University of Oulu

Rovira Rubió J, Megremis S, Pasioti M, et al. Respiratory virome profiles reflect antiviral immune responses. Allergy. 2023;78:1258-1268. doi:10.1111/all.15634

Respiratory virome profiles reflect antiviral immune responses

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Author: Rovira Rubió, Judit1; Megremis, Spyridon1; Pasioti, Maria2;
Organizations: 1Division of Infection, Immunity & Respiratory Medicine, University of Manchester, Manchester, UK
2Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
3Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
4Upper Airway Research Laboratory, Ghent University Hospital, Ghent, Belgium
5Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, Erlangen, Germany
6PEDEGO Research Unit, University of Oulu, Oulu, Finland
7Department of Pediatrics and Adolescent Medicine, University of Oulu, Oulu, Finland
8Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
9Biomedical Research Foundation of the Academy of Athens, Athens, Greece
10Swiss Institute of Allergy and Asthma Research (SIAF), University Zurich, Davos, Switzerland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 3.4 MB)
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Language: English
Published: John Wiley & Sons, 2023
Publish Date: 2023-08-11


Background: From early life, respiratory viruses are implicated in the development, exacerbation and persistence of respiratory conditions such as asthma. Complex dynamics between microbial communities and host immune responses shape immune maturation and homeostasis, influencing health outcomes. We evaluated the hypothesis that the respiratory virome is linked to systemic immune responses, using peripheral blood and nasopharyngeal swab samples from preschool-age children in the PreDicta cohort.

Methods: Peripheral blood mononuclear cells from 51 children (32 asthmatics and 19 healthy controls) participating in the 2-year multinational PreDicta cohort were cultured with bacterial (Bacterial-DNA, LPS) or viral (R848, Poly:IC, RV) stimuli. Supernatants were analysed by Luminex for the presence of 22 relevant cytokines. Virome composition was obtained using untargeted high throughput sequencing of nasopharyngeal samples. The metagenomic data were used for the characterization of virome profiles and the presence of key viral families (Picornaviridae, Anelloviridae, Siphoviridae). These were correlated to cytokine secretion patterns, identified through hierarchical clustering and principal component analysis.

Results: High spontaneous cytokine release was associated with increased presence of Prokaryotic virome profiles and reduced presence of Eukaryotic and Anellovirus profiles. Antibacterial responses did not correlate with specific viral families or virome profile; however, low antiviral responders had more Prokaryotic and less Eukaryotic virome profiles. Anelloviruses and Anellovirus-dominated profiles were equally distributed among immune response clusters. The presence of Picornaviridae and Siphoviridae was associated with low interferon-λ responses. Asthma or allergy did not modify these correlations.

Conclusion: Antiviral cytokine responses at a systemic level reflect the upper airway virome composition. Individuals with low innate interferon responses have higher abundance of Picornaviruses (mostly Rhinoviruses) and bacteriophages. Bacteriophages, particularly Siphoviridae, appear to be sensitive sensors of host antimicrobial capacity, while Anelloviruses are not correlated with TLR-induced immune responses.

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Series: Allergy
ISSN: 0105-4538
ISSN-E: 1398-9995
ISSN-L: 0105-4538
Volume: 78
Issue: 5
Pages: 1258 - 1268
DOI: 10.1111/all.15634
Type of Publication: A1 Journal article – refereed
Field of Science: 3121 General medicine, internal medicine and other clinical medicine
Funding: The study acquired funding from the European Union's Horizon 2020 research and innovation programme CURE under grant agreement No 767015, and the European FP7-Health programme PREDICTA under Grant agreement ID: 260895. CURE: ‘Constructing a ‘Eubiosis Reinstatement Therapy’ for Asthma’. PREDICTA: ‘Post-infectious immune reprogramming and its association with persistence and chronicity of respiratory allergic diseases’. Disclaimer of EU responsibility: The content of this publication reflects only the views of its authors. The European Commission is not responsible for any use that may be made of the information it contains.
Copyright information: © 2023 The Authors. Allergy published by European Academy of Allergy and Clinical Immunology and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.