Cases of Q fever detected in residents of the novosibirsk region hospitalized with suspection of infections transmitted by ticks

Coxiella burnetii is the causative agent of Q fever (coxiellosis), which, in addition to acute manifestations, often occurs in a latent form, is prone to chronic course and, in the absence of antibiotic therapy, has a high risk of disability or death. As a result of the presence of a wide range of clinical manifestations specific to other infectious diseases, the use of laboratory test methods (LTM) is required to make a diagnosis. The presence of Q fever anthropurgic foci in the Novosibirsk region was described in the 90s of the last century, but due attention to its laboratory diagnostics is not paid in this region. The aim of the study was to identify genetic and serological markers of the causative agent, C. burnetii, in patients of the Novosibirsk region who were admitted for treatment with fever with suspected tick-borne infections (TBIs). DNA marker of the causative agent of Q fever was detected in blood samples by real time PCR in 9 out of 325 patients. In three patients, the presence of C. burnetii DNA was confirmed by sequencing of the IS1111 and htpB gene fragments. In ELISA tests, antibodies against the causative agent of coxiellosis were detected in the blood sera of 4 patients with positive results of PCR analysis. Contact with tick was registered in 7 out of 9 patients who had C. burnetii DNA and lacked markers of other TBIs. Six people were infected in the Novosibirsk region, two suffered from tick's bite in Altai, and one case was from the Republic of Kyrgyzstan. Thus, a complex approach using both PCR analysis and ELISA provided the identification of markers of the Q fever causative agent in patients admitted with suspected TBIs, thereby differentiating it from other infections. Contact with ticks in most cases suggests that infection with C. burnetii had a transmissible pathway.

Genetic diversity and geographical distribution of the Siberian subtype of the tick-borne encephalitis virus

The tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is currently subdivided into three main subtypes-the European (TBEV-Eu), the Far-Eastern (TBEV-FE), and the Siberian (TBEV-Sib). The TBEV-Sib is the most common subtype and found in all regions where TBEV was detected, except for Central and Western Europe. Currently, four genetic lineages have been described within TBEV-Sib. In this study, detailed analysis of TBEV-Sib genetic diversity, geographic distribution, phylogeography and divergence time of different TBEV-Sib genetic lineages based on E gene fragments, complete genome sequences, and all currently available data in the GenBank database was performed. As a result, a novel Bosnia lineage within the TBEV-Sib was identified. It was demonstrated that the Zausaev lineage is the most widely distributed among the TBEV-Sib lineages, and was detected in all studied regions except the Far East. The Vasilchenko lineage was found from Western Siberia to the Far East. The Baltic lineage is presented from Europe to Western Siberia. The Obskaya lineage was found only in Western Siberia. TBEV strains from a newly described Bosnia lineage were detected in Bosnia, the Crimean peninsula, Kyrgyzstan and Kazakhstan. The greatest divergence of the TBEV-Sib genetic variants was observed in Western Siberia. Within the TBEV-Sib, the Obskaya lineage diverged from the common ancestor the earliest, after that the Bosnia lineage was separated, then the Baltic lineage, and the Zausaev and Vasilchenko lineages diverged most recently.

DEFINITION AND COMPARATIVE ANALYSIS OF THE GENOMIC STRUCTURE OF SIBERIAN STRAINS OF TICK-BORNE ENCEPHALITIS VIRUS OF THE EUROPEAN SUBTYPE

Tick-borne encephalitis virus (TBEV) is classified into three subtypes: Far Eastern (TBEV-FE), European (TBEV-EU) and Siberian (TBEV-SIB). In Russia, these are also called genotypes 1, 2 and 3, respectively. Geographically, TBEV-EU dominates in Central and Northern Europe, but its representatives are also found to the east - along the southern part of the forest zone of extratropical Eurasia - up to Eastern Siberia and South Korea. However, the strains isolated outside Europe remain poorly investigated. In the proposed study, eight full genomes of the Siberian isolates of TBEV-EU were determined and 13 complete genomes were compared. The analysis of 152 full-genome TBEV sequences showed that the TBEV-EU has a higher degree of stability of the genome-coding region in the entire Eurasian area (3.1% of differences) compared to TBEV-FE (6.6%) and TBEV-SIB (7.8%). At the same time, the maximum differences are observed not between European and Siberian strains, as one could expect, but between the representatives from Europe - TBEV strains Mandl-2009 from Norway and Hypr from the Czech Republic. The studied strains from Siberia form the compact genetic cluster of 42 TBEV-EU strains and are divided into two subclusters - West Siberian and East Siberian variants. These variants differ in the combinations of amino acid substitutions in all proteins except NS2B. The West Siberian variant mostly circulates in the territory of Altai, and the closest relative of its representatives is Absettarov strain from the European part of Russia. The strains similar to the East Siberian variant of the European subtype were recorded in the Altai (strain 84.2, 2007) and in Belarus (N256, about 1940).

