1
|
Kovalev SY, Okulovskaya VY. The First Record of Omsk Hemorrhagic Fever Virus and Tick-Borne Encephalitis Virus of Baltic Lineage from the Kemerovo Region of Russia. Vector Borne Zoonotic Dis 2024; 24:443-450. [PMID: 38593456 DOI: 10.1089/vbz.2023.0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Sergey Y Kovalev
- Institute of Natural Science and Mathematics, Ural Federal University, Yekaterinburg, Russia
| | - Viktoriya Y Okulovskaya
- Institute of Natural Science and Mathematics, Ural Federal University, Yekaterinburg, Russia
| |
Collapse
|
2
|
Ma R, Li C, Gao A, Jiang N, Li J, Hu W, Feng X. Tick species diversity and potential distribution alternation of dominant ticks under different climate scenarios in Xinjiang, China. PLoS Negl Trop Dis 2024; 18:e0012108. [PMID: 38683839 PMCID: PMC11081513 DOI: 10.1371/journal.pntd.0012108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 05/09/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Ticks are a hematophagous parasite and a vector of pathogens for numerous human and animal diseases of significant importance. The expansion of tick distribution and the increased risk of tick-borne diseases due to global climate change necessitates further study of the spatial distribution trend of ticks and their potential influencing factors. This study constructed a dataset of tick species distribution in Xinjiang for 60 years based on literature database retrieval and historical data collection (January 1963-January 2023). The distribution data were extracted, corrected, and deduplicated. The dominant tick species were selected for analysis using the MaxEnt model to assess their potential distribution in different periods under the current and BCC-CSM2.MR mode scenarios. The results indicated that there are eight genera and 48 species of ticks in 108 cities and counties of Xinjiang, with Hyalomma asiaticum, Rhipicephalus turanicus, Dermacentor marginatus, and Haemaphysalis punctatus being the top four dominant species. The MaxEnt model analysis revealed that the suitability areas of the four dominant ticks were mainly distributed in the north of Xinjiang, in areas such as Altay and Tacheng Prefecture. Over the next four periods, the medium and high suitable areas within the potential distribution range of the four tick species will expand towards the northwest. Additionally, new suitability areas will emerge in Altay, Changji Hui Autonomous Prefecture, and other local areas. The 60-year tick dataset in this study provides a map of preliminary tick distribution in Xinjiang, with a diverse array of tick species and distribution patterns throughout the area. In addition, the MaxEnt model revealed the spatial change characteristics and future distribution trend of ticks in Xinjiang, which can provide an instrumental data reference for tick monitoring and tick-borne disease risk prediction not only in the region but also in other countries participating in the Belt and Road Initiative.
Collapse
Affiliation(s)
- Rui Ma
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chunfu Li
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Ai Gao
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Na Jiang
- College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jian Li
- College of Life Sciences, Inner Mongolia University, Hohhot, China
- Basic Medical College, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Wei Hu
- College of Life Sciences, Inner Mongolia University, Hohhot, China
- Department of Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xinyu Feng
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, China
| |
Collapse
|
3
|
Schelling J, Einmahl S, Torgler R, Larsen CS. Evidence for a 10-year TBE vaccine booster interval: an evaluation of current data. Expert Rev Vaccines 2024; 23:226-236. [PMID: 38288983 DOI: 10.1080/14760584.2024.2311359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/24/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Tick-borne encephalitis (TBE) is rapidly spreading to new areas in many parts of Europe. While vaccination remains the most effective method of protection against the disease, vaccine uptake is low in many endemic countries. AREAS COVERED We conducted a literature search of the MEDLINE database to identify articles published from 2018 to 2023 that evaluated the immunogenicity and effectiveness of TBE vaccines, particularly Encepur, when booster doses were administered up to 10 years apart. We searched PubMed with the MeSH terms 'Encephalitis, Tick-Borne/prevention and control' and 'Vaccination' for articles published in the English language. EXPERT OPINION Long-term immunogenicity data for Encepur and real-world data on vaccine effectiveness and breakthrough infections following the two European TBE vaccines, Encepur and FSME-Immun, have shown that extending the booster interval from 3-5 years to 10 years does not negatively impact protection against TBE, regardless of age. Such extension not only streamlines the vaccination schedules but may also increase vaccine uptake and compliance among those living in endemic regions.
