Sergey Yu. Kovalev

Introduction. Tick-borne encephalitis virus (TBEV) is a neurotropic flavivirus endemic to Eurasia and traditionally classified into three major subtypes: Far Eastern, Siberian, and European. However, the current classification remains incomplete and partly inconsistent with the rapidly growing amount of genomic data. The aim of this study was to refine the clusteron structure of TBEV populations, reassess the evolutionary relationships among viral lineages, and determine the taxonomic position of strain 178–79 (EF469661). Material and methods. In this study, we analyzed TBEV diversity using the clusteron approach combined with phylogenetic and phylogeographic analyses of viral sequences retrieved from GenBank. A total of 2,214 sequences from GenBank were examined. Results. Twelve previously unrecognized clusterons were identified, expanding the TBEV clusteron structure to 81 units. Importantly, we identified and propose a second Far Eastern subtype, designated TBEV-FE2. This subtype is represented by five recently identified isolates from northeastern China and the historical strain 178–79 isolated in Eastern Siberia in 1979. These viruses form a well-supported monophyletic clade exhibiting more than 11% whole-genome divergence from the classical TBEV-FE subtype, exceeding previously proposed thresholds for subtype differentiation. Conclusion. The results obtained refine current understanding of the population structure and evolution of the tick-borne encephalitis virus and provide a rationale for the recognition of a second Far Eastern subtype of TBEV. The identification of TBEV-FE2 expands current knowledge of the virus’s genetic diversity and highlights the need for further molecular epidemiological studies in the natural foci of Northeast Asia.

Lyme borreliosis is caused by species of the Borrelia burgdorferi sensu lato complex. Genospecies vary in human pathogenicity, reservoir host and tick vector adaptation. What causes these differences is currently unknown, but some answers are likely to be found within the fragmented genomes containing linear and circular plasmids (and even fusions). These plasmids are highly variable and challenging to reconstruct completely. We aimed to analyze plasmid presence/absence and to identify trends in plasmid numbers and/or types associated with specific ecological adaptations or pathogenic potentials. For this, we used the most complete, reliable, and currently available 86 B. burgdorferi s.l. genomes (30 newly sequenced, 56 publicly available) belonging to 21 of the 28 known species. The plasmid types per isolate vary from 6-21 (median: 12) and linear plasmid numbers (3–12, median: 7) are significantly higher than circular plasmids (2–11, median: 5). The only plasmids found in all isolates are lp54 and cp26 and only a few species- or population-specific plasmids are identified, demonstrating the high variability. Species with smaller plasmid counts (median < 11) tend to have fewer lp28 and cp32 plasmids than larger plasmid counts species (median ≥ 15). Significantly higher total and circular plasmid numbers are found in rodents-only compared to birds-only associated species. Interestingly, plasmid numbers are not significantly reduced in species associated with a single reservoir host/vector compared to multiple. Analyses of the plasmid-location of the vls/vlsE antigenic variation system highlighted the dynamic nature of B. burgdorferi s.l. plasmids. Surprisingly, whilst the plasmid repertoire of B. burgdorferi s.l. is very plastic and variable, our analyses rarely reveal plasmids associated with specific ecological adaptations or pathogenic potentials. However, some plasmids were more frequently found in one of the groups and will be of interest for gene-based analyses that will be required for further progress in this research area.

Tick-borne encephalitis virus (TBEV) is the etiological agent of tick-borne encephalitis. TBEV is maintained in nature by the ixodid ticks Ixodes ricinus and I. persulcatus , which are its hosts and main vectors. The classification distinguishes three TBEV subtypes: Far Eastern, European (TBEV-Eu) and Siberian. Each subtype is characterized by its own range, reflected in its name. Nevertheless, numerous findings of TBEV subtypes in non-endemic areas have been reported. This phenomenon may be the result of virus introduction due to natural causes such as bird and mammal migrations. Detection of TBEV-Eu in South Korea in 2005 and in Siberia in the second half of the 20th century are significantly different from other cases of virus introduction. This paper presents the results of a comprehensive study including phylogenetic analysis, clusteron approach, establishing specificity of viral population dynamics, etc. The age of viral populations and the probable time of their emergence in non-endemic regions were determined. Using the example of TBEV-Eu in South Korea, we conclude that there is negative population dynamics of the virus after its introduction. This conclusion, in conjunction with several other features, indicates that human activity played a pivotal role in the TBEV-Eu introduction into South Korea and Siberia.