The phylodynamics of the rabies virus in the Russian Federation

Near complete rabies virus N gene sequences (1,110 nt) were determined for 82 isolates obtained from different regions of Russia between 2008 and 2016. These sequences were analyzed together with 108 representative GenBank sequences from 1977-2016 using the Bayesian coalescent approach. The timing of the major evolutionary events was estimated. Most of the isolates represented the steppe rabies virus group C, which was found over a vast geographic region from Central Russia to Mongolia and split into three groups (C0-C2) with discrete geographic prevalence. A single strain of the steppe rabies virus lineage was isolated in the far eastern part of Russia (Primorsky Krai), likely as a result of a recent anthropogenic introduction. For the first time the polar rabies virus group A2, previously reported in Alaska, was described in the northern part of European Russia and at the Franz Josef Land. Phylogenetic analysis suggested that all currently circulating rabies virus groups in the Russian Federation were introduced within the few last centuries, with most of the groups spreading in the 20th century. The dating of evolutionary events was highly concordant with the historical epidemiological data.

[Detection of potential sites of recombination in the Tick-borne encephalitis virus by the methods of comparative genomics]

The results of the bioinformatic search for the potential sites of the recombination in the genome-wide structures of the tick-borne encephalitis virus (TBEV) through a series of software techniques were presented in this work. The genomes of the 55 TBEV strains were assayed, 21 of them showed the presence of the recombination sites. Recombinant strains belonged to the Far Eastern (19 strains) and European (2 strains) genotypes. 22 sites of the recombination attributed were identified to five types based on position, strain, and regional characteristics. The parental strains were identified based on the genotypic and geographical parameters, which do not contradict the possibility of the formation of the recombinants. Nearly two-thirds of the sites are located in the regions of NS4a and NS4b genes, which are the "hot spots" of the recombination, most of them being concentrated in the gene NS4. It was shown that the recombination processes did not occur at the level of the genotypes (European genotype) or certain groups within the genotype (Far East) and were typical of the peripheral populations.

The correlation between tick (Ixodes persulcatus Sch.) questing behaviour and synganglion neuronal responses to odours

We examined the behavioural and electrophysiological responses of taiga ticks (Ixodes persulcatus) to several olfactory stimuli: Osmopherone® (5-a-androst-16-en-3-ol), Osmopherine® (butanoic and 3-methylbutanoic acids), DEET® (N,N-diethyl-meta-toluamide), ethanol (96%), and water (control stimulus). To study individual tick behavioural reactions to these stimuli, we used a Y-shaped glass maze (n=50). To study the electrophysiological reactions of the ticks' synganglia to these olfactory stimuli, we recorded the shifts of total potential (TP) of pre-oesophageal neurons in response to odour stimulation of Haller's organ (n=25). We found that Osmopherine® attracted ticks and frequently evoked negative shifts of TP, whereas the response to Osmopherone® did not differ from the reaction to water. DEET® and ethanol acted as tick repellents and generally evoked positive shifts of TP. We also tested each tick for its questing height (QH) on a glass rod that was at an incline of 75°, and we tested for the presence of pathogens i.e., DNA of Borrelia burgdorferi sp. s.l. and RNA of tick-borne encephalitis virus (TBEV). The degree of response to Osmopherine® positively correlated with the QH. The ticks with the highest values of QH showed a greater prevalence of the tick-borne pathogen Borrelia sp. s.l. compared with the ticks that did not reach the maximum QH. The present results show a correlation between the electrophysiological reaction of the synganglia of ticks and their behavioural responses to different odours.

[Genotypes 4 and 5 of the tick-borne encephalitis virus: features of the genome structure and possible scenario for its formation]

On the basis of the comparison of complete genome structures of 32 strains and gene E fragments (160 ndt) of 643 strains and RNA isolates of tick-borne encephalitis (TBE) virus, we confirmed our previously expressed assumption (Zlobin V.I. et al, 2001) of existence, along with the three major genotypes, of genotypes 4 (strain 178-79) and 5 (strain 886-84). "Mosaic" structure of the polyprotein in the two strains was established. It manifests itself in particular in the sequences of 14 positions (C-3, E-206, NS1-54, NS-285, NS2A-100, NS2A-127, NS2A-174, NS2A-175, NS2A-225, NS3-376, NS4B-28, NS4B-96, NS5-18, NS5-671) containing the amino acids strictly conserved for each of the three major genotypes and is consistent with a uniform pattern of distribution of nucleotide substitutions that are specific for genotypes 1, 2 and 3. Possible scenario of the origin of TBE genotypes 4 and 5 was suggested.

