Reporting of New tick-borne encephalitis virus strains isolated in Eastern Siberia (Russia) in 1960-2011 and explaining them in an evolutionary context using Bayesian phylogenetic inference.

Tick-borne encephalitis virus (TBEV) is one of the main tick-borne viral pathogens of humans. Infection may induce signs of meningitis, encephalitis, paralysis and high fever. TBEV is well studied by molecular phylogenetic methods. The present-day implementation of Bayesian phylogenetic models allows population dynamics to be tracked, providing changes in population size that were not directly observed. However, the description of the past population dynamics of TBEV is rare in the literature. In our investigation, we provide data on the dynamics of viral genetic diversity of TBEV in Zabaikalsky Krai (Eastern Siberia, Russia) revealed by the Bayesian coalescent inference in a BEAST program. As a data set, we used the envelope (E) protein partial gene sequences (1308 nt) of 38 TBEV strains (including six "886-84-like" or Baikalian subtype strains (TBEV-B)), isolated in Zabaikalsky Krai (Eastern Siberia, Russia) in 1960-1963 and 1995-2011. To increase estimations reliability, we compared 9 model combinations by Path sampling and Stepping-stone sampling methods. It has been shown that the genetic diversity decline in the population history of TBEV in the 1950s coincides with the date of the beginning of wide dichlorodiphenyltrichloroethane forest dusting in Siberia. We assumed that the TBEV population on the territory of Siberia went through a genetic bottleneck. Also, we provide data estimating the divergence time of TBEV-B strains and indicate the specific evolution rate of an ancestor lineage of the Baikalian subtype, illustrated on a phylogenetic tree, and reconstructed under a relaxed clock model.

"886-84-like" tick-borne encephalitis virus strains: Intraspecific status elucidated by comparative genomics.

Tick-borne encephalitis virus (TBEV) can cause severe meningitis, encephalitis, and meningoencephalitis. TBEV represents a pathogen of high zoonotic potential and an emerging global threat. There are three known subtypes of TBEV: Far-Eastern, Siberian and European. Since 2001 there have been suggestions that two new subtypes may be distinguished: "178-79" and "886-84". These assumptions are based on the results of the envelope gene fragment sequencing (Zlobin et al., 2001; Kovalev and Mukhacheva, 2017) and genotype-specific probes molecular hybridization (Demina et al., 2010). There is only one full-genome sequence of "178-79" strain and two identical ones of "886-84" strain can be found in GenBank. For clarification of the intraspecific position of the "886-84-like" strains group we completely sequenced six previously unknown "886-84-like" strains isolated in Eastern Siberia. As a result of applying different bioinformatics approaches, we can confirm that "886-84-like" strains group is a distinct subtype of TBEV.

Molecular identification and phylogeny of Dermacentor nuttalli (Acari: Ixodidae).

Dermacentor nuttalli is an epidemiologically important tick in Palearctic Asia which transmits several infectious diseases including tularemia, North Asian tick-borne rickettsiosis, Lyme disease and tick-borne encephalitis. The genetic specificity and phylogeny of D. nuttalli from four geographic localities in Eastern Siberia were characterized using the mitochondrial (mt) 16S ribosomal RNA (rRNA) gene and internal transcribed spacer 2 (ITS2). Low genetic diversity was observed in the populations of ticks distributed from South Siberia to North China. From 11 detected mt 16S haplotypes, one was found in all populations, whereas the others were restricted to specific localities. These results suggested that the genetic structure of D. nuttalli represents integrated populations with no geographic isolation across the distribution area. The phylogenetic reconstructions inferred from the mt 16S rRNA gene and ITS2 were in agreement and showed a distinct D. nuttalli clade within a monophyletic Eurasian lineage of Dermacentor sp.