Once inside the body, the SARS-CoV-2 coronavirus first reproduces in the upper respiratory tract. Usually, the number of virus particles increases to a maximum within the first week after infection. The higher the virus replication in the nasopharynx, the more likely it is to infect another person. Thus, in the first week, the patient with coronavirus is most contagious. In addition, with a high level of viral replication, the probability of severe COVID-19 is higher. Therefore, effective antiviral response from the body at an early stage of the disease can reduce the transmission of the virus and the progression of COVID-19 disease.

In response to the invasion of the virus, the dendritic cells of the innate immune system produce antiviral interferon (IFN). The interferon response limits the early replication of the virus on the mucous membranes. However, the SARS-CoV-2 coronavirus suppresses and delays this response. In addition, studies have shown that interferon protects against severe COVID-19. However, it is unclear exactly when this protective mechanism is activated at an early stage of infection.

The mucosal interferon response is triggered when epithelial and immune cell pattern recognition receptors detect viral RNA. This event triggers the expression of IFN types I and III and interferon-stimulated genes (ISG). The secreted IFNs, in turn, binds to the cell surface receptors on neighboring cells, enhancing the expression of ISG and creating antiviral protection of the mucosa.

Most respiratory viruses cause an IFN response in the respiratory tract. The SARS-CoV-2 coronavirus can trigger the expression of IFN and ISG in the airway epithelium, but the IFN response will be slowed. Therefore, in some cases, virus replication will be suppressed ineffectively. Studies have shown that while pretreatment with exogenous IFN blocks SARS-CoV-2, IFN is much less effective when administered after infection is established. Analysis of epithelial cells from the nasopharynx of patients with COVID-19 showed that ISGS are present only in patients with mild or moderate, but not severe, disease. It is consistent with the observation that patients with severe COVID-19 are more likely to have defects in the interferon signaling pathways. These results together suggest that epithelial cells can trigger an IFN response when SARS-CoV-2 enters the body, but the timing and magnitude of the interferon response are crucial in suppressing infection.

At Yale University (USA), scientists examined samples of nasopharyngeal swabs (NP) of patients with coronavirus obtained at different periods after infection, including specimens collected close to the beginning of the disease in asymptomatic subjects. The researchers analyzed the expression of ISG in the respiratory mucosa of patients with COVID-19. The increase and decrease in ISG expression correlated with the growth and reduction of viral load. The researchers found that prior rhinovirus infection increased ISG activity at an early stage of SARS-CoV-2 disease and completely prevented SARS-CoV-2 replication. Moreover, there was no such effect when blocking ISG expression. Blocking the expression of ISG during SARS-CoV-2 increased the rate of virus replication under low infectious dose conditions.

