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Hemorrhagic fever with renal syndrome (HFRS) is registered annually among residents of Khabarovsk city, Russia. The aim of the study was to conduct a genetic analysis of hantaviruses, the causative agents of HFRS, in residents of Khabarovsk city and in Norway rats (Rattus norvegicus), a natural reservoir of Seoul virus (SEOV), captured in Khabarovsk and its suburbs. Materials and methods. Blood sera samples from 75 patients with HFRS, collected in 2016–2023 (blood plasma – in 2017) and samples from 1468 Norway rats, captured during 2011–2023, were investigated. Results and discussion. We have demonstrated the presence of the Seoul virus (SEOV) in samples of Norway rats from the city of Khabarovsk and the suburban settlement Priamursky, Jewish Autonomous Region; 2 RNA isolates of the SEOV virus, 33 isolates of the Hantaan virus (HTNV), 9 isolates of the Amur virus (AMRV) – in patients with HFRS from Khabarovsk. Phylogenetic analysis of partial S and L segments of the genome has revealed that three RNA isolates of SEOV from Norway rats and two isolates from HFRS patients are most closely related (99 % homology) to strains from China and are different from the variant of SEOV from Vladivostok. It is assumed that the urban focus of the Seoul virus in Khabarovsk and its environs was formed as a result of the importation of virus carriers from China, where this variant of the virus is widespread. The data obtained indicate that the incidence of HFRS in residents of Khabarovsk, caused by infection with the HTNV and AMRV viruses, is associated with visits to various rural areas of the Far East.

Coronaviruses (family Coronaviridae, genera Alphacoronavirus, Betacoronavirus) are dangerous viral pathogens that have caused three outbreaks of severe respiratory diseases, SARS, MERS, COVID-19. In Russia, data on coronaviruses in natural reservoirs are limited, as investigations began only during the COVID-19 pandemic.The aim. To study the diversity of coronaviruses among rodents and insectivores in the Republic of Altai.Materials and methods. Rodents (n = 67) and shrews (n = 52) were captured in 2022. Samples were analyzed by reverse transcription-polymerase chain reaction followed by sequencing.Results and conclusions. Four samples from rodents (Myodes rutilus, M. glareolus, Apodemus peninsulae, A. agrarius) and two samples from an insectivore (Crocidura sibirica) were positive for coronaviruses, among which three different coronaviruses were detected. Rodent-borne coronaviruses are classified in the genus Betacoronavirus, subgenera Embecovirus, and have shown host associated clustering. The nucleotide sequences of Siberian coronaviruses from rodents were identical for closely related species (M. rutilus and M. glareolus, A. agrarius and A. peninsulae) and close (> 94 % homology) to previously published sequences in each of the groups of carriers found in the territory Novosibirsk region, Europe and China. The coronavirus identified from the insectivore, possibly belonging to a new subgenera of the family Coronaviridae, has also been assigned to the genus Betacoronavirus.Conclusion. Five species of natural carriers of three different coronaviruses were detected in the Altai Republic. A high level of identity of coronaviruses genomes from rodents has been revealed, indicating a relatively low rate of their evolution.

Coronaviruses (family Coronaviridae, genera Alphacoronavirus and Betacoronavirus) are the causative agents of respiratory, intestinal and neurological diseases in humans and animals. Natural reservoirs of coronaviruses include bats, rodents and insectivores, however, the circulation of coronaviruses among rodents and insectivores in the Russian Federation has been unexplored. The aim of the study was to investigate the diversity of coronaviruses among rodents and insectivores co-inhabiting natural biotopes. Materials and methods. Rodents (68 specimens) and shrews of the genus Sorex (23 specimens) were caught in a limited forest area not exceeding 1.5 sq. km, in the vicinity of Novosibirsk. All samples were screened using reverse transcription polymerase chain reaction followed by sequencing. Results and discussion. Four distinct coronaviruses have been detected in four species of small mammals. Rodent-borne coronaviruses were classed within subgenera Embecovirus, genus Betacoronavirus, and demonstrated host-associated phylogenetic clustering. The level of homology between the new RNA isolates from red-backed vole (Myodes rutilus), root vole (Microtus oeconomus) and field mouse (Apodemus agrarius) is 85.5–87.7 %. The nucleotide sequences of Siberian coronavirus isolates are closely related (>93 % homology) to previously published sequences in each of the carrier groups found in Europe and China, which suggests their common evolutionary origin. The coronavirus identified in the common shrew (Sorex araneus) belongs to the genus Alphacoronavirus, but is significantly different (>36 % difference) from earlier identified strains included in the genus. It has been shown that different coronaviruses co-circulate in a limited area among rodents and insectivores.

