Molecular Detection and Phylogenetic Analysis of Tick-Borne Encephalitis Virus in Rodents Captured in the Transdanubian Region of Hungary Re ´ ka Pinte ´ r, 1,2 Mo ´ nika Madai, 1,2 Gy} oz} o Horva ´ th, 2 Vikto ´ ria Ne ´ meth, 1,2 Miklo ´ s Oldal, 1,2 Ga ´ bor Kemenesi, 1,2 Bianka Dallos, 1,2 Krisztia ´n Ba ´ nyai, 3 and Ferenc Jakab 1,2 Abstract Tick-borne encephalitis virus (TBEV) infection is a common zoonotic disease affecting humans in Europe and Asia. To determine whether TBEV is present in small mammalian hosts in Hungary, liver samples of wild rodents were tested for TBEV RNA. Over a period of 7 years, a total of 405 rodents were collected at five different geographic locations of the Transdanubian region. TBEV nucleic acid was identified in four rodent species: Apodemus agrarius, A. flavicollis, Microtus arvalis, and Myodes glareolus. Out of the 405 collected rodents, 17 small mammals (4.2%) were positive for TBEV. The present study provides molecular evidence and sequence data of TBEV from rodents in Hungary. Key Words: Tick-borne encephalitis—Small mammals—Prevalence—RT-PCR—Hungary. Introduction T ick-borne encephalitis virus (TBEV) infection is one of the most important vector-transmitted viral diseases, with thousands of cases reported annually from Europe and Asia. TBEV is a member of the family Flaviviridae, genus Flavivirus, which causes meningitis, meningoencephalitis, or meningoencephalomyelitis in humans (Kaiser et al. 1999). TBEV has a single-stranded RNA genome of about 11 kilo- bases, which encodes three structural, and seven nonstruc- tural proteins (Lindquist and Vapalahti 2008). There are three genotypes of TBEV that have been identified: Far Eastern, European, and Siberian. The European subtype is transmitted by Ixodes ricinus, whereas I. persulcatus is the primary ar- thropod vector of the Siberian and the Far Eastern subtypes. Small mammals play a central role in the ecology of TBEV (Mansfield et al. 2009). In Central Europe, the major hosts of the virus are Apodemus and Myodes species, although other species from the orders Rodentia and Insectivora may also participate in the natural transmission cycle of TBEV (Labuda et al. 1997, Pfeffer and Dobler 2010). TBEV in- fection is a notifiable communicable disease in Hungary. In an overview of serologically confirmed cases reported from 1958 to 2004, most TBEV infections had occurred in the western and northern counties of Hungary; therefore, these regions have been classified as high-risk areas of TBEV (Ra ´cz et al. 2006). In the past years, mostly sporadic TBEV infections were identified in the country; however, clusters of cases have been also reported more recently (Balogh et al. 2010, Caini et al. 2012). The case fatality rate associated with TBEV is estimated at 0.2% (Balogh et al. 2010). In spite of the medical importance of TBEV infection in Hungary, a fairly low number of ecological studies about vectors, hosts, and related issues have been published over the past several decades. Therefore, we aimed at investigating the prevalence of TBEV in wild rodents collected in different parts of high- risk areas of Hungary. Materials and Methods As part of an ecological study run in parallel, small mam- mals were collected in five different locations in the Southern Transdanubian Region (STR) between 2005 and 2011. All trapping sites were located in high-risk areas of TBEV. Ro- dents were captured with live trapping methods, and each trap was checked twice per day (morning and evening). Prioritizing the needs of the parallel ecological study, only those animals that perished in the trap naturally were used for our research. After sex determination and measuring the specimens’ weight and size, collected rodents were frozen 1 Virological Research Group, Ja ´nos Szenta ´gothai Research Center, University of Pe ´cs, Pe ´cs, Hungary. 2 Institute of Biology, Faculty of Sciences, University of Pe ´cs, Pe ´cs, Hungary. 3 Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary. VECTOR-BORNE AND ZOONOTIC DISEASES Volume 14, Number 8, 2014 ª Mary Ann Liebert, Inc. DOI: 10.1089/vbz.2013.1479 621