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Monitoring infectious diseases is one of the most important pillars of preventative veterinary medicine in zoological collections. The zoo environment offers a great variety of different animal species living in proximity and in contact with small wild animals and vectors (e.g., ticks and mosquitos). In this context, tick-borne encephalitis virus (TBEV), Usutu virus (USUV), and West Nile virus (WNV) causing vector-borne diseases are emerging pathogens that raise concern. The aim of the study was to detect antibodies to selected flaviviruses in various animal species in the Ljubljana Zoo, Slovenia. In total, 874 sera from 96 animal species were tested for antibodies to TBEV by enzyme-linked immunosorbent assays (ELISA); positive samples were confirmed by a virus neutralization test (VNT) using TBEV, WNV, and USUV antigens. Antibodies to TBEV were detected by ELISA in 3.9% (34/874) of zoo animals, with 4% (30/753) in mammals and 5% (4/86) in birds; the sera of reptiles (n = 34) and amphibians (n = 1) were negative. Antibodies to TBEV were confirmed by VNT in 11 mammals; one bird was positive for both WNV and USUV. The mixture of exotic animal species and their contact with wild animals and vectors such as ticks and mosquitos suggest that screening of infectious diseases in zoo animals might provide good insight into the epizootological situation of the area. This is the first survey of TBEV, WNV, and USUV in a zoological collection in Slovenia.

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosal infections in humans and various domestic and wild animals. Nevertheless, there is limited knowledge about PVs in wildlife hosts, including mustelid species. This study describes a case in stone marten (Martes foina) with a clinical manifestation of skin tumor, which is rather atypical for infections with PVs. The result of the papillomavirus PCR performed on the skin tumor sample was positive, and the complete PV genome was determined in the studied sample using next-generation sequencing technology. The analysis of the PV genome revealed infection of the stone marten with a putative new PV type belonging to the Dyonupapillomavirus genus. The proposed new stone marten PV type was named MfoiPV1.

The family Picornaviridae includes important human and animal pathogens that are associated with a wide range of diseases and, in some cases, have zoonotic potential. During epidemiological surveillance of bats, we identified, by next-generation sequencing (NGS) techniques, the presence of picornavirus RNA in a common pipistrelle bat (Pipistrellus pipistrellus). By coupling NGS, primer-walking strategies, and sequence-independent protocols to obtain the sequences of the 5′ and 3′ termini, we reconstructed the genome sequence of picornavirus strain ITA/2017/189/18-155. The genome of the bat picornavirus is 8.2 kb in length and encodes a polyprotein of 2462 amino acids. A comparison of polyprotein sequences revealed that this virus is distantly related (65.1% and 70.9% sequence identity at the nucleotide and amino acid level, respectively) to a bat aichivirus identified in 2010. Phylogenetic analysis showed that this picornavirus clustered closely with members of the genus Kobuvirus, which also includes human and animal aichiviruses. The identification of aichiviruses in several animal hosts is providing hints that will lead to an understanding of their origin and evolutionary patterns.