Veterinarni Medicina, 54, 2009 (9): 393–398 Original Paper 393 Genotyping of bovine viral diarrhoea virus isolates from the Czech Republic B. Robesova 1 , K. Kovarcik 1 , S. Vilcek 2 1 Veterinary Research Institute, Brno, Czech Republic 2 University of Veterinary Medicine, Kosice, Slovakia ABSTRACT: This study was focused on the genetic typing of bovine viral diarrhoea virus (BVDV) isolates obtained from 41 serum samples of persistently infected cattle in the Czech Republic in the period of 2004 to 2007. For the differentiation of BVDV isolates, the 5’-UTR and N pro regions were selected. A 288-bp fragment from 5’-UTR and 428-bp fragment from N pro of the selected isolates were amplified by RT-PCR and subsequently sequenced and analysed by computer-assisted phylogenetic analysis. The isolates belong to BVDV-1 genotype and the following subtypes were identified: b (n = 16), d (n = 16), e (n = 2) and f (n = 7). In this collection of viral samples, no isolate belonged to BVDV-2 genotype. Keywords: BVDV; phylogenetic analysis; genotyping; cattle Supported by the Ministry of Agriculture Supported by the Ministry of Agriculture of the Czech Republic (Grants No. 1B44021 and No. MZE 0002716202), the Slovak Research and Development Agency (Grant No. APVV-20-019605) and the Scientiic Grant Agency (VEGA) of the Ministry of Education of the Slovak Republic (Grant No. 1/0389/08). The bovine viral diarrhoea virus (BVDV) is a significant pathogen of cattle that occurs world- wide. Different manifestations of BVDV infection have been reported, e.g. diarrhoea, respiratory problems, abortion and immunosuppression. In pregnant cows, the resorption of the foetus can also occur (Radostits and Littlejohns, 1988). Viral infection during the first trimester of pregnancy in cows can result in the development of persist- ently infected (PI) animals. PI animals carrying virus during their lifetime are immunotolerant to BVDV and become a source of infection for healthy cattle in their proximity (Nettleton and Entrican, 1995). The number of PI individuals in herds ranges between 0.1 and 1.8% (Houe, 1999). According to the accepted taxonomy, BVDV type 1 (BVDV-1) and BVDV type 2 (BVDV-2) species are recognised. BVDV-2 causes similar clinical symp- toms as BVDV-1. Further, highly viraemic strains may develop a serious haemorrhagic syndrome with high mortality of cattle (Pellerin et al., 1994; Ridpath et al., 1994). BVDV-1 and BVDV-2 are single-stranded posi- tive sense RNA viruses forming together with classical swine fever (CSFV) and border disease virus (BDV) the genus Pestivirus in the Flaviviridae family (Fauquet et al., 2005). The length of RNA genome is approximately 12.3 kbp. The viral ge- nome comprises a single open reading frame (ORF) encoding about 4 000 amino acids (Collet et al., 1988; Demoerlooze et al., 1993). At the 5’ and 3’ ends, the genome is surrounded by untranslated regions (UTR). The 5’-UTR region consists of ap- proximately 380 nucleotides. This part of the ge- nome is highly conservative and it has been used as a target sequence for diagnostic RT-PCR (Vilcek et al., 1994; Letellier and Kerkhofs, 2003). Since 5’- UTR also contains variable regions and it is easy to obtain a fragment by RT-PCR for sequencing, it was widely used for the preliminary genetic typing of pestiviruses. In addition, the N pro and E2 regions were used for the typing of BVDV isolates at the genetic level (Becher et al., 1997, 1999; Tajima et al., 2001; Vilcek et al., 2001; Couvreur et al., 2002).