Paramyxoviruses are widespread among numerous vertebrate species, particularly mammals and birds. The subfamily Orthoparamyxovirinae includes genetically diverse viruses, many of which have also been detected in rodents and shrews. In these hosts, members of the genus Jeilongvirus predominate, while viruses from the genera Parahenipavirus, Paramorbillivirus and Narmovirus are also present. Despite the increasing number of studies, data on orthoparamyxoviruses in small mammals in Slovenia are scarce. Therefore, the aim of this master’s thesis was to determine their presence and genetic diversity in rodents and shrews. We analysed 127 kidney samples from five species of small mammals that were collected between 2005 and 2024. Viral RNA was detected using RT-PCR and nested PCR, positive products were Sanger sequenced, and the obtained nucleotide sequences were compared with sequences in the GenBank database and analysed phylogenetically. Orthoparamyxovirus RNA was detected in 85 out of 127 samples (66.9%), with the highest proportion of positive samples found in Apodemus flavicollis (81.1%). Among the 78 sequences included in the phylogenetic analysis, 33 distinct nucleotide variants were identified that clustered into several phylogenetic groups. Some sequences clustered with reference viruses from the genus Jeilongvirus, while others were associated with more genetically distant orthoparamyxoviruses. Due to the short analysed fragment of the L gene, reliable taxonomic classification at the genus or species level was not possible. The results indicate the presence and genetic diversity of orthoparamyxoviruses in the analysed small mammals from Slovenia.
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