Interferon Responses Could Explain Susceptibility to Severe COVID-19
Impaired or delayed antiviral signaling could be a treatable cause of serious COVID-19.
What are interferons?
Interferons are proteins made by cells in response to infection. In humans, there are 3 categories of interferons: type I, type II, and type III. Insufficient or inappropriately timed activation of interferon signaling may contribute to severe cases of COVID-19, which is caused by the coronavirus SARS-CoV-2. Too little interferons at the beginning and too much later in the infection could contribute to severe or even lethal cases.
In humans, type I interferons consist of IFN-α, β, ε, κ, and ω. Type I interferons are mostly produced by infected cells and cells of the immune system. There is a single member of the type II interferon family: IFN-γ. Type II interferon is also produced by immune cells. Type III interferons consist of 4 subtypes of IFN-λ. Although some immune cells produce type III interferons, these are also produced by epithelial cells or cells that are from the same developmental path as epithelial cells.
Epithelial cells are the cells that line the parts of the body that come into contact with the outside world: the respiratory tract, the gastrointestinal tract, and the urogenital tract. Cells with a similar developmental source include liver cells called hepatocytes.
Each type of interferon has a specific receptor complex that is activated by all members of the family. The type I interferon receptor and the type II interferon receptor are present on many types of immune cells and other cell types. Fewer immune cells have the receptor for type III interferons. Instead, the type III interferon receptor complex is found on epithelial cells in the respiratory tract, gastrointestinal tract, and urogenital tract, as well as liver cells (hepatocytes) and skin cells (keratinocytes). The presence of this type III interferon receptor on respiratory tract epithelial cells is particularly relevant for respiratory infections.
Interferons are proteins that are released by cells in response to detection of pathogens either outside the cell or inside the cell. Interferons are also released if cells detect signals released by other cells that have detected pathogens. When they bind to their receptors on cells, they initiate a set of events that lead to activation of genes involved in pro- and anti-inflammatory responses. Not only can interferons signal other types of cells with the matching receptor, but sometimes even the cells that make the interferon have the matching receptor. So, interferons can stimulate the cells that produced the interferon. This is called a feed-forward loop and lets interferons rapidly amplify the response.
Type I and type III interferons both activate a transcription factor called ISGF3, which stimulates genes with a specific sequence called ISRE. Type I and type III interferons both activate another transcription factor, which turns on genes with a sequence called GAS. Thus, type I interferons stimulate both sets of genes, the ones with ISRE and the ones with GAS. Type II and type III interferons produce a more limited response.
Type I and type II interferons produce a pro-inflammatory response through the genes that they stimulate in other immune cells. Some of these immune cells then proceed to either kill infected cells or neutralize the virus with antibodies. Others take up the viruses and parts of dead infected cells.
In contrast, type III interferons are less inflammatory, because these mostly reduce viral replication in the cells that they stimulate. Another important distinction between the type III interferons and the others is that type III interferons promote epithelial barrier stability. Studies in mice showed that there is less tissue damage if the response to a respiratory virus includes the type III interferon response.
An effective interferon response can eliminate a viral infection. Indeed, specific subtypes of IFN-α are used to treat chronic viral infections, such as hepatitis, and can even cure the infection in some patients. IFN-β is used to treat some autoimmune diseases, such as multiple sclerosis. IFN-γ is used to treat a bone disorder and an immune deficiency syndrome. Thus, there are multiple clinical applications of interferons, including in treatment of viral diseases.
How can a virus avoid interferon-mediated elimination?
If interferons are so powerful, why do people get so sick from virus infections? Viruses are nucleic acid (either RNA or DNA) usually bound with one or more proteins. This genetic core is surrounded by a protein shell with lipids. The genetic material of the virus encodes more than just proteins needed for the virus to reproduce itself and the proteins that bind the nucleic acid and those that form the outer shell. Some of these extra proteins have important functions in making the final proteins from longer precursors, but others interfere with the antiviral responses of the host.
