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Gonzalo-Nadal V, Kohl A, Rocchi M, Brennan B, Hughes J, Nichols J, Da Silva Filipe A, Dunlop JI, Fares M, Clark JJ, Tandavanitj R, Patel AH, Cloquell-Miro A, Bongers J, Deacon J, Kaczmarska A, Stalin C, Liatis T, Irving J, Gutierrez-Quintana R. Suspected tick-borne flavivirus meningoencephalomyelitis in dogs from the UK: six cases (2021). J Small Anim Pract 2024; 65:132-143. [PMID: 37956993 DOI: 10.1111/jsap.13682] [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: 02/20/2023] [Revised: 06/30/2023] [Accepted: 10/01/2023] [Indexed: 11/21/2023]
Abstract
OBJECTIVES Tick-borne encephalitis virus and louping ill virus are neurotropic flaviviruses transmitted by ticks. Epidemiologically, tick-borne encephalitis is endemic in Europe whereas louping ill's predominant geographical distribution is the UK. Rarely, these flaviviruses affect dogs causing neurological signs. This case series aimed to describe the clinical, clinicopathological, and imaging findings, as well as the outcomes in six dogs with meningoencephalitis and/or meningomyelitis caused by a flavivirus in the UK in 2021. MATERIALS AND METHODS Observational retrospective case-series study. Clinical data were retrieved from medical records of dogs with positive serological or immunohistochemical results from three different institutions from spring to winter 2021. RESULTS Six dogs were included in the study. All dogs presented an initial phase of pyrexia and/or lethargy followed by progressive signs of spinal cord and/or intracranial disease. Magnetic resonance imaging showed bilateral and symmetrical lesions affecting the grey matter of the thalamus, pons, medulla oblongata, and thoracic or lumbar intumescences with none or mild parenchymal and meningeal contrast enhancement. Serology for tick-borne encephalitis virus was positive in five dogs with the presence of seroconversion in two dogs. The viral distinction between flaviviruses was not achieved. One dog with negative serology presented positive immunohistochemistry at post-mortem examination. Three dogs survived but presented neurological sequelae. Three dogs were euthanased due to the rapid progression of the clinical signs or static neurological signs. CLINICAL SIGNIFICANCE These cases raise awareness of the presence of tick-borne encephalitis as an emergent disease or the increased prevalence of louping ill virus affecting dogs in the UK.
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Affiliation(s)
- V Gonzalo-Nadal
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - A Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - M Rocchi
- Moredun Research Institute, Midlothian, UK
| | - B Brennan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - J I Dunlop
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - M Fares
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J J Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - R Tandavanitj
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - A H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - A Cloquell-Miro
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - J Bongers
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Moorview Vets, Cramlington, UK
| | | | - A Kaczmarska
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - C Stalin
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Moorview Vets, Cramlington, UK
| | - T Liatis
- Queen Mother Hospital for Animals, Royal Veterinary College, University of London, London, UK
| | - J Irving
- Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire, UK
- Harper & Keele Veterinary School, Newport, Shropshire, UK
| | - R Gutierrez-Quintana
- Division of Small Animal Clinical Sciences, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Bondaryuk AN, Belykh OI, Andaev EI, Bukin YS. Inferring Evolutionary Timescale of Omsk Hemorrhagic Fever Virus. Viruses 2023; 15:1576. [PMID: 37515262 PMCID: PMC10385366 DOI: 10.3390/v15071576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Until 2020, there were only three original complete genome (CG) nucleotide sequences of Omsk hemorrhagic fever virus (OHFV) in GenBank. For this reason, the evolutionary rate and divergence time assessments reported in the literature were based on the E gene sequences, but notably without temporal signal evaluation, such that their reliability is unclear. As of July 2022, 47 OHFV CG sequences have been published, which enables testing of temporal signal in the data and inferring unbiased and reliable substitution rate and divergence time values. Regression analysis in the TempEst software demonstrated a stronger clocklike behavior in OHFV samples for the complete open reading frame (ORF) data set (R2 = 0.42) than for the E gene data set (R2 = 0.11). Bayesian evaluation of temporal signal indicated very strong evidence, with a log Bayes factor of more than 5, in favor of temporal signal in all data sets. Our results based on the complete ORF sequences showed a more precise OHFV substitution rate (95% highest posterior density (HPD) interval, 9.1 × 10-5-1.8 × 10-4 substitutions per site per year) and tree root height (416-896 years ago) compared with previous assessments. The rate obtained is significantly higher than tick-borne encephalitis virus by at least 3.8-fold. The phylogenetic analysis and past population dynamics reconstruction revealed the declining trend of OHFV genetic diversity, but there was phylogenomic evidence that implicit virus subpopulations evolved locally and underwent an exponential growth phase.
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Affiliation(s)
- Artem N Bondaryuk
- Laboratory of Natural Focal Viral Infections, Irkutsk Antiplague Research Institute of Siberia and the Far East, Irkutsk 664047, Russia
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Olga I Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
| | - Evgeny I Andaev
- Laboratory of Natural Focal Viral Infections, Irkutsk Antiplague Research Institute of Siberia and the Far East, Irkutsk 664047, Russia
| | - Yurij S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia
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Kjær LJ, Johansson M, Lindgren PE, Asghar N, Wilhelmsson P, Fredlund H, Christensson M, Wallenhammar A, Bødker R, Rasmussen G, Kjellander P. Potential drivers of human tick-borne encephalitis in the Örebro region of Sweden, 2010-2021. Sci Rep 2023; 13:7685. [PMID: 37169798 PMCID: PMC10175290 DOI: 10.1038/s41598-023-34675-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
Incidence of tick-borne encephalitis (TBE) has increased during the last years in Scandinavia, but the underlying mechanism is not understood. TBE human case data reported between 2010 and 2021 were aggregated into postal codes within Örebro County, south-central Sweden, along with tick abundance and environmental data to analyse spatial patterns and identify drivers of TBE. We identified a substantial and continuing increase of TBE incidence in Örebro County during the study period. Spatial cluster analyses showed significant hotspots (higher number of cases than expected) in the southern and northern parts of Örebro County, whereas a cold spot (lower number of cases than expected) was found in the central part comprising Örebro municipality. Generalised linear models showed that the risk of acquiring TBE increased by 12.5% and 72.3% for every percent increase in relative humidity and proportion of wetland forest, respectively, whereas the risk decreased by 52.8% for every degree Celsius increase in annual temperature range. However, models had relatively low goodness of fit (R2 < 0.27). Results suggest that TBE in Örebro County is spatially clustered, however variables used in this study, i.e., climatic variables, forest cover, water, tick abundance, sheep as indicator species, alone do not explain this pattern.