Introduction. Insectivores are newly recognized hantaviral reservoir worldwide. Four distinct shrew-borne hantaviruses (family Hantaviridae) have been identified in two regions located in southern and northern part of the Russian Far East, two genetic variants of Seewis virus (SWSV), Lena River virus (LENV), Kenkeme virus (KKMV) and Yakeshi virus (YKSV). Here, we describe geographic distribution of shrew-borne hantaviruses in southern part of the Russian Far East: Jewish Autonomous region, Khabarovsk Krai, Primorsky Krai and Sakhalin region. Materials and methods. Lung samples from shrews of genus Sorex, captured in the four regions of Far Eastern Russia, were examined for hantavirus RNA using reverse transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis of the partial nucleotide sequences of viral genome was conducted using MEGA X software. Results. New genetic variant of YKSV was identified in new reservoir host, long-clawed shrew (S. ungiuculatus) from Sakhalin Island. Genetic variant of SWSV, ARTV-Sc, has been found to circulate among S. caecutiens on the seacoast of Khabarovsk and Primorsky Krai. KKMV virus and second genetic variant of SWSV, ARTV-St, were found in S. roboratus and S. tundrensis, respectively from Jewish Autonomous region. Conclusion. Sorex-borne hantaviruses were found in all studied regions of Far Eastern Russia. Our results demonstrated co-evolution of SWSV, KKMV, and YKSV viruses throughout the geographic distribution of its hosts.

Pathogenic hantaviruses, belonging to the family Hantaviridae, genus Orthohantavirus, are widely spread in many regions of the world and cause hemorrhagic fever with renal syndrome (HFRS) in Europe and Asia. In the European Russia, the most active HFRS foci are located in the optimum habitat area of natural reservoir of the Puumala virus (PUUV), bank voles (Myodes glareolus), – in the Middle Volga and Cis-Urals. The largest number of cases of HFRS was registered in the Volga Federal District. In 2019, an outbreak of HFRS was registered among the residents of Saratov and the Saratov Region, the number of cases was 2702. Objective of the study was genetic identification of hantaviruses from HFRS patients and rodent carriers and phylogenetic analysis of full-size genomes from natural hosts during HFRS outbreak in the Saratov Region, 2019. Materials and methods. Blood samples of 8 HFRS patients from Saratov and 3 lung samples of bank voles captured in the suburb of Saratov were analyzed using reverse transcription polymerase chain reaction, followed by sequencing and phylogenetic analysis. Results and discussion. A total of 6 viral RNA isolates from HFRS patients were genetically typed, full-length RNA-isolate genomes were obtained for 3 natural carriers. Our data indicate that PUUV virus was associated with HFRS outbreak in Saratov. Genetic analysis revealed that the virus belonged to RUS lineage of PUUV, related most closely to strains from Udmurtia and Tatarstan and differed from strains circulating in the territory of Bashkortostan and Samara Region.

Human pathogenic hantaviruses, belonging to the family Hantaviridae, genus Orthohantavirus, are disseminated worldwide and cause hemorrhagic fever with renal syndrome (HFRS) in Europe and Asia. In the Far East of Russia Hantaan (HTNV), Amur (AMRV) and Seoul (SEOV) viruses are etiologic agent of HFRS, while the human pathogenic potential of other seven hantaviruses, circulating in this region, has not been researched adequately yet. Objective of the study was genetic identification of hantaviruses, associated with HFRS in the Far East of Russia during 2015-2018. Materials and methods. Blood samples of 64 HFRS patients from Jewish Autonomous Region, Khabarovsk and Primorsky Territories were analyzed for hantavirus RNA using reverse transcription polymerase chain reaction. Results and discussion. A total of 19 viral RNA isolates from HFRS patients were genetically typed. Etiologic agents of HFRS were three pathogenic hantaviruses: HTNV (13 isolates), AMRV (3 isolates), SEOV (3 isolates). Three genetic lineages were identified among HTNV, two lineages among AMRV One genetic variant of SEOV virus was identified among HFRS patients, which was more close to the strains from South-Eastern Asia than to those from the neighboring countries.

Objective of the study was investigation of hantaviruses in a new natural reservoir - insectivores, their diversity and geographic distribution in the Western and Eastern Siberia. Materials and methods. Sorex shrews (71 specimens) were captured in Altai Republic, Altai, and Krasnoyarsk Territories, and Omsk Region. All samples were analyzed for hantavirus RNA using reverse transcription polymerase chain reaction with subsequent sequencing. Results and conclusions. A total of 12 viral RNA isolates from two Sorex species (S. araneus and S. roboratus) were genetically typed. Sequence analysis of the partial L and S segments identified two distinct hantaviruses. Kenkeme (KKMV) virus was detected in a flat-skulled shrew (S. roboratus) in Altai Territory. This virus was previously found in geographically remote sites in the Sakha Republic and China. New foci of Seewis virus circulation among common shrews (S. araneus), were found in the Omsk Region, Altai and Krasnoyarsk Territories. Previously published and new findings suggest that hantaviruses among shrews are widely distributed over the Russian Federation territory. The widespread circulation of SWSV and KKMV throughout Siberia is an important argument for investigation of their role in human infections.