Collapse
Affiliation(s)
- Jörg Schelling
- Department of Medicine IV, LMU University Hospital, LMU Munich, University of Munich, Munich, Germany
| | - Suzanne Einmahl
- Department of Medical Strategy, Bavarian Nordic AG, Zug, Switzerland
| | - Ralph Torgler
- Department of Medical Strategy, Bavarian Nordic AG, Zug, Switzerland
| | | |
Collapse
|
4
|
Kwasnik M, Rola J, Rozek W. Tick-Borne Encephalitis-Review of the Current Status. J Clin Med 2023; 12:6603. [PMID: 37892741 PMCID: PMC10607749 DOI: 10.3390/jcm12206603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The tick-borne encephalitis virus (TBEV) is the arboviral etiological agent of tick-borne encephalitis (TBE), considered to be one of the most important tick-borne viral diseases in Europe and Asia. In recent years, an increase in the incidence of TBE as well as an increasing geographical range of the disease have been noted. Despite the COVID-19 pandemic and the imposition of restrictions that it necessitated, the incidence of TBE is rising in more than half of the European countries analyzed in recent studies. The virus is transmitted between ticks, animals, and humans. It seems that ticks and small mammals play a role in maintaining TBEV in nature. The disease can also affect dogs, horses, cattle, and small ruminants. Humans are incidental hosts, infected through the bite of an infected tick or by the alimentary route, through the consumption of unpasteurized milk or milk products from TBEV-infected animals. TBEV infections in humans may be asymptomatic, but the symptoms can range from mild flu-like to severe neurological. In Europe, cases of TBE are reported every year. While there is currently no effective treatment for TBE, immunization and protection against tick bites are critical in preventing this disease.
Collapse
Affiliation(s)
- Malgorzata Kwasnik
- Department of Virology, National Veterinary Research Institute, Al. Partyzantow 57, 24-100 Pulawy, Poland; (J.R.); (W.R.)
| | | | | |
Collapse
|
5
|
Sukhorukov GA, Paramonov AI, Lisak OV, Kozlova IV, Bazykin GA, Neverov AD, Karan LS. The Baikal subtype of tick-borne encephalitis virus is evident of recombination between Siberian and Far-Eastern subtypes. PLoS Negl Trop Dis 2023; 17:e0011141. [PMID: 36972237 PMCID: PMC10079218 DOI: 10.1371/journal.pntd.0011141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 04/06/2023] [Accepted: 02/06/2023] [Indexed: 03/29/2023] Open
Abstract
Tick-borne encephalitis virus (TBEV) is a flavivirus which causes an acute or sometimes chronic infection that frequently has severe neurological consequences, and is a major public health threat in Eurasia. TBEV is genetically classified into three distinct subtypes; however, at least one group of isolates, the Baikal subtype, also referred to as “886-84-like”, challenges this classification. Baikal TBEV is a persistent group which has been repeatedly isolated from ticks and small mammals in the Buryat Republic, Irkutsk and Trans-Baikal regions of Russia for several decades. One case of meningoencephalitis with a lethal outcome caused by this subtype has been described in Mongolia in 2010. While recombination is frequent in Flaviviridae, its role in the evolution of TBEV has not been established. Here, we isolate and sequence four novel Baikal TBEV samples obtained in Eastern Siberia. Using a set of methods for inference of recombination events, including a newly developed phylogenetic method allowing for formal statistical testing for such events in the past, we find robust support for a difference in phylogenetic histories between genomic regions, indicating recombination at origin of the Baikal TBEV. This finding extends our understanding of the role of recombination in the evolution of this human pathogen.
