An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations

Abstract

Multisystem Inflammatory Syndrome in Children (MIS-C) associated with Coronavirus Disease 2019 (COVID-19) is a newly recognized condition in which children with recent SARS-CoV-2 infection present with a constellation of symptoms including hypotension, multiorgan involvement, and elevated inflammatory markers. These symptoms and the associated laboratory values strongly resemble toxic shock syndrome, an escalation of the cytotoxic adaptive immune response triggered upon the binding of pathogenic superantigens to MHCII molecules and T cell receptors (TCRs). Here, we used structure-based computational models to demonstrate that the SARS-CoV-2 spike (S) exhibits a high-affinity motif for binding TCR, interacting closely with both the α- and β-chains variable domains' complementarity-determining regions. The binding epitope on S harbors a sequence motif unique to SARS-CoV-2 (not present in any other SARS coronavirus), which is highly similar in both sequence and structure to bacterial superantigens. Further examination revealed that this interaction between the virus and human T cells is strengthened in the context of a recently reported rare mutation (D839Y/N/E) from a European strain of SARS-CoV-2. Furthermore, the interfacial region includes selected residues from a motif shared between the SARS viruses from the 2003 and 2019 pandemics, which has intracellular adhesion molecule (ICAM)-like character. These data suggest that the SARS-CoV-2 S may act as a superantigen to drive the development of MIS-C as well as cytokine storm in adult COVID-19 patients, with important implications for the development of therapeutic approaches.

Keywords: Covid-19; Cytokine storm; SARS-CoV-2 Spike; Superantigen; Toxic shock syndrome.

Figure 1:. Binding of TCR to SARS-CoV-2 spike trimer near the “PRRA” insert region.

Overall (A) and closeup (B) views of the complex and interfacial interactions. In (B) the spike monomers are colored white, ice blue, and spectrally from blue (N-terminal domain) to red, all displayed in surface representation. For better visualization, the spike trimer is oriented such that its receptor binding domains (RBDs) are at the bottom. TCR α- and β-chains are in red and cyan ribbons. In (B), the segment S₆₈₀PPRAR₆₈₅ including the PRRA insert and highly conserved cleavage site R685 is shown in van der Waals representation (black labels) and nearby CDR residues of the TCRVβ domain are labeled in blue/white. See additional information in Supplementary Fig. S1.

Figure 2:. Sequence and structural properties of the insert “PRRA” motif.

A–B SARS-CoV-2 encodes both a cleavage site (1) and neurotoxin motifs (21) near the insertion PRRA that distinguishes it from SARS-CoV. (A) Sequence alignment of SARS-CoV-2 and multiple SARS-CoV and Bat SARS-like CoV strains (1) near the insertion PRRA. (B) Structural alignment of SARS-CoV-2 and SARS-CoV at the same region. The PRRARS motif is shown in red sticks. (C) Sequence similarity between neurotoxin motifs and the close neighborhood of the PRRA insert, reported earlier (21) as well as HIV-1 gp120 SAg motif (22) in the last row. (D) SARS-CoV-2 S trimer composed of S1 subunits only. The protomers are colored orange, red and gray, and displayed in van der Waals format. The protruding motifs E661-R685 are highlighted in white, green, red, and blue representing the hydrophobic, hydrophilic, acidic, and basic residues.

Figure 3:. The “PRRA” insert in SARS-CoV-2 spike exhibits sequence and structure properties similar to those of bacterial superantigen SEB.

(A) Alignment of the superantigenic sequence of SEB (23) against a homologous sequence of SARS-CoV-2 spike near the PRRA insert and corresponding SARS-CoV segment. Alignments are displayed for both forward (left) and reverse (right) ordering of the SEB sequence. Note the similarity between the former two, while the third (SARS-CoV) shows similarities to SARS-CoV-2, but not SEB, sequence. (B) Structure of the superantigenic peptide (T150 - D161) observed in the crystal structure of SEB (25) (PDB: 3SEB). (C) Structural model for SARS-CoV-2 S palindromic motif E661 - R685. (D) Homologous region in SARS-CoV S exhibits totally distinctive structural features: a salt bridge, K152-E159 (in SEB) or R685-E661 (SARS-CoV-2), is absent in SARS-CoV spike; the former two are poly-basic (with three lysines and three arginines in the respective motifs), whereas SARS-CoV spike counterpart has one basic residue (R667) only; and the former two possess a scaffolding ASN, which is absent on SARS1. (E) Structural alignment of CD28, the receptor binding SEB, onto TCRVβ domain, in support of the adaptability of the putative SAg site to accommodate spike-TCRβ or SEB-CD28 interactions.

Figure 4:. The interfacial interactions between SARS-CoV-2 spike and αβTCR are further stabilized by the association of an ICAM-like motif with TCRVα domain.

(A) Interface between SARS-CoV-2 spike and TCR variable domains. Spike is shown in yellow; TCR Vα and Vβ are in magenta and cyan, respectively. The PRRARS insert is highlighted in red; The mutation site D839 identified in recent study (28) is in green; SARS-CoV-2 counterpart of CD54-like motif identified for SARS-CoV spike (26) is in orange. Residues involved in close interfacial contacts are shown in sticks, with nitrogen and oxygen atoms colored blue and red, respectively. Interactions between atom pairs separated by less than 2.5Å are indicated by black dashed lines. (B) A close-up view of the interactions between the PRRARS insert/motif and TCR Vβ. (C) Same for the D839 mutation site. (D) Interactions between selected residues on ICAM-1-like motif (labeled, orange) TCRVα CDRs.