Background. Hantavirus infections are one of the most important zoonotic diseases in the Russian Federation. However, the pathogenicity of Hantaviruses circulating in Siberia is still unknown. The aim of the study was to assess the incidence of Hantavirus infection in patients with fever of unknown origin from Irkutsk region and adjacent territories. Materials and methods. Serum samples collected in 2016 from individuals with symptoms of health deterioration were screened by ELISA to investigate possible Hantavirus infection, in addition to tick-borne infections. Depending on date of tick bite specific immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies to tick-borne encephalitis, borreliosis and Hantavirus were tested by ELISA or screened by PCR for tick-borne encephalitis, borreliosis, human granulocytic anaplasmosis and monocytic erlychiosis RNA/DNA. Results. Out of 92 serum samples, 6.5 % were positive for hantavirus-specific antibodies, which is at least twice higher than the seroprevalence among healthy people in the Irkutsk region. IgM and IgM+IgG antibodies were found in 5.4 % of cases, while IgG antibodies - in 1.1 % of cases. The clinical symptoms among sero-positive patients were fever, skin lesion, fatigue syndrome, headache and lymphadenitis. IgM antibodies to borreliosis were found in two hantavirus sero-positive cases. Lung tissues from small mammals captured in 2016 were screened by ELISA for the presence of Hantavirus antigen. Hantaviral antigen was detected in 6.3 % of 48 samples. Conclusions. Thus, present and previous studies demonstrate existence of natural foci of Hantavirus infections in addition to tick-born infections in the territory of the Irkutsk region.

The article describes the results of recognaissance surveys of blood serums of humans in Baikal area for hantavirus antibodies and of tissue specimens (lungs) of small mammal for hantavirus antigens. This investigation demonstrated that Baikal area inhabitants contact such dangerous pathogens as hantaviruses. It's proved by the presence of hantavirus antibodies in human serum samples. IgG or IgM antibodies to hantaviruses were found in 3,7 % of 379 tested serum samples. IgM were found in 1,6 % of cases, IgG - in 2,1 % of cases. 2 patients with IgG and IgM with suspected traces of hantavirus infection had complaints to hyperthermia (up to 40,5 °C) and wasting. Blood serums with positive results of hantavirus antibodies were found in residents of Irkutsk region. Hantavirus antigens weren't found in researched lung samples of mouse-like rodent and insectivores from Angarsk, Irkutsk, Zalari and Ust-Kut districts of Irkutsk region and Tunkinsky district of Republic of Buryatia.

Hokkaido hantavirus (HOKV) identified originally in the grey red-backed vole (Myodes rufocanus) in Hokkaido, Japan. Subsequent studies showed different genetic lineages of HOKV in Sakhalin, Buryatia and Far Eastern regions of Russia and in China. Tissuesfrom 68 arvicolid rodents, captured in regions south and west of Baikal Lake, were initially tested for hantaviral antigen by ELISA, and tissues from antigen-positive rodents were analyzed for hantavirus RNA by RT-PCr. Taxonomic identification of host species was based on phylogenetic analysis of partial cytochrome b gene sequences. Hantavirus Land S-segment sequences were detected in two antigen-positive M. rufocanus, from the Tunka region of Buryatia Republic (south side) and the Olhon region of Irkutsk Oblast (west side). Sequence analysis showed that the newfound hantavirus strains, designated Baikal and Siberia, represented genetic variants of HOKV Previously unknown genetic variant designated Siberia was identified in M. rufocanus captured in Olhon region. Second genetic variant from Tunka region, designated Baikal, was closely related to previously described hantavirus strain from the same region. Alignment and comparison of the nucleotide and amino acid sequences showed intra-strain differences of 18,4 % and 5,3 % for the L segment and 17,4 % and 3,5 % for the S segment, respectively. Sequence divergence from geographically distant HOKV strains were 17,4-21,5 % and 3,9-6,8 % for the L segment and 15,2-17,0 % and 3,3-4,0 % for the S segment, respectively. Phylogenetic analysis, based on a 346-nucleotide region of the L segment, revealed four lineages represented by previously reported variants from Japan and Sakhalin (strains Kitahiyama128L/2008, Tobetsu35L/2010 and Sakhalin99L/1998), Shkotovo in Far-Eastern Russia (strain Khekhtsir37L/2002) and the new variants from Baikal Lake. Analysis of the N protein, coding by the S segment, identified specific amino acid signatures for YJRV of Lys5, Arg26, Val/Ile68, Val/Ala9 He262, Pro283. Conclusions: HOKV is widespread across the geographic range of its arvicolid rodent reservoir host.

Genetic evidence of shrew-borne hantavirus in Russia is presented here. Impressive distribution of a hantavirus Seewis (SWSV), previously discovered in the Eurasian common shrew from Switzerland, was demonstrated in Siberia among closely related shrew species: Sorex araneus, S. tundrensis and. S. daphaenodon. SWSV circulation was shown in Altai Republic, Krasnoyarsk Krai, Kemerovo and. Novosibirsk regions, surburbs of Novosibirsk and Irkutsk Cities.