Collapse
Affiliation(s)
- Grigorii A. Sukhorukov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
- * E-mail: (GAS); (GAB); (ADN)
| | - Alexey I. Paramonov
- Laboratory of molecular Epidemiology and genetic diagnosis, Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Oksana V. Lisak
- Laboratory of molecular Epidemiology and genetic diagnosis, Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Irina V. Kozlova
- Laboratory of molecular Epidemiology and genetic diagnosis, Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Georgii A. Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Laboratory of Molecular Evolution, Kharkevich Institute for Information Transmission Problems of the RAS, Moscow, Russia
- * E-mail: (GAS); (GAB); (ADN)
| | - Alexey D. Neverov
- HSE University, Moscow, Russia
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
- * E-mail: (GAS); (GAB); (ADN)
| | - Lyudmila S. Karan
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
| |
Collapse
|
6
|
Bondaryuk AN, Kulakova NV, Belykh OI, Bukin YS. Dates and Rates of Tick-Borne Encephalitis Virus-The Slowest Changing Tick-Borne Flavivirus. Int J Mol Sci 2023; 24:ijms24032921. [PMID: 36769238 PMCID: PMC9917962 DOI: 10.3390/ijms24032921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
We evaluated the temporal signal and substitution rate of tick-borne encephalitis virus (TBEV) using 276 complete open reading frame (ORF) sequences with known collection dates. According to a permutation test, the TBEV Siberian subtype (TBEV-S) data set has no temporal structure and cannot be applied for substitution rate estimation without other TBEV subtypes. The substitution rate obtained suggests that the common clade of TBEV (TBEV-common), including all TBEV subtypes and louping-ill virus (LIV), is characterized by the lowest rate (1.87 × 10-5 substitutions per site per year (s/s/y) or 1 nucleotide substitution per ORF per 4.9 years; 95% highest posterior density (HPD) interval, 1.3-2.4 × 10-5 s/s/y) among all tick-borne flaviviruses previously assessed. Within TBEV-common, the TBEV European subtype (TBEV-E) has the lowest substitution rate (1.3 × 10-5 s/s/y or 1 nucleotide substitution per ORF per 7.5 years; 95% HPD, 1.0-1.8 × 10-5 s/s/y) as compared with TBEV Far-Eastern subtype (3.0 × 10-5 s/s/y or 1 nucleotide substitution per ORF per 3.2 years; 95% HPD, 1.6-4.5 × 10-5 s/s/y). TBEV-common representing the species tick-borne encephalitis virus diverged 9623 years ago (95% HPD interval, 6373-13,208 years). The TBEV Baikalian subtype is the youngest one (489 years; 95% HPD, 291-697 years) which differs significantly by age from TBEV-E (848 years; 95% HPD, 596-1112 years), LIV (2424 years; 95% HPD, 1572-3400 years), TBEV-FE (1936 years, 95% HPD, 1344-2598 years), and the joint clade of TBEV-S (2505 years, 95% HPD, 1700-3421 years) comprising Vasilchenko, Zausaev, and Baltic lineages.
Collapse
Affiliation(s)
- Artem N. Bondaryuk
- Laboratory of Natural Focal Viral Infections, Irkutsk Antiplague Research Institute of Siberia and the Far East, 664047 Irkutsk, Russia
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Nina V. Kulakova
- Department of Biodiversity and Biological Resources, Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Olga I. Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
- Correspondence:
| | - Yurij S. Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| |
Collapse
|
7
|
Kutschera LS, Wolfinger MT. Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology. Virus Evol 2022; 8:veac051. [PMID: 35822110 PMCID: PMC9272599 DOI: 10.1093/ve/veac051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/17/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is the aetiological agent of tick-borne
encephalitis, an infectious disease of the central nervous system that is often associated
with severe sequelae in humans. While TBEV is typically classified into three subtypes,
recent evidence suggests a more varied range of TBEV subtypes and lineages that differ
substantially in the architecture of their 3ʹ untranslated region (3ʹUTR). Building on
comparative genomic approaches and thermodynamic modelling, we characterize the TBEV UTR
structureome diversity and propose a unified picture of pervasive non-coding RNA structure
conservation. Moreover, we provide an updated phylogeny of TBEV, building on more than 220
publicly available complete genomes, and investigate the molecular epidemiology and
phylodynamics with Nextstrain, a web-based visualization framework for real-time pathogen
evolution.