Objectives: Tick-borne encephalitis virus Siberian subtype (TBEV-Sib) and Omsk hemorrhagic fever virus (OHFV) are causative agents of natural focal infections in Western Siberia, Russia. The distribution of TBEV phylogenetic lineages and OHFV in the Kemerovo Region of Western Siberia remains poorly investigated. Methods: The phylogenetic analyses of fragment genome sequences 26 flaviviruses identified in 2019 were performed, and the amino acid variation was determined to reveal to which clusteron they belong. The age of Baltic and Asian lineages of the TBEV-Sib was calculated for Kemerovo District and Region, respectively. Results: Twenty-five isolates were members of three TBEV-Sib phylogenetic lineages: Baltic (48%), Asian (36%), and East Siberian (16%). The Baltic lineage's eastern boundary is commonly thought to be in the Novosibirsk Region, but our data suggest that it may reach further east. Analysis of the Baltic lineage clusteron structure showed that the isolates found are unique (6) or belong to clusteron-founder 3D (1) and derived clusteron 3O (5). Based on the age of 3O clusteron, Baltic lineage could have appeared in the Kemerovo Region by the late 1970s. One of the isolated viruses turned out to be the OHFV of the first subtype and not to belong to any known clusteron. This finding is the first known detection of the virus outside the endemic area of Russia. Given the recent discovery of OHFV in Kazakhstan, it can be assumed that the area of this virus distribution is much wider than previously thought. Conclusions: This report provides insights into the population structure of TBEV and OHFV, which may be helpful for epidemiological investigation and surveillance of the viruses.

This paper describes the first discovery of Sinanodonta woodiana and S. lauta in the artificially heated section of the Reft Reservoir (Sverdlovsk oblast, Reft River, Ob–Irtysh River basin). The discovered Sinanodonta populations are represented by invasive haplotypes E3 (S. woodiana) and C3 (S. lauta). The alien populations include S. woodiana and S. lauta individuals belonging to various size and age groups, which indirectly indicates the successful naturalization of these species. Old-aged individuals (over 10 years) predominate in the S. woodiana population (56%), while middle-aged ones prevail in the S. lauta population (48%). Sinanodonta individuals under 1 year old (shell length less than 25 mm) were not found, and specimens aged 2–3 years occur rarely. On the basis of the molecular data and archival fishery records, it can be assumed that this invasion of S. woodiana and S. lauta into the Reft Reservoir is associated with the introduction of commercial fish species from Volga fish farms at the end of the 20th and the beginning of the 21st century.

Early knowledge about novel emerging viruses and rapid determination of their characteristics are crucial for public health. In this context, development of theoretical approaches to model viral evolution are important. The clusteron approach is a recent bioinformatics tool which analyzes genetic patterns of a specific E protein fragment and provides a hierarchical network structure of the viral population at three levels: subtype, lineage, and clusteron. A clusteron is a group of strains with identical amino acid (E protein fragment) signatures; members are phylogenetically closely related and feature a particular territorial distribution. This paper announces TBEV Analyzer 3.0, an analytical platform for rapidly characterizing tick-borne encephalitis virus (TBEV) strains based on the clusteron approach, workflow optimizations, and simplified parameter settings. Compared with earlier versions of TBEV Analyzer, we provide theoretical and practical enhancements to the platform. Regarding the theoretical aspect, the model of the clusteron structure, which is the core of platform analysis, has been updated by analyzing all suitable TBEV strains available in GenBank, while the practical enhancements aim at improving the platform’s functionality. Here, in addition to expanding the strain sets of prior clusterons, we introduce eleven novel clusterons through our experimental results, predominantly of the European subtype. The obtained results suggest effective application of the proposed platform as an analytical and exploratory tool in TBEV surveillance.