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Affiliation(s)
- Lene Jung Kjær
- Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Magnus Johansson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Per-Eric Lindgren
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Region Jönköping County, Jönköping, Sweden
| | - Naveed Asghar
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Peter Wilhelmsson
- Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Region Jönköping County, Jönköping, Sweden
| | - Hans Fredlund
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Örebro County Council, Örebro, Sweden
| | - Madeleine Christensson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU), Riddarhyttan, Sweden
| | - Amélie Wallenhammar
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - René Bødker
- Section for Animal Welfare and Disease Control, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Gunløg Rasmussen
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Örebro County Council, Örebro, Sweden
| | - Petter Kjellander
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU), Riddarhyttan, Sweden
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Xu G, Gao T, Wang Z, Zhang J, Cui B, Shen X, Zhou A, Zhang Y, Zhao J, Liu H, Liang G. Re-Emerged Genotype IV of Japanese Encephalitis Virus Is the Youngest Virus in Evolution. Viruses 2023; 15:626. [PMID: 36992335 PMCID: PMC10054483 DOI: 10.3390/v15030626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
An outbreak of viral encephalitis caused by a Japanese encephalitis virus (JEV) genotype IV infection occurred in Australia between 2021 and 2022. A total of 47 cases and seven deaths were reported as of November 2022. This is the first outbreak of human viral encephalitis caused by JEV GIV since it was first isolated in Indonesia in the late 1970s. Here, a comprehensive phylogenetic analysis based on the whole genome sequences of JEVs revealed it emerged 1037 years ago (95% HPD: 463 to 2100 years). The evolutionary order of JEV genotypes is as follows: GV, GIII, GII, GI, and GIV. The JEV GIV emerged 122 years ago (95% HPD: 57-233) and is the youngest viral lineage. The mean substitution rate of the JEV GIV lineage was 1.145 × 10-3 (95% HPD values, 9.55 × 10-4, 1.35 × 10-3), belonging to rapidly evolving viruses. A series of amino acid mutations with the changes of physico-chemical properties located in the functional important domains within the core and E proteins distinguished emerging GIV isolates from old ones. These results demonstrate the JEV GIV is the youngest JEV genotype at a rapid evolution stage and has good host/vector adaptability for introduction to non-endemic areas. Thus, surveillance of JEVs is highly recommended.
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Affiliation(s)
- Guanlun Xu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Tingting Gao
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Zhijie Wang
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Jun Zhang
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Baoqiu Cui
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Xinxin Shen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Anyang Zhou
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Yuan Zhang
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Jie Zhao
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo 255049, China
| | - Guangdong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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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.
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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
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Lang D, Chitimia-Dobler L, Bestehorn-Willmann M, Lindau A, Drehmann M, Stroppel G, Hengge H, Mackenstedt U, Kaier K, Dobler G, Borde J. The Emergence and Dynamics of Tick-Borne Encephalitis Virus in a New Endemic Region in Southern Germany. Microorganisms 2022; 10:2125. [PMID: 36363717 PMCID: PMC9693875 DOI: 10.3390/microorganisms10112125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 06/11/2024] Open
Abstract
Tick-borne encephalitis (TBE) is the most important viral tick-borne infection in Europe and Asia. It is emerging in new areas. The mechanisms of emergence are fairly unknown or speculative. In the Ravensburg district in southern Germany, TBE emerged, mainly over the last five years. Here, we analyzed the underlying epidemiology in humans. The resulting identified natural foci of the causal TBE virus (TBEV) were genetically characterized. We sampled 13 potential infection sites at these foci and detected TBEV in ticks (Ixodes ricinus) at eight sites. Phylogenetic analysis spurred the introduction of at least four distinct TBEV lineages of the European subtype into the Ravensburg district over the last few years. In two instances, a continuous spread of these virus strains over up to 10 km was observed.