Viruses can interfere with the host proteins that sense viruses inside cells or viral proteins or particles outside of cells and thus prevent interferon genes from being turned on. This reduces the production of interferons by infected cells. Another way viruses block production of the interferons is to prevent the transcription factors from getting into the nucleus and turning on the interferon genes or genes that produce signals indicating a cell is infected. At least 10 different viral proteins in human coronaviruses function to reduce interferon production or signaling by infected cells.
Viruses can interfere with the interferon signaling in cells with the receptors. Virus proteins can physically bind interferons so that the interferons cannot bind to their receptors. At least 2 proteins in human coronaviruses block the ability of interferons to stimulate gene expression. Viruses can also interfere with the function of some of the antiviral proteins produced by genes stimulated by interferons.
The coronaviruses that only cause mild symptoms (like colds) stimulate a strong interferon response. Like SARS-CoV-2, SARS and MERS are two coronaviruses that cause serious, even fatal, disease in humans. Compared with the coronavirus that causes mild disease, SARS and MERS induce a much smaller interferon response. Thus, a reduced interferon response likely contributes to the differences in their disease-causing abilities (virulence).
By comparing the amino acid sequences of SARS-CoV-2 with those of SARS, MERS, and coronaviruses that cause mild disease, researchers can predict which interferon evasion systems are likely present in SARS-CoV-2. This information could help in the development of treatment strategies.
What is known about the interferon response in COVID-19 patients?
Most of the studies of COVID-19 patients have been of those that are seriously sick and require hospitalization or of patients that died of COVID-19. Even these are small studies with limited numbers of patients. Additionally, information about mild cases of this viral infection is lacking. Despite these limitations, the studies provide information that could be useful both in explaining how some patients develop such severe illness and in developing strategies for treatment.
Because interferons stimulate the expression of specific genes, one way that researchers examine the interferon response is by determining the gene expression profile of blood cells from patients. One study reported results from profiling the expression of genes in white blood cells from 4 patients before, during, and after the patients were hospitalized in the intensive care unit. They found that the genes indicating a type I interferon response were stimulated the most at the time when the patients were sickest.
Another study used both gene expression profiling and detection of some of the encoded gene products to evaluate the interferon response. Comparison of the gene expression profiles in lung tissue from 2 patients that had died of COVID-19 and 2 samples of healthy lung tissue from biopsies showed that the COVID-19 patients did not have high expression of genes associated with either a type I or type III interferon response and the genes encoding type I and type III interferons were also not expressed. Despite this apparent lack of a type I and type III interferon response, the lung samples from the COVID-19 patients had high expression of inflammatory genes and genes that produce signals to recruit inflammatory immune cells.
These researchers also measured proteins important in regulating immune response in the serum of hospitalized COVID-19 patients and patients with respiratory issues that were not related to COVID-19. In this case, the study included 24 patients of each type. The proteins measured are called chemokines and cytokines; these serve as signals for immune cells or cause inflammatory responses.
Both groups of patients were negative for IFN-β and IFN-λ, indicative of a poor type I and type III interferon response. Instead, the COVID-19 patients had increased amounts of proteins associated with generalized inflammation, not necessarily viral infection. These signals included proteins that attract cytotoxic immune cells (T cells and NK cells), immune cells that take up damaged cells or cellular debris and that activate the cytotoxic cells (macrophages and monocytes), and another type of immune cell that takes up viral particles if the particles are coated by antibodies (neutrophils).
The finding of signals for recruiting neutrophils is particularly important because neutrophils can cause tissue damage and form structures called neutrophil extracellular traps (NETs). These NETs trap pathogens, but they also cause blood clots to form. Thus, excessive recruitment of neutrophils in the context of an impaired antiviral interferon response could be a factor that contributes to the compromised lung function, leakage of fluid into the lungs, and formation of blood clots that lead to the death of patients with COVID-19.
