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Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease

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Abstract

Viral infections are implicated in the pathogenesis of autoimmune diseases, including Sjögren’s disease (SjD), but the mechanisms linking viral antigens to disease development remain poorly understood. To address this, we conducted shotgun metagenomic sequencing of saliva samples from 35 patients with SjD and 25 healthy controls. The salivary virome of the patients with SjD, particularly those with high disease activity, had an expansion of Siphoviridae bacteriophages and increased eukaryotic viral sequences, including Vientovirus. This virus was associated with lacrimal gland dysfunction and elevated anti-SSA/Ro52 autoantibody levels. Alignment analysis and cross-blocking assay identified molecular mimicry between the Vientovirus capsid protein and the autoantigen SSA/Ro52. Mice immunized with a Vientovirus capsid peptide developed anti-SSA/Ro52 antibodies and showed immunological features resembling those of patients with SjD. These findings highlight distinct virome profiles in SjD and provide mechanistic evidence supporting the role of Vientovirus in triggering autoimmunity through molecular mimicry.

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Fig. 1: Overview of salivary virome analysis and differences in salivary virome composition.
Fig. 2: Taxonomic signatures of the salivary virome of patients with SjD and their clinical significance.
Fig. 3: Vientovirus genomes in saliva samples from patients with SjD.
Fig. 4: Detection of Vientovirus in oral swab samples and its association with anti-SSA/Ro52 and Schirmer’s tests.
Fig. 5: Molecular mimicry of SjD-enriched Vientovirus.
Fig. 6: Immunization with the Vientovirus capsid peptide induced anti-SSA/Ro52 production and lacrimal dysfunction.

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Data availability

The sequence data generated in this study can be found in the Sequence Read Archive (SRA) of NCBI under BioProject accession numbers PRJNA1223632 and PRJNA1272653. Source data are provided with this paper.

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (82471833, Y. Liu; 82101841, X.Z.; 82171779 and 82371802, G.S.), the Natural Science Foundation of Fujian Province (2023J06055, Y. Liu), the Fujian Health and Family Planning Commission (2024GGB20, X.Z.) and the Scientific and Technological Projects of Xiamen City (2022XMSLCYX01, G.S.).

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Y. Liu, G.S. and X.Z. conceptualized the project. X.Z., Y. Li (0000-0003-3020-6424) and Y.Q. designed the methodology. Y.Q., Z.L. and Y.C. collected the specimens. X.Z., Y. Li (0000-0003-3020-6424), C.D. and H.Q. conducted the investigations. Y. Li (0000-0003-3020-6424) and X.Z. wrote the original draft of the paper. Y. Li (0000-0002-5587-2784), G.S., S.C., Y.H. and Y.Q. reviewed and edited the paper. G.S., Y. Liu and X.Z. acquired funding and resources.

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Correspondence to Guixiu Shi or Yuan Liu.

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Extended data

Extended Data Fig. 1 Differences in salivary virome composition of SjD patients.

