Comparative analysis of genomes of tick-borne encephalitis virus strains isolated from mosquitoes and ticks.

The tick-borne encephalitis virus (TBEV) strain Lazo MP36 was isolated from the pool of mosquitoes Aedes vexans collected in Lazo region of Khabarovsk territory in August 2014. Phylogenetic analysis of the strain Lazo MP36 complete genome (GenBank accession number KT001073) revealed its correspondence to the TBEV Far Eastern subtype and differences from the following strains: 1) from ticks Ixodes persulcatus P. Schulze, 1930 [vaccine strain 205 (JX498939) and strains Khekhtzir 1230 (KF880805), Chichagovka (KP844724), Birobidzhan 1354 (KF880805) isolated in 2012-2013]; 2) from mosquitoes [strain Malyshevo (KJ744034) isolated in 1978 from Aedes vexans nipponii in Khabarovsk territory; strain Sakhalin 6-11 isolated from the pool of mosquitoes in 2011 (KF826916)]; 3) from human brain [vaccine strain Sofjin (JN229223), Glubinnoe/2004(DQ862460). Kavalerovo (DQ862460), Svetlogorie (DQ862460)]. The fusion peptide necessary for flavivirus entry to cells of the three TBEV strains isolated from mosquitoes (Lazo MP36, Malyshevo and Sakhalin 6-11) has the canonical structure 98-DRGWGNHCGLFGKGSI-113 for the tick-borne flaviviruses. Amino acid transition H104G typical for the mosquito-borne flaviviruses was not found. Structures of 5'- and 3'-untranslated (UTR) regions of the TBEV strains from mosquitoes were 85-98% homologous to the TBEV strains of all subtypes without recombination with mosquito-borne flaviviruses found in the Far East of Russia. Secondary structures of 5'- and 3'-UTR as well as cyclization sequences (CS) of types a and B are highly homologous for all TBEV isolates independently of the biological hosts and vectors. similarity of the genomes of the TBEV isolates from mosquitoes, ticks and patients as well as pathogenicity of the isolates for new-borne laboratory mice and tissue cultures might suggest a possible role of mosquitoes in the TBEV circulation in natural foci as an accidental or additional virus carrier.

Molecular-genetic and ultrastructural characteristics of 'Candidatus Ehrlichia khabarensis', a new member of the Ehrlichia genus.

Recently, a new Ehrlichia genetic variant, Ehrlichia sp. Khabarovsk, was identified in tissue samples of small mammals captured in the Russian Far East. To further characterize Ehrlichia sp. Khabarovsk, tissue homogenate from a naturally infected gray red-backed vole (Myodes rufocanus) was passaged three times in newborn laboratory mice. Using nested PCR Ehrlichia sp. Khabarovsk DNA was detected in tissue samples from infected mice at 1-4 weeks post inoculation. Electron microscopic examination revealed morulae containing gram-negative bacterial cells in monocytes of mouse spleen and liver. The size and ultrastructure of these cells corresponded to those described previously and allowed us to identify the bacteria as Ehrlichia sp. The comparison of ehrlichial 16S rRNA, groEL and gltA genes and putative GroEL and GltA amino acid sequences has demonstrated that Ehrlichia sp. Khabarovsk, like Ehrlichia ruminantium, is more distant from all other Ehrlichia species than these species are between themselves. Phylogenetic analysis has shown that Ehrlichia sp. Khabarovsk belongs to the clade formed by Ehrlichia spp. but clusters separately from other Ehrlichia species and genetic variants. These data indicate that Ehrlichia sp. Khabarovsk can be considered as a new candidate species. We propose to designate it as 'Candidatus Ehrlichia khabarensis' according to the territory where this species was found.

Genetic variability of Babesia parasites in Haemaphysalis spp. and Ixodes persulcatus ticks in the Baikal region and Far East of Russia.