Studies of SARS and MERS suggest that the interferon response is delayed. Compared with coronaviruses that cause mild disease and with milder cases of these two coronaviruses that can cause severe disease, the patients with severe SARS or MERS had higher viral loads and delayed interferon responses. Thus, it could be that the patients most susceptible to severe disease are those that cannot mount an effective early antiviral immune response.
A study of 50 patients with cases ranging from mild to severe found that gene expression profiles indicating type I and type II interferon responses were highest in patients with mild to moderate disease and were low in the patients with severe or critical disease. A similar difference in type I interferon activity was detected in the serum from the patients: Patients with more severe disease had less type I interferon activity in their blood.
What conditions can cause an impaired antiviral interferon response?
The idea that an impaired early antiviral immune response contributes to susceptibility to severe COVID-19 is consistent with those at high risk. Older people are among the most at risk for severe COVID-19. Older people have a well-documented impairment in type I and type III interferon production from immune cells in response to virus infection. Diabetes and cancer can also suppress type I interferon production, which could explain the increased risk of people with these conditions for developing severe COVID-19.
Obesity is another condition that is associated with high risk of developing severe COVID-19 and a poor type I interferon response. In addition, obesity is associated with chronic inflammation. So, these people may be even at a higher risk. In addition to not effectively clearing the virus due to the impaired antiviral interferon response, SARS-CoV-2 infection could push the existing chronic inflammatory response past a critical threshold that results in severe disease.
Thus, patients that develop severe COVID-19 may have an initially poor antiviral interferon response and an exaggerated inflammatory response. This inflammatory response does not effectively eliminate the virus.
How can interferons be used to treat or prevent COVID-19?
Clinical trials with various interferons have been started. Studies with cells and preliminary results in people support these trials. Studies with cultured cells that showed a reduction in viral replication in cells pretreated with IFN-α or IFN-β (Mantlo and colleagues, and Lokugamage and colleagues). A study with primary intestinal epithelial cells or organoids (cultures of mixed cell types that form structures like those in the body) also showed that viral infection was reduced by treatment of the cells with either IFN-β or IFN-λ.
A Chinese study reported no cases of COVID-19 in ~3000 healthcare workers receiving nasal drops with IFN-α, suggesting that this could be an effective prophylactic strategy. Indeed, the timing of the treatment may be critical. Type I interferons, which could exacerbate tissue damage, may be inappropriate for patients with late stage, severe COVID-19. Instead, those patients may benefit more from type III interferon therapy. Either type I or type III interferons could potentially be beneficial as prophylactic agents.
However, it is also possible that genetic variations in people will also contribute to the effectiveness of such approaches. More information about how interferon responses vary among COVID-19 patients and the association with disease outcomes will help guide effective trials of possible treatment and prevention strategies.
Acknowledgment: Thanks to Dr. Akiko Iwasaki for critical reading.
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Reviews and Commentary
Agrawal, Mechanisms and Implications of Age-Associated Impaired Innate Interferon Secretion by Dendritic Cells: A Mini-Review. Gerontology 59, 421- 426 (2013). DOI: https://doi.org/10.1159/000350536
Broggi, et al., Type III Interferons: Balancing Tissue Tolerance and Resistance to Pathogen Invasion. J. Exp. Med. (2019) DOI: https://doi.org/10.1084/jem.20190295
Park and Iwasaki, Type I and Type III Interferons — Induction, Signaling, Evasion, and Application to Combat COVID-19. Cell Host & Microbe (2020). DOI: https://doi.org/10.1016/j.chom.2020.05.008
Prokunina-Olsson, et al., COVID-19 and Emerging Viral Infections: The Case for Interferon lambda. J. Exp. Med. 217, e20200653 (2020). DOI: https://doi.org/10.1084/jem.20200653
Rönnblom and Leonard, Interferon Pathway in SLE: One Key to Unlocking the Mystery of Disease. Lupus Science & Medicine 6, e000270 (2019). DOI: 10.1136/lupus-2018–000270
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