Collapse
Affiliation(s)
- Lena S Kutschera
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| |
Collapse
|
8
|
Mel'nikova OV, Adel'shin RV, Lopatovskaya KV, Trushina YT, Yakovchits NV, Andaev EI. [Biological properties and phylogenetic relationships of tick-borne encephalitis virus (Flaviviridae, Flavivirus) isolates of siberian subtype isolated in the south of East siberia in modern period]. Vopr Virusol 2021; 66:310-321. [PMID: 34545723 DOI: 10.36233/0507-4088-55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 09/18/2021] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Tick-borne encephalitis virus (TBEV) is medically most important representative of the same-name serogroup of genus Flavivirus (Flaviviridae). In the view of various researchers there are 3 to 5 TBEV subtypes, of them siberian being the most prevalent. The aim of the work is to compare the biological properties and to reveal phylogenetic relationships of large group of modern (2006-2019) TBEV isolates of siberian subtype from natural foci in southern East Siberia. MATERIAL AND METHODS Ixodid ticks (Ixodidae) and small mammals (Mammalia) from tick-borne encephalitis (TBE) natural foci in Irkutsk Region, Republic of Buryatia and Republic of Tuva, as well as specimens from TBE patients, were examined for TBEV markers using enzyme-linked immunosorbent assay (ELISA) and reverse transcription polymerase chain reaction (RT-PCR). Virus was isolated from suspensions with positive result, and its pathogenicity for white mice (Mus) (WM) was studied by different inoculation ways. Analysis of the nucleotide sequences of E gene was performed for isolates at 1st passage. Phylogenetic tree was constructed using MEGA X program. RESULTS The phylogenetic analysis has shown that TBEV of siberian subtype that circulates in natural foci of the studied territory belong to two genetic lines. These lines are «Vasilchenko» and «Zausaev» with a strong predominance of the first. The differences in biological properties between the two groups of strains have been demonstrated. Most of the strains from both groups showed high virulence for WM both after intracerebral and subcutaneous inoculation. Only four strains demonstrated the reduced ability to overcome the blood-brain barrier. However, the analysis of the E protein coding sequences revealed evident correlation between phylogenetic clustering and geographical origin of isolates, but not with TBE host or pathogenicity for WM. CONCLUSION Further search for TBE genome regions associated with pathogenicity require the analysis of complete genome sequences of representative group of strains with different biological properties.
Collapse
Affiliation(s)
- O V Mel'nikova
- FSHI «Irkutsk Anti-plague Research Institute of Siberia and Far East» of the Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - R V Adel'shin
- FSHI «Irkutsk Anti-plague Research Institute of Siberia and Far East» of the Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor); FSBEI HE «Irkutsk State University»
| | - K V Lopatovskaya
- FSHI «Irkutsk Anti-plague Research Institute of Siberia and Far East» of the Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - Yu T Trushina
- FSHI «Irkutsk Anti-plague Research Institute of Siberia and Far East» of the Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - N V Yakovchits
- FSHI «Irkutsk Anti-plague Research Institute of Siberia and Far East» of the Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| | - E I Andaev
- FSHI «Irkutsk Anti-plague Research Institute of Siberia and Far East» of the Surveillance of Consumer Rights Protection and Human Wellbeing (Rospotrebnadzor)
| |
Collapse
|
9
|
Deviatkin AA, Karganova GG, Vakulenko YA, Lukashev AN. TBEV Subtyping in Terms of Genetic Distance. Viruses 2020; 12:E1240. [PMID: 33142676 PMCID: PMC7692686 DOI: 10.3390/v12111240] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/24/2020] [Accepted: 10/29/2020] [Indexed: 01/07/2023] Open
Abstract
Currently, the lowest formal taxon in virus classification is species; however, unofficial lower-level units are commonly used in everyday work. Tick-borne encephalitis virus (TBEV) is a species of mammalian tick-borne flaviviruses that may cause encephalitis. Many known representatives of TBEV are grouped into subtypes, mostly according to their phylogenetic relationship. However, the emergence of novel sequences could dissolve this phylogenetic grouping; in the absence of strict quantitative criterion, it may be hard to define the borders of the first TBEV taxonomic unit below the species level. In this study, the nucleotide/amino-acid space of all known TBEV sequences was analyzed. Amino-acid sequence p-distances could not reliably distinguish TBEV subtypes. Viruses that differed by less than 10% of nucleotides in the polyprotein-coding gene belonged to the same subtype. At the same time, more divergent viruses were representatives of different subtypes. According to this distance criterion, TBEV species may be divided into seven subtypes: TBEV-Eur, TBEV-Sib, TBEV-FE, TBEV-2871 (TBEV-Ob), TBEV-Him, TBEV-178-79 (TBEV-Bkl-1), and TBEV-886-84 (TBEV-Bkl-2).
