Previously, the main studies were focused on viruses that cause disease in commercial and farmed shellfish and cause damage to food enterprises (for example, Ostreavirusostreidmalaco1, Aurivirus haliotidmalaco1 and Aquabirnavirus tellinae). Advances in high-throughput sequencing technologies have extended the studies to natural populations of mollusks (and other invertebrates) as unexplored niches of viral diversity and possible sources of emerging diseases. These studies have revealed a huge diversity of mostly previously unknown viruses and filled gaps in the evolutionary history of viruses. In the present study, we estimated the viral diversity in samples of the Baikal endemic gastropod Benedictia baicalensis using metatranscriptomic analysis (total RNA-sequencing); we were able to identify a wide variety of RNA-containing viruses in four samples (pools) of mollusks collected at three stations of Lake Baikal. Most of the identified viral genomes (scaffolds) had only distant similarities to known viruses or (in most cases) to metagenome-assembled viral genomes from various natural samples (mollusks, crustaceans, insects and others) mainly from freshwater ecosystems. We were able to identify viruses similar to those previously identified in mollusks (in particular to the picornaviruses Biomphalaria virus 1 and Biomphalaria virus 3 from the freshwater gastropods); it is possible that picorna-like viruses (as well as a number of other identified viruses) are pathogenic for Baikal gastropods. Our results also suggested that Baikal mollusks, like other species, may bioaccumulate or serve as a reservoir for numerous viruses that infect a variety of organisms (including vertebrates).

We evaluated the temporal signal and substitution rate of tick-borne encephalitis virus (TBEV) using 276 complete open reading frame (ORF) sequences with known collection dates. According to a permutation test, the TBEV Siberian subtype (TBEV-S) data set has no temporal structure and cannot be applied for substitution rate estimation without other TBEV subtypes. The substitution rate obtained suggests that the common clade of TBEV (TBEV-common), including all TBEV subtypes and louping-ill virus (LIV), is characterized by the lowest rate (1.87 × 10⁻⁵ substitutions per site per year (s/s/y) or 1 nucleotide substitution per ORF per 4.9 years; 95% highest posterior density (HPD) interval, 1.3–2.4 × 10⁻⁵ s/s/y) among all tick-borne flaviviruses previously assessed. Within TBEV-common, the TBEV European subtype (TBEV-E) has the lowest substitution rate (1.3 × 10⁻⁵ s/s/y or 1 nucleotide substitution per ORF per 7.5 years; 95% HPD, 1.0–1.8 × 10⁻⁵ s/s/y) as compared with TBEV Far-Eastern subtype (3.0 × 10⁻⁵ s/s/y or 1 nucleotide substitution per ORF per 3.2 years; 95% HPD, 1.6–4.5 × 10⁻⁵ s/s/y). TBEV-common representing the species tick-borne encephalitis virus diverged 9623 years ago (95% HPD interval, 6373–13,208 years). The TBEV Baikalian subtype is the youngest one (489 years; 95% HPD, 291–697 years) which differs significantly by age from TBEV-E (848 years; 95% HPD, 596–1112 years), LIV (2424 years; 95% HPD, 1572–3400 years), TBEV-FE (1936 years, 95% HPD, 1344–2598 years), and the joint clade of TBEV-S (2505 years, 95% HPD, 1700–3421 years) comprising Vasilchenko, Zausaev, and Baltic lineages.

The aim of the review was to conduct a comparative analysis of the epidemiological situation on tick-borne encephalitis (TBE) over 2014–2023 in the constituent entities of the Russian Federation located in the European and Asian parts of the country and to give a forecast of incidence for 2024. The incidence of TBE in 2023 only marginally decreased as compared to the peak values in 2022, which leveled down the ten-year trend towards reduction. Grouping of the entities of the Russian Federation according to the average incidence of TBE over a decade made it possible to classify 17 of them as regions of low, 15 – of medium, and 17 – of high epidemiological risk. In general, the epidemiological situation regarding TBE is more unfavorable in the Asian part of the country. A list of species of Ixodidae ticks, the main vectors of the tick-borne encephalitis virus, is provided, as well as subtypes and genetic variants of the latter, identified in the European and Asian parts of the country. The peculiarities of the epidemiological situation on TBE and the scope of preventive measures undertaken in Russia in 2023 are considered. It is shown that there are no clearly outlined trends in the nature of changes in the incidence of TBE in endemic federal districts and entities of the country, and the expected incidence rates in 2024 will remain at the long-term average level.

The aim of the review is to conduct a comparative analysis of the epidemiological situation on tick-borne viral encephalitis (TBVE) in the constituent entities of the Russian Federation in 2015–2024 and to provide a forecast of the incidence rate for 2025. According to the data for 2015–2024, the number of visits to medical organizations by people that suffered from tick bites remained approximately at the same level and averaged 491,871.2 cases per year. The Siberian, Volga, and Ural Federal Districts are of primary importance for the formation of the incidence rate, accounting for more than 75 % of all cases. In 2024, 1 659 patients with TBVE were identified, which is only slightly less than in the previous year (1 778). The morbidity rate per 100 thousand population (1.13) was lower than the long-term average for the period of 2015–2024 (1.17). 46 lethal outcomes were registered (mortality rate 2.7 %), which is 1.3 times higher than the long-term average. The epidemic process in 2024 was most active in the territories of 11 entities of the Russian Federation: Krasnoyarsk and Perm Territories, Sverdlovsk, Kirov, Irkutsk, Novosibirsk and Kemerovo Regions, TransBaikal Territory, St. Petersburg city, Udmurt Republic, and Arkhangelsk Region. The number of virus containing ticks removed from people and from environmental objects, when studied using PCR and ELISA, in the Russian Federation as a whole in 2024 did not exceed the long-term average value. The infection rate of ticks removed from people has statistically significantly decreased over a ten-year period. The review examines the volumes of specific and non-specific TBVE prevention measures taken in Russia in 2024 and compares them with the data from previous years. It is predicted that the situation on TBVE incidence in 2025 will remain at the average long-term level in six federal districts of the country. However, in the Far Eastern Federal District, mainly due to the change in the epidemiological situation in the TransBaikal Territory, a statistically significant trend towards an increase in the morbidity and mortality has emerged, which is taken into account when making the forecast of the TBVE incidence rate for this federal district in 2025.