[Detection of recombinations in tick-borne encephalitis virus by using computer analysis of viral genomes]

Computer programs were used to search for tick-borne encephalitis (TBE) virus recombinants among the isolates whose complete nucleotide sequences are deposited in the GenBank database. The application of RDP, Chimaera, Maximum chi2, and TOPAL programs has revealed recombinant sites in a number of sequences, which indicates that TBE virus has recombinations and that the programs are suitable for their detection.

Omsk haemorrhagic fever

Omsk haemorrhagic fever is an acute viral disease prevalent in some regions of western Siberia in Russia. The symptoms of this disease include fever, headache, nausea, severe muscle pain, cough, and moderately severe haemorrhagic manifestations. A third of patients develop pneumonia, nephrosis, meningitis, or a combination of these complications. The only treatments available are for control of symptoms. No specific vaccine has been developed, although the vaccine against tick-borne encephalitis might provide a degree of protection against Omsk haemorrhagic fever virus. The virus is transmitted mainly by Dermacentor reticulatus ticks, but people are mainly infected after contact with infected muskrats (Ondatra zibethicus). Muskrats are very sensitive to Omsk haemorrhagic fever virus. The introduction of this species to Siberia in the 1930s probably led to viral emergence in this area, which had previously seemed free from the disease. Omsk haemorrhagic fever is, therefore, an example of a human disease that emerged owing to human-mediated disturbance of an ecological niche. We review the biological properties of the virus, and the epidemiological and clinical characteristics of Omsk haemorrhagic fever.

[The genetic variability and genotyping of tick-borne encephalitis virus with deoxyoligonucleotide probes]

A panel of genotype-specific molecular probes has been designed, which is used to indicate and differentiate tickborne encephalitis (TBE) virus. It assesses the individual genetic structure of each strain since the targets for the probes are the variable sequences of all 10 virus genes, which are specific for each of three genotypes. The molecular nucleic acid hybridization by means of the panel was used to study 273 TBE virus strains. Isolated from a Eurasian area; along with the representatives of three genotypes, the virus strains, the genomic structures of which do not fit in the established concept on three genotypes, circulate in Eastern Siberia.

The brain 5-HT1Areceptor gene expression in hibernation

Hibernation is a unique physiological state characterized by profound reversible sleep-like state, depression in body temperature and metabolism. The serotonin 5-hydroxytryptamine(1A) (5-HT(1A)) receptor gene sequence in typical seasonal hibernator, ground squirrel (Spermophilus undulatus), was specified. It was found that the fragment encoding the fifth transmembrane domain showed 93.6% of homology with the analogous fragment of the mouse and rat genes and displayed 88.5% homology with the human 5-HT(1A) receptor gene. Using primers designed on the basis of obtained sequence, the expression of 5-HT(1A) receptor gene in the brain regions in active, entering into hibernation, hibernating and coming out of hibernation ground squirrels was investigated. Significant structure-specific changes were revealed in the 5-HT(1A) messenger RNA (mRNA) level in entry into hibernation and in arousal. An increase in the 5-HT(1A) gene expression was found in the hippocampus during the prehibernation period and in ground squirrels coming out of hibernation, thus confirming the idea of the hippocampus trigger role in the hibernation. Significant decrease in 5-HT(1A) receptor mRNA level in the midbrain was found in animals coming out of hibernation. There was no considerable changes in 5-HT(1A) receptor mRNA level in different stages of sleep-wake cycle in the frontal cortex. Despite drastically decreased body temperature in hibernating animals (about 37 degrees C in active and 4-5 degrees C in hibernation), 5-HT(1A) receptor mRNA level in all examined brain regions remained relatively high, suggesting the essential role of this 5-HT receptor subtype in the regulation of hibernation and associated hypothermia.

