Sergey Kovalev

Institute of Natural Sciences and Mathematics, Ural Federal University

Early knowledge about novel emerging viruses and rapid determination of their characteristics are crucial for public health. In this context, development of theoretical approaches to model viral evolution are important. The clusteron approach is a recent bioinformatics tool which analyzes genetic patterns of a specific E protein fragment and provid...

Vector‐borne pathogens exist in obligate transmission cycles between vector and reservoir host species. Host and vector shifts can lead to geographic expansion of infectious agents and the emergence of new diseases in susceptible individuals. Three bacterial genospecies (Borrelia afzelii, Borrelia bavariensis, and Borrelia garinii) predominantly ut...

Omsk hemorrhagic fever was first described in the early 1940s and is a natural focal infection, spread exclusively in four regions of Western Siberia and associated with muskrat (Ondatra zibethicus). The etiological agent of this disease is the Omsk hemorrhagic fever virus (OHFV) which is closely related to the tick-borne encephalitis virus (TBEV),...

Viral surveillance is an essential task in public health that yields specific data, such as biological and epidemiological characteristics, crucial in the fight against viruses. We have recently developed an online platform for monitoring of Tick-Borne Encephalitis Virus, TBEV Analyzer, equipped with phylogenetic analysis and geographic map visuali...

Vector-borne pathogens exist in obligate transmission cycles between vector and reservoir host species. Host shifts can lead to geographic expansion and the emergence of new diseases. Three etiological agents of human Lyme borreliosis (Borrelia afzelii, Borrelia bavariensis, and Borrelia garinii) predominantly utilize two distinct tick species as v...

According to modern classification, tick-borne flaviviruses have been divided into a mammalian tick-borne virus group and a seabird tick-borne virus group (STBVG). The STBVG includes the Tyuleniy virus, Meaban virus, Saumarez Reef virus, and the recently discovered Kama virus (KAMV). The latter was isolated from Ixodes lividus, an obligate parasiti...

Omsk hemorrhagic fever virus (OHFV) is the etiological agent of Omsk hemorrhagic fever, a disease described in the 1940s in Western Siberia. However, until now, it has been represented in GenBank by just four complete genome sequences, which does not reflect the real genetic diversity of the virus in nature. In this study, we analyzed the molecular...

Background: Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis, is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge. Results: We pres...

Background Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis , is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge. Results We present...

Background Borrelia bavariensis is one of the agents of Lyme Borreliosis (or Lyme disease) in Eurasia. The genome of the Borrelia burgdorferi sensu lato species complex, that includes B. bavariensis , is known to be very complex and fragmented making the assembly of whole genomes with next-generation sequencing data a challenge. Results We present...

Anaplasma phagocytophilum is a tick-transmitted bacterium that replicates in neutrophil granulocytes and elicits febrile disease in humans and animals; it is widely distributed in the Americas, Europe, Africa, and Asia. A. phagocytophilum is commonly regarded as a single species, but several genetic variants with distinct host distribution and geog...

Anaplasma phagocytophilum is the bacterial agent of granulocytic anaplasmosis in humans and animals; it is widely distributed in Eurasia and North America and transmitted mainly by Ixodes ticks. Several approaches have been used to study genetic diversity in A. phagocytophilum, multilocus sequence typing (MLST) currently being the most reliable and...

Background. In 2016 WHO classification of myeloid neoplasms and acute leukemias a new provisional entity 'B-lymphoblastic leukemia/lymphoma, BCR-ABL1-like' has been introduced. Two current strategies of BCR-ABL1-like ALL detection are based on gene expression profile revealed either by microarray ('BCR-ABL-like') or by NGS / patented TaqMan low-den...

Ticks of the Ixodes ricinus group are important vectors of human pathogens in both Eurasia and North America; therefore, many studies have focused on their molecular systematics and evolutionary relationships. However, there are species that have not been characterized by molecular genetic methods so far. For the first time, we obtained nucleotide...

Tick-borne encephalitis is widespread in Eurasia and transmitted by Ixodes ticks. Classification of its causative agent, tick-borne encephalitis virus (TBEV), includes three subtypes, namely Far-Eastern, European, and Siberian (TBEV-Sib), as well as a group of 886-84-like strains with uncertain taxonomic status. TBEV-Sib is subdivided into three ph...

Ixodes ticks transmit infectious agents and also harbor their own parasites and symbionts. The presumptive endosymbiont of Ixodes ricinus, ‘Candidatus Midichloria mitochondrii’, has a unique ability to invade mitochondria within tick ovarian cells and is transovarially transmitted with 100% efficiency. A closely related bacterium, provisionally nam...

Molecular genetic techniques and approaches in epidemiological studies were breakthrough in the understanding of the laws, ways, and mechanisms of the spread of the pathogens. However, lack of standard methods makes it difficult to compare results obtained by different scientific groups. In this work we propose to choose one fragment of the TBEV ge...

Hybridization of ticks of the genus Ixodes has been described for several species under laboratory conditions although no molecular genetics evidence confirming interspecific hybridization in nature is available. We have designed a real time PCR targeted on nuclear (ITS2) and mitochondrial (cox1) markers to accurately identify tick species and to d...

Table S1. Clusterons and unique TBEV strains used in the present study.

Tick-borne encephalitis is the most important human arthropod-borne virus disease in Europe and Russia, with an annual incidence of about 13 thousand people. Tick-borne encephalitis virus (TBEV) is distributed in the natural foci of forest and taiga zones of Eurasia, from the Pacific to the Atlantic coast. Currently, there are three mutually exclus...