Collapse
Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
| | - Galina G. Karganova
- Department of Organization and Technology of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexander N. Lukashev
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
| |
Collapse
|
10
|
Abdiyeva K, Turebekov N, Yegemberdiyeva R, Dmitrovskiy A, Yeraliyeva L, Shapiyeva Z, Nurmakhanov T, Sansyzbayev Y, Froeschl G, Hoelscher M, Zinner J, Essbauer S, Frey S. Vectors, molecular epidemiology and phylogeny of TBEV in Kazakhstan and central Asia. Parasit Vectors 2020; 13:504. [PMID: 33023633 PMCID: PMC7539389 DOI: 10.1186/s13071-020-04362-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND In the South of Kazakhstan, Almaty Oblast' (region) is endemic for tick-borne encephalitis, with 0.16-0.32 cases/100,000 population between 2016-2018. The purpose of this study was to determine the prevalence and circulating subtypes of tick-borne encephalitis virus (TBEV) in Almaty Oblast' and Kyzylorda Oblast'. METHODS In 2015 we investigated 2341 ticks from 7 sampling sites for the presence of TBEV. Ticks were pooled in 501 pools and isolated RNA was tested for the presence of TBEV by RT-qPCR. For the positive samples, the E gene was amplified, sequenced and a phylogenetic analysis was carried out. RESULTS A total of 48 pools were TBEV-positive by the RT-qPCR. TBEV-positive ticks were only detected in three districts of Almaty Oblast' and not in Kyzylorda Oblast'. The positive TBEV pools were found within Ixodes persulcatus, Haemaphysalis punctata and Dermacentor marginatus. These tick species prevailed only in Almaty Oblast' whereas in Kyzylorda Oblast' Hyalomma asiaticum and D. marginatus are endemic. The minimum infection rates (MIR) in the sampling sites were 4.4% in Talgar, 2.8% in Tekeli and 1.1% in Yenbekshikazakh, respectively. The phylogenetic analysis of the generated sequences indicates that TBEV strains found in Almaty Oblast' clusters in the Siberian subtype within two different clades. CONCLUSIONS We provided new data about the TBEV MIR in ticks in Almaty Oblast' and showed that TBEV clusters in the Siberian Subtype in two different clusters at the nucleotide level. These results indicate that there are different influences on the circulating TBEV strains in south-eastern Kazakhstan. These influences might be caused by different routes of the virus spread in ticks which might bring different genetic TBEV lineages to Kazakhstan. The new data about the virus distribution and vectors provided here will contribute to an improvement of monitoring of tick-borne infections and timely anti-epidemic measures in Kazakhstan.