Study results

  • SARS-CoV-2 triggers an IFN response in the nasopharynx. All NP samples positive for SARS-CoV-2 showed an increase in ISG expression compared to the healthy control group. In addition, levels of IFN-λ1 and IFN-γ, but not other IFN subtypes, were significantly higher in patients with COVID-19 than in the control group.
  • The level of the NP CXCL10 protein correlates with the expression of ISG at the RNA level.
  • The level of CXCL10 correlates with the viral load.
  • CXCL10 shows the kinetics of the body’s response to SARS-CoV-2 at the onset of infection.
  • SARS-CoV-2 RNA increases exponentially, doubling time is about 6 hours, infection causes a sustained ISG response on the 4th day after infection.
  • Rhinovirus infection (RV) increases the level of dACE2 mRNA, but not full-size ACE2, in an IRF3-dependent manner.
    In organoid cultures, SARS-CoV-2 causes ISG expression with a time delay relative to viral replication. Prior infection with another virus can accelerate these ISG responses. RV causes colds. It is the most commonly detected virus in the human upper respiratory tract. Scientists have suggested that RV may limit SARS-CoV-2 infection by enhancing the antiviral response. However, it can also contribute to infection by increasing the expression of SARS-CoV-2 entry receptors. The scientists found that rhinovirus infection increases the level of dACE2 mRNA, but not the full-size ACE2, in an IRF3-dependent manner. When infected with rhinovirus, the shortened form of the ACE2 – dACE2 receptor, which is not a functional receptor for coronavirus entry into the cell, significantly increases. The expression of the whole–size ACE2 receptor also increases, but to a lesser extent-about 2 times less than dACE2. The expression of TMPRSS2 is not affected by rhinovirus infection.
  • Prior RV infection blocks SARS-CoV-2 replication.
    RV triggers ISG expression on the 3rd day after infection. The organoids infected with RV were found to be healthy 3 days after infection with the coronavirus. The viral load of SARS-CoV-2 increased exponentially in infected cultures without prior RV infection, but did not increase significantly between 24 and 72 hours when the cultures were exposed to RV 3 days prior. Thus, despite the slight increase in full-size ACE2 mRNA caused by RV, RV infection results 3 days before SARS-CoV-2 infection is a blockage of coronavirus replication. Evaluation of ISG expression during infection showed that in the early stages of SARS-CoV-2 infection, ISG expression was significantly higher in cultures pre-infected with RV than in cultures infected with SARS-CoV-2 without prior RV exposure.
  • RV triggers an IFN response in the witness cells.
    Scientists have evaluated the expression of ISG for 5 days. After infection, RV replicated steadily, peaking after 24 hours, and then replication declined significantly, but RV was still detected on day 5 – a time point corresponding to 48 hours after SARS-CoV-2 infection in a sequential infection experiment. ISG expression increased and decreased in parallel with virus replication but was still significantly higher than in cells subjected to false treatment on day 5 after RV infection. In addition, on day 5 after RV infection, high levels of IFN-λ1 protein were detected in cell cultures. Although RV RNA was detected only in a small subset of cells in infected cultures on day 5 (1.67%), ISG was elevated in all cells compared to cultures subjected to false treatment. It indicates that RV elicits a robust antiviral response in uninfected cells and is consistent with detecting high levels of IFN-λ1. These data together suggest that RV infection triggers sustained ISG expression in all cells of infected cultures, many of which are witness cells.
  • RV blocks SARS-CoV-2 replication by expressing ISG.
    Scientists have blocked the expression of ISG with the signal-transfer inhibitor BX795. Under these conditions, the ISG response to SARS-CoV-2 did not limit virus replication since BX795 suppressed SARS-CoV-2 ISG expression but did not alter the viral load. However, BX795 dramatically altered SARS-CoV-2 replication in the context of RV infection. Prior RV infection suppressed SARS-CoV-2 replication by more than 1,000 times. However, after pretreatment of BX795, SARS-CoV-2 replication was restored. These results indicate that ISG expression is necessary to suppress SARS-CoV-2 replication by prior RV infection.
    72 hours after SARS-CoV-2 infection and 6 days after RV infection, RV RNA was detected at much lower levels than SARS-CoV-2 RNA and showed a slight decrease during SARS-CoV-2 co-infection without BX795, but significantly higher levels when both viruses were detected in the presence of BX795. This result indicates that the antiviral response also restricts RV replication under SARS-CoV-2 co-infection conditions at the same point in time. In other words, in the presence of a natural antiviral response, the viral load of both viruses decreased, but if ISG expression was suppressed, the viral load was equal (for SARS-CoV-2) or higher (for RV) during co-infection.
  • The ISG response restricts SARS-CoV-2 replication in low-dose infectious conditions.

Conclusions

At the beginning of the infection, SARS-CoV-2 replication occurs exponentially. The coronavirus triggers an ISG response, with the highest IGG level being reached just before the viral load drops in the airway epithelium. The body’s response to prior rhinovirus infection accelerates ISG expression and suppresses SARS-CoV-2 replication in the airway epithelium. The ISG response triggered by the coronavirus significantly reduces virus replication due to the low initial viral load. These results show that the protective response of ISG in the airway epithelium is dynamic and, in some instances, significantly restricts the replication of SARS-CoV-2 at the beginning of infection.

Source

Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics

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