Virome diversity and novel virus discovery in Italian ticks through metatranscriptomics

Ticks are parasites of a wide range of animal species and the main vectors of many viruses of health concern. However, a genome-scale characterization of tick diversity in Italy remains lacking, although several areas of the country are known to be affected by tick-borne viral infections. To begin addressing this important knowledge gap, we sequenced 22 tick transcriptomes from three different locations along a north-south gradient in Italy. We found that viral richness, prevalence, and abundance varied among samples. In our dataset, northern populations showed a higher presence of viruses of potential health concern; however, given the unbalanced and temporally split sampling design, these observations should be interpreted with caution. Using a combination of metagenomics and phylogenomics, we recovered 99 viral contigs, which were assembled into 89 uncultivated viral genomes (UViGs), as some viral species possess segmented genomes composed of multiple contigs. These 89 UViGs correspond to 31 viral operational taxonomic units, including 10 new putative species (i.e., unclassified viruses) and 19 species reported in Italy for the first time. We present the updated phylogenies of viruses of known or new potential zoonotic concern including Haseki tick virus, members of the Orthototiviridae and Phenuiviridae families, Tick-borne encephalitis virus, and four different phleboviruses (Brown dog tick phlebovirus 2, Norway phlebovirus 1, Leuven phlebovirus and Tick phlebovirus). These results increase our general understanding of the evolution of tick-borne viruses, provide a comprehensive look at their diversity in Italy, and represent a source of information for implementing future surveillance activities.