Detection and Phylogenetic Characterization of Canine Distemper Virus from a Red Fox in Hungary

Canine distemper virus (CDV) affects both domestic and wild carnivores and is associated with a high mortality rate. The virus can cross species barriers, infecting a wide range of mammals, which raises concerns for both wildlife conservation and domestic animal health. During our study, we processed a total of <i>n</i> = 552 oral and rectal swab samples from <i>n</i> = 260 red foxes (<i>Vulpes vulpes</i>) and <i>n</i> = 16 golden jackals (<i>Canis aureus</i>). The samples were collected by the National Food Chain Safety Office (NÉBIH) as part of a Rabies monitoring programme from Hungary in 2024. We performed a Real-Time RT-PCR, followed by a CDV-specific amplicon-based sequencing method using Oxford Nanopore Technologies to obtain the complete genome. All golden jackal samples tested negative, while both oral and rectal samples of one red fox tested positive for viral RNA. From this positive sample, we were able to sequence a partial CDV genome. Based on phylogenetic analysis of the haemagglutinin gene, our CDV sequence was assigned to the Europe lineage, one of the endemic lineages in the continent, infecting both threatened and common animals. This finding highlights the ongoing presence of CDV in wildlife populations and illustrates the value of integrated monitoring systems.