Spirochetes of the Borrelia burgdorferi sensu lato complex are the causative agent of Lyme borreliosis which is widespread in Russia. Nowadays, three clinically important B. burgdorferi s.l. genospecies, B. afzelii, B. garinii, B. bavariensis sp. nov., can be found in Russia, as well as B. miyamotoi, which belongs to the tick-borne relapsing fever...

We performed clinical and laboratory characterization of patients with rare translocation t(1;11)(p32;q23) leading to MLL-EPS15 fusion gene formation. Study cohort consisted of 33 primary acute leukemia (AL) cases including 6 newly diagnosed and 27 patients previously described in literature. Among study group patients t(1;11)(p32;q23) was found mo...

Tick-borne encephalitis (TBE) is a natural focal viral neuroinfection that is widespread in the temperate zone of Eurasia. Knowledge of the genetic structure of tick-borne encephalitis virus (TBEV) populations is important for understanding, not only the origin and evolution of the virus, but also the formation and maintenance of natural foci. A ne...

Tick-borne encephalitis is a natural focal transmissible zooanthroponosis. The causative agent of the disease is a tick-borne encephalitis virus (TBEV) belonging to the genus Flavivirus of the family Flaviviridae and is widespread in Eurasia. Current TBEV classification based on molecular genetic data comprises three phylogenetically separate subty...

Although the history of the tick-borne encephalitis in Urals dates back to 75 years ago, the problem of the spread and evolution of the tick-borne encephalitis virus (TBEV] largely remains terra incognita. Any research in this area is of great basic and practical importance. A few years ago, a hypothesis about the change of the TBEV genotype in the...

The Sofjin strain is one of the first isolates of tick-borne encephalitis virus and, due to its wide distribution in virus collections, it has become the reference strain. Until now, GenBank has recorded several sequences associated with the Sofjin strain that have significant differences between each other. We have sequenced the complete genome of...

117 cases of infant acute lymphoblastic leukemia without Down syndrome (aged from 1 to 365 days) were included in the current study. Rearrangements of 11q23 (MLL) were revealed in 74 patients (63.2%). Among this group the most common rearrangement was t(4;11)(q21;q23)/MLL-AF4 detected in 63.5% cases, less frequently was found t(11;19)(q23;p13)/MLL-...

European and Asian viruses within the tick-borne encephalitis flavivirus complex are known to show temporal, spatial and phylogenetic relationships that imply a clinal pattern of evolution. However, the isolation of recognized Far-Eastern tick-borne encephalitis virus (TBEV) strains in the European region of the former Soviet Union (SU), i.e. thous...

Tick-borne encephalitis virus (TBEV) plays an important role in infectious human morbidity, particularly in Russia and the Middle Urals. The Siberian subtype of TBEV (S-TBEV) is dominant in the Middle Urals. Determining the origin of S-TBEV strains in this territory and also in the European part of Russia and the Baltic countries is very important...

Studies and complete awareness of the regional and epidemiological properties of tick-borne encephalitis virus (TBEV) allow one to improve methods for preventing, diagnosing, and treating its severe neurological infection. The authors have developed reverse-transcriptase polymerase chain reaction (RT-PCR) systems for the detection of RNA of TBEV an...

Translocation t(1;11)(p32;q23) leading to the MLL/EPS15 fusion gene (FG) is relatively rare event in infants leukemia. Purpose. To develop quantitative real-time PCR(qRT-PCR) assay for detection and MRD monitoring of MLL/EPS15 FG. Methods. Since September 2003 till November 2007 twenty three infants with ALL were enrolled in MLL-Baby study, conta...

The Ural region in Russia is one of the areas most affected by a high incidence of tuberculosis (TB). Molecular epidemiological studies able to trace Mycobacterium tuberculosis transmission are of particular significance. To characterize the population of M. tuberculosis strains circulating in the Ural region, to detect the predominant genotypes an...

A study of distributions of different genetic variations (subtypes) of hepatitis C virus (HCV), circulating in the territories of Yekaterinburg and Chelyabinsk among infected population categories of different social statuses and age, is reported in the paper. The predominance of 1b subtype was shown in the HCV-infected patients at the hemodialysis...

Homozygous mutations of the gene mutated in ataxia telangiectasia (ATM) causes the AT syndrome, a pleiotropic phenotype that includes an increased risk of cancer. Most of the known mutations at the ATM gene lead to truncations which are usually associated with instability of mRNA and protein. A decrease or loss of ATM protein expression is associat...

The p73 gene is a structural and, in overexpression systems, functional p53 homologue. Ectopic p73 expression can activate a broad subset of p53-responsive genes, induce apoptosis, and act as a growth suppressor. Yet, viral oncoproteins that antagonize p53 (adenovirus E1B 55K, SV40 large T, and human papillomavirus E6) do not antagonize p73. This c...

The novel p73 gene is a structural and, in overexpression systems, functional p53 homologue. p73 resides on chromosome 1p36.33 within a commonly deleted region in neuroblastoma (NB) and other human tumors. To evaluate p73's candidacy for a NB suppressor, we analyzed 28 primary NB tumors, 14 NB cell lines, and 5 non-NB malignant pediatric tumors. We...

In contrast to endometrioid carcinoma, uterine papillary serous carcinoma (UPSC) is an aggressive type of endometrial cancer. Loss of p53 function is critical for the molecular pathogenesis of UPSC. Both UPSC and its putative precursor, endometrial intraepithelial carcinoma (EIC), show abnormal p53 overexpression in most tumors. To further assess t...