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Affiliation(s)
- Daniel Lang
- National Reference Laboratory for TBEV, Bundeswehr Institute for Microbiology, 80937 Munich, Germany
| | - Lidia Chitimia-Dobler
- National Reference Laboratory for TBEV, Bundeswehr Institute for Microbiology, 80937 Munich, Germany
| | - Malena Bestehorn-Willmann
- National Reference Laboratory for TBEV, Bundeswehr Institute for Microbiology, 80937 Munich, Germany
| | - Alexander Lindau
- Department of Parasitology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Marco Drehmann
- Department of Parasitology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Gabriele Stroppel
- Public Health Office, District Ravensburg, 88212 Ravensburg, Germany
| | - Helga Hengge
- Public Health Office, District Ravensburg, 88212 Ravensburg, Germany
| | - Ute Mackenstedt
- Department of Parasitology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Klaus Kaier
- Institute of Medical Biometry and Statistics (IMBI), University Medical Center Freiburg im Breisgau, 79106 Freiburg im Breisgau, Germany
| | - Gerhard Dobler
- National Reference Laboratory for TBEV, Bundeswehr Institute for Microbiology, 80937 Munich, Germany
- Department of Parasitology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Johannes Borde
- Praxis Prof. Borde & Kollegen, Gesundheitszentrum Oberkirch, 77704 Oberkirch, Germany
- Division of Infectious Diseases, Department of Internal Medicine, University Medical Center Freiburg im Breisgau, 79106 Freiburg im Breisgau, Germany
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Delimitation of the Tick-Borne Flaviviruses. Resolving the Tick-Borne Encephalitis virus and Louping-Ill Virus Paraphyletic Taxa. Mol Phylogenet Evol 2022; 169:107411. [PMID: 35032647 DOI: 10.1016/j.ympev.2022.107411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/22/2021] [Accepted: 12/27/2021] [Indexed: 11/22/2022]
Abstract
The tick-borne flavivirus (TBFV) group contains at least 12 members where five of them are important pathogens of humans inducing diseases with varying severity (from mild fever forms to acute encephalitis). The taxonomy structure of TBFV is not fully clarified at present. In particular, there is a number of paraphyletic issues of tick-borne encephalitis virus (TBEV) and louping-ill virus (LIV). In this study, we aimed to apply different bioinformatic approaches to analyze all available complete genome amino acid sequences to delineate TBFV members at the species level. Results showed that the European subtype of TBEV (TBEV-E) is a distinct species unit. LIV, in turn, should be separated into two species. Additional analysis of TBEV and LIV antigenic determinant diversity also demonstrate that TBEV-E and LIV are significantly different both from each other and from the other TBEV subtypes. The analysis of available literature provided data on other virus phenotypic particularities that supported our hypothesis. So, within the TBEV+LIV paraphyletic group, we offer to assign four species to get a more accurate understanding of the TBFV interspecies structure according to the modern monophyletic conception.
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Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data. BIOLOGY 2021; 10:biology10121282. [PMID: 34943197 PMCID: PMC8698833 DOI: 10.3390/biology10121282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 12/03/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary The evolution of human pathogenic viruses is one of the pressing problems of modern biology and directly relevant to public health. Many important aspects of virus evolution (e.g., evolutionary rate, population size, and migration history) are ‘hidden’ from the naked eye of a researcher. Modern bioinformatics methods make it possible to evaluate and visualize such evolutionary particularities of viruses. In this paper, we reconstructed the migration history and estimated the evolutionary rate of one of the most dangerous neuroinvasive and neurotropic tick-borne flaviviruses—Powassan virus (POWV)—distributed in North America and the Far East of Russia. Using the dates obtained, we hypothesized that the divergence of the most recent common ancestor of POWV into two independent genetic lineages most likely occurred because of the melting of glaciers that began at 11.72 Kya in the Holocene due to the climate warming-caused flooding of the isthmus between Eurasia and North America. Abstract In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary rate of this virus. In addition, we proposed a simple Bayesian technique for the evaluation and visualization of ‘temporal signal dynamics’ along the phylogenetic tree. We showed that the evolutionary rate value of POWV is 3.3 × 10−5 nucleotide substitution per site per year (95% HPD, 2.0 × 10−5–4.7 × 10−5), which is lower than values reported in the previous studies. Divergence of the most recent common ancestor (MRCA) of POWV into two independent genetic lineages most likely occurred in the period between 2600 and 6030 years ago. We assume that the divergence of the virus lineages happened due to the melting of glaciers about 12,000 years ago, which led to the disappearance of the Bering Land Bridge between Eurasia and North America (the modern Alaskan territory) and spatial division of the viral areal into two parts. Genomic data provide evidence of the virus migrations between two continents. The mean migration rate detected from the Far East of Russia to North America was one event per 1750 years. The migration to the opposite direction occurred approximately once per 475 years.
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Egyed L, Biksi I, Varga T, Zöldi V, Dán Á. Analysing the genomes of two tick-borne encephalitis viruses isolated in Hungary in 1952 and 2019. Ticks Tick Borne Dis 2021; 12:101806. [PMID: 34455141 DOI: 10.1016/j.ttbdis.2021.101806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/20/2021] [Accepted: 08/09/2021] [Indexed: 11/24/2022]
Abstract
The genomes of two Tick-borne encephalitis virus (TBEV) strains were fully sequenced and compared to those of known Hungarian strains. One was a laboratory strain (KEM-1) isolated in 1952, which had gone through hundreds of passages both on Vero cell cultures and in laboratory mice, while the other was a recent isolate (2019) from questing female ticks. The laboratory strain formed a monophyletic group with the already published 4 Hungarian strains on the evolutionary tree, located relatively close to Finnish (Kumlinge) and Russian (Absettarov) strains. This KEM-1 strain was phylogenetically distantly related both to the geographically close reference strain Neudörfl and the chronologically close Czech isolates from 1953. The 2019 isolate, KEM-195 was related to TBEV isolates from Southern Slovakia and Styria, and had the longest (328 nucleotides) deletion in its 3'-non-coding region among published sequences of strains of European subtype. Our results show that decades of laboratory passage have not altered the viral genome too much and that at least two distinct branches of TBEV strains circulate in Hungary.
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Affiliation(s)
- L Egyed
- Veterinary Medical Research Institute, ELKH, Hungária krt. 21, Budapest 1143, Hungary.
