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Rotaviral RNA was detected in the stool sample of an asymptomatic fattening pig at a Slovenian pig farm. To characterize the rotavirus, RT-PCR was used, employing primers specific for the VP7, VP4 and NSP4 genes. Specific products were purified and the sequencing reaction was performed for the molecular analysis of amplified genes. Nucleotide and amino acid sequences of the VP7 gene were found highly identical (85.3-88.1% and 90.7-91.6%) to G1 genotype strains. Phylogenetic and molecular analyses of the VP7 antigen regions revealed the sample to be from a new lineage of G1 genotype. In the molecular analysis of the VP4 gene, only 70.9% nucleotide (76.2% amino acid) identity was found with the most related rotavirus VP4 gene from GenBank. Following this, the NSP4 gene was also analyzed. After the phylogenetic analysis, it clustered with the NSP4 B genotype, but also seemed to represent a new lineage of this genotype. This new rotavirus strain, named P21-5, differed greatly from all rotaviruses characterized so far in all three genes analyzed. The virulence of this strain is not clear yet and has to be investigated.

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Group C rotaviruses are associated with sporadic gastroenteritis and outbreaks of diarrhea in children and adults worldwide. Three cases with group C rotavirus infection are described, and the molecular characterization of the gene for the major capsid protein VP6 is reported. Patients described in this report were 10 years old or more and had mild to moderate clinical symptoms. A high nucleotide (>98%) and amino acid (100%) identity was observed among all three isolated Slovenian group C rotavirus strains. The similar identity is confirmed of Slovenian strains with other human group C rotavirus isolates, which were seen to cluster separately from the animal group C rotavirus isolates by a phylogenetic analysis. This is the first report of group C rotavirus detection in Slovenia.