Characteristics of genetic variability of tick-borne encephalitis virus in the Ekhirit-Bulagatsky district of the Irkutsk region

Background . The Ekhirit-Bulagatsky district of the Irkutsk region is the only area in the world where the simultaneous circulation of all known tick-borne encephalitis virus (TBEV) subtypes, with the exception of the Himalayan subtype, has been documented. The unique ecology of this region justifies its selection as a model for studying the influence of environmental factors on the formation of a heterogeneous viral population, and the genetic variability of TBEV circulating in this area merits a more detailed description. The aim . To characterize the genetic diversity of tick-borne encephalitis virus circulating in the Ekhirit-Bulagatsky district of the Irkutsk region. Materials and Methods . Thirty-nine TBEV strains from the collection of the Scientific Centre for Family Health and Human Reproduction Problems isolated from various sources in the Ekhirit-Bulagatsky district were analyzed. A combination of molecular genetic methods (MHNA, Sanger sequencing, and NGS) was used for strain genotyping. Results . Based on genome coding sequence analysis, the circulation of four TBEV subtypes (Siberian, Far Eastern, European, and Baikalian) in the Ekhirit-Bulagatsky district was confirmed, and strain 178-79 with an original genetic structure was identified. The differences in TBEV genotypic composition depending on the landscape type and the source of isolation were demonstrated. An assumption was made about the important role of taiga ticks in the selection of the Siberian subtype of the virus. It was hypothesized that the long-term co-circulation of several TBEV subtypes in one area creates the preconditions for the emergence of strains with a “mosaic” genetic structure. A comparative analysis of the genomes of strains from the Ekhirit-Bulagatsky district and other districts of the Irkutsk region was conducted. The unique amino acid substitutions in the structural and non-structural virus proteins, characteristic of strains from the studied district, were identified. Conclusion . The Ekhirit-Bulagatsky district has been proven to be unique in terms of TBEV genetic variability, characterized by a wide range of circulating subtypes and the presence of unique genotypic amino acid substitutions within each identified subtype.