SARS-CoV-2 RNA levels, IFN-1, ISGs, and NF-κB gene responses within the respiratory tract of mild and severe COVID-19 patients

In a recent study published in medRxiv* preprint server A team of researchers characterized the expression of type 1 and type 2 interferon (IFN-1 and IFN-2), interferon-stimulating genes (ISGs), and nuclear factor kappa B (NF-κB) in the upper respiratory tract of infected patients. with mild and severe coronavirus disease 2019 (COVID-19), to understand innate immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.

Study: Innate antiviral immunity is diminished in the upper respiratory tract of severe COVID-19 patients.  Image credit: ktsdesign/Shutterstock
Stady: Innate antiviral immunity is diminished in the upper respiratory tract of severe COVID-19 patients. Image credit: ktsdesign/Shutterstock


The severe clinical consequences of COVID-19 are a cumulative effect of SARS-CoV-2 infection and the body’s immune response against the virus, leading to cell damage and dysfunction.

Early immune responses to SARS-CoV-2 infection and proliferation in type 2 pneumonia cells located on the alveoli of the upper and lower respiratory tract consist of the secretion of IFN-1 such as interferon alpha-2 (IFNα2), interferon beta-1 (IFNβ1), and IFN-γ 2 as interferon-gamma (IFNγ). Interferons also stimulate the gene expression of ISGs, which produce a local antiviral state.

In addition, during SARS-CoV-2 infection, NF-κB mediates the expression of pro-inflammatory chemokines and cytokines and activates innate and adaptive immune cells. However, the pro-inflammatory responses activated by NF-κB can also cause tissue and organ damage and dysfunction.

Studies indicate that interferon responses during COVID-19 vary with severity and across anatomical segments. Understanding the differences in innate immune responses during SARS-CoV-2 infection can aid in the development of therapies that mitigate the organ damage and dysfunction caused by viral infection and the subsequent pro-inflammatory response.

about studying

In this study, blood, mouth, and nasopharyngeal swabs were collected from hospitalized (severe) and outpatient (mild) cases of patients at the US National Institute of Health. Blood and respiratory samples obtained from healthy individuals were used as a control.

Total RNA was extracted from the swab and blood samples. A droplet digital polymerase chain reaction (ddPCR) was used to amplify SARS-CoV-2 RNA from the RNA extracts of the swab sample. RNA extracted from blood samples was used for the NanoString assay to determine the expression of specific genes. The geometric mean expressions of the 28 ISGs and 11 NF-κBs were determined to calculate the scores of 28 type-1 ISG genes and 11 NF-κB genes, respectively.

An expression vector containing pre-fusion stable SARS-CoV-2 Spike protein A Trimer was used to transfect FreeStyle293F cells. The spike protein was then obtained from the cell supernatant using size exclusion chromatography and used to characterize antibody responses by surface RNA resonance.

Fluorescence reduction neutralization assays were performed to detect neutralizing antibodies in serum samples. The half-maximal inhibitory concentration (IC50) for each serum sample by logistic regression for each dilution series.


Results reported significantly higher ISG and NF-B responses in the upper respiratory tracts of mild COVID-19 patients than in patients with severe COVID-19. Gene expression analysis of ISGs indicated that mild COVID-19 patients had increased expression of 13 genes in the upper respiratory tract compared to severe COVID-19 cases.

A significant portion of the upregulated ISGs had antiviral or regulatory functions, such as CXC motif chemokine ligand 10 (CXCL10), which recruits T cells and natural killer cells presenting type 3 CXC chemoreceptor (CXCR3) and orchestrates adaptive immune responses in the early stages of infection. . Decreased CXCL10 expression in the upper respiratory tracts of severe COVID-19 patients reduces early immune responses, inhibiting clearance of virus-infected cells from the upper respiratory tract.

Moreover, mild COVID-19 cases showed significantly higher IFNα2 and IFNγ levels in the upper respiratory tract compared to severe COVID-19 patients, suggesting an early antiviral response that prevented the spread of SARS-CoV-2 to the lower respiratory tract. In contrast, in severe cases of COVID-19, decreased IFNα2 and IFNγ responses led to increased burden or viral load in the lower respiratory tract within 10 days.

In addition, increased expression of the IFNβ1 gene was observed in severe COVID-19 patients, followed by increased expression of cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase (cGAS) and interferon-stimulatory (STING) genes, which has been linked to brain dysfunction. lining of blood vessels. Lower respiratory tract samples from severe COVID-19 patients also showed NF-κB responses compared to upper respiratory tract and blood samples during the peak of infection.


Overall, the results indicated that weak interferon responses in the upper respiratory tract during the early stages of SARS-CoV-2 infection, followed by strong pro-inflammatory responses such as increased NF-κB responses in the lower respiratory tract during peak stages of infection, contribute to the pathogenesis. with severe COVID-19.

*Important note

medRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, directing clinical practice/health-related behaviour, or treated as hard information.

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