Human Paramyxovirus Infections Induce T Cells That Cross-React with Zoonotic Henipaviruses

Abstract

Humans are infected with paramyxoviruses of different genera early in life, which induce cytotoxic T cells that may recognize conserved epitopes. This raises the question of whether cross-reactive T cells induced by antecedent paramyxovirus infections provide partial protection against highly lethal zoonotic Nipah virus infections. By characterizing a measles virus-specific but paramyxovirus cross-reactive human T cell clone, we discovered a highly conserved HLA-B*1501-restricted T cell epitope in the fusion protein. Using peptides, tetramers, and single cell sorting, we isolated a parainfluenza virus-specific T cell clone from a healthy adult and showed that both clones cleared Nipah virus-infected cells. We identified multiple conserved hot spots in paramyxovirus proteomes that contain other potentially cross-reactive epitopes. Our data suggest that, depending on HLA haplotype and history of paramyxovirus exposures, humans may have cross-reactive T cells that provide protection against Nipah virus. The effect of preferential boosting of these cross-reactive epitopes needs to be further studied in light of paramyxovirus vaccination studies.IMPORTANCE Humans encounter multiple paramyxoviruses early in life. This study shows that infection with common paramyxoviruses can induce T cells cross-reactive with the highly pathogenic Nipah virus. This demonstrates that the combination of paramyxovirus infection history and HLA haplotype affects immunity to phylogenetically related zoonotic paramyxoviruses.

Keywords: Nipah virus; T cells; human parainfluenza virus; measles virus; paramyxovirus.

FIG 1

Conservation between MeV and CDV. (A) Heat map indicating homology between MeV and CDV for the respective open reading frames (ORFs). Green represents fully homologous residues, and red shows nonhomologous residues. Proteins and total percentage of conservation are indicated above the heat map. (B) Stretches of fully conserved homologous amino acids when comparing all ORFs from MeV and CDV, containing potential cross-reactive T cell epitopes. Stretches of 1 to 5, 6 to 10, 11 to 20, and 21 or more homologous amino acids are indicated in shades of gray. MeV, measles virus; CDV, canine distemper virus; N, nucleoprotein; P, phosphoprotein; M, matrix protein; F, fusion protein; H, hemagglutinin; L, large protein or polymerase.

FIG 2

Characterization of cross-reactive TCC. A panel of well-characterized MeV-specific T cell clones (TCC) was tested for cross-reactivity with CDV. (A) Two representative examples of CD4⁺ TCC, one solely reactive with MeV (CD4^MeV1), the other one reactive with both MeV and CDV (CD4^Xreact1) as tested by IFN-γ ELISPOT. (B) Two representative examples of CD8⁺ TCC, one solely reactive with MeV (CD8^MeV1), the other one reactive with both MeV and CDV (CD8^Xreact1). (C) In vitro virus suppression assay in which CD8^MeV1 and CD8^Xreact1 were cocultured with MeV- and CDV-infected autologous B-LCL. MeV, measles virus; CDV, canine distemper virus; B-LCL, B-lymphoblastic cell line; TCC, T cell clone.

FIG 3

Epitope mapping for CD4^Xreact1 and CD8^Xreact1. Overlapping peptide-pulsed autologous B-LCL were used to determine the minimal epitope recognized by CD4^Xreact1 and CD8^Xreact1 in IFN-γ ELISPOT. (A and D) Overlapping 15-mer peptides with 11 overlap were initially used. (B and E) Fine-tuning of recognized region using overlapping 10-mer peptides with 9 overlap. (C and F) Confirmation of recognition of F^129–137 (F^AQITAGIAL) by both TCC. MeV, measles; F, fusion protein; SFC, spot-forming cells.

FIG 4

Isolation of a novel F^129–137-specific TCC. (A) AQITAGIAL^PE tetramer fluorescence-activated cell sorting (FACS) staining of TCC CD8^Xreact1 confirming that the TCC is CD8⁺ and recognizes F^AQITAGIAL in the context of HLA-B*15:01. (B) CD3^APCCy7 and AQITAGIAL^PE tetramer staining of PBMC obtained from three human HLA-B*15:01-positive donors. CD3⁺ CD8⁺ T cells that were positively stained by the HLA-B*15:01-AQITAGIAL tetramer were single cell sorted by FACS and clonally expanded from donor 3. (C) AQITAGIAL^PE tetramer FACS staining of TCC CD8^Xreact2 confirming that the TCC is CD8⁺ and recognizes F^AQITAGIAL in the context of HLA-B*15:01.

FIG 5

CD8^Xreact1 and CD8^Xreact2 cross-recognize NiV-infected cells. (A) Cross-reactive TCC were evaluated for reactivity with different F^129–137 regions from relevant viruses by IFN-γ ELISPOT. B-LCL pulsed with different with F^129–137 peptides at a concentration of 1 μM were cocultured with TCC. (B and C) IFN-γ ELISPOT with B-LCL pulsed at different concentrations of peptides for CD8^Xreact1 (B) and CD8^Xreact2 (C). (D and E) FACS-based assay showing interaction strength between TCC and tetramers. Interaction strength was calculated as mean fluorescence intensity (MFI) at 2 M urea divided by MFI at 0 M urea (Fig. S5). CDV, canine distemper virus; MeV, measles virus; ND, not done; NiV, Nipah virus; HPIV, human parainfluenza virus; MuV, mumps virus; TCC, T cell clone.

FIG 6

CD8^Xreact1 and CD8^Xreact2 clear NiV-infected cells. (A) CD8^Xreact1 suppressed MeV, CDV, and NiV replication. (B) CD8^Xreact2 suppressed MeV, CDV, HPIV3, and NiV replication. (C) As a control, we included CD8^MeV1, which exclusively suppressed MeV replication. CDV, canine distemper virus; MeV, measles virus; NiV, Nipah virus; HPIV, human parainfluenza virus; MuV, mumps virus; TCC, T cell clone.

FIG 7

Systematic search for conserved regions in paramyxo- and pneumoviruses. (A) Number of conserved regions in the different ORFs when comparing NiV with MeV, HPIV3, and HPIV2, respectively. Conserved regions were most abundant in the L protein. (B) Selection of conserved regions with an average of more than 50% homology among all paramyxo- and pneumoviruses; F^117–134 is the full fusion peptide (NiV numbering). Graph shows how conserved the regions of interest are in a selection of viruses, using NiV as a reference sequence. CDV, canine distemper virus; MeV, measles virus; NiV, Nipah virus; HeV, Hendra virus; HPIV, human parainfluenza virus; MuV, mumps virus; HMPV, human metapneumovirus; HRSV, human respiratory virus.

FIG 8

“Original antigenic sin” model. (A) In this model, we suggest that it is crucial in which order paramyxo- and pneumoviruses are encountered to develop cross-immunity to the highly pathogenic henipaviruses (or other paramyxoviruses). (B) Initially committing T cell immunity to epitopes present in pneumoviruses or MeV could lead to a relative narrow immunity and therefore no protection and death upon encountering a highly pathogenic virus. (C) Encountering HPIV2 or -3 before MeV vaccination or infection could lead to committing to broadly reactive T cell epitopes and therefore (partial) immunity to highly pathogenic viruses.