Collapse
Affiliation(s)
- Karlygash Abdiyeva
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
- National Scientific Center for Highly Dangerous Infections, Almaty, Kazakhstan
| | - Nurkeldi Turebekov
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
- National Scientific Center for Highly Dangerous Infections, Almaty, Kazakhstan
| | | | | | | | - Zhanna Shapiyeva
- Scientific Practical Center of Sanitary Epidemiological Expertise and Monitoring, Almaty, Kazakhstan
| | - Talgat Nurmakhanov
- National Scientific Center for Highly Dangerous Infections, Almaty, Kazakhstan
| | - Yerlan Sansyzbayev
- National Scientific Center for Highly Dangerous Infections, Almaty, Kazakhstan
| | - Guenter Froeschl
- Center for International Health, Ludwig-Maximilians-Universität, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany
| | | | | | - Stefan Frey
- Institute of Microbiology, Munich, Germany
- present Address: Bundeswehr Research Institute for Protective Technologies and CBRN Protection, Munster, Germany
| |
Collapse
|
11
|
De Carli S, Wolf JM, Gräf T, Lehmann FKM, Fonseca ASK, Canal CW, Lunge VR, Ikuta N. Genotypic characterization and molecular evolution of avian reovirus in poultry flocks from Brazil. Avian Pathol 2020; 49:611-620. [PMID: 32746617 DOI: 10.1080/03079457.2020.1804528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Avian reovirus (ARV) is one of the main causes of infectious arthritis/tenosynovitis and malabsorption syndrome (MAS) in poultry. ARVs have been disseminated in Brazilian poultry flocks in the last years. This study aimed to genotype ARVs and to evaluate the molecular evolution of the more frequent ARV lineages detected in Brazilian poultry-producing farms. A total of 100 poultry flocks with clinical signs of tenosynovitis/MAS, from all Brazilian poultry-producing regions were positive for ARV by PCR. Seventeen bird tissues were submitted to cell culture and ARV RNA detection/genotyping by two PCRs. The phylogenetic classification was based on σC gene alignment using a dataset with other Brazilian and worldwide ARVs sequences. ARVs were specifically detected by both PCRs from the 17 cell cultures, and σC gene partial fragments were sequenced. All these sequences were aligned with a total of 451 ARV σC gene data available in GenBank. Phylogenetic analysis demonstrated five well-defined clusters that were classified into lineages I, II, III, IV, and V. Three lineages could be further divided into sub-lineages: I (I vaccine, Ia, Ib), II (IIa, IIb, IIc) and IV (IVa and IVb). Brazilian ARVs were from four lineages/sub-lineages: Ib (48.2%), IIb (22.2%), III (3.7%) and V (25.9%). The Bayesian analysis demonstrated that the most frequent sub-lineage Ib emerged in the world around 1968 and it was introduced into Brazil in 2010, with increasing spread soon after. In conclusion, four different ARV lineages are circulating in Brazilian poultry flocks, all associated with clinical diseases. RESEARCH HIGHLIGHTS One-hundred ARV-positive flocks were detected in all main poultry-producing regions from Brazil. A large dataset of 468 S1 sequences was constructed and divided ARVs into five lineages. Four lineages/sub-lineages (Ib, IIb, III and V) were detected in commercial poultry flocks from Brazil. Brazilian lineages shared a low identity with the commercial vaccine lineage (I vaccine). Sub-lineage Ib emerged around 1968 and was introduced into Brazil in 2010.
Collapse
Affiliation(s)
- Silvia De Carli
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular aplicada à Saúde, Universidade Luterana do Brasil (ULBRA), Canoas, Brazil.,Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jonas Michel Wolf
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular aplicada à Saúde, Universidade Luterana do Brasil (ULBRA), Canoas, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Fernanda K M Lehmann
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular aplicada à Saúde, Universidade Luterana do Brasil (ULBRA), Canoas, Brazil
| | | | - Cláudio W Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Vagner R Lunge
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular aplicada à Saúde, Universidade Luterana do Brasil (ULBRA), Canoas, Brazil.,Simbios Biotecnologia, Cachoeirinha, Brazil
| | - Nilo Ikuta
- Laboratório de Diagnóstico Molecular, Programa de Pós-Graduação em Biologia Celular e Molecular aplicada à Saúde, Universidade Luterana do Brasil (ULBRA), Canoas, Brazil.,Simbios Biotecnologia, Cachoeirinha, Brazil
| |
Collapse
|
12
|
Clark JJ, Gilray J, Orton RJ, Baird M, Wilkie G, Filipe ADS, Johnson N, McInnes CJ, Kohl A, Biek R. Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Negl Trop Dis 2020; 14:e0008133. [PMID: 32925939 PMCID: PMC7515184 DOI: 10.1371/journal.pntd.0008133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 09/24/2020] [Accepted: 08/07/2020] [Indexed: 12/30/2022] Open
Abstract
