Comparative analysis of complete genome sequences of European subtype tick-borne encephalitis virus strains isolated from Ixodes persulcatus ticks, long-tailed ground squirrel ( Spermophilus undulatus ), and human blood in the Asian part of Russia

Bartonella, Blechomonas and Trypanosoma in fleas from the long-tailed ground squirrel (Spermophilus undulatus) in northwestern China

Fleas are known to be vectors for a variety of pathogens in veterinary medicine. However, no information is available on the presence of Bartonella and Trypanosomatidae in fleas of the long-tailed ground squirrel (LTGR, Spermophilus undulatus). The present study shows detection of these pathogens in LTGR fleas. During 2022-2023, a total of 396 fleas were collected from 91 LTGRs in 4 alpine regions of Xinjiang Uygur Autonomous Region (northwestern China) and grouped into 54 flea pools. Flea species were identified according to morphological characteristics and molecular data. In addition, all flea samples were analyzed for Bartonella with amplification and sequencing of a 380-bp part of the gltA gene and Trypanosomatidae with targeting the 18S rRNA (850-bp) and gGAPDH (820-bp) genes. The flea species included Frontopsylla elatoides elatoides (203), Neopsylla mana (49), and Citellophilus tesquorum dzetysuensis (144). Of 54 flea pools, seven (12.96%) tested positive for Bartonella, and three (5.56%) were positive for Trypanosomatidae. Based on BLASTn and phylogenetic analyses, i) Bartonella washoensis in F. elatoides elatoides and C. tesquorum dzetysuensis, and Bartonella rochalimae in F. elatoides elatoides were identified. Interestingly, a new haplotype within the species Ba. washoensis was discovered in C. tesquorum dzetysuensis; and ii) Blechomonas luni was confirmed in C. tesquorum dzetysuensis and Trypanosoma otospermophili in F. elatoides elatoides. Two Bartonella species and two Trypanosomatidae members were discovered for the first time in fleas from LTGRs. This study broadens our understanding of the geographic distribution and potential vectors for Bartonella and Trypanosomatidae.

The First Record of Omsk Hemorrhagic Fever Virus and Tick-Borne Encephalitis Virus of Baltic Lineage from the Kemerovo Region of Russia

Objectives: Tick-borne encephalitis virus Siberian subtype (TBEV-Sib) and Omsk hemorrhagic fever virus (OHFV) are causative agents of natural focal infections in Western Siberia, Russia. The distribution of TBEV phylogenetic lineages and OHFV in the Kemerovo Region of Western Siberia remains poorly investigated. Methods: The phylogenetic analyses of fragment genome sequences 26 flaviviruses identified in 2019 were performed, and the amino acid variation was determined to reveal to which clusteron they belong. The age of Baltic and Asian lineages of the TBEV-Sib was calculated for Kemerovo District and Region, respectively. Results: Twenty-five isolates were members of three TBEV-Sib phylogenetic lineages: Baltic (48%), Asian (36%), and East Siberian (16%). The Baltic lineage's eastern boundary is commonly thought to be in the Novosibirsk Region, but our data suggest that it may reach further east. Analysis of the Baltic lineage clusteron structure showed that the isolates found are unique (6) or belong to clusteron-founder 3D (1) and derived clusteron 3O (5). Based on the age of 3O clusteron, Baltic lineage could have appeared in the Kemerovo Region by the late 1970s. One of the isolated viruses turned out to be the OHFV of the first subtype and not to belong to any known clusteron. This finding is the first known detection of the virus outside the endemic area of Russia. Given the recent discovery of OHFV in Kazakhstan, it can be assumed that the area of this virus distribution is much wider than previously thought. Conclusions: This report provides insights into the population structure of TBEV and OHFV, which may be helpful for epidemiological investigation and surveillance of the viruses.

