Anastasiya Alexandrovna Derko

Wild waterfowl constitute the primary natural reservoir of influenza A viruses, and wetlands at the convergence of major migratory flyways serve as critical hubs for viral genetic exchange. Baikal Siberia, situated at the intersection of the East African–West Asian, Central Asian, and East Asian–Australasian flyways, represents a unique yet understudied region in this context. Here we report the results of long-term virological surveillance of wild birds in the Lake Baikal basin conducted between 2018 and 2024. A total of 1036 cloacal swab samples from 28 bird species were screened, yielding 42 influenza A virus isolates belonging to 12 HA/NA subtype combinations: H1N1, H3N1, H3N2, H3N5, H3N6, H3N8, H4N6, H6N1, H6N2, H6N3, H6N8, and H12N5. Among the detected subtypes, H6 viruses—identified with four distinct neuraminidase combinations (N1, N2, N3, N8)—are of particular public health relevance owing to their documented capacity for dual-receptor binding and potential for zoonotic transmission to mammals, including humans. Full-genome sequencing followed by cluster analysis of internal gene segments identified 16 distinct segment constellations, indicating extensive reassortment. BLAST searches against the GISAID database revealed closest genetic relatives in Mongolia, South Korea, Japan, China, and Western Siberia, with more distant links to Bangladesh, Europe, and a possible intercontinental connection via the Pacific flyway. Maximum-likelihood phylogenetic analysis of the HA and NA segments confirmed that all isolates belong to the Eurasian genetic lineage, yet they are distributed across multiple clades rather than forming a single monophyletic group, reflecting the role of Buryatia as a mixing zone for genetically diverse viral populations. These findings substantially expand the understanding of influenza A virus ecology in the Lake Baikal basin and underscore the importance of continued surveillance at this key migratory crossroads in Northern Asia.

Highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b has recently emerged as a major threat to wildlife, agriculture, and public health due to its expanding host range and the increasing frequency of spillover into mammals. In July–August 2023, the mass death of over 3500 northern fur seals (Callorhinus ursinus) and at least one Steller sea lion (Eumetopias jubatus) was recorded on Tyuleniy Island in the Sea of Okhotsk, Russia. Two HPAI A(H5N1) viruses were isolated from fur seal carcasses and designated A/Northern_fur_seal/Russia_Tyuleniy/74/2023 and A/Northern_fur_seal/Russia_Tyuleniy/75/2023. Both viruses exhibited high pathogenicity in chickens (IVPI 2.7–3.0) and mice (MLD₅₀ 1.9–2.5 log₁₀EID₅₀/mL), with distinct differences in disease progression, histopathology, and organ tropism. Experimental infection of mice revealed that strain A/74/2023 induced more severe pulmonary and neurological lesions than A/75/2023. Whole-genome sequencing and phylogenetic analysis demonstrated close relatedness to HPAI H5N1 strains circulating in the Russian Far East and Japan from 2022 to 2023, with several mutations associated with mammalian adaptation, including NP-N319K and, in one isolate, PB2-E627K. According to our findings, northern fur seals (Callorhinus ursinus) on Tyuleniy Island acted as spillover hosts for the highly pathogenic avian influenza (HPAI) H5N1 virus of clade 2.3.4.4b. Furthermore, the high population density of fur seals and the extensive mortality observed during the outbreak highlight these animals’ potential role as another vessel for the evolution of avian influenza viruses. This study represents the first documented case of HPAI H5N1 in pinnipeds in the North Pacific region and supports previous reports indicating that pinnipeds, including northern fur seals, are highly susceptible to HPAI H5N1 clade 2.3.4.4b viruses.

Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.

Ixodid ticks are blood-sucking ectoparasites of vertebrates. They are an integral part of any natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) are found, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks are being identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in people with fever symptoms after tick bites in Japan and China from 2014 to 2025. For the first time, we performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The subsequent phylogenetic analysis demonstrated that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. These findings expand the geographic range and the number of vector species for YEZV and highlight the importance of molecular monitoring of viral agents circulating among ticks in Western Siberia.

Wild waterbirds are circulating important RNA viruses, such as avian coronaviruses, avian astroviruses, avian influenza viruses, and avian paramyxoviruses. Waterbird migration routes cover vast territories both within and between continents. The breeding grounds of many species are in the Arctic, but research into this region is rare. This study reports the first Newcastle disease virus (NDV) detection in Arctic Russia. As a result of a five-year study (from 2019 to 2023) of avian paramyxoviruses and avian influenza viruses in wild waterbirds of the Taimyr Peninsula, whole-genome sequences of NDV and H3N8 were obtained. The resulting influenza virus isolate was phylogenetically related to viruses that circulated between 2021 and 2023 in Eurasia, Siberia, and Asia. All NDV sequences were obtained from the Herring gull, and other gull sequences formed a separate gull-like clade in the sub-genotype I.1.2.1, Class II. This may indirectly indicate that different NDV variants adapt to more host species than is commonly believed. Further surveillance of other gull species may help to test the hypothesis of putative gull-specific NDV lineage and better understand their role in the evolution and global spread of NDV.

