Virome studies of squirrels in Germany

Rodents in general are reservoir hosts for zoonotic pathogens, and also squirrels in particular have been described as hosts of putative zoonotic viruses (https://doi.org/10.3390/v10070373). In squirrel rescue centres, contact between humans and animals is intense. Selected samples collected in rescue centres were analysed for the presence of viruses. Next-generation sequencing combined with subsequent metagenomics analysis was used to examine samples from animals with pre-reported clinical signs of diarrhoea. Detected viral sequence reads were assembled and genetically and phylogenetically analysed. Subsequently, primers were designed and specific real-time PCR systems were developed and used for a small-scale screening for the detected viruses. More than 500 samples of different tissues from 135 different animals were analysed. Different new viruses of the families *Picornaviridae*, *Astroviridae*, and *Tombusviridae* were detected. According to the results of our sequence analyses, no viruses with suspected or proven zoonotic potential were among the closest relatives. The new viruses were predominantly found in animals belonging to the indigenous species *Sciurus vulgaris* and showed mainly an intestinal tropism. They were also frequently detected in liver, and sporadically in lung and kidney, but never in brain. The association of the occurrence of the viruses with specific clinical signs like diarrhoea and sudden death remains to be confirmed.