Beschreibung:
<jats:p>Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (<jats:italic>Linepithema humile</jats:italic>, Dolichoderinae), the invasive garden ant (<jats:italic>Lasius neglectus</jats:italic>, Formicinae) and the red ant (<jats:italic>Myrmica rubra</jats:italic>, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in <jats:italic>Li. humile</jats:italic>, followed by <jats:italic>La. neglectus</jats:italic> and <jats:italic>M. rubra</jats:italic>. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in <jats:italic>M. rubra</jats:italic>. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.</jats:p>