| | - I Biksi
- SCG Diagnosztika Ltd., Délegyháza, Hungary
| | - T Varga
- SCG Diagnosztika Ltd., Délegyháza, Hungary
| | - V Zöldi
- Department of Pest control, National Centre for Epidemiology, Budapest, Hungary
| | - Á Dán
- Danam.Vet. Molbiol, Kőszeg, Hungary
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LOUPING-ILL VIRUS SEROSURVEY OF WILLOW PTARMIGAN (LAGOPUS LAGOPUS LAGOPUS) IN NORWAY. J Wildl Dis 2021; 57:282-291. [PMID: 33822153 DOI: 10.7589/jwd-d-20-00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/27/2020] [Indexed: 11/20/2022]
Abstract
In Norway, the Willow Ptarmigan (Lagopus lagopus lagopus) is experiencing population declines and is nationally Red Listed as Near Threatened. Although disease has not generally been regarded as an important factor behind population fluctuations for Willow Ptarmigan in Norway, disease occurrence has been poorly investigated. Both louping-ill virus (LIV) and the closely related tick-borne encephalitis virus are found along the southern part of the Norwegian coast. We assessed whether and where Norwegian Willow Ptarmigan populations have been infected with LIV. We expected to find infected individuals in populations in the southernmost part of the country. We did not expect to find infected individuals in populations further north and at higher altitudes because of the absence of the main vector, the sheep tick (Ixodes ricinus). We collected serum samples on Nobuto filter paper and used a hemagglutination inhibition assay for antibodies against LIV. We collected data at both local and country-wide levels. For local sampling, we collected and analyzed 87 hunter-collected samples from one of the southernmost Willow Ptarmigan populations in Norway. Of these birds, only three positives (3.4%) were found. For the country-wide sampling, we collected serum samples from 163 Willow Ptarmigan carcasses submitted from selected locations all over the country. Of these birds, 32% (53) were seropositive for LIV or a cross-reacting virus. Surprisingly, we found seropositive individuals from locations across the whole country, including outside the known distribution of the sheep tick. These results suggest that either LIV or a cross-reacting virus infects ptarmigan in large parts of Norway, including at high altitudes and latitudes.
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Liebig K, Boelke M, Grund D, Schicht S, Bestehorn-Willmann M, Chitimia-Dobler L, Dobler G, Jung K, Becker SC. The Stable Matching Problem in TBEV Enzootic Circulation: How Important Is the Perfect Tick-Virus Match? Microorganisms 2021; 9:microorganisms9010196. [PMID: 33477924 PMCID: PMC7833397 DOI: 10.3390/microorganisms9010196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV), like other arthropod-transmitted viruses, depends on specific vectors to complete its enzootic cycle. It has been long known that Ixodes ricinus ticks constitute the main vector for TBEV in Europe. In contrast to the wide distribution of the TBEV vector, the occurrence of TBEV transmission is focal and often restricted to a small parcel of land, whereas surrounding areas with seemingly similar habitat parameters are free of TBEV. Thus, the question arises which factors shape this focal distribution of TBEV in the natural habitat. To shed light on factors driving TBEV-focus formation, we used tick populations from two TBEV-foci in Lower Saxony and two TBEV-foci from Bavaria with their respective virus isolates as a showcase to analyze the impact of specific virus isolate-tick population relationships. Using artificial blood feeding and field-collected nymphal ticks as experimental means, our investigation showed that the probability of getting infected with the synonymous TBEV isolate as compared to the nonsynonymous TBEV isolate was elevated but significantly higher only in one of the four TBEV foci. More obviously, median viral RNA copy numbers were significantly higher in the synonymous virus–tick population pairings. These findings may present a hint for a coevolutionary adaptation of virus and tick populations.
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Affiliation(s)
- Katrin Liebig
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (K.L.); (M.B.); (D.G.); (S.S.)
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine Hanover, 30559 Hanover, Germany
| | - Mathias Boelke
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (K.L.); (M.B.); (D.G.); (S.S.)
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine Hanover, 30559 Hanover, Germany
| | - Domenic Grund
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (K.L.); (M.B.); (D.G.); (S.S.)
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine Hanover, 30559 Hanover, Germany
| | - Sabine Schicht
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (K.L.); (M.B.); (D.G.); (S.S.)
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625 Hanover, Germany
| | - Malena Bestehorn-Willmann
- Bundeswehr Institute of Microbiology, Neuherbergstraße 11, 80937 Munich, Germany; (M.B.-W.); (L.C.-D.); (G.D.)
| | - Lidia Chitimia-Dobler
- Bundeswehr Institute of Microbiology, Neuherbergstraße 11, 80937 Munich, Germany; (M.B.-W.); (L.C.-D.); (G.D.)
| | - Gerhard Dobler
- Bundeswehr Institute of Microbiology, Neuherbergstraße 11, 80937 Munich, Germany; (M.B.-W.); (L.C.-D.); (G.D.)
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559 Hanover, Germany;
| | - Stefanie C. Becker
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (K.L.); (M.B.); (D.G.); (S.S.)
- Research Center for Emerging Infections and Zoonosis, University of Veterinary Medicine Hanover, 30559 Hanover, Germany
- Correspondence: ; Tel.: +49-511-9538717
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12
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Tick populations from endemic and non-endemic areas in Germany show differential susceptibility to TBEV. Sci Rep 2020; 10:15478. [PMID: 32968088 PMCID: PMC7511395 DOI: 10.1038/s41598-020-71920-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is endemic in twenty-seven European countries, transmitted via the bite of an infected tick. TBEV is the causative agent of one of the most important viral diseases of the central nervous system (CNS). In Germany, 890 human cases were registered between the years 2018–2019. The castor bean tick, Ixodes ricinus, is the TBEV vector with the highest importance in Central Europe, including Germany. Despite the nationwide distribution of this tick species, risk areas of TBEV are largely located in Southern Germany. To increase our understanding of TBEV-tick interactions, we collected ticks from different areas within Germany (Haselmühl/Bavaria, Hanover/Lower Saxony) and infected them via an in vitro feeding system. A TBEV isolate was obtained from an endemic focus in Haselmühl. In two experimental series conducted in 2018 and 2019, ticks sampled in Haselmühl (TBEV focus) showed higher artificial feeding rates, as well as higher TBEV infections rates than ticks from the non-endemic area (Hanover). Other than the tick origin, year and month of the infection experiment as well as co-infection with Borrelia spp., had a significant impact on TBEV Haselmühl infection rates. Taken together, these findings suggest that a specific adaptation of the tick populations to their respective TBEV virus isolates or vice versa, leads to higher TBEV infection rates in those ticks. Furthermore, co-infection with other tick-borne pathogens such as Borrelia spp. can lower TBEV infection rates in specific populations.
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13
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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.
