Infant gut anellovirus composition associates with early life factors and childhood atopic disease

Anelloviruses are single-stranded circular DNA viruses that infect eukaryotic cells. They are acquired in infancy and can be found in most body compartments. The Anelloviridae family is highly prevalent and genetically diverse, but factors shaping the composition and the relationship with disease remain elusive. Here, we characterise 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, 111 unique anellovirus species are identified and reveal immense prevalence and individual variability. The anellovirus and bacteriophage compositions are slightly correlated, while no correlation is observed with the bacterial composition. Early-life exposures such as attending day care and having older siblings are associated with a reduced anellovirus abundance and diversity, and influence the anellovirus composition. Additionally, genetic secretors of the FUT2 enzyme have a higher anellovirus abundance compared to non-secretors. Minor associations are observed between anelloviruses and later allergic rhinitis, but no associations are found for concurrent acute 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.