The Lack of the Association of the CCR5 Genotype with the Clinical Presentation and Frequency of Tick-Borne Encephalitis in the Polish Population

Background: The host factors influencing the susceptibility to and the severity of tick-borne encephalitis (TBE) are poorly defined. The loss-of-function Δ32 mutation in the chemokine receptor gene CCR5 was identified as a risk factor for West Nile encephalitis and possibly for TBE, suggesting a protective role of CCR5 in Flavivirus encephalitis. Methods: We studied the CCR5 genotype in 205 TBE patients stratified by a clinical presentation and 257 controls from the same endemic area (Podlasie, Poland). The genotype distribution between the groups and differences between TBE patients with different genotypes were analyzed. Results: There were 36 (17.6%) CCR5Δ32 heterozygotes and 3 (1.5%) homozygotes in the TBE group, with no statistically significant difference in comparison with the controls. The CCR5Δ32 allele did not associate with the clinical presentation or the severity of TBE. The cerebrospinal fluid (CSF) inflammatory parameters did not differ between the wild-type (wt/wt) and wt/Δ32 genotype patients. The TBE clinical presentation and CSF parameters in three Δ32/Δ32 homozygotes were unremarkable. Conclusions: The lack of association of CCR5Δ32 with the risk and clinical presentation of TBE challenges the suspected CCR5 protective role. CCR5 is not indispensable for the effective immune response against the TBE virus.

Y-shaped RNA Secondary Structure of a Noncoding Region in the Genomic RNA of Tick-Borne Encephalitis Virus Affects Pathogenicity

Tick-borne encephalitis virus (TBEV) is a zoonotic virus that causes encephalitis in humans. Various deletions have been reported in a variable region of the 3' untranslated region of the TBEV genome. In this study, we analyzed the role of a Y-shaped secondary structure in the pathogenicity of TBEV by using reverse genetics. Deletion of the structure increased the mortality rate of virus-infected mice but did not affect virus multiplication in cultured cells and organs. Our results indicated that the secondary structure is involved in the regulation of TBEV pathogenesis. This article is protected by copyright. All rights reserved.

European subtype of tick-borne encephalitis virus. Literature review

This review is devoted to the European subtype of tick-borne encephalitis virus (TBEV). It summarizes and analyzes the information available at the scientific literature on the genetic and biological properties of strains of this virus subtype. A comparative analysis of the complete coding sequences of all currently recognized tick-borne flaviviruses was carried out. It was noted that the differences in TBEV strains included in the European subtype are minimal, which indicates a higher degree of their genetic homogeneity than in strains of the Far Eastern and Siberian subtypes. The level of differences in the genome of strains of the European subtype, depending on the region and the source of isolation, was analyzed. No relationship was found between the level of homology of nucleotide sequences of TBEV strains of the European subtype and the source of isolation. The proposed models for the evolution of TBE are described. The area of TBE of the European subtype in Eurasia is analyzed. The maps of the geographical distribution of the European subtype are presented. It shows the European subtype TBE is found in 14 regions of Russia. TBE of this subtype, as a rule, causes a disease with a milder course in comparison with TBE caused by a virus of the Far Eastern or Siberian subtypes. An analysis of the main vectors and reservoir hosts of the European subtype TBEV in Europe and in Siberia has been carried out. It is emphasized that in Eurasia the European TBEV circulates in territories that differ significantly in climatic conditions, relief, landscape, and characteristics of biotopes. However, analysis of scientific literature data showed that, despite these differences, it has a high degree of genome stability.

Exploring the Reservoir Hosts of Tick-Borne Encephalitis Virus

Tick-borne encephalitis virus (TBEV) is an important arbovirus, which is found across large parts of Eurasia and is considered to be a major health risk for humans. Like any other arbovirus, TBEV relies on complex interactions between vectors, reservoir hosts, and the environment for successful virus circulation. Hard ticks are the vectors for TBEV, transmitting the virus to a variety of animals. The importance of these animals in the lifecycle of TBEV is still up for debate. Large woodland animals seem to have a positive influence on virus circulation by providing a food source for adult ticks; birds are suspected to play a role in virus distribution. Bank voles and yellow-necked mice are often referred to as classical virus reservoirs, but this statement lacks strong evidence supporting their highlighted role. Other small mammals (e.g., insectivores) may also play a crucial role in virus transmission, not to mention the absence of any suspected reservoir host for non-European endemic regions. Theories highlighting the importance of the co-feeding transmission route go as far as naming ticks themselves as the true reservoir for TBEV, and mammalian hosts as a mere bridge for transmission. A deeper insight into the virus reservoir could lead to a better understanding of the development of endemic regions. The spatial distribution of TBEV is constricted to certain areas, forming natural foci that can be restricted to sizes of merely 500 square meters. The limiting factors for their occurrence are largely unknown, but a possible influence of reservoir hosts on the distribution pattern of TBE is discussed. This review aims to give an overview of the multiple factors influencing the TBEV transmission cycle, focusing on the role of virus reservoirs, and highlights the questions that are waiting to be further explored.