Natural tick-borne encephalitis virus infection among wild small mammals in the southeastern part of western Siberia, Russia

Infestation of small mammals, including common shrews Sorex araneus L., field mice Apodemus agrarius Pallas, and red voles Clethrionomus rutilus Schreber, with immature Ixodes persulcatus ticks and their infection with tickborne encephalitis virus (TBEV) were studied in the forest-steppe habitat in the vicinity of Novosibirsk, Russia. Larval ticks parasitize all three host species, but virtually all nymphs were found only on field mice and red voles. Detection of the viral RNA using reverse transcription (RT) with subsequent nested polymerase chain reaction (nPCR) and of viral antigen using enzyme-linked immunosorbent assay (ELISA) revealed a high prevalence of TBEV-positive animals in both the summer and winter. The proportion of small mammals with hemagglutination inhibition (HI) antibodies was significantly lower than with ELISA-detected antibodies. Taken together, the data suggest that small mammals may maintain TBEV as a persistent infection throughout the year.

[Detection of RNA in vaccine " EnceVir" against tick-borne encephalitis virus]

Fractionation of RNA isolated from the inactivated purified concentrated vaccine "EnceVir" ("Virion", Tomsk, Russia) allowed the authors to reveal predominantly double-stranded RNA and trace quantities of single-stranded RNA sizing mainly less than 200 n. The fragments of tick-borne encephalitis virus (TBEV) were detected among the total RNA by the reverse transcription test, followed by nested polymerase chain reaction with the primers specific to the E gene of TBEV. The findings may suggest that immunity may be induced through activation of Th1 and Th2 after immunization with such an inactivated vaccine for effective elimination of intracellular infection and intracellular virions, respectively.

PCR detection of Borrelia burgdorferi sensu lato, tick-borne encephalitis virus, and the human granulocytic ehrlichiosis agent in Ixodes persulcatus ticks from Western Siberia, Russia

PCR assays were used to test adult Ixodes persulcatus ticks from Western Siberia, Russia, for Borrelia burgdorferi sensu lato, tick-borne encephalitis virus (TBEV), and the human granulocytic ehrlichiosis (HGE) agent. Of the 150 ticks that were studied, 38% were infected with B. burgdorferi, 46% were infected with TBEV, and 8% were infected with the HGE agent. These three pathogens were distributed in the ticks independently of one another.

[Newly isolated mink parvovirus strain]

A new mink enteritis virus (MEV) strain, called Cherepanovo, was isolated in the Novosibirsk region (West Siberia). The level of this strain's accumulation in cell culture is lower than that of commercial MEV strains Rodniki or Beregovoi. Identification of Cherepanovo strain by hemagglutination inhibition test, protein electrophoresis in denaturing polyacrylamide gel, and PCR showed its similarity to the previously described MEV strains. Comparative analysis of this strain's 5' and 3' nucleotide sequences of VP2 gene showed its more than 98% homology with other feline parvoviruses. Nucleotide residues 2920, 2971, and 4245 in the Cherepanovo strain VP2 gene differed from those of all previously described MEV strains. It is noteworthy that transition at the position 4245 led to Phe-->Cys replacement in amino acid residue.

[Genetic analysis of tick-borne encephalitis virus strains from West Siberia]

Tick-borne encephalitis (TBE) virus strains were isolated in West Siberia in the forest-steppe region near the Ob river in 1981-1992. Hybridization of genome RNA of 46 TBE strains with [32P]cDNA of TBE Sofyin strain revealed essential differences in the genomes of West-Siberian and Far-Eastern Sofyin strains of TBE virus. Nucleotide sequences of 6 TBE strains (1348-1503 n.) have been determined. A 89-98% homology of Siberian TBE strains has been shown, while the similarity of the respective fragment of E gene for West Siberian and Sofyin strains was no more than 81%. No significant changes in E gene of TBE strains have been detected over a 12-year period.

Tick-borne encephalitis virus strains of Western Siberia

Tick-borne encephalitis virus (TBEV) strains were isolated from ticks in Western Siberia for 12 years. Molecular hybridization of the 46 viral RNA with the TBEV cDNA and oligonucleotide probes revealed differences between the Siberian and Far Eastern strains. A comparison of the viral E gene fragment nucleotide sequence showed 89-98% homology between Siberian TBEV strains, whereas their similarity with strains from other populations was less than 83%. However, the viral E and NS1 glycoprotein antigenic structures appeared to be conservative because of the degenerate genetic code. This was shown by enzyme-linked immunosorbent assay with the corresponding monoclonal antibodies (MAb). The single exception was the MAb 17C3 against nonstructural glycoprotein NS1, which could distinguish Siberian from Far Eastern strains. Moreover, the neurovirulence differed between strains from the two natural populations. Lower neuroinvasiveness of the Siberian strains in comparison with Far Eastern Sofyin strain might be caused by both E and NS1 glycoprotein mutations.