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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)
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14
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Bondaryuk AN, Sidorova EA, Adelshin RV, Andaev EI, Balakhonov SV. Reporting of New tick-borne encephalitis virus strains isolated in Eastern Siberia (Russia) in 1960-2011 and explaining them in an evolutionary context using Bayesian phylogenetic inference. Ticks Tick Borne Dis 2020; 11:101496. [PMID: 32723652 DOI: 10.1016/j.ttbdis.2020.101496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022]
Abstract
Tick-borne encephalitis virus (TBEV) is one of the main tick-borne viral pathogens of humans. Infection may induce signs of meningitis, encephalitis, paralysis and high fever. TBEV is well studied by molecular phylogenetic methods. The present-day implementation of Bayesian phylogenetic models allows population dynamics to be tracked, providing changes in population size that were not directly observed. However, the description of the past population dynamics of TBEV is rare in the literature. In our investigation, we provide data on the dynamics of viral genetic diversity of TBEV in Zabaikalsky Krai (Eastern Siberia, Russia) revealed by the Bayesian coalescent inference in a BEAST program. As a data set, we used the envelope (E) protein partial gene sequences (1308 nt) of 38 TBEV strains (including six "886-84-like" or Baikalian subtype strains (TBEV-B)), isolated in Zabaikalsky Krai (Eastern Siberia, Russia) in 1960-1963 and 1995-2011. To increase estimations reliability, we compared 9 model combinations by Path sampling and Stepping-stone sampling methods. It has been shown that the genetic diversity decline in the population history of TBEV in the 1950s coincides with the date of the beginning of wide dichlorodiphenyltrichloroethane forest dusting in Siberia. We assumed that the TBEV population on the territory of Siberia went through a genetic bottleneck. Also, we provide data estimating the divergence time of TBEV-B strains and indicate the specific evolution rate of an ancestor lineage of the Baikalian subtype, illustrated on a phylogenetic tree, and reconstructed under a relaxed clock model.
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Affiliation(s)
- Artem N Bondaryuk
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
| | - Elena A Sidorova
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
| | - Renat V Adelshin
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia; Irkutsk State University, Irkutsk, Russia.
| | - Evgeny I Andaev
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
| | - Sergey V Balakhonov
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
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15
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Ott D, Ulrich K, Ginsbach P, Öhme R, Bock-Hensley O, Falk U, Teinert M, Lenhard T. Tick-borne encephalitis virus (TBEV) prevalence in field-collected ticks (Ixodes ricinus) and phylogenetic, structural and virulence analysis in a TBE high-risk endemic area in southwestern Germany. Parasit Vectors 2020; 13:303. [PMID: 32527288 PMCID: PMC7291635 DOI: 10.1186/s13071-020-04146-7] [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: 12/11/2019] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Tick-borne encephalitis (TBE) is the most common viral CNS infection with incidences much higher than all other virus infections together in many risk areas of central and eastern Europe. The Odenwald Hill region (OWH) in southwestern Germany is classified as a TBE risk region and frequent case numbers but also more severe infections have been reported within the past decade. The objective of the present study was to survey the prevalence of tick-borne encephalitis virus (TBEV) in Ixodes ricinus and to associate TBEV genetic findings with TBE infections in the OWH. METHODS Ticks were collected by the flagging methods supported by a crowdsourcing project implementing the interested public as collectors to cover completely and collect randomly a 3532 km2 area of the OWH TBE risk region. Prevalence of TBEV in I. ricinus was analysed by reversed transcription quantitative real-time PCR. Phylogeographic analysis was performed to classify OWH TBEV isolates within a European network of known TBEV strains. Mutational sequence analysis including 3D modelling of envelope protein pE was performed and based on a clinical database, a spatial association of TBE case frequency and severity was undertaken. RESULTS Using the crowd sourcing approach we could analyse a total of 17,893 ticks. The prevalence of TBEV in I. ricinus in the OWH varied, depending on analysed districts from 0.12% to 0% (mean 0.04%). Calculated minimum infection rate (MIR) was one decimal power higher. All TBEV isolates belonged to the European subtype. Sequence analysis revealed a discontinuous segregation pattern of OWH isolates with two putative different lineages and a spatial association of two isolates with increased TBE case numbers as well as exceptional severe to fatal infection courses. CONCLUSIONS TBEV prevalence within the OWH risk regions is comparatively low which is probably due to our methodological approach and may more likely reflect prevalence of natural TBEV foci. As for other European regions, TBEV genetics show a discontinuous phylogeny indicating among others an association with bird migration. Mutations within the pE gene are associated with more frequent, severe and fatal TBE infections in the OWH risk region.
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Affiliation(s)
- Daniela Ott
- Neuroinfectious Diseases Group, Department of Neurology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
| | - Kristina Ulrich
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA Scotland, UK
| | | | - Rainer Öhme
- Molecular Biology Laboratory, Landesgesundheitsamt Stuttgart, Nordbahnhofstraße 135, 70191 Stuttgart, Germany
| | - Oswinde Bock-Hensley
- Gesundheitsamt Rhein-Neckarkreis, Kurfürsten-Anlage 38-40, 69115 Heidelberg, Germany
| | - Ulrich Falk
- Gesundheitsamt Odenwaldkreis, Michelstädter Str. 12, 64711 Erbach, Germany
| | - Martina Teinert
- Gesundheitsamt Neckar-Odenwaldkreis, Neckarelzer Str. 7, 74821 Mosbach, Germany
| | - Thorsten Lenhard
- Neuroinfectious Diseases Group, Department of Neurology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 350, 69120 Heidelberg, Germany
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16
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Alfano N, Tagliapietra V, Rosso F, Ziegler U, Arnoldi D, Rizzoli A. Tick-borne encephalitis foci in northeast Italy revealed by combined virus detection in ticks, serosurvey on goats and human cases. Emerg Microbes Infect 2020; 9:474-484. [PMID: 32100632 PMCID: PMC7054962 DOI: 10.1080/22221751.2020.1730246] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tick-borne encephalitis (TBE) is a severe zoonotic neurological disease endemic in northeast Italy since 1992. In the Province of Trento, a sharp increase in TBE incidence has been recorded since 2012, despite the vaccination efforts. To assess current TBE infection hazard in this area, we applied an integrated approach combining the distribution of human cases, the seroprevalence of tick-borne encephalitis virus (TBEV) in sentinel hosts and the screening of questing ticks for TBEV. A total of 706 goat sera from 69 farms were screened for TBEV-specific antibodies resulting in 5 positive farms, while the location of human cases was provided by the local Public Health Agency. Tick sampling was concentrated in areas where TBEV circulation was suggested by either seroprevalence in goats or human cases, resulting in 2,410 Ixodes ricinus collected and analyzed by real-time RT-PCR. Four tick samples from 2 areas with record of human cases were positive to TBEV corresponding to a 0.17% prevalence in the region, while risk areas suggested by serology on goats were not confirmed by tick screening. Our results revealed an increase in TBEV prevalence in ticks and the emergence of new active TBE foci, compared to previous surveys, and demonstrated the importance of an integrated approach for TBE risk assessment. A phylogenetic analysis of the partial E gene confirmed that the European TBEV subtype is circulating in northeast Italy and suggested that the different Italian TBEV strains originated independently as a result of different introductions from neighbouring countries, presumably through migratory birds.
