In silico analysis suggests less effective MHC-II presentation of SARS-CoV-2 RBM peptides: Implication for neutralizing antibody responses

PLoS One. 2021 Feb 11;16(2):e0246731. doi: 10.1371/journal.pone.0246731. eCollection 2021.

Abstract

SARS-CoV-2 antibodies develop within two weeks of infection, but wane relatively rapidly post-infection, raising concerns about whether antibody responses will provide protection upon re-exposure. Here we revisit T-B cooperation as a prerequisite for effective and durable neutralizing antibody responses centered on a mutationally constrained RBM B cell epitope. T-B cooperation requires co-processing of B and T cell epitopes by the same B cell and is subject to MHC-II restriction. We evaluated MHC-II constraints relevant to the neutralizing antibody response to a mutationally-constrained B cell epitope in the receptor binding motif (RBM) of the spike protein. Examining common MHC-II alleles, we found that peptides surrounding this key B cell epitope are predicted to bind poorly, suggesting a lack MHC-II support in T-B cooperation, impacting generation of high-potency neutralizing antibodies in the general population. Additionally, we found that multiple microbial peptides had potential for RBM cross-reactivity, supporting previous exposures as a possible source of T cell memory.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Antibodies, Neutralizing / immunology*
  • Antibodies, Viral / immunology
  • Antibody Formation
  • B-Lymphocytes / immunology
  • COVID-19 / immunology*
  • Computer Simulation
  • Epitopes, B-Lymphocyte / chemistry
  • Epitopes, B-Lymphocyte / immunology*
  • Histocompatibility Antigens Class II / immunology*
  • Humans
  • Models, Molecular
  • Peptides / chemistry
  • Peptides / immunology
  • SARS-CoV-2 / chemistry
  • SARS-CoV-2 / immunology*
  • Spike Glycoprotein, Coronavirus / chemistry
  • Spike Glycoprotein, Coronavirus / immunology*
  • T-Lymphocytes / immunology

Substances

  • Antibodies, Neutralizing
  • Antibodies, Viral
  • Epitopes, B-Lymphocyte
  • Histocompatibility Antigens Class II
  • Peptides
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2