Immune States in Severe COVID19 Cases

This article was reviewed by E. Idil Temel, one of our subject matter experts.

The paper we’re demystifying today can be found here, if you would like to follow along. 


The researchers in this study wanted to investigate and get a better understanding of how the immune system cells respond to mild-to-moderate and severe cases of COVID-19. This meant studying the progress of the immune cells throughout the course of disease to understand the pathology. The scientists investigated different immune cells and found that patients with mild-to-moderate cases of COVID-19 had a coordinated pattern of expression of a class of genes involved in activating the interferon response, the interferon-stimulated genes (ISGs). The interferon response occurs when there is a viral infection. The infected cells will release a signal protein to nearby cells to prepare an anti-viral defense in case those cells get infected. They also found that those who had severe COVID-19 had more antibodies for SARS-CoV-2, when the serum from these patients were studied, and that these antibodies block ISG expressing immune cells. The researchers suggest that their findings may help reveal potential targets for immunotherapies to help combat severe COVID-19. 


It has been documented that many people who test positive for SARS-CoV-2, the virus, will end up with a mild or moderate case of COVID-19, the disease that is caused by the virus. These scientists set out to get an answer for a holistic understanding of the COVID-19 pathology, and its origin between severe and mild cases of the disease. This is an important field to investigate as it will allow us to understand how the different cells in the immune system respond to SARS-CoV-2 infection and how they progress throughout the course of disease in COVID-19. 


To address their question, the scientists in this group focused on understanding the immune biology that is present in COVID-19 patients. They compared 21 inpatients that tested positive for SARS-CoV-2 and presented a mild-to-moderate (n=11) or severe (n=10) case of COVID-19 to 11 inpatients who had a similar clinical presentation that is consistent with acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). These inpatients were all tested negative for SARS-CoV-2, and it is believed that their respiratory distress was caused by other infections. From this group, there were six patients who presented with mild-to-moderate non-COVID-19 ALI/ARDS and five patients who presented with severe non-COVID-19 ALI/ARDS. The researchers also ensured they had a control group of 14 individuals. 

The researchers noted that all but one patient who presented with mild-to-moderate disease remained mild-to-moderate throughout their hospital stay, which suggests that mild-to-moderate and severe disease states are stable and may not be transient phases of diseases for this cohort that was studied. 


Many papers have shown that the majority of COVID-19 mortality is among patients with ARDS. This typically meant that there was an exuberant immune response from the innate immune system. Because of this, the scientists set out to collect different immune cells from the innate immune system (the innate immune system provide a generalized and  immediate response to pathogens) and other types of cells in our body that are involved in the immune response from their patients. All collected cells were then run using a technology called single-cell-RNA sequencing (or scRNA-seq for short). scRNA-seq is used when scientists want to identify different cell types and study the expression levels of certain genes in each cell group from a sample of mixed cell populations (in this case blood samples). 

From the scRNA-seq data, our scientists were able to identify, neutrophils, platelets, mononuclear phagocytes, T and Natural killer cells, B cells, plasma cells and eosinophils. These cells are components of white blood cells, and we will discuss what these cells do as we go through the paper.   

Neutrophils are a type of white blood cells, who are part of the innate immune response. They are usually one of the first to respond when you have a microbial infection and will die in the front lines after killing the foreign microbial organism. Believe it or not, there are different subtypes of neutrophils, and the scientists were able to identify seven of them. They found that SARS-CoV-2 positive patients with severe cases of COVID-19 had a highly enriched population of strong interferon-stimulated gene (ISG) neutrophils. Their analysis showed the ISG subtype is altered significantly between mild-to-moderate and severe patients and specifically with those who tested positive for SARS-CoV-2. 

So, what does that mean? The most important thing you need to know is that this type of neutrophil has the ability to induce anti-viral regulators which can restrict the ability of a virus to enter the cell. The scientists then investigated the expression levels of the genes in the different subtypes of neutrophils from all SARS-CoV-2 positive versus negative patients and compared the mild-to-moderate patients to the severe cases. They found that the genes for anti-viral regulators in ISG neutrophils were expressed much higher levels especially in patients who had mild-to-moderate cases of COVID-19.

After investigating the neutrophils, the mononuclear phagocytes were investigated next. These are also part of the innate immune response and consist of different white blood cells, like the monocytes, macrophages, dendritic cells, and plasmacytoid dendritic cells. You don’t have to worry about their functions, but what is important to note is that the scientists found that there were ISG expressing monocytes that were enriched in SARS-CoV-2 positive patients, especially those with mild-to-moderate cases of disease. This was similar to what was found about neutrophils! The ISG monocytes and neutrophils frequencies also correlated with one another in mild to moderate SARS-CoV-2 positive individuals. It’s also important to note that the scientists found B and T cell populations were also enriched with ISG expressing cells. 

The next main thing the scientists investigated after observing the ISG expression profiles increased in each cell type, was to look at the holistic view of the disease states. When we talk about expression profiles, what we mean here is that we want to look at how much is the interferon-stimulated gene (ISG) being expressed in the cell to make the immune cell respond to a viral infection.

Using a method called Phenotypic earth mover’s distance (PhEMD), scientists were able to look at each patient and investigate how the different cell types in the immune system progressed. There were eight distinct groups of patients, who all had increasing enrichment of neutrophils, while four of the eight groups had a relative enrichment of monocytes and one out of the eight groups had an enrichment of ISG neutrophils who were mainly SARS-CoV-2 positive patients with mild-to-moderate disease. The main thing to get out of this stage of the research was that there was an inverse correlation between ISG expression level and higher antibody expression against SARS-CoV-2. What this essentially means is that those who have a high antibody response to severe disease tend to have a low ISG expressing cell populations. 

So knowing about this inverse correlation, the scientists then asked if the serum from patients who have severe disease also contain antibodies against ISG-expressing cells when the serum is applied to healthy blood samples in the presence or absence of IFNα (known as interferon alpha). INFα’s job is to essentially alert the immune system that there is a viral infection. So, this test can help the scientist figure out what kind of specificities are seen for these antibodies produced by severe patients. The specificities of these antibodies are for antibodies that either recognize the spike protein and/or the nucleocapsid protein on SARS-CoV-2. Their work suggested that each patient may actually have unique combinations of specificities for their antibodies, when the blood cells had or did not have INFα stimulation. A unique patient sample had serum without ISG-cells but they still had antibodies to INFα, this told scientists that they cannot explain why severe patients lacked ISG cells. Another type of testing was able to show the scientists that severe patients’ serum can potentially block or partially block INFα response and the antibodies produced by these patients were responsible for this blocking. 

The main thing to get out of this study is that there is a complex mechanism that takes place when antibodies attempt to trigger an INFα response, contrarily this mechanism downregulates the INFα response. However, if you block one part of the mechanism, that is CD32 (CD32 is a receptor that helps trigger or block a certain immune response), you can restore INFα based induction. 


Overall, this study showed that almost all patients with severe disease showed that they had a general antibody mediated response. When patients had high antibody responses, it resulted in an inhibition of ISG-expressing immune cell populations. The main thing this work revealed was that depending on the severity of the disease a patient had, they would have a different distribution of ISG expressing immune cell populations. Another major thing this research shows us is that antibodies produced by patients with severe disease of COVID-19 is the reason for the absence of ISG-expressing cell groups in their immune response profile.

Additional research will be needed to characterize the different subclasses of antibodies that contribute to the immune response and their specificities. The main thing to get out of this study, was that the scientists suggest that the ISG expression profile severe patients have may be addressable with drugs to help restore these patients’ immune responses.  

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