Radiograph of inflamed lungs.

Radiograph of inflamed lungs. GETTY

Covid-19 patients have reported a vast array of symptoms, including issues related to the heart, kidneys, liver, brain, and a number of other areas. Neurological problems following SARS-CoV-2 infection, ranging from the inability to concentrate to overwhelming fatigue, have been especially concerning. Exactly how this happens, however, remains somewhat of a mystery. By and large, these kinds of symptoms were considered a result of direct viral infection of host cells. Yet increasingly we’re realizing that indirect mechanisms may play a larger role than initially assumed— whether through secondary effects from viral proteins or through the release of inflammatory cytokines and chemokines.

A recent study by researchers at Cleveland State University, led by Abhijit Basu with senior author Barsanjit Mazumder, might help shed some light into this dark corner of Covid-19 pathogenesis. The key discovery is that the SARS-CoV-2 virus need not enter a cell to disturb its function in profound ways; it may be sufficient for the spike (S) protein to simply bind to the outside of a cell to cause significant, and even lethal, changes. 

Nearly two decades ago, Mazumder and his then colleagues were researching how our immune system autoregulates inflammation. They knew that a protein called ceruloplasmin (Cp) was involved in this process, but weren’t sure how. Looking into it, Mazumder et al. discovered that ceruloplasmin messenger RNA contains a special “hairpin” loop structure (figure 1). When this structure gets bound by a specific bundle of proteins, ceruloplasmin production is halted, restricting inflammation and preventing our immune response from accidentally harming our own bodies. All of this happens via signals sent from outside the cell, kickstarted by a small protein called interferon-gamma (IFN-γ).

The researchers called the mRNA structure a gamma interferon inhibitor of translation (GAIT) element, and the bundle of proteins that binds to it a GAIT complex

GAIT element of human ceruloplasmin


Since then, it has been discovered that some viruses also carry GAIT-like elements in their genome. For example, a common pig coronavirus, transmissible gastroenteritis coronavirus (TGEV), has been shown to have a GAIT-like element that allows it to modulate the host’s innate immune response. 

Curious to see whether something similar could be seen in SARS-CoV-2, Basu et al. analyzed the entirety of the viral genome. They found two sequences, one located within ORF1a and a second in the S gene, that could form structures akin to those of canonical GAIT elements (Figures 2 & 3), albeit with dissimilar genetic sequences.

Location of VAIT elements in Genome

FIGURE 2. Schematic representation showing the location of ORF1a RNA and Spike mRNA within the … [+]BASU ET AL. 2022

VAIT Elements

FIGURE 3. GAIT-like hairpin loop structures in SARS-CoV-2 ORF1a RNA and S mRNA. BASU ET AL. 2022

The researchers discovered that the GAIT-like elements in SARS-CoV-2 help silence the production of ORF1a and S. This process kicks off when the SARS-CoV-2 spike protein binds to our lung cells’ ACE2 receptors. They decided to call the hairpin loop structures found in SARS-CoV-2 virus-activated inhibitor of translation (VAIT) elements, emphasizing the fact that genomic silencing takes place on the basis of viral signals rather than signals from IFN-γ.

Although Basu et al. aren’t exactly sure of the first steps of the signaling pathway, they suggest that it may happen by way of the ERK1/2 “kinase cascade.” Kinase cascades link extracellular signals to a number of different cellular processes, generally through the phosphorylation of proteins— essentially, they provide a means of giving a cell a set of instructions without needing to enter into it. 

This activates another kinase cascade, DAPK-ZiPK, which causes the release of L13a from our ribosomes— the cellular “machinery” used in the production of proteins. L13a binds with other proteins, as of yet still unknown, to form the VAIT protein complex that ultimately binds to the VAIT RNA elements. Figure 4 outlines a proposed pathway for VAIT element binding. 

VAIT Pathway (full)

FIGURE 4. A model of the VAIT-dependent signaling pathway that silences synthesis of SARS-CoV-2 … [+]BASU ET AL. 2022

It’s important to note that death-associated kinase 1 (DAPK-1) is involved in apoptosis and autophagy. Apoptosis is a process by which stressed cells commit suicide in such a way as to not induce inflammation; they just quietly digest themselves. But regardless, it leads to cell death. In this sense, the virus may be triggering a very potent reaction by activating DAPK-1. 

Basu et al.’s research shows that, independent of its role as an entry receptor for SARS-CoV-2, extracellular binding of the spike protein to host ACE2 triggers an intracellular cascade that has the potential to alter both cell physiology and expression of viral proteins. 

An independent study by Elisa Avolio et al. found that SARS-CoV-2 spike binding to another receptor, C147, initiates a signaling cascade that disrupts pericyte function and induces death of vascular endothelial cells. Together these studies show that signal transduction induced by sarbecovirus S protein binding to surface receptors are likely to contribute to viral pathogenesis independent of the virus’s ability to enter and to replicate in the target cell.