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The south of Western Siberia traditionally belongs to the regions with unfavorable epidemiological situation for tick-transmitted infections. In Novosibirsk and its suburbs, approximately 20 thousand people annually seek for medical care after tick bites. The purpose of this work was to determine human-attacking tick species composition in the territory of Novosibirsk and its suburbs by identifying nucleotide sequence of tick mitochondrial gene cytochrome oxidase COI fragment during the 2018 spring-summer season, determination of infections of individual ticks with viral and bacterial tick-borne infections, followed by genotyping identified pathogens by PCR methods, by determining nucleotide sequences and phylogenetic analysis. It is established that ticks of five species attack the humans: Ixodes persulcatus, Ixodes pavlovskyi, Dermacentor reticulatus, Dermacentor marginatus, Dermacentor nuttali in the Novosibirsk metropolis. The majority of tick attacks on humans are associated with I. pavlovskyi (43.6%) and D. reticulatus (41.2%) ticks. The genetic material of the tick-borne encephalitis virus was detected in 3.6%, borrelia 13.8% and Rickettsia 23.1% individual ticks collected from humans. Genotyping of the tick-borne encephalitis virus (TBEV) in the collected ticks showed the presence of TBEV Siberian and Far Eastern genotype in 83% and 17% cases, respectively. The Kemerovo virus could not be detected. Genetic material from Borrelia spp. and Rickettsia spp. has been detected in all five tick species attacking the local human population. The bulk of the identified Borrelia spp. isolates were genotyped as Borrelia garinii (86%) and 13% of the isolates as Borrelia afzelii species. The genetic material of Borrelia miyamotoi was found in one individual tick. Ticks of the genus Dermacentor have been found to be infected by Rickettsia raoultii, and ticks of the genus Ixodes were largely infected with Rickettsia tarasevichiae, and I. persulcatus tick was infected by Rickettsia helvetica in a single case. Thus, the human population of Novosibirsk and its suburbs is attacked by five species of ixodid ticks dominated by I. pavlovskyi and D. reticulatus ticks. The genetic material of the following tick-borne pathogens was found: Siberian and Far Eastern TBEV genotype, B. garinii, B. afzelii, B. miyamotoi, R. raoulti, R. tarasevichiae and R. helvetica in the individual ticks collected from humans.

Objective of the studywas to assess the level of infection with Borrelia miyamotoi in ticks Ixodes persulcatus and Ixodes pavlovskyi collected in the south of Western Siberia.Materials and methods.688 ticks I. persulcatus and I. pavlovskyi collected on the territory of Novosibirsk, Tomsk and Kemerovo Regions were examined. Borrelia DNA was detected by a two-round polymerase chain reaction with specifc primers to the omp66 gene region, followed by sequencing of the isolated fragments and phylogenetic analysis, including the sequences of prototype isolates published in the international GenBank database. Comparison and analysis of nucleotide sequences was carried out using the MEGA 7 software package. In parallel, the samples were examined for the presence of the agents of transmissible infections – West Nile fever and tick-borne encephalitis, anaplasmosis, ehrlichiosis, babesiosis, bartonellosis and candidate pathogens of tick-borne rickettsiosis through RT-PCR and PCR with species-specifc and genus-specifc primers.Results and discussion.The genetic material of B. miyamotoi was found in 2.2 % of I. persulcatus and I. pavlovskyi ticks in the Tomsk, Novosibirsk, and Kemerovo Regions and their appurtenance to the Asian genotype was determined. It was revealed that the degree of similarity of the omp66 gene fragments within the group of isolates of the Asian genotype was 100 %. No relation between B. miyamotoi and a specifc vector species was identifed.

This paper reports the analysis of the nucleotide sequences of the 5'-untranslated region (5'-UTR) of tick-borne encephalitis virus (TBEV) genomic RNA isolated from 39 individual taiga ticks collected in several regions of Northern Eurasia. The sequences of 5'-UTRs of the Siberian and Far East TBEV genotypes were 89% and 95% identical to the prototype strains (Zausaev and 205), respectively. The detected nucleotide substitutions were typical for these two TBEV genotypes, which made possible unambiguous identification. Both conservative and variable motifs were detected in the 5'-UTR RNA. The B2, C1, and C2 elements of the Y-shaped 5'-UTR structure and the presumable viral RNA-dependent RNA-polymerase binding site were the most variable. The A2, CS A, CS В elements as well as the start codon were conservative. Interestingly, five substitutions in the 5'-UTR C1 variable element of the TBEVs isolated in different geographical regions were strictly conservative, while 11 different substitutions were detected in this element among the laboratory TBEV variants. A little less that a third of all nucleotide substitutions were mapped outside the main elements of the Y-shaped structure. In general, nucleotide substitutions were localized to stem structures, not being found in the hairpin regions of the TBEV 5'-UTR. The results indicated significant variability of the genomic RNA 5'-UTR in the TBEV laboratory strains and field isolates obtained from different geographical regions. It has been suggested that genetic variability of 5'-UTR is characteristic of the TBEV genome 5'-UTR organization and may serve as a structural basis for virus efficient replication in various avian, mammalian, and ixodic tick cells.