Yakutia, the largest breeding ground for wild migratory birds in Northeastern Siberia, plays a big role in the global ecology of avian influenza viruses (AIVs). In this study, we present the results of virological surveillance conducted between 2018 and 2023, analyzing 1970 cloacal swab samples collected from 56 bird species. We identified 74 AIVs of H3N6, H3N8, H4N6, H5N3, H7N7, H10N3, and H11N9 subtypes in Anseriformes order. Phylogenetic analysis showed that the isolates belong to the Eurasian lineage and have genetic similarities with strains from East Asia, Europe, and North America. Cluster analysis has demonstrated the circulation of stable AIV genotypes for several years. We assume that Yakutia is an important territory for viral exchange on the migratory routes of migrating birds. In addition, several amino acid substitutions have been found to be associated with increased virulence and adaptation to mammalian hosts, highlighting the potential risk of interspecific transmission. These results provide a critical insight into the ecology of the AIV and highlight the importance of continued monitoring in this geographically significant region.

Rhinoviruses and respiratory enteroviruses remain among the leading causes of acute respiratory infections, particularly in children. Little is known about the genetic diversity of enteroviruses and rhinoviruses in pediatric patients with acute respiratory infections in Russia. We assessed the prevalence of human rhinoviruses/enteroviruses (HRV/EV) in 1992 children aged 0 to 17 years hospitalized with acute respiratory infections during the 2023–2024 epidemic season using PCR. The detection rate of HRV/EV was 11% (220/1992). We performed typing of 58 HRV and 28 EV viruses by partial sequencing of the VP1 gene. Rhinovirus A was the most common among HRV, followed by rhinovirus C; rhinovirus B was detected in only three cases. Enteroviruses were represented by all four species, with the EV-D68 genotype being the most frequently detected. Phylogenetic analysis of the VP1 fragment of EV-D68 showed that all our sequences belonged to the B3 subclade. We identified the first case of EV-C105 infection in Russia in a two-year-old girl hospitalized with pneumonia. Phylogenetically, the Novosibirsk strain EV-C105 was closely related to a strain discovered in France in 2018. This research helped to fill a critical gap in understanding the epidemiological landscape of HRV/EV in pediatric populations within Russia.

Rhinoviruses and respiratory enteroviruses remain among the leading causes of acute respiratory infections, particularly in children. Little is known about the genetic diversity of enteroviruses and rhinoviruses in pediatric patients with acute respiratory infections in Russia. We assessed the prevalence of human rhinoviruses/enteroviruses (HRV/EV) in 1992 children aged 0 to 17 years hospitalized with acute respiratory infections during the 2023-2024 epidemic season using PCR. The detection rate of HRV/EV was 11% (220/1,992). We performed typing of 58 HRV and 28 EV viruses by partial sequencing of the VP1 gene. Rhinovirus A was the most common among HRV, followed by rhinovirus C; rhinovirus B was detected in only three cases. Enteroviruses were represented by all four species, with the EV-D68 genotype being the most frequently detected. Phylogenetic analysis of the VP1 fragment of EV-D68 showed that all our sequences belonged to the B3 subclade. We identified the first case of EV-C105 infection in Russia in a two-year-old girl hospitalized with pneumonia. Phylogenetically, the Novosibirsk strain EV-C105 was closely related to a strain discovered in France in 2018. This research helped to fill a critical gap in understanding the epidemiological landscape of HRV/EV in pediatric populations within Russia.

More than 20 years after the discovery of the first anelloviruses (AVs), they still remain a mysterious group of viruses. To date, there is no clear understanding of their impact on the host organism, although information is emerging about their participation in various pathologies. However, it is well known that AVs are an important component of the human virome. In the current study we assessed the abundance of AVs in viromes from four nasal and pharyngeal samples from children with respiratory symptoms using a metagenomic approach. It is worth noting that three patients had known respiratory viruses and one did not have any. Regarding AVs, they were detected in all samples, namely Torque teno mini virus (TTMV). The greatest abundance and diversity of AVs (Torque teno virus (TTV), TTMV and Torque teno midi virus (TTMDV)) were shown in a diseased patient with an absence of respiratory viruses, which may indicate the potential involvement of AVs in the maintenance of respiratory symptoms. An activated immune system to combat the main pathogens, against the background of which the number of AVs decreases, is discussed as a possible reason for the reduced diversity of anellome in other patients. We also compared the results of the metagenomic approach and qPCR for major respiratory viruses, which were in agreement. In addition, metagenomic sequencing made it possible to obtain additional data on viral genomes in order to establish their taxonomic identification and characterize individual viral profiles in patients from the Siberian part of Russia.