Phylogenetic Characterization of Rabies Virus Field Isolates Collected from Animals in European Russian Regions in 2009-2022.

Rabies is a fatal disease of mammals that poses a high zoonotic risk to humans as well. The distribution of rabies is mainly driven by host animal migration and human-mediated dispersion. To contribute to the global understanding of the rabies virus (RABV) molecular epidemiology, 94 RABV field isolates collected from animals in 13 European Russian regions were phylogenetically characterized using the nearly full-size N gene nucleotide sequences. According to phylogenetic inferences, all isolates belonged to one of the two established phylogenetic groups, either group C (n = 54) or group D (n = 40), which are part of the clade Cosmopolitan of RABVs. Some representatives of group C collected from regions located far apart from each other had a remarkably high level of nucleotide identity. The possibility of the contribution of local bat species to the distribution of RABVs was discussed. Interestingly, over the years, the fraction of group D isolates has been constantly decreasing compared with that of group C isolates. The phylogenetic insights generated herein might have an important contribution to the control and surveillance of animal rabies epidemiology in the region.

Fox rabies outbreaks in the republic of Buryatia: Connections with neighbouring areas of Russia, Mongolia and China.

The Republic of Buryatia (RB) is located southeast of Lake Baikal and shares a long border with Mongolia. This region of Russia was rabies-free from 1982 to 2010. The first outbreak of fox rabies in RB was identified in 2011, about 30 km from the Russian-Mongolian border. We assessed the possible pathways to further spread the 'steppe' phylogenetic lineage of the rabies virus near the northeastern limits of its known distribution. All rabies cases were located 30-210 km north of the Russia-Mongolia border, with a distance of up to 320 km from each other. Rabies has spread to the north across steppe landscapes and river valleys, with foxes being the main natural hosts of the infection. All RABV isolates from RB belong to the 'steppe' phylogenetic lineage, and three major phylogenic groups could be separated. Group 1 contains sequences from RB, Mongolia, China (Inner Mongolia), and bordering regions of Russia. Group 2 is formed by isolates from other regions of Eastern Siberia, which have no borders with RB and foreign countries. Group 3 contains samples from Western Siberia with endemic fox rabies since the 1950s. The most probable cause of fox rabies epizooty in the RB was multiple drift of the RABV across the Russian-Mongolian border. Our data show that after 2010, fox rabies affected new areas in Central Asia and extended to the north and northeast. Affected areas are similar to the Mongolian-type steppes in their zoogeographical aspect. Closely related genetic lineages of RABV are circulating in RB, Mongolia and the nearest areas of China. International cooperation is necessary to prevent the spread of rabies in the bordering territories of these countries.

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.

Brown Rot Syndrome and Changes in the Bacterial Сommunity of the Baikal Sponge Lubomirskia baicalensis.

Mass mortality events have led to a collapse of the sponge fauna of Lake Baikal. We describe a new Brown Rot Syndrome affecting the endemic species Lubomirskia baicalensis. The main symptoms are the appearance of brown patches at the sponge surface, necrosis, and cyanobacterial fouling. 16S rRNA gene sequencing was used to characterize the bacterial community of healthy versus diseased sponges, in order to identify putative pathogens. The relative abundance of 89 eubacterial OTUs out of 340 detected has significantly changed between healthy and diseased groups. This can be explained by the depletion of host-specific prokaryotes and by the appearance and proliferation of disease-specific OTUs. In diseased sponges, the most represented OTUs belong to the families Oscillatoriaceae, Cytophagaceae, Flavobacteriaceae, Chitinophagaceae, Sphingobacteriaceae, Burkholderiaceae, Rhodobacteraceae, Comamonadaceae, Oxalobacteraceae, and Xanthomonadaceae. Although these families may contain pathogenic agents, the primary causes of changes in the sponge bacterial community and their relationship with Brown Rot Syndrome remain unclear. A better understanding of this ecological crisis will thus require a more integrative approach.

Actinobacteria possessing antimicrobial and antioxidant activities isolated from the pollen of scots pine (Pinus sylvestris) grown on the Baikal shore.

Isolated ecosystems existing under specific environmental conditions have been shown to be promising sources of new strains of actinobacteria. The taiga forest of Baikal Siberia has not been well studied, and its actinobacterial population remains uncharacterized. The proximity between the huge water mass of Lake Baikal and high mountain ranges influences the structure and diversity of the plant world in Siberia. Here, we report the isolation of eighteen actinobacterial strains from male cones of Scots pine trees (Pinus sylvestris) growing on the shore of the ancient Lake Baikal in Siberia. In addition to more common representative strains of Streptomyces, several species belonging to the genera Rhodococcus, Amycolatopsis, and Micromonospora were isolated. All isolated strains exhibited antibacterial and antifungal activities. We identified several strains that inhibited the growth of the pathogen Candida albicans but did not hinder the growth of Saccharomyces cerevisiae. Several isolates were active against Gram-positive and Gram-negative bacteria. The high proportion of biologically active strains producing antibacterial and specific antifungal compounds may reflect their role in protecting pollen against phytopathogens.

Complete Genome Sequences of Four European Subtype Strains of Tick-Borne Encephalitis Virus from Eastern Siberia, Russia.

Three tick-borne encephalitis virus (TBEV) strains were isolated from Ixodes persulcatus ticks, and one was isolated from a shrew in the territory of eastern Siberia (Russia). The level of sequence identity compared to Neudoerfl (the European prototype strain) is 97.2 to 97.3%.

Microsporidian Parasites Found in the Hemolymph of Four Baikalian Endemic Amphipods.

At present, approximately 187 genera and over 1300 species of Microsporidia have been described, among which almost half infect aquatic species and approximately 50 genera potentially infect aquatic arthropods. Lake Baikal is the deepest and one of the oldest lakes in the world, and it has a rich endemic fauna with a predominance of arthropods. Among the arthropods living in this lake, amphipods (Crustacea) are the most dominant group and are represented by more than 350 endemic species. Baikalian amphipods inhabit almost all depths and all types of substrates. The age and geographical isolation of this group creates excellent opportunities for studying the diversity, evolution and genetics of host-parasite relationships. However, despite more than 150 years of study, data investigating the microsporidia of Lake Baikal remain incomplete. In this study, we used molecular genetic analyses to detect microsporidia in the hemolymph of several endemic species of amphipods from Lake Baikal. We provide the first evidence that microsporidian species belonging to three genera (Microsporidium, Dictyocoela and Nosema) are present in the hemolymph of Baikalian endemic amphipods. In the hemolymph of Eulimnogammarus verrucosus, we detected SSU rDNA of microsporidia belonging to the genus Nozema. In the hemolymph of Pallasea cancellous, we found the DNA of Microsporidium sp. similar to that in other Baikalian endemic amphipods; Dictyocoela sp. was found in the hemolymph of Eulimnogammarus marituji and Acanthogammarus lappaceus longispinus.