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Affiliation(s)
- Niccolò Alfano
- Fondazione Edmund Mach, Research and Innovation Centre, Trento, Italy
| | | | - Fausta Rosso
- Fondazione Edmund Mach, Research and Innovation Centre, Trento, Italy
| | - Ute Ziegler
- Friederich-Loeffler-Institute, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Daniele Arnoldi
- Fondazione Edmund Mach, Research and Innovation Centre, Trento, Italy
| | - Annapaola Rizzoli
- Fondazione Edmund Mach, Research and Innovation Centre, Trento, Italy
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17
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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.
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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.
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18
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Smura T, Tonteri E, Jääskeläinen A, von Troil G, Kuivanen S, Huitu O, Kareinen L, Uusitalo J, Uusitalo R, Hannila-Handelberg T, Voutilainen L, Nikkari S, Sironen T, Sane J, Castrén J, Vapalahti O. Recent establishment of tick-borne encephalitis foci with distinct viral lineages in the Helsinki area, Finland. Emerg Microbes Infect 2019; 8:675-683. [PMID: 31084456 PMCID: PMC6522972 DOI: 10.1080/22221751.2019.1612279] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Number of tick-borne encephalitis (TBE) cases has increased and new foci have emerged in Finland during the last decade. We evaluated risk for locally acquired TBE in the capital region inhabited by 1.2 million people. We screened ticks and small mammals from probable places of TBE virus (TBEV) transmission and places without reported circulation. The TBEV positive samples were sequenced and subjected to phylogenetic analysis. Within the study period 2007–2017, there was a clear increase of both all TBE cases and locally acquired cases in the Helsinki area. The surveillance of ticks and small mammals for TBEV confirmed four distinct TBEV foci in the Helsinki area. All detected TBEV strains were of the European subtype. TBEV genome sequences indicated that distinct TBEV lineages circulate in each focus. Molecular clock analysis suggested that the virus lineages were introduced to these foci decades ago. In conclusion, TBE has emerged in the mainland of Helsinki area during the last decade, with at least four distinct virus lineages independently introduced into the region previously. Although the overall annual TBE incidence is below the threshold for recommending general vaccinations, the situation requires further surveillance to detect and prevent possible further emergence of local TBE clusters.
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Affiliation(s)
- Teemu Smura
- a Department of Virology , University of Helsinki , Helsinki , Finland.,b Division of Clinical Microbiology , Helsinki University Hospital Laboratory Services (HUSLAB) , Helsinki , Finland
| | - Elina Tonteri
- c Centers for Military Medicine and Biothreat Preparedness , Helsinki , Finland
| | - Anu Jääskeläinen
- b Division of Clinical Microbiology , Helsinki University Hospital Laboratory Services (HUSLAB) , Helsinki , Finland
| | | | - Suvi Kuivanen
- a Department of Virology , University of Helsinki , Helsinki , Finland
| | - Otso Huitu
- e Natural Resources Institute Finland (Luke) , Helsinki , Finland
| | - Lauri Kareinen
- a Department of Virology , University of Helsinki , Helsinki , Finland
| | - Joni Uusitalo
- a Department of Virology , University of Helsinki , Helsinki , Finland
| | - Ruut Uusitalo
- a Department of Virology , University of Helsinki , Helsinki , Finland.,f Department of Geosciences and Geography , University of Helsinki , Helsinki , Finland.,g Department of Veterinary Biosciences , University of Helsinki , Helsinki , Finland
| | | | - Liina Voutilainen
- c Centers for Military Medicine and Biothreat Preparedness , Helsinki , Finland
| | - Simo Nikkari
- c Centers for Military Medicine and Biothreat Preparedness , Helsinki , Finland
| | - Tarja Sironen
- a Department of Virology , University of Helsinki , Helsinki , Finland
| | - Jussi Sane
- h Department of Health Security, Infectious Disease Control and Vaccinations Unit , National Institute for Health and Welfare , Helsinki , Finland
| | | | - Olli Vapalahti
- a Department of Virology , University of Helsinki , Helsinki , Finland.,b Division of Clinical Microbiology , Helsinki University Hospital Laboratory Services (HUSLAB) , Helsinki , Finland.,g Department of Veterinary Biosciences , University of Helsinki , Helsinki , Finland
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19
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Litov AG, Deviatkin AA, Goptar IA, Dedkov VG, Gmyl AP, Markelov ML, Shipulin GA, Karganova GG. Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing. J Gen Virol 2019; 99:240-245. [PMID: 29393021 DOI: 10.1099/jgv.0.001003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We studied minor variants within two tick-borne encephalitis virus (TBEV) populations with a common ancestor: the mouse brain-adapted variant EK-328c and the tick-adapted variant M. High-throughput sequencing with custom amplicons from RT-PCR viral RNA was performed on Illumina MiSeq 2*250 paired-end v2 chemistry. Using the LowFreq program (default settings) and Sanger-sequenced consensus as a reference, variants with an abundance of 1 % and above within the studied populations were identified. Using the obtained data in the context of our previous studies, we concluded that TBEV variants, which are different from the major population phenotype and can become a major part of the viral population under favourable environmental conditions, can exist at abundances of less than 1 % in the long-term. The comparison of our data with the literature allowed us to conclude that the laboratory variant EK-328c and variant M have similar SNV counts to TBEV variants from natural populations and some fast-evolving RNA viruses.
