Tick-Borne Encephalitis with Hemorrhagic Syndrome, Novosibirsk Region, Russia, 1999

Eight fatal cases of tick-borne encephalitis with unusual hemorrhagic syndrome were identified in 1999 in the Novosibirsk Region, Russia. To study these strains, we sequenced cDNA fragments of protein E gene from six archival formalin-fixed brain samples. Phylogenetic analysis showed tick-borne encephalitis variants clustered with a Far Eastern subtype (homology 94.7%) but not with the Siberian subtype (82%)

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

Rotavirus Seasonality: An Application of Singular Spectrum Analysis and Polyharmonic Modeling

The dynamics of many viral infections, including rotaviral infections (RIs), are known to have a complex non-linear, non-stationary structure with strong seasonality indicative of virus and host sensitivity to environmental conditions. However, analytical tools suitable for the identification of seasonal peaks are limited. We introduced a two-step procedure to determine seasonal patterns in RI and examined the relationship between daily rates of rotaviral infection and ambient temperature in cold climates in three Russian cities: Chelyabinsk, Yekaterinburg, and Barnaul from 2005 to 2011. We described the structure of temporal variations using a new class of singular spectral analysis (SSA) models based on the “Caterpillar” algorithm. We then fitted Poisson polyharmonic regression (PPHR) models and examined the relationship between daily RI rates and ambient temperature. In SSA models, RI rates reached their seasonal peaks around 24 February, 5 March, and 12 March (i.e., the 55.17 ± 3.21, 64.17 ± 5.12, and 71.11 ± 7.48 day of the year) in Chelyabinsk, Yekaterinburg, and Barnaul, respectively. Yet, in all three cities, the minimum temperature was observed, on average, to be on 15 January, which translates to a lag between the peak in disease incidence and time of temperature minimum of 38–40 days for Chelyabinsk, 45–49 days in Yekaterinburg, and 56–59 days in Barnaul. The proposed approach takes advantage of an accurate description of the time series data offered by the SSA-model coupled with a straightforward interpretation of the PPHR model. By better tailoring analytical methodology to estimate seasonal features and understand the relationships between infection and environmental conditions, regional and global disease forecasting can be further improved

Immunochernical and single molecule force spectroscopy studies of specific interaction between the laminin binding protein and the West Nile virus surface glycoprotein E domain II

ELISA and Western blot immunochemical data attest an effective and highly specific interaction of the surface glycoprotein E domain II (DII) of the tick born encephalitis and Dengue viruses with the laminin binding protein (LBP). Based on a highly conservative structure of the DII in different flaviviruses we propose a similarly effective interaction between the LBP and the DII of the surface glycoprotein E of the West Nile virus. We report the results of studies of this interaction by immunochemical and single molecule force spectroscopy methods. The specific binding between these species is confirmed by both methods. Copyright (c) 2007 John Wiley & Sons, Ltd

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

Novel Variant of Tickborne Encephalitis Virus, Russia

We isolated a novel strain of tickborne encephalitis virus (TBEV), Glubinnoe/2004, from a patient with a fatal case in Russia. We sequenced the strain, whose landmark features included 57 amino acid substitutions and 5 modified cleavage sites. Phylogenetically, Glubinnoe/2004 is a novel variant that belongs to the Eastern type of TBEV

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