The objectives of our study were to survey the prevalence of genetic markers for Rickettsia spp., Ehrlichia spp., Anaplasma spp., Babesia spp., and Theileria spp. in Hyalomma anatolicum ticks collected in southwestern Tajikistan and to perform sequencing and phylogenetic analysis of fragments of the 16S rRNA gene and groESL operon from Ehrlichia spp. and fragments of the 18S rRNA gene of Theileria spp. detected in H. anatolicum ticks. Hyalomma anatolicum ticks collected in the Tursunzade and Rudaki districts of Tajikistan were tested for DNA of Rickettsia spp., Ehrlichia spp., Anaplasma spp., Babesia spp., and Theileria spp. by PCR with specific primers. The amplified fragments were sequenced and analyzed. DNA of Ehrlichia spp. (3.3 %) and Theileria spp. (3.3 %) was detected only in H. anatolicum ticks collected from the Rudaki district, and DNA of Ehrlichia spp. (0.7 %) was found in H. anatolicum ticks from the Tursunzade district. Sequence analysis of fragments of the 16S rRNA gene and groESL operon from Ehrlichia spp. revealed high similarity to Ehrlichia spp. The Tajik isolates of Theileria spp. were genotyped as Theileria annulata based on the analysis of 18S rRNA gene sequences. The phylogenetic analysis demonstrates that Ehrlichia spp. isolates are highly similar to Ehrlichia spp. circulating in China and Brazil. The isolate Tajikistan-5 is closely related to the putative novel species Ehrlichia mineirensis. The Tajik isolates of Theileria spp. were clustered with T. annulata isolates from Turkey, Iran, Pakistan, and China by phylogenetic analyses.

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 regi...

In this work we tested two reagent kits developed by us for detecting SARS-CoV-2 RNA using a fragment of the ORF1ab gene in digital PCR and real-time PCR formats. Data were obtained on the detection of SARS-CoV-2 virus RNA in nasopharyngeal swabs of patients with COVID-19 and asymptomatic carriers. The developed reagent kits provided 100% sensitivity and a detection limit of 103 GE / ml for qPCR, and at least 200 copies / ml of viral RNA when performing digital PCR. These methods were tested using a panel of 1,328 samples collected from patients with suspected COVID-19 at the beginning of 2020 in the Russian Federation. It has been shown that dPCR is more sensitive and can be used to analyze samples with low viral load, including those from patients without clinical symptoms. dPCR significantly improves the accuracy of laboratory research and significantly reduces the number of false negative results in the diagnosis of SARS-CoV-2. Determination of the concentration of SARS-CoV-2 RNA in patients with different clinical course of the disease showed that the concentration of viral RNA can sharply decrease in the first days of the disease. A low concentration of viral RNA in samples from patients is also characteristic of asymptomatic disease. Digital PCR provides a higher detection rate for asymptomatic cases, which is approximately 75% of those infected, as opposed to 45% for real-time PCR. The results obtained on the use of the digital PCR method for detecting SARS-CoV-2 RNA showed that this method is especially suitable for detecting RNA in case of its low concentration in contacts, as well as for monitoring changes in viral load in convalescent patients.

This paper reports the analysis of the nucleotide sequences of the 5'-untranslated region (5'-UTR) of tick-borne encephalitis virus (TBEV) genomic RNA isolated from 39 individual taiga ticks collected in several regions of Northern Eurasia. The sequences of 5'-UTRs of the Siberian and Far East TBEV genotypes were 89% and 95% identical to the prototype strains (Zausaev and 205), respectively. The detected nucleotide substitutions were typical for these two TBEV genotypes, which made possible unambiguous identification. Both conservative and variable motifs were detected in the 5'-UTR RNA. The B2, C1, and C2 elements of the Y-shaped 5'-UTR structure and the presumable viral RNA-dependent RNA-polymerase binding site were the most variable. The A2, CS A, CS В elements as well as the start codon were conservative. Interestingly, five substitutions in the 5'-UTR C1 variable element of the TBEVs isolated in different geographical regions were strictly conservative, while 11 different substitutions were detected in this element among the laboratory TBEV variants. A little less that a third of all nucleotide substitutions were mapped outside the main elements of the Y-shaped structure. In general, nucleotide substitutions were localized to stem structures, not being found in the hairpin regions of the TBEV 5'-UTR. The results indicated significant variability of the genomic RNA 5'-UTR in the TBEV laboratory strains and field isolates obtained from different geographical regions. It has been suggested that genetic variability of 5'-UTR is characteristic of the TBEV genome 5'-UTR organization and may serve as a structural basis for virus efficient replication in various avian, mammalian, and ixodic tick cells.