Omsk hemorrhagic fever was first described in the early 1940s and is a natural focal infection, spread exclusively in four regions of Western Siberia, and associated with muskrat (Ondatra zibethicus). The etiological agent of this disease is the Omsk hemorrhagic fever virus (OHFV) which is closely related to the tick‐borne encephalitis virus (TBEV), and its range entirely lies within the TBEV area. OHFV belongs to the mammalian tick‐borne flaviviruses and the ecological group of arboviruses. The problem concerning the origin of OHFV remains unresolved to date. This study analyzed all nucleotide sequences of the OHFV genome obtained in the present study and available in GenBank, including the E gene fragment and the amino acid sequences of the surface glycoprotein encoded by it. The conclusions, based on the clusteron approach, suggest that OHFV originated directly from the TBEV of the Far Eastern subtype due to the host‐jump phenomenon, that is, through a rapid change from an arthropod host,Ixodes persulcatus, to a rodent,O. zibethicus. The muskrat was introduced to Western Siberia in the second half of the 1930s. The peculiarities of the biology and ecology of the muskrat in the new habitat became the reason for the TBEV cross‐species transmission. Calculations show that host‐jumping occurred between 1931 and 1947 and accompanied a cascade of adaptive amino acid substitutions in protein E. As a result, the virus changed its transmission to contact, alimentary, and airborne routes. Based on the data obtained, OHFV would be more correctly attributed to zoonotic viruses transmitted by rodents and, accordingly, to the ecological group of roboviruses.

Viral surveillance is an essential task in public health that yields specific data, such as biological and epidemiological characteristics, crucial in the fight against viruses. We have recently developed an online platform for monitoring of Tick-Borne Encephalitis Virus, TBEV Analyzer, equipped with phylogenetic analysis and geographic map visualization functions. The phylogenetic analysis employs the clusteron approach, which has been earlier proposed by one of the authors of this paper. The analysis is based on a genetic pattern and provides three-fold hierarchical information about subtype, phylogenetic lineage, and clusteron. A clusteron is a group of TBEV strains with identical amino acid sequences of the glycoprotein E fragment, as a rule phylogeographically close, and having a certain type of territorial distribution. We enhance the algorithms and quality of visualization by integrating our platform with the GenBank database, adding a heat map distribution, and providing more details in the analysis report. To demonstrate the performance of the upgraded system, we analyze recent strains published in GenBank and compare them with the results of the manual analysis performed by a specialist. The results show that the system can rapidly and accurately determine query strain characteristics. This suggests possible applications in the field of public health.

Vector-borne pathogens exist in obligate transmission cycles between vector and reservoir host species. Host shifts can lead to geographic expansion and the emergence of new diseases. Three etiological agents of human Lyme borreliosis (Borrelia afzelii, Borrelia bavariensis, and Borrelia garinii) predominantly utilize two distinct tick species as vectors in Asia (Ixodes persulcatus) and Europe (Ixodes ricinus) but how and in which order they colonized each continent remains unknown. Here, by reconstructing the evolutionary history of 142 Eurasian isolates, we show that all three Borrelia genospecies evolved from an Asian origin, suggesting that successful expansion into Europe resulted through invading a novel vector. The pattern of gene flow between continents is different between genospecies and most likely conditioned by reservoir host association and their dispersal. Our results highlight that Eurasian Lyme borreliosis agents are all capable of geographic expansion through vector shifts, but potentially differ in their capacity as emergent pathogens.

According to modern classification, tick-borne flaviviruses have been divided into a mammalian tick-borne virus group and a seabird tick-borne virus group (STBVG). The STBVG includes the Tyuleniy virus, Meaban virus, Saumarez Reef virus, and the recently discovered Kama virus (KAMV). The latter was isolated from Ixodes lividus, an obligate parasitic tick of the sand martin (Riparia riparia), in 1989 in the central part of the Russian Plain. In 2014, based on molecular genetic analysis, it was shown that KAMV is a new virus belonging to STBVG, genus Flavivirus, fam. Flaviviridae. Very little is known about the Kama virus concerning its range, vectors, and reservoir hosts. GenBank contains a single sequence of the complete genome of this virus. In the present study, the complete genome sequences of two strains, isolated in 1983 in the Omsk region (Western Siberia) from gamasid mites in the nests of rooks (Corvus frugilegus), have been determined. Phylogenetic analyses of their genomes showed a close relationship both with each other (approx. 98.9% nucleotide identity) and with KAMV isolated in European Russia (approx. 98.4% nucleotide identity). The ecological features of KAMV that are due to the species of the vector (gamasid mites) and its hosts (colonial birds of the mainland of Eurasia) indicate that KAMV is an atypical representative STBVG.