Rickettsia raoultii and Rickettsia sibirica in ticks from the long-tailed ground squirrel near the China-Kazakhstan border

Spotted fever group (SFG) rickettsiae cause infection in humans, domestic animals and wildlife. To date, no rickettsial agents have been reported in hard ticks from the long-tailed ground squirrel (Spermophilus undulatus). A total of 50 adult ticks and 48 nymphs were collected from S. undulatus in the border region of northwestern China. Tick species (identified according to morphological and molecular characteristics) included Dermacentor nuttalli, Dermacentor silvarum and Ixodes kaiseri. Based on the cytochrome c oxidase subunit I (COI) haplotype analysis, I. kaiseri from S. undulatus belongs to an ancestral. In addition, all tick samples were analyzed for the presence of rickettsiae by PCR amplification and sequencing of six genetic markers. Rickettsia raoultii and Rickettsia sibirica subsp. sibirica were shown to occur in adults and nymphs of D. nuttalli and D. silvarum. Rickettsia sibirica subsp. sibirica was also detected in an I. kaiseri adult. Dermacentor silvarum and I. kaiseri were found for the first time on S. undulatus. Rickettsia raoultii and R. sibirica subsp. sibirica were detected in two Dermacentor and one Ixodes species, respectively, suggesting that these rickettsiae circulate in the region of the China-Kazakhstan border by hard ticks infesting S. undulatus.

Are tree squirrels involved in the circulation of flaviviruses in Italy?

West Nile virus (WNV), Usutu virus (USUV) and tick-borne encephalitis virus (TBEV) are emerging zoonotic flaviviruses (family Flaviviridae), which have circulated in Europe in the past decade. A cross-sectional study was conducted to assess exposure to these antigenically related flaviviruses in eastern grey squirrels (Sciurus carolinensis) in Italy. Seventeen out of 158 (10.8%; CI_95% : 5.9-15.6) squirrels' sera tested through bELISA had antibodies against flaviviruses. Specific neutralizing antibodies to WNV, USUV and TBEV were detected by virus neutralization tests. Our results indicate that tree squirrels are exposed to Culex and tick-borne zoonotic flaviviruses in Italy. Moreover, this study shows for the first time USUV and TBEV exposure in grey squirrels, broadening the host range reported for these viruses. Even though further studies are needed to define the real role of tree squirrels in the epidemiology of flaviviruses in Europe, this study highlights that serology could be an effective approach for future investigations aimed at broadening our knowledge about the species exposed to these zoonotic infections.

New genetic lineage within the Siberian subtype of tick-borne encephalitis virus found in Western Siberia, Russia

Tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is a causative agent of a severe neurological disease. There are three main TBEV subtypes: the European (TBEV-Eu), Far Eastern (TBEV-FE), and Siberian (TBEV-Sib). Currently, three lineages within TBEV-Sib have been recorded. In this study, the genetic and biological characteristics of a new original strain, TBEV-2871, isolated in the Novosibirsk province of Western Siberia, Russia were investigated. The strain has low neuroinvasiveness in mice. Phylogenetic analysis demonstrated that TBEV-2871 belongs to TBEV-Sib, but does not cluster with any of the TBEV-Sib lineages. The TBEV-2871 strain has 88-89% nucleotide sequence identity with the other TBEV-Sib strains, 84-86% nucleotide sequence identity with the TBEV-FE and TBEV-Eu subtypes and is genetically close to the subtype division border. The TBEV-2871 polyprotein sequence includes 43 unique amino acid substitutions, 30 of which are recorded at positions that are conserved among all TBEV subtypes. Strain TBEV-2871 and two similar but not identical isolates found in Kemerovo province, Western Siberia are separated into a new lineage tentatively named Obskaya after the name of Ob riber, in the vicinity of which the TBEV-2871 was first found. A molecular evolution investigation demonstrated that within TBEV-Sib, the Obskaya lineage likely separated 1535years ago, which is even earlier than the Baltic lineage.