(a) Alpha diversity of eukaryotic RNA virome comparisons based on observed richness, Chao1 richness, Shannon diversity, and Simpson diversity of the HC (n = 25 biological replicates), ESSDAI-low SjD (n = 23 biological replicates) and ESSDAI-high SjD (n = 12 biological replicates) groups. One-way ANOVA and two-sided Mann‒Whitney U test was used. Each data point is shown, the boxplot represents the median and interquartile range values, and whiskers represent the minimum and maximum values. (b) Observed richness, Chao1 richness, Shannon diversity, and Simpson diversity the eukaryotic DNA virome of the HC (n = 25), ESSDAI-low SjD (n = 23) and ESSDAI-high SjD (n = 12) groups. One-way ANOVA and two-sided Mann‒Whitney U test was used. Each data point is shown, the boxplot represents the median and interquartile range values, and whiskers represent the minimum and maximum values. (c) Observed richness, Chao1 richness, Shannon diversity, and Simpson diversity of prokaryotic virome of the HC (n = 25), ESSDAI-low SjD (n = 23) and ESSDAI-high SjD (n = 12) groups. One-way ANOVA and two-sided Mann‒Whitney U test was used. Each data point is shown, the boxplot represents the median and interquartile range values, and whiskers represent the minimum and maximum values. (d) Multivariate sparse partial least-squares discriminant analysis (sPLS-DA) of relative abundance at the family level of the saliva virome, comparing the HC and SjD groups. Two-sided PERMANOVA was used. (e) sPLS-DA of relative abundance at the species level of the saliva virome, comparing the HC and SjD groups. Two-sided PERMANOVA was used. (f) sPLS-DA of the relative abundance of the saliva virome at the family level, comparing the HC, ESSDAI-low SjD and ESSDAI-high SjD groups. Two-sided PERMANOVA was used. (g) sPLS-DA of the relative abundance of the saliva virome at the species level, comparing the HC, ESSDAI-low SjD and ESSDAI-high SjD groups. Two-sided PERMANOVA was used. ESSDAI, EULAR Sjögren’s Syndrome Disease Activity Index.

Source data

Extended Data Fig. 2 Detection of RdRp gene of Tomato mosaic virus (ToMV) and indicated genes of EBV from oral swabs of SjD and HC subjects.

(a) Representative PCR bands of indicated genes from oral swabs. (b) Quantifications of relative band intensities normalized to ACTB and the semi-quantitative levels were shown in the heatmap. (c) Two-sided Spearman’s correlation between relative band intensity of ToMV and anti-SSA/Ro52 level was shown. (d) Two-sided Spearman’s correlation between the relative band intensity of ToMV and unstimulated salivary flow rate (uSFR) was shown. (e) Two-sided Spearman’s correlation between relative band intensity of EBV genes and indicated clinical parameter were shown in the heatmap. uSFR, unstimulated salivary flow rate; sSFR, stimulated salivary flow rate; ESSPRI, EULAR Sjögren’s Syndrome Patient Reported Index; ESSDAI, EULAR Sjögren’s Syndrome Disease Activity Index. *, P < 0.05, **, P < 0.01, ***, P < 0.001.

Source data

Extended Data Fig. 3 Salivary glands change in mice immunized with Vientovirus capsid peptide.

(a) Saliva flow rates were measured in BSA-, mimotope 1-, and mimotope 2-immunization groups. Dots plot with mean ± SD. n = 7 mice for the BSA group, n = 6 mice for the mimotope 1 group, n = 5 for mimotope 2 group. Statistical significances were determined by Two-way ANOVA test with two-sided Tukey’s multiple comparisons test. (b) The serum IgG against SG antigens was detected by ELISA. n = 7 mice for the BSA group, n = 6 mice for the mimotope 1 group, n = 5 for mimotope 2 group. Statistical significance was determined by two-way ANOVA with two-sided Tukey’s multiple comparisons test. Dots plot with mean ± SD. (c) Immune deposits were detected by immunofluorescence staining for IgM (green) and complement C3 (red) in a representative salivary gland section from three groups. Scale bars, 250 µm. (d) Histological evaluation of lymphocyte infiltration in three groups was performed on tissue sections of salivary glands with H&E staining. Scale bars, 250 µm (left panel),100 µm (right panel).

Source data

Supplementary information

Supplementary Information

Supplementary Figs. 1–6, Supplementary Tables 1–3 and 5–8, and uncropped scans of gels for Supplementary Fig. 3.

Reporting Summary

Supplementary Table 4

Sequence identity of vOTU_2333 and vOTU_3152 Rep sequences with other reference strains.

Supplementary Table 9

PCR primers used in this study.

Supplementary Data

Source data for supplementary figures.

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Unprocessed gels for Fig. 4b.

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Unprocessed gels for Extended Data Fig. 2a.

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Zhang, X., Li, Y., Qin, Y. et al. Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren’s disease. Nat Microbiol 10, 2591–2602 (2025). https://doi.org/10.1038/s41564-025-02115-3

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