The complete genome of Lake Sinai virus 3 (LSV3) was sequenced by the Ion Torrent next-generation sequencing (NGS) technology from an archive sample of honey bees collected in 2010. This strain M92/2010 is the first complete genome sequence of LSV lineage 3. From October 2016 to December 2017, 56 honey bee samples from 32 different locations and 41 bumble bee samples from five different locations were collected. These samples were tested using a specific reverse transcriptase-polymerase chain reaction (RT-PCR) method; 75.92% of honey bee samples and 17.07% of bumble bee samples were LSV-positive with the RT-PCR method. Phylogenetic comparison of 557-base pair-long RNA-dependent RNA polymerase (RdRp) genome region of selected 23 positive samples of honey bees and three positive bumble bee samples identified three different LSV lineages: LSV1, LSV2, and LSV3. The LSV3 lineage was confirmed for the first time in Slovenia in 2010, and the same strain was later detected in several locations within the country. The LSV strains detected in bumble bees are from 98.6 to 99.4% identical to LSV strains detected among honey bees in the same territory.

The distribution and abundance of macrophytes, land-use beyond the riparian zone, characteristics of the riparian zone and selected channel properties have been studied in 9 streams flowing through an agricultural landscape in the north-eastern part of Slovenia. The streams studied supported a rich macrophyte community. Altogether, 53 plant taxa were observed on 93 km of the streams. Canonical correspondence analysis indicated that 10 out of the 11 parameters examined significantly influenced macrophyte distribution. Of these, substrate characteristics and riparian vegetation type were the most influential. Species composition analysis revealed that the majority of species indicated moderate nutrient load while, in the more strongly modified reaches, species indicating eutrophic conditions, i.e. Myriophyllum spicatum and different species of genus Potamogeton, were more abundant.

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a b s t r a c tWe present the process of developing a macrophyte based index (River Macrophyte Index -RMI) for assessing river ecological status, that would be applicable for rivers with moderate to high water alkalinity, flowing over low slope terrain. A reference value and boundary values were determined for five ecological classes. The relation between the developed index and two existing indices, the Reference Index (RI) and the Trophic Index of Macrophytes (TIM), and selected environmental variables was established. The RMI is based on species composition and abundance from 208 sampling sites being in reference or good hydromorphological conditions and differing in the catchment land use. The percentage of natural areas in the sub-catchment was used for classifying macrophyte taxa into 5 ecological groups. 65 plant taxa, of which 47 were identified as indicator taxa, were included in the analysis. To assess the ecological status of a river site, the presence of at least 3 indicator taxa is necessary, otherwise the assessment is considered inconclusive. RMI is expected to indicate multiple pressures on the river, including trophic level. The developed index and RI and TIM indices differed in relation to slope, distance to source and catchment size.

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Porcine epidemic diarrhea virus (PEDV) was detected for the first time in Slovenia in January 2015. The complete genome sequence of PEDV strain SLO/JH-11/2015, obtained from a fecal sample of a fattening pig with diarrhea in September 2015, is closely related to recently detected European strains.

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BackgroundRecently, mammalian orthoreoviruses (MRVs) were detected for the first time in European bats, and the closely related strain SI-MRV01 was isolated from a child with severe diarrhoea in Slovenia. Genetically similar strains have also been reported from other mammals, which reveals their wide host distribution. The aim of this study was to retrospectively investigate the occurrence and genetic diversity of MRVs in bats in Slovenia, from samples obtained throughout the country in 2008 to 2010, and in 2012 and to investigate the occurrence of the novel SI-MRV01 MRV variant in Slovenian bats.ResultsThe detection of MRVs in bat guano was based on broad-range RT-PCR and specific bat MRV real-time RT-PCR. Subsequently, MRV isolates were obtained from cell culture propagation, with detailed molecular characterisation through whole-genome sequencing.Overall, bat MRVs were detected in 1.9% to 3.8% of bats in 2008, 2009 and 2012. However, in 2010 the prevalence was 33.0%, which defined an outbreak of the single SI-MRV01 strain. Here, we report on the identification of five MRV isolates of different serotypes that are designated as SI-MRV02, SI-MRV03, SI-MRV04, SI-MRV05 and SI-MRV06. There is high genetic variability between these characterised isolates, with evident genome reassortment seen across their genome segments.ConclusionsIn conclusion, we have confirmed the presence of the SI-MRV01 strain in a Slovenian bat population. Moreover, according to genetic characterisation of S1 genome segment, all three MRV serotypes were present in the bat population. In this study, five independent MRV isolates were obtained and detailed whole genome analysis revealed high diversity between them. This study generates new information about the epidemiology and molecular characteristics of emerging bat MRV variants, and provides important molecular data for further studies of their pathogenesis and evolution.Electronic supplementary materialThe online version of this article (10.1186/s12917-018-1585-y) contains supplementary material, which is available to authorized users.