Detection of tick-borne pathogens in wild birds and their ticks in Western Siberia and high level of their mismatch

Abstract: The Tomsk region located in the south of Western Siberia is one of the most high-risk areas for tick-borne diseases due to elevated incidence of tick-borne encephalitis and Lyme disease in humans. Wild birds may be considered as one of the reservoirs for tick-borne pathogens and hosts for infected ticks. A high mobility of wild birds leads to unpredictable possibilities for the dissemination of tick-borne pathogens into new geographical regions. The primary goal of this study was to evaluate the prevalence of tick-borne pathogens in wild birds and ticks that feed on them as well as to determine the role of different species of birds in maintaining the tickborne infectious foci. We analysed the samples of 443 wild birds (60 species) and 378 ticks belonging to the genus Ixodes Latraille, 1795 collected from the wild birds, for detecting occurrence of eight tick-borne pathogens, the namely tick-borne encephalitis virus (TBEV), West Nile virus (WNV), and species of Borrelia, Rickettsia, Ehrlichia, Anaplasma, Bartonella and Babesia Starcovici, 1893, using RT-PCR/or PCR and enzyme immunoassay. One or more tick-borne infection markers were detected in 43 species of birds. All markers were detected in samples collected from fieldfare Turdus pilaris Linnaeus, Blyth’s reed warbler Acrocephalus dumetorum Blyth, common redstart Phoenicurus phoenicurus (Linnaeus), and common chaffinch Fringilla coelebs Linnaeus. Although all pathogens have been identified in birds and ticks, we found that in the majority of cases (75.5%), there were mismatches of pathogens in birds and ticks collected from them. Wild birds and their ticks may play an extremely important role in the dissemination of tick-borne pathogens into different geographical regions

Prevalence and genetic diversity of the <i>Alongshan virus (Flaviviridae)</i> circulating in ticks in the south of Eastern Siberia

Introduction. Tick-borne infections are of great importance for many regions of Russia, including Eastern Siberia. This unfavorable epidemiological situation can be characterized not only by the circulation of well-known tick-borne infections, but also by the identification of new pathogens, the role of which remains little or generally unexplored. Multicomponent flavi-like viruses can cause infectious diseases in humans and pose a threat to public health. The purpose of the study was the identification and molecular genetic characterization of the Alongshan virus (Flaviviridae, ALSV) isolates, transmitted by ticks in the south of Eastern Siberia. Materials and methods. Total 1060 ticks were collected and analyzed from the territory of the Republics of Khakassia, Tuva, Buryatia, Irkutsk Region and Transbaikal Territory (Zabaykalsky Krai) in the spring-summer period 2023. ALSV RNA was detected by RT-PCR followed by nucleotide sequence determination and phylogenetic analysis for each segment of the genome. Results. The ALSV infection rate in Ixodes persulcatus ticks collected in the Republic of Khakassia was 3.3% (95% CI: 1.4–7.5); in Irkutsk Oblast – 1.0% (95% CI: 0.3–3.7); in the Republic of Tuva – 0.9% (95% CI: 0.3–3.4) and in Transbaikal Krai – 0.7% (95% CI: 0.2–3.6). Sequences of all four segments of ALSV genetic variants circulating in I. persulcatus ticks in the south of Eastern Siberia are grouped with sequences found in China and clustered into the Asian subgroup transmitted by taiga ticks. The level of difference in the nucleotide sequences of genome fragments among the identified genetic variants of ALSV ranged from 2 to 3%. Conclusion. The article shows the widespread distribution of ALSV in I. persulcatus ticks in the Republics of Khakassia and Tyva, Irkutsk Oblast and Transbaikal Territory. The obtained data actualize monitoring of changes in the area of distribution of potentially dangerous for humans flavi-like viruses and their vectors

Untranslated Regions of a Segmented Kindia Tick Virus Genome Are Highly Conserved and Contain Multiple Regulatory Elements for Viral Replication

Novel segmented tick-borne RNA viruses belonging to the group of Jingmenviruses (JMVs) are widespread across Africa, Asia, Europe, and America. In this work, we obtained whole-genome sequences of two Kindia tick virus (KITV) isolates and performed modeling and the functional annotation of the secondary structure of 5′ and 3′ UTRs from JMV and KITV viruses. UTRs of various KITV segments are characterized by the following points: (1) the polyadenylated 3′ UTR; (2) 5′ DAR and 3′ DAR motifs; (3) a highly conserved 5′-CACAG-3′ pentanucleotide; (4) a binding site of the La protein; (5) multiple UAG sites providing interactions with the MSI1 protein; (6) three homologous sequences in the 5′ UTR and 3′ UTR of segment 2; (7) the segment 2 3′ UTR of a KITV/2017/1 isolate, which comprises two consecutive 40 nucleotide repeats forming a Y-3 structure; (8) a 35-nucleotide deletion in the second repeat of the segment 2 3′ UTR of KITV/2018/1 and KITV/2018/2 isolates, leading to a modification of the Y-3 structure; (9) two pseudoknots in the segment 2 3′ UTR; (10) the 5′ UTR and 3′ UTR being represented by patterns of conserved motifs; (11) the 5′-CAAGUG-3′ sequence occurring in early UTR hairpins. Thus, we identified regulatory elements in the UTRs of KITV, which are characteristic of orthoflaviviruses. This suggests that they hold functional significance for the replication of JMVs and the evolutionary similarity between orthoflaviviruses and segmented flavi-like viruses

Complete mitogenome of the ixodid tick Dermacentor reticulatus (Acari: Ixodida)

Here, we present the complete mitochondrial DNA sequence of Dermacentor reticulatus. The mitogenome is 14,806 bp and contains 13 protein-coding, 2 rRNA, and 22 tRNA genes, along with 2 control regions. Dermacentor reticulatus mitogenome has the common mitochondrial gene order of Metastriata ticks. It is phylogenetically close to the mitogenomes of Dermacentor ticks, of which D. everestanus mitogenome is the closest with 85.7% similarity. These data provide insights into the phylogenetic relations among Dermacentor ticks

The Viromes of Mosquitoes from the Natural Landscapes of Western Siberia

The metagenomic analysis of mosquitoes allows for the genetic characterization of mosquito-associated viruses in different regions of the world. This study applied a metagenomic approach to identify novel viral sequences in seven species of mosquitoes collected from the Novosibirsk region of western Siberia. Using NGS sequencing, we identified 15 coding-complete viral polyproteins (genomes) and 15 viral-like partial sequences in mosquitoes. The complete sequences for novel viruses or the partial sequences of capsid proteins, hypothetical viral proteins, and RdRps were used to identify their taxonomy. The novel viral sequences were classified within the orders Tymovirales and Picornavirales and the families Partitiviridae, Totiviridae, Tombusviridae, Iflaviridae, Nodaviridae, Permutotetraviridae, and Solemoviridae, with several attributed to four unclassified RNA viruses. Interestingly, the novel putative viruses and viral sequences were mainly associated with the mosquito Coquillettidia richardii. This study aimed to increase our understanding of the viral diversity in mosquitoes found in the natural habitats of Siberia, which is characterized by very long, snowy, and cold winters