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A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro

Cheng, M.H. et al. (BioRxiv) DOI: 10.1101/2020.11.24.395079



  • Neutralizing antibodies

  • Superantigen

  • Furin-cleavage site


Main Findings

  • It has been hypothesized that the mechanism leading to the hyperinflammatory state following severe SARS-CoV-2 infection is similar to that of toxic shock syndrome which is caused by the binding of unprocessed bacterial toxins directly to the major histocompatibility (MHC) molecule and one of the variable domains of the T cell receptor (TCR). This TCR/MHC cross-linking causes an excessive release of inflammatory cytokines leading to toxic shock. The toxins responsible for this non-specific T cell activation are referred to as superantigens (SAgs)

  • in silico, it has been shown that TCRs are capable of engaging a superantigen motif adjacent to the SARS-CoV-2 S1/S2 cleavage site with a sequence and structure similar to staphylococcal enterotoxin B (SEB) (Chan et al. PNAS. 2020.

  • In this preprint (Chan et al.), molecular docking simulations confirmed that this SAg insert enters the catalytic cavities of transmembrane protease serine 2 (TMPRSS2) and furin, stabilizing S prior to S1/S2 cleavage (which is critical for S priming prior to membrane fusion)

  • SEB antibodies were screened in silico for their ability to bind the SAg motif on S. The monoclonal antibody (mAb) 6D3 exhibited comparable binding affinity to TMPRSS2 and furin 

  • 6D3 was capable of inhibiting infection with live virus assessed by immunofluorescent staining of dsRNA and S in Vero-E6 cells. 6D3 also possesses a cluster of acidic residues in CDR2 similar to the SARS-CoV-2 neutralizing antibody (NAb) 4A8

  • Docking simulations also showed that both 6D3 and 4A8 are predicted to bind      the S1/S2 furin cleavage site of HCoV-OC43 S (a pathogenic betacoronavirus 

      similar to SARS-CoV-2)


  • Viral challenge studies in vivo are necessary to confirm the therapeutic and prophylactic potential of 6D3 

  • Stimulation with the S SAg and SEB using patient PBMC’s ex vivo is needed to confirm the phenomenon of non-specific T cell activation in severe COVID-19

  • in vitro assays are needed to confirm whether SAg recognition in severe COVID-19 patients takes place in a TCR Vβ-dependent manner

  • in vitro assays are also needed to determine whether these mAbs can block non-specific T cell activation by SAg binding


TCR Vβ skewing, an indicator of superantigen-mediated T cell activation, has been observed in patients with severe COVID-19 and the Multisystem Inflammatory Syndrome (MIS-C) following SARS-CoV-2 infection. Meanwhile, though monoclonal antibodies represent an exciting treatment opportunity for COVID-19 patients, most neutralizing antibodies (NAbs) previously isolated from convalescent patients have been structurally characterized with S proteins possessing a mutated S1/S2 cleavage site. This helps to stabilize the complex for structural analysis but fails to capture NAbs that bind the cleavage site. Therefore, this study shows that mAbs targeting the cleavage site are potentially capable of virus neutralization and mitigation of shock following infection with SARS-CoV-2 and other human coronaviruses that encode furin-like cleavage sites such as MERS, HKu1, and OC43.


Reviewed by Matthew Brown as part of the cross-institutional journal club of the Immunology Institute of the Icahn School of Medicine, Mount Sinai and the Kennedy Institute of Rheumatology, University of Oxford.

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