Marcin Smreczak, Anna Orłowska, Paweł Trębas and Jan F. Żmudziński
The paper describes the data concerning rabies in domestic animals and in wildlife as well as in bats in Poland in 2009 and 2010. Analysis of rabies situation was based on species involved and geographical distribution of rabies outbreaks. Favourable decreasing trend in rabies epidemic in 2009 was stopped by the outbreak of rabies in the Malopolska province in 2010. This resulted in dramatic increase in the number of rabies cases. Emergency vaccination in the zone of rabies outbreak with increased number of vaccines per km2 in bordering areas of the province has improved epizootic situation, which returned to the state before the outbreak. To monitor rabies situation a strict supervision of all elements of the ORV and surveillance of rabies is necessary.
Anna Orłowska, Jan F. Żmudziński, Marcin Smreczak, Paweł Trębas and Anna Marzec
Introduction: The reverse transcription polymerase chain reaction (RT-PCR) is one of the most extensively used methods for identification of animals infected with bluetongue virus (BTV). There are several RT-PCR protocols published and several real-time RT-PCR (rtRT-PCR) commercial kits available on the market. Because Poland faced BTV-14 infection in 2012, different protocols were implemented in the country to confirm the RT-PCR results positive for this virus. The article presents a comparative study of several RT-PCR protocols and discusses their diagnostic reliability and applicability.
Material and Methods: Six rtRT-PCR/RT-PCR protocols were compared for the laboratory diagnostic of fourteen BTV-14 isolates circulating in Poland in 2012–2014.
Results: All 14 isolates were positive in the protocols of Shaw et al. (18), a commercial LSI NS3 kit, and Eschbaumer et al. (5). Four out of fourteen BTV-14 isolates gave positive results in Hoffmann’s 2 and 6 protocols and none of the 14 isolates yielded positive results in Maan et al. (8) method. Phylogenetic study of a short fragment of 450 nt of BTV segment 2 (258–696 positions) revealed 100% identity within Polish variants and with Russian and Spanish isolates.
Conclusion: The paper points to the possible false negative results in the diagnosis of BTV infections depending on the protocol used.
Anna Orłowska, Ewelina Iwan, Marcin Smreczak and Jerzy Rola
High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs).
Material and Methods
The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes.
Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71.
Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.
Marcin Świtoniak, Cezary Kabała, Marek Podlasiński and Bożena Smreczak
Agricultural soil maps (ASM), prepared since mid-1960s until 1980s and digitalised recently, are important source of information on the quality and spatial variability of arable soils in Poland. Basic standard information in each map contour includes the indication of a (genetic) soil type (often also the subtype or variety related to parent material or other specific properties), soil texture classes throughout the profile, and the category of soil agricultural suitability, which covers the complex information about the soil conditions, land morphology, climate and moisture regime. Unfortunately, the genetic classification on ASM is simplified compared to soil classifications in Poland and does not reflect numerous modernisations of the classification systems, including the modifications of existing units and newly introduced soil types and subtypes. Thus, the reinterpretation of ASM is necessary to simplify the further use of ASM by various users, to allow the creation of modern soil maps based on archival databases, and to correlate the soil data with other modern national and international classifications. This paper includes a proposal of equivalents for the soil units indicated in agricultural soil map (using all soil data available in a map contour), correlated with a recent, the 6th edition of Polish Soil Classification.
Cezary Kabała, Przemysław Charzyński, Jacek Chodorowski, Marek Drewnik, Bartłomiej Glina, Andrzej Greinert, Piotr Hulisz, Michał Jankowski, Jerzy Jonczak, Beata Łabaz, Andrzej Łachacz, Marian Marzec, Łukasz Mendyk, Przemysław Musiał, Łukasz Musielok, Bożena Smreczak, Paweł Sowiński, Marcin Świtoniak, Łukasz Uzarowicz and Jarosław Waroszewski
The sixth edition of the Polish Soil Classification (SGP6) aims to maintain soil classification in Poland as a modern scientific system that reflects current scientific knowledge, understanding of soil functions and the practical requirements of society. SGP6 continues the tradition of previous editions elaborated upon by the Soil Science Society of Poland in consistent application of quantitatively characterized diagnostic horizons, properties and materials; however, clearly referring to soil genesis. The present need to involve and name the soils created or naturally developed under increasing human impact has led to modernization of the soil definition. Thus, in SGP6, soil is defined as the surface part of the lithosphere or the accumulation of mineral and organic materials permanently connected to the lithosphere (through buildings or permanent constructions), coming from weathering or accumulation processes, originated naturally or anthropogenically, subject to transformation under the influence of soil-forming factors, and able to supply living organisms with water and nutrients. SGP6 distinguishes three hierarchical categories: soil order (nine in total), soil type (basic classification unit; 30 in total) and soil subtype (183 units derived from 62 unique definitions; listed hierarchically, separately in each soil type), supplemented by three non-hierarchical categories: soil variety (additional pedogenic or lithogenic features), soil genus (lithology/parent material) and soil species (soil texture). Non-hierarchical units have universal definitions that allow their application in various orders/types, if all defined requirements are met. The paper explains the principles, classification scheme and rules of SGP6, including the key to soil orders and types, explaining the relationships between diagnostic horizons, materials and properties distinguished in SGP6 and in the recent edition of WRB system as well as discussing the correlation of classification units between SGP6, WRB and Soil Taxonomy.