Human Memory B Cells Harbor Diverse Cross-Neutralizing Antibodies against BK and JC Polyomaviruses

Abstract

Graphical Abstract Highlights d Latent polyomavirus infections generate a potent, neutralizing antibody response d The anti-BKV repertoire is clonally diverse and harbors crossreactive antibodies d Memory IgM B cell receptors are affinity matured and isotype restricted d A monoclonal cross-neutralizing IgG binds a conserved quaternary viral epitope SUMMARY Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with minimal clinical manifestations. However, viral reactivation can cause severe pathology in immunocompromised individuals. We developed a high-throughput, functional antibody screen to examine the humoral response to BK polyomavirus. This approach enabled the isolation of antibodies from all peripheral B cell subsets and revealed the anti-BK virus antibody repertoire as clonally complex with respect to immunoglobulin sequences and isotypes (both IgM and IgG), including a high frequency of monoclonal antibodies that broadly neutralize BK virus subtypes and the related JC polyomavirus. Cryo-electron microscopy of a broadly neutralizing IgG single-chain variable fragment complexed with BK virus-like particles revealed the quaternary nature of a conserved viral epitope at the junction between capsid pentamers. These features unravel a potent modality for inhibiting polyomavirus infection in kidney transplant recipients and other immunocompromised patients.

Antibody Escape by Polyomavirus Capsid Mutation Facilitates Neurovirulence

“…Refinement of both datasets produced maps at 3.9 Å and 4.2 Å resolution for the A2 and A2-Fab complex, respectively ( Figure 4B and Table S2) (Punjani et al, 2017;Zivanov et al, 2018). In contrast to the 60 epitopes present in the BKPyV:scFv structure (one per asymmetric unit), our complex map revealed density for 360 copies of 8A7H5Fab, corresponding to six copies per asymmetric unit, that is 1 Fab per each VP1 ( Figures S3A and S3B) (Lindner et al, 2019).…”

“…recognized an epitope comprised of residues from VP1 proteins between hexavalent capsomers (Lindner et al, 2019). Thus, mutations may disrupt recognition by antibodies with epitopes distinct from that of 8A7H5.…”

“…Notably a 4.2 Å map of BKPyV interacting with single chain variable fragment (scFv) provided insight into antibody neutralization of polyomavirus (Lindner et al, 2019). Structural studies typically use the fragment antigen-binding (Fab) to avoid potential cross-linking of capsids by and multiple points of intrinsic flexibility of intact antibodies that interfere with cryo EM analysis.…”

JCPyV VP1 Mutations in Progressive Multifocal Leukoencephalopathy: Altering Tropism or Mediating Immune Evasion?

“…The majority of this antibody’s epitope lies in the EF loop, distant from the receptor binding pocket and sites of PML mutations. However, a portion of the epitope contains several residues in the BC loop in the immediate vicinity of the frequently mutated L54 residue [ 126 ]. JCPyV mAbs generated from a natalizumab-treated PML patient provide evidence for a dominant nAb target in VP1 [ 127 ].…”

“…The tissue, cell type(s), and mechanisms responsible for generating VP1 mutations are not known; for JCPyV, kidney epithelia and certain glia have been suggested as possible locations [ 67 , 84 ]. PyV antibody-escape mutants can arise by serial passage in epithelial cells, indicating that these cells are capable of generating VP1 mutations [ 106 , 126 ]. Human glia engrafted in Mbps shi/shi Rag2 −/− mice also generate VP1 point mutations in JCPyV [ 67 ].…”