To study Babesia diversity in Ixodid ticks in Russia, Ixodes persulcatus, Haemaphysalis japonica, Haemaphysalisconcinna, Dermacentor silvarum, and Dermacentor nuttalli ticks collected in the Far East and Baikal region were assayed for the presence of Babesia spp. using nested PCR. In total, Babesia DNA was detected in 30 of the 1125 (2.7%) I. persulcatus, 17 of the 573 (3.0%) H. concinna, and 12 of the 543 (2.2%) H. japonica but was undetectable in any of the 294 analyzed Dermacentor spp. Partial 18S rRNA gene sequences were determined for all of the positive samples. Among the positive ticks, nine I. persulcatus were infected by Babesia microti 'US'-type, five I. persulcatus were infected by Babesia divergens-like parasites, and 11 I. persulcatus were infected by Babesia venatorum. For all three of these species, the determined 18S rRNA gene sequences were identical to those of the Babesia genetic variants found previously in I. persulcatus in Russia. In addition, five I. persulcatus from the Baikal region and all of the positive Haemaphysalis spp. ticks carried 13 different sequence variants of Babesia sensu stricto belonging to distinct phylogenetic clusters. Babesia spp. from 29 ticks of different species collected in distinct locations belonged to the cluster of cattle and ovine parasites (Babesia crassa, Babesiamajor, Babesiamotasi, Babesiabigemina, etc.). Babesia spp. from four H. japonica ticks in the Far East belonged to the cluster formed by parasites of carnivores. One more Babesia sequence variant detected in an I. persulcatus tick from the Baikal region belonged to the cluster formed by parasites of cattle and wild cervids (B. divergens, Babesiacapreoli, B. venatorum, Babesiaodocoilei, etc.).

[Genetic variability of anaplasmataceae bacteria determined in Haemaphysalis spp. and Dermacentor sp. ticks in the territory of the Russian Far East].

Totally 484 Haemaphysalis japonica, 359 Haemaphysalis concinna and 221 Dermacentor silvarumn collected in Amur region and Khabarovsk Territory of the Russian Far East were examined on the presence of Anaplasmataceae bacteria using nested PCR. All positive samples were characterized by analysis of the 16S rRNA gene and/or groESL operone nucleotide sequences. Forty nine H. japonica and three H. concinna were shown to contain DNA of two new Ehrlichia genetic variants. These genetic variants on the basis of the 16S rRNA gene and groESL operone nucleotide sequences analysis were most closely related to Ehrlichia spp. revealed in Haemaphysalis spp. ticks in Japan. Four H. concinna from Amur region were shown to contain DNA of a new Anaplasma bovis genetic variant, which corresponded to A. bovis genetic variant revealed in a red gray-backed vole and a Siberian chipmunk from the Far East. Three H. concinna and nine D. silvarum contained DNA of non-typical bacteria which can't be attributed to any Anaplasmataceae genera based on the determined sequences of the 16S rRNA gene fragments. The revealed non-typical bacteria on the basis of 16S rRNA gene sequences significantly differed from each other and didn't form a separate genetic group.

[Study of the heterogeneity of 16s rRNA gene and groESL operone in the dna samples of Anaplasma phagocytophilum, Ehrlichia muris, and "Candidatus Neoehrlichia mikurensis" determined in the Ixodes persulcatus ticks in the area of Urals, Siberia, and far east of Russia].

