Abstract
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, 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 analyzed by Luminex for the presence of 22 relevant cytokines. Virome composition was obtained using untargeted high troughput 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 amongst immune response clusters. The presence of Picornaviridae and Siphoviridae was associated with low interferon-λ responses. Asthma or allergy did not modify these correlations.
Conclusions: Antiviral cytokines 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 affected by TLR-induced immune responses.
Keywords: Asthma, bacteriophages, Interferon-λ, Rhinoviruses, virome
Introduction
The role of the microbiome in shaping health and disease is increasingly understood and substantiated [1]. Nevertheless, the focus on the gut microbiome has left other important niches, such as the respiratory tract, or agents, such as viruses, less well studied [2]. Particularly, little is known about the role of the respiratory virome in homeostasis across the ages, despite several studies showing that common respiratory viruses can often be found in the airways of asymptomatic individuals [3,4].
It has been suggested that the virome may be able to mold the immune system, affecting the development of asthma and respiratory diseases in childhood [5]. Specific viruses, or viral families may be able to modulate the immune responses and hence drive immune maturation, influence health and disease and be candidates for intervention strategies [6]. Clearly, infection with common cold viruses is closely linked with the development of respiratory and other allergic diseases [7,8].
In addition, to maintain homeostasis the immune system needs to control the density and composition of the microbiome [9]. When it comes specifically to the respiratory virome, much less is known, nevertheless, there is increasing understanding regarding the development of immune surveillance to eukaryotic viruses [10], the interplay between inert viruses such as the Anelloviruses and immune competence [11] and the non-host immune support conveyed by bacteriophages [12].
It is therefore clear that a continuous interplay between immune surveillance, established microbial self and incoming microbes, defines a dynamic balance shaping health and disease in an interactive complexity, in which the local virome has a considerable share.
We have previously described the respiratory virome (DNA and RNA viruses) in a cohort of well-characterized preschool-age children with asthma and healthy controls across Europe, in the context of the PreDicta study [13]. Among the viral genomes identified, the most prevalent and diversified between health and asthma, involved Picornaviruses, Anelloviruses and bacteriophages of the Siphoviridae family. Depending on their virome composition, individuals could be grouped into three profiles: a Eukaryotic prevailing profile (E-VPG), an Anellovirus prevailing profile (A-VPG) and a Prokaryotic prevailing profile (P-VPG).
We hypothesized that any biological interactions between the respiratory virome and the host antiviral immune responses may be reflected in associations between viral and immune signatures. The aim of this study was to evaluate links between the presence of the prevailing viral families, as well as of the respiratory virome profile groups, with cytokine production from peripheral blood cells at baseline and following stimulation with viral- and bacterial-mimicking stimuli.
This helps characterize immune-microbiome interactions and biomarkers that identify health/disease gradients and unravel novel therapeutic targets.