From 2006 to 2011, in the Tomsk region (south of Western Siberia), eight species of pathogens were detected in birds and the ticks feeding on them: Tick-borne encephalitis virus (TBEV), West Nile virus (WNV), Borrelia spp., Rickettsia spp., Bartonella spp., Anaplasma spp., Ehrlichia spp., and Babesia spp. The identification of a number of strains of viruses and bacterial genovariants related geographically with the Russian Far East, Eastern Siberia, China and Japan and confirms the possibility of the role of birds in the spread of pathogens in the direction of Western Siberia and back. Most of the species that breed and migrate in Western Siberia are of Eastern origin and mostly fly for wintering to South-East Asia. Among these species in our samples, Phylloscopus proregulus was a carrier of both TBEV and Bartonella spp.; Luscinia calliope were infected with both TBEV and Borrelia, while Tarsiger cyanurus were infected with WNV.

The role of birds in the focus of tick-borne infections was studied from 2006 to 2011. The frequency index of ticks carried by ground dwelling birds is about 49.7%. The index of their abundance is 3.8. The larvae of ticks have been found on birds in 43.8% of cases. Nymphs and adult ticks have been found in 39.9 and 16.3%, respectively. It was revealed that Ixodex pavlovskyi was transferred and dominated in the urban microfoci because of its ornithophily. The markers of infectious agents have been recorded in 42 of 60 bird species under study.

Determined is the complete genome sequence of Kolarovo-2008 strain (Siberia subtype) of Tick-borne encephalitis virus (TBEV), isolated from a tick in the suburbs of the Tomsk city. Nucleotide sequence analysis testifies of the fact that the level of genetic differences within the Siberian subtype of TBEV amounts to 10 % of the nucleotide sequence and to 7 % of amino-acid sequence for certain virus genes. 3'-HTO of the genome of Siberian subtype has the highest rate of variability and the homology level ranging from 65 to 97 %. Kolarovo-2008 and Vasilchenko (isolated in Novosibirsk in 1969) strains have the highest level of genome homology. The level of dissimilarity between the two Tomsk strains is substantially higher: the total number of amino-acid substitutions in Tomsk Zausaev and Kolarovo-2008 strains equals to 124, and 3'HTO level of homology is 79 %. Identified genetic variability of the Siberian subtype of TBEV is of a great importance for further development and enhancement of tick-borne encephalitis virus diagnostics.

The role of birds in the focus of tick-borne infections was studied from 2006 to 2011. The frequency index of ticks carried by ground dwelling birds is about 49.7%. The index of their abundance is 3.8. The larvae of ticks have been found on birds in 43.8% of cases. Nymphs and adult ticks have been found in 39.9 and 16.3%, respectively. It was revealed that Ixodex pavlovskyi was transferred and dominated in the urban microfoci because of its ornithophily. The markers of infectious agents have been recorded in 42 of 60 bird species under study.

To study the role of wild birds in the transmission of tick borne encephalitis virus (TBEV), we investigated randomly captured wild birds bearing ixodid ticks in a very highly endemic TBE region located in Tomsk city and its suburbs in the south of Western Siberia, Russia. The 779 wild birds representing 60 species were captured carrying a total of 841 ticks, Ixodes pavlovskyi Pom., 1946 ( n = 531), Ixodes persulcatus P. Sch., 1930 ( n = 244), and Ixodes plumbeus Leach. 1815 ( n = 66). The highest average number of ticks per bird in a particular species was found for the fieldfare ( Turdus pilaris Linnaeus, 1758) (5.60 ticks/bird) and the tree pipit ( Anthus trivialis Linnaeus, 1758) (13.25 ticks/bird). Samples from wild birds and ticks collected in highly endemic periods from 2006 to 2011 were tested for the TBEV markers using monoclonal modified enzyme immunoassay (EIA) and RT-PCR. TBEV RNA and antigen were found in 9.7% and 22.8% samples collected from wild birds, respectively. TBEV markers were also detected in 14.1% I. persulcatus ticks, 5.2% I. pavlovskyi , and 4.2% I. plumbeus ticks collected from wild birds. Two TBEV strains were also isolated on PKE (pig kidney embryo) cells from fieldfare and Blyth's reed warbler ( Acrocephalus dumetorum Blyth, 1849). Sequencing of 5′-NCR of TBEV revealed that all TBEV isolates belong to Far Eastern (dominate) and Siberian genotypes. Several phylogenetic subgroups included TBEV sequences novel for the Tomsk region. Our data suggest that wild birds are potential disseminators of TBEV, TBEV-infected ixodid ticks, and possibly other tick-borne infections.