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Affiliation(s)
- Alexander G Litov
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
- Lomonosov MSU, Faculty of Biology, Lenin Hills, 1/12, Moscow 119234, Russia
| | - Andrey A Deviatkin
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Research Institute of Occupational Health, Moscow, Russia
| | - Irina A Goptar
- Research Institute of Occupational Health, Moscow, Russia
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Vladimir G Dedkov
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Anatoly P Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - German A Shipulin
- Central Research Institute for Epidemiology (CRIE), Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, Moscow, Russia
| | - Galina G Karganova
- Lomonosov MSU, Faculty of Biology, Lenin Hills, 1/12, Moscow 119234, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
- Chumakov Institute of Poliomyelitis and Viral Encephalitides (Chumakov FSC R&D IBP), prem. 8, k.17, pos. Institut Poliomielita, poselenie Moskovskiy, Moscow 108819, Russia
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Andersen NS, Bestehorn M, Chitimia-Dobler L, Kolmos HJ, Jensen PM, Dobler G, Skarphédinsson S. Phylogenetic characterization of tick-borne encephalitis virus from Bornholm, Denmark. Ticks Tick Borne Dis 2018; 10:533-539. [PMID: 30704909 DOI: 10.1016/j.ttbdis.2018.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 12/17/2018] [Accepted: 12/27/2018] [Indexed: 12/30/2022]
Abstract
The Danish island of Bornholm in the Baltic Sea has been known as a tick-borne encephalitis (TBE) natural focus for more than 60 years. TBE in humans is diagnosed on a regular basis either in inhabitants or tourists of the island. Other areas in Denmark have been suggested as possible risk areas of TBE. Despite the long-known endemicity on Bornholm and the possibility of the virus circulating in other areas, no data on the prevalences of TBE virus (TBEV) in ticks, or adequate molecular characterization and phylogenetic studies are available for the circulating TBEV strains. This study aimed to detect TBEV in ticks collected on the island of Bornholm and other possible risk areas, with the attempt to isolate the circulating viruses for molecular and phylogenetic analysis and confirm the presence of virus in the predicted risk areas. From 2014 to 2016, 9321 I. ricinus (nymphs, females, and males) were collected by flagging 31 locations in Denmark. The ticks were pooled and tested for TBEV by qPCR. The envelope gene of the detected TBE virus strains was amplified and sequenced by RT-PCR. After successful virus isolation, whole genome sequencing was performed. Phylogenetic analysis of the obtained sequences was done by the Maximum Likelihood method. One pool of 11 females and one pool of eight males from a total of 34 tick pools collected from the northwestern shore of lake Rubinsøen on Bornholm tested positive, resulting in a local estimated point prevalence of 0.6% [CI95% 0,1-1.85%] in this microfocus. We were not successful in confirming any other of the predicted TBEV-endemic areas. Alignment of the two complete E genes from Bornholm revealed identical sequences. Virus isolation and whole genome sequencing were succeeded from one of the positive samples. Phylogenetic analysis showed that the isolated virus had the closest phylogenetic relationship to TBEV sequences detected in Eastern and Central Europe.
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Affiliation(s)
- Nanna Skaarup Andersen
- Clinical Centre of Emerging and Vector-borne Infections, Odense University Hospital, Sdr. Boulevard 29, DK-5000, Odense C, Denmark; Research Unit of Clinical Microbiology, University of Southern Denmark, J.B. Winsløvsvej 21.2, DK-5000, Odense C, Denmark.
| | - Malena Bestehorn
- Parasitology Unit, Institute of Zoology, University of Hohenheim, Hans-Wolff-Strasse 34, DE-70955, Stuttgart, Germany; Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, DE-80937, Munich, Germany; German Center of Infection Research (DZIF) Partner Munich, Neuherbergstrasse 11, DE-80937, Munich, Germany
| | - Lidia Chitimia-Dobler
- Parasitology Unit, Institute of Zoology, University of Hohenheim, Hans-Wolff-Strasse 34, DE-70955, Stuttgart, Germany; Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, DE-80937, Munich, Germany; German Center of Infection Research (DZIF) Partner Munich, Neuherbergstrasse 11, DE-80937, Munich, Germany
| | - Hans Jørn Kolmos
- Research Unit of Clinical Microbiology, University of Southern Denmark, J.B. Winsløvsvej 21.2, DK-5000, Odense C, Denmark
| | - Per Moestrup Jensen
- Department of Plant- and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Copenhagen, Denmark
| | - Gerhard Dobler
- Parasitology Unit, Institute of Zoology, University of Hohenheim, Hans-Wolff-Strasse 34, DE-70955, Stuttgart, Germany; Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, DE-80937, Munich, Germany; German Center of Infection Research (DZIF) Partner Munich, Neuherbergstrasse 11, DE-80937, Munich, Germany
| | - Sigurdur Skarphédinsson
- Clinical Centre of Emerging and Vector-borne Infections, Odense University Hospital, Sdr. Boulevard 29, DK-5000, Odense C, Denmark; Department of Infectious Diseases, Odense University Hospital, Sdr. Boulevard 29, DK-5000, Odense C, Denmark
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21
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Egyed L, Rónai Z, Dán Á. Hungarian tick-borne encephalitis viruses isolated from a 0.5-ha focus are closely related to Finnish strains. Ticks Tick Borne Dis 2018; 9:1064-1068. [PMID: 29655579 DOI: 10.1016/j.ttbdis.2018.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/02/2018] [Accepted: 03/30/2018] [Indexed: 12/30/2022]
Abstract
Four tick-borne encephalitis virus strains were isolated from a small 0.5-ha focus over a six-year-long period (2011-2016) in Hungary. Two strains with identical genomes were isolated from Ixodes ricinus and Haemaphysalis concinna two months apart, which shows that the virus had not evolved separately in these tick species. Whole-genome sequencing of the virus revealed that the isolates differed from each other in 4 amino acids and 9 nucleotides. The calculated substitution rates indicated that the speed of genome evolution differs from habitat to habitat, and continuously changes even within the same focus. The amino acid changes affected the capsid, envelope, NS2a and NS5 genes, and one mutation each occurred in the 5' and 3' NCR as well as the premembrane, NS2a and NS5 genes. Phylogenetic analyses based on complete coding ORF sequences showed that the isolates belong to the European subtype of the virus and are closely related to the Finnish Kumlinge strains, the Bavarian isolate Leila and two isolates of Russian origin, but more distantly related to viruses from the neighbouring Central European countries. These isolates obviously have a common origin and are probably connected by migrating birds. These are the first published complete Hungarian TBEV sequences.