The emergence and spread of tick-borne arboviruses pose an increased challenge to human and animal health. In Europe this is demonstrated by the increasingly wide distribution of tick-borne encephalitis virus (TBEV, Flavivirus, Flaviviridae), which has recently been found in the United Kingdom (UK). However, much less is known about other tick-borne flaviviruses (TBFV), such as the closely related louping ill virus (LIV), an animal pathogen which is endemic to the UK and Ireland, but which has been detected in other parts of Europe including Scandinavia and Russia. The emergence and potential spatial overlap of these viruses necessitates improved understanding of LIV genomic diversity, geographic spread and evolutionary history. We sequenced a virus archive composed of 22 LIV isolates which had been sampled throughout the UK over a period of over 80 years. Combining this dataset with published virus sequences, we detected no sign of recombination and found low diversity and limited evidence for positive selection in the LIV genome. Phylogenetic analysis provided evidence of geographic clustering as well as long-distance movement, including movement events that appear recent. However, despite genomic data and an 80-year time span, we found that the data contained insufficient temporal signal to reliably estimate a molecular clock rate for LIV. Additional analyses revealed that this also applied to TBEV, albeit to a lesser extent, pointing to a general problem with phylogenetic dating for TBFV. The 22 LIV genomes generated during this study provide a more reliable LIV phylogeny, improving our knowledge of the evolution of tick-borne flaviviruses. Our inability to estimate a molecular clock rate for both LIV and TBEV suggests that temporal calibration of tick-borne flavivirus evolution should be interpreted with caution and highlight a unique aspect of these viruses which may be explained by their reliance on tick vectors. Tick-borne pathogens represent a major emerging threat to public health and in recent years have been expanding into new areas. LIV is a neglected virus endemic to the UK and Ireland (though it has been detected in Scandinavia and Russia) which is closely related to the major human pathogen TBEV, but predominantly causes disease in sheep and grouse. The recent detection of TBEV in the UK, which has also emerged elsewhere in Europe, requires more detailed understanding of the spread and sequence diversity of LIV. This could be important for diagnosis and vaccination, but also to improve our understanding of the evolution and emergence of these tick-borne viruses. Here we describe the sequencing of 22 LIV isolates which have been sampled from several host species across the past century. We have utilised this dataset to investigate the evolutionary pressures that LIV is subjected to and have explored the evolution of LIV using phylogenetic analysis. Crucially we were unable to estimate a reliable molecular clock rate for LIV and found that this problem also extends to a larger phylogeny of TBEV sequences. This work highlights a previously unknown caveat of tick-borne flavivirus evolutionary analysis which may be important for understanding the evolution of these important pathogens.
Collapse
Affiliation(s)
- Jordan J. Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Moredun Research Institute, Edinburgh, United Kingdom
- * E-mail: (JC); (RB)
| | - Janice Gilray
- Moredun Research Institute, Edinburgh, United Kingdom
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Margaret Baird
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Gavin Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicholas Johnson
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
- Faculty of Health and Medical Science, University of Surrey, Guildford, Surrey, United Kingdom
| | | | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine - University of Glasgow, Glasgow, United Kingdom
- * E-mail: (JC); (RB)
| |
Collapse
|
13
|
Deviatkin AA, Kholodilov IS, Vakulenko YA, Karganova GG, Lukashev AN. Tick-Borne Encephalitis Virus: An Emerging Ancient Zoonosis? Viruses 2020; 12:v12020247. [PMID: 32102228 PMCID: PMC7077300 DOI: 10.3390/v12020247] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Tick-borne encephalitis (TBE) is one of the most important viral zoonosis transmitted by the bite of infected ticks. In this study, all tick-borne encephalitis virus (TBEV) E gene sequences available in GenBank as of June 2019 with known date of isolation (n = 551) were analyzed. Simulation studies showed that a sample bias could significantly affect earlier studies, because small TBEV datasets (n = 50) produced non-overlapping intervals for evolutionary rate estimates. An apparent lack of a temporal signal in TBEV, in general, was found, precluding molecular clock analysis of all TBEV subtypes in one dataset. Within all subtypes and most of the smaller groups in these subtypes, there was evidence of many medium- and long-distance virus transfers. These multiple random events may play a key role in the virus spreading. For some groups, virus diversity within one territory was similar to diversity over the whole geographic range. This is best exemplified by the virus diversity observed in Switzerland or Czech Republic. These two countries yielded most of the known European subtype Eu3 subgroup sequences, and the diversity of viruses found within each of these small countries is comparable to that of the whole Eu3 subgroup, which is prevalent all over Central and Eastern Europe. Most of the deep tree nodes within all three established TBEV subtypes dated less than 300 years back. This could be explained by the recent emergence of most of the known TBEV diversity. Results of bioinformatics analysis presented here, together with multiple field findings, suggest that TBEV may be regarded as an emerging disease.
