Early life factors shaping infant gut anellovirus composition and associations with childhood atopic disease

Abstract The Anelloviridae family is highly prevalent and genetically diverse, but factors shaping the composition and the relationship with disease remain elusive. Here, we characterised faecal viromes of 647 one-year-old children from the deeply phenotyped Copenhagen Prospective Studies on Asthma in Childhood₂₀₁₀ (COPSAC₂₀₁₀) mother-child cohort. In this study, the anelloviruses showed immense prevalence and individual variability. Early-life exposures such as being in day care and having older siblings were associated with a reduced anellovirus abundance and diversity, and influenced the anellovirus composition. Additionally, genetic secretors of the FUT2 enzyme had a higher anellovirus abundance compared to non-secretors. We observed an association between anelloviruses and allergic rhinitis, but no associations with infections or the development of other atopic traits. Our findings indicate that anelloviruses are a commensal component of all infants' faecal virome, and further investigations into how immune-training factors influence their composition longitudinally are pertinent.