike protein, which can remove the source of these long-term persistent infection or remnants of the virus, and that could be making the improvement in these people.

Or it can be the inflammatory cytokines that are induced as a result of the vaccination could have impact on these auto-reactive cells. So we're very excited to start the study. We are almost at the cusp of studying this, recruiting long-hauler patients to look at immune response before and after the vaccination so we can make some connections between these dots.”

As more studies and research are conducted on COVID patients, more data will help the medical community have a better understanding of the virus, and ultimately, a better understanding of how to treat the complicated disease.

Submitted by Amy Anderson on August 11, 2021