A total of 3552 Ixodes persulcatus from Sverdlovsk, Chelyabinsk, Novosibirsk, Irkutsk regions and Khabarovsk Territory were examined on the Ehrlichia and Anaplasma presence by nested PCR based on the 16S rRNA gene. Both Anaplasma phagocytophilum and Ehrlichia muris DNA were found in I. persulcatus in all studied regions. A. Phagocytophilum was detected in 1.3-6.3% of ticks and E. muris - in 2.0-14.1% of ticks. Moreover, "Candidatus Neoehrlichia mikurensis" DNA was found in 8 ticks collected in Novosibirsk, Irkutsk Regions and Khabarovsk Territory. Partial nucleotide sequences of 16S rRNA gene and groESL operone (1240-1300 bp) were determined for 65 samples of A. Phagocytophilum, 17 samples of E. muris and 4 samples of "Candidatus Neoehrlichia mikurensis". Nucleotide sequences of 16S rRNA gene and groESL operone of E. muris and "Candidatus Neoehrlichia mikurensis" were shown to be highly conservative, and nucleotide sequences of groESL operone of both E. muris and "Candidatus Neoehrlichia mikurensis" differed from the sequences found previously in other species of Ixodid tick. On the basis of analysis of the 16S rRNA gene and groESL operone sequences it was concluded that all revealed samples A. Phagocytophilum could be divided into 2 groups. GroESL operone sequences of A. Phagocytophilum from the first group were identical to each other but significantly differed from the known groESL operone sequences (less than 98.2% of similarity), whereas their 16S rRNA gene sequences were identical to the sequence of widely distributed and pathogenic for human A. Phagocytophilum genetic variant (CAHU-HGEl, GenBank AF093788) or differed from it by a single nucleotide substitution. The nucleotide sequences of groESL operone of A. Phagocytophilum from the second group differed from each other by 1-4 nucleotides and were closely related (99.2-99.4% of similarity) to the sequences of groESL operone ofA. phagocytophilum isolates found in Europe in Ixodes ricinus and roe deer. The nucleotide sequences of the 16S rRNA gene of A. Phagocytophilum from the second group were most similar to the sequence of the rare A. Phagocytophilum genetic variant previously found only in China (GenBank DQ342324).

[Detection of Babesia spp. DNA in small mammals and ixodic ticks on the territory of north Ural, west Siberia and far east of Russia].

Totally, 932 small mammals and 458 questing adult Ixodes persulcatus from Sverdlovsk and Novosibirsk regions and Khabarovsk Territory, as well as 128 Haemaphysalis japonica, 34 H. concinna and 29 Dermacentor silvarum from Khabarovsk Territory were examined for the presence of Babesia by nested PCR based on the 18S rRNA gene. Babesia microti DNA was found in samples of small mammals from all the studied regions--in 36.2% of samples from Sverdlovsk region, 5.3% of samples from Novosibirsk region, and 6.7% of samples from Khabarovsk Territory. The determined B. microti 18S rRNA gene sequences from Novosibirsk region (6 sequences) and from Khabarovsk Territory (10 sequences) were identical to each other and to the sequences of pathogenic for human B. microti US-type, while the determined B. microti 18S rRNA gene sequences from Sverdlovsk region (12 sequences) were identical to those of B. microti strain Munich. B. microti were found most frequently in samples of Myodes spp., they were found also in Microtus spp., Apodemus spp., Sorer spp., and Sicista betulinav. It was shown that one of 347 analyzed I. persulcatus from Novosibirsk region and one of 77 I. persulcatus from Khabarovsk Territory contained B. microti US-type DNA. One I. persulcatus from Novosibirsk region contained B. divergens DNA. In this work B. divergens was for the first time determined in I. persulcatus and B. microti in I. persulcatus in Asian part of Russia. Three different genetic variants of Babesia sensu stricto were found in three H. japonica from Khabarovsk Territory. The first genetic variant was closely related to Babesia sp. revealed in a feral raccoon in Japan (99.9% similarity on the basis of 18S rRNA gene sequences). Two others Babesia genetic variants were most similar to the ovine pathogen Babesia crassa (97.1-97.6% similarity on the basis of 18S rRNA gene sequences).

[PCR detection of the causative agents of infections transmitted by ticks on the Kamchatka Peninsula].

There has been recently a rise in referrals for Ixodes tick bites in the spring and summer periods in the Kamchatka Territory. Among the dominant tick species, there has been the taiga tick Ixodes persulcatus habiting the extensive areas of the southern and central parts of the peninsula. Examination of 84 I. persulcatus females collected from human beings and domestic animals in 2003 to 2007 detected DNA of the pathogens of tick-borne borreliosis (B. burgdorferi sensu lato), rickettsiasis (R. tarasevichiae and R. helvetica), and Ehrlichiosis/anaplasmosis (A. phagocytophilum). Tick-borne encephalitis RNA and antigens and babesiasis DNA were not found in the study samples. Despite the small number of taiga ticks in Kamchatka, the detection of the pathogens of various infectious diseases in the ticks suggests that there may be a risk for contamination of the peninsula's population with these pathogens.