Collapse
Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Laboratory of Postgenomic Technologies, Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia
- Correspondence: ; Tel.: +7-906-739-0860
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (G.G.K.)
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, Chumakov Institute of Poliomyelitis and Viral Encephalitides (FSBSI “Chumakov FSC R&D IBP RAS), 108819 Moscow, Russia; (I.S.K.); (G.G.K.)
- Department of Organization and Technology of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Alexander N. Lukashev
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia;
| |
Collapse
|
14
|
Tkachev SE, Babkin IV, Chicherina GS, Kozlova IV, Verkhozina MM, Demina TV, Lisak OV, Doroshchenko EK, Dzhioev YP, Suntsova OV, Belokopytova PS, Tikunov AY, Savinova YS, Paramonov AI, Glupov VV, Zlobin VI, Tikunova NV. Genetic diversity and geographical distribution of the Siberian subtype of the tick-borne encephalitis virus. Ticks Tick Borne Dis 2019; 11:101327. [PMID: 31767494 DOI: 10.1016/j.ttbdis.2019.101327] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/21/2019] [Accepted: 11/06/2019] [Indexed: 11/16/2022]
Abstract
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.
Collapse
Affiliation(s)
- S E Tkachev
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Acad. Lavrentyev's pr., 8, Novosibirsk, 630090, Russia.
| | - I V Babkin
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Acad. Lavrentyev's pr., 8, Novosibirsk, 630090, Russia
| | - G S Chicherina
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, Novosibirsk, 630091, Russia
| | - I V Kozlova
- Scientific Centre for Family Health and Human Reproduction Problems, Timiryazev Str., 16, Irkutsk, 664003, Russia
| | - M M Verkhozina
- Center for Hygiene and Epidemiology in the Irkutsk Region, Trilisser Str., 51, Irkutsk, 664047, Russia
| | - T V Demina
- Irkutsk State Agrarian University by A.A. Ezhevsky, Molodezhny Settlement, Irkutsk District, Irkutsk, 664038, Russia
| | - O V Lisak
- Scientific Centre for Family Health and Human Reproduction Problems, Timiryazev Str., 16, Irkutsk, 664003, Russia
| | - E K Doroshchenko
- Scientific Centre for Family Health and Human Reproduction Problems, Timiryazev Str., 16, Irkutsk, 664003, Russia
| | - Yu P Dzhioev
- Research Institute of Biomedical Technology of Irkutsk State Medical University, Krasnogo Vosstaniya Str., 1/3, Irkutsk, 664003, Russia
| | - O V Suntsova
- Scientific Centre for Family Health and Human Reproduction Problems, Timiryazev Str., 16, Irkutsk, 664003, Russia
| | - P S Belokopytova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Acad. Lavrentyev's pr., 8, Novosibirsk, 630090, Russia
| | - A Yu Tikunov
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Acad. Lavrentyev's pr., 8, Novosibirsk, 630090, Russia
| | - Yu S Savinova
- Scientific Centre for Family Health and Human Reproduction Problems, Timiryazev Str., 16, Irkutsk, 664003, Russia
| | - A I Paramonov
- Scientific Centre for Family Health and Human Reproduction Problems, Timiryazev Str., 16, Irkutsk, 664003, Russia
| | - V V Glupov
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str., 11, Novosibirsk, 630091, Russia
| | - V I Zlobin
- Research Institute of Biomedical Technology of Irkutsk State Medical University, Krasnogo Vosstaniya Str., 1/3, Irkutsk, 664003, Russia
| | - N V Tikunova
- Institute of Chemical Biology and Fundamental Medicine of the SB RAS, Acad. Lavrentyev's pr., 8, Novosibirsk, 630090, Russia.
| |
Collapse
|
15
|
Adaptive genetic diversifications among tick-borne encephalitis virus subtypes: A genome-wide perspective. Virology 2019; 530:32-38. [DOI: 10.1016/j.virol.2019.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/30/2022]
|