The aim of the study is to determine molecular markers for the detection of Schmallenberg virus by standard PCR, taking into account the genetic structure of the pathogen. International databases GenBank, EMBL, DDBJ were used to obtain genomic RNA sequences of viruses. MEGA v. 4.0.2 was used for phylogenetic analysis. Traditional dendrograms were constructed using the Neighbor joining method. The analysis of the phylogenetic tree was performed by visual assessment of its topology and pairwise distances between the components of the sample. Multiple alignment of selected sequences, determination of molecular markers for the Schmallenberg virus detection was performed using BioEdit v. 7.0.0 and ClustalW module of MEGA 4. The assumptions regarding Schmallenberg virus reassortment have been confirmed. It has been found that the segment S of the Schmallenberg virus is the most suitable molecular marker for the Schmallenberg virus detection by the PCR standard variant. A suitable primers system which can be further used to develop a method for indicating the Schmallenberg virus genetic material has been selected
Keywords: molecular marker, PCR, RNA
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