Multisystem Inflammatory Syndrome in Children and Long COVID: The SARS-CoV-2 Viral Superantigen Hypothesis

Abstract

Multisystem inflammatory syndrome in children (MIS-C) is a febrile pediatric inflammatory disease that may develop weeks after initial SARS-CoV-2 infection or exposure. MIS-C involves systemic hyperinflammation and multiorgan involvement, including severe cardiovascular, gastrointestinal (GI) and neurological symptoms. Some clinical attributes of MIS-C-such as persistent fever, rashes, conjunctivitis and oral mucosa changes (red fissured lips and strawberry tongue)-overlap with features of Kawasaki disease (KD). In addition, MIS-C shares striking clinical similarities with toxic shock syndrome (TSS), which is triggered by bacterial superantigens (SAgs). The remarkable similarities between MIS-C and TSS prompted a search for SAg-like structures in the SARS-CoV-2 virus and the discovery of a unique SAg-like motif highly similar to a Staphylococcal enterotoxin B (SEB) fragment in the SARS-CoV-2 spike 1 (S1) glycoprotein. Computational studies suggest that the SAg-like motif has a high affinity for binding T-cell receptors (TCRs) and MHC Class II proteins. Immunosequencing of peripheral blood samples from MIS-C patients revealed a profound expansion of TCR β variable gene 11-2 (TRBV11-2), which correlates with MIS-C severity and serum cytokine levels, consistent with a SAg-triggered immune response. Computational sequence analysis of SARS-CoV-2 spike further identified conserved neurotoxin-like motifs which may alter neuronal cell function and contribute to neurological symptoms in COVID-19 and MIS-C patients. Additionally, autoantibodies are detected during MIS-C, which may indicate development of post-SARS-CoV-2 autoreactive and autoimmune responses. Finally, prolonged persistence of SARS-CoV-2 RNA in the gut, increased gut permeability and elevated levels of circulating S1 have been observed in children with MIS-C. Accordingly, we hypothesize that continuous and prolonged exposure to the viral SAg-like and neurotoxin-like motifs in SARS-CoV-2 spike may promote autoimmunity leading to the development of post-acute COVID-19 syndromes, including MIS-C and long COVID, as well as the neurological complications resulting from SARS-CoV-2 infection.

Keywords: MIS-C multisystem inflammatory syndrome in children; SARS-CoV-2; long COVID; neurotoxin-like segment; post-acute sequelae of COVID-19 (PASC); superantigen; superantigen-like motif.

Figure 1

SARS-CoV-2 spike glycoprotein structure, its structural subunits, putative SAg and neurotoxin-like motifs. (A) The SARS-CoV-2 spike trimer in the pre-fusion state, where one of the protomers is shown in spectral colors from blue (N-terminal domain, NTD) to red (C-terminus), and the other two protomers are shown in white and gray. Each protomer has a Receptor-Binding Domain (RBD) that can assume up and down conformations in the receptor-bound and unbound states. (B) Structure of S1 subunit, shown for the spectrally colored protomer, in the same format and perspective as in (A). Pink color showed the “PRRA” insert unique to SARS-CoV-2. (C) S1 trimer after shedding of the S2 trimer, shown from top. Each protomer is shown in a different color (orange, brick, and gray). The SAg-like motifs (E661 to R685) in the SARS-CoV-2 spike S1 trimer are shown in van der Waals (VDW) format; white, green, red, and blue represent hydrophobic, hydrophilic, acidic and basic residues. (D) S2 subunits after cleavage, forming a fusion trimer [same color and format as in (A)]. (E) Neurotoxin motifs on the spike glycoprotein. Side (left panel) and top (middle panel) views of the spike in the presence of a bound TCR (yellow ribbon) are shown. The spike protomers are colored green, cyan and magenta in this case, and the neurotoxin motif [residues 299-351; reported in (44)] belonging to the cyan and magenta protomers are displayed in blue and red spheres, respectively. Note that the portion C336-Y351 (orange spheres on the right panel) is exposed to interact with the host cell receptor or substrates. The homology model [44] constructed based on the cryo-EM structure resolved by Wrapp et al. (2020) (PDB id: 6vsb) has been used in the ribbon diagrams.

Figure 2

Schematic of the proposed hypothesis. (A) SARS-CoV-2 spike (blue) proteins expressed at the surface of SARS-CoV-2 interact with host cell ACE2 receptor (yellow) and transmembrane protease TMPRSS2 (purple). After SARS-CoV-2 spike proteins bind to ACE2, they are cleaved at the S1/S2 junction by human proteases (TMPRSS2 and furin), which mediate membrane fusion and viral cellular entry. Protease binds the spike trimer near the PRRA insert unique to SARS-CoV-2 and located in the SAg-like motif adjacent to the S1/S2 cleavage site. Cleavage of S1/S2 separates each subunit of the spike trimer into 2 subunits, S1 and S2, resulting in the S2 fusion trimer (bound to viral membrane) and the S1 trimer (released to extracellular space). The SAg and neurotoxin-like motifs are exposed in S1. (B) The neurotoxin-like motif in circulating SARS-CoV-2 S1 crosses the BBB and contributes to the neurological symptoms associated with MIS-C and individuals recovering from COVID infection. (C) SARS-CoV-2 persists in extra-pulmonary organs, including the GI tract. (D) Persistent presence of SARS-CoV-2 antigens in the gut results in Zonulin-mediated increased intestinal permeability and leakage of S1 and the SAg-like motif into the circulation. (E) The SAg-like motif in SARS-CoV-2 S1 activates a large fraction of T cell and leads to TCR skewing. (F) SARS-CoV-2 and the SAg-like motif in S1 triggers maladapted immune responses and autoimmunity. The SAg-like motif in shed S1 triggers T cells expansion, TCR skewing and hyperinflammation/cytokine storm, resulting in host tissue damage and autoantigen release. SARS-CoV-2 persistence in tissue reservoirs also activates autoreactive T and B cells via molecular mimicry. Autoreactive T and B cells may also be activated by either repeated exposure to the SAg-like motif in S1 and bystander activation. Release of autoantigens and activation of autoreactive lymphocytes leads to the production of autoantibodies that further damage host tissues. Figure created with BioRender.com.