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Affiliation(s)
- László Egyed
- Veterinary Medical Research Institute, Agricultural Research Center of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Zsuzsanna Rónai
- Molecular Biology Department, National Food Chain Safety Office, Veterinary Diagnostic Institute, Budapest, Hungary
| | - Ádám Dán
- Molecular Biology Department, National Food Chain Safety Office, Veterinary Diagnostic Institute, Budapest, Hungary
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22
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New genetic lineage within the Siberian subtype of tick-borne encephalitis virus found in Western Siberia, Russia. INFECTION GENETICS AND EVOLUTION 2017; 56:36-43. [PMID: 29069610 DOI: 10.1016/j.meegid.2017.10.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/06/2017] [Accepted: 10/21/2017] [Indexed: 11/20/2022]
Abstract
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.
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23
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Demina T, Tkachev S, Kozlova I, Doroshchenko E, Lisak O, Suntsova O, Verkhozina M, Dzhioev YP, Paramonov A, Tikunov A, Tikunova N, Zlobin V, Ruzek D. 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. Ticks Tick Borne Dis 2017; 8:547-553. [DOI: 10.1016/j.ttbdis.2017.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 03/08/2017] [Accepted: 03/08/2017] [Indexed: 10/20/2022]
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24
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Grubaugh ND, Rückert C, Armstrong PM, Bransfield A, Anderson JF, Ebel GD, Brackney DE. Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution. Virus Evol 2016; 2:vew033. [PMID: 28058113 PMCID: PMC5210029 DOI: 10.1093/ve/vew033] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Arthropod-borne RNA viruses exist within hosts as heterogeneous populations of viral variants and, as a result, possess great genetic plasticity. Understanding the micro-evolutionary forces shaping these viruses can provide insights into how they emerge, adapt, and persist in new and changing ecological niches. While considerable attention has been directed toward studying the population dynamics of mosquito-borne viruses, little is known about tick-borne virus populations. Therefore, using a mouse and Ixodes scapularis tick transmission model, we examined Powassan virus (POWV; Flaviviridae, Flavivirus) populations in and between both the vertebrate host and arthropod vector. We found that genetic bottlenecks, RNAi-mediated diversification, and selective constraints collectively influence POWV evolution. Together, our data provide a mechanistic explanation for the slow, long-term evolutionary trends of POWV, and suggest that all arthropod-borne viruses encounter similar selective pressures at the molecular level (i.e. RNAi), yet evolve much differently due to their unique rates and modes of transmission.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Microbiology Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA
| | - Claudia Rückert
- Department of Microbiology Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA
| | - Philip M Armstrong
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
| | - Angela Bransfield
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
| | - John F Anderson
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
| | - Gregory D Ebel
- Department of Microbiology Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA
| | - Doug E Brackney
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
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25
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Bertrand YJK, Johansson M, Norberg P. Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach. PLoS One 2016; 11:e0164435. [PMID: 27760182 PMCID: PMC5070875 DOI: 10.1371/journal.pone.0164435] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/26/2016] [Indexed: 12/02/2022] Open
Abstract
The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.
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Affiliation(s)
- Yann J. K. Bertrand
- Science and Historical Investigations of Evolution Laboratory of Dubá, Dubá, Czech Rep
| | - Magnus Johansson
- School of Medical Sciences Örebro University, Örebro, Sweden
- School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden
- iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Peter Norberg
- Department of Clinical Microbiology, Sahlgrenska University, Gothenburg, Sweden
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26
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Levanov L, Jääskeläinen A, Vapalahti O. Test based on subtype-specific μ-capture IgM immunoassay can distinguish between infections of European and Siberian subtypes of tick-borne encephalitis virus. J Clin Virol 2015; 73:81-83. [DOI: 10.1016/j.jcv.2015.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/29/2015] [Accepted: 11/01/2015] [Indexed: 10/22/2022]
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27
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Jääskeläinen A, Tonteri E, Pieninkeroinen I, Sironen T, Voutilainen L, Kuusi M, Vaheri A, Vapalahti O. Siberian subtype tick-borne encephalitis virus in Ixodes ricinus in a newly emerged focus, Finland. Ticks Tick Borne Dis 2015; 7:216-223. [PMID: 26548609 DOI: 10.1016/j.ttbdis.2015.10.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/28/2015] [Accepted: 10/16/2015] [Indexed: 11/26/2022]
Abstract
The first tick-borne encephalitis (TBE) cases in Kotka, Finland appeared in 2010. Altogether ten human cases have been diagnosed by 2014. Four had long-lasting sequelae. We collected 195 Ixodes ricinus ticks, nine rodents, and eleven shrews from the archipelago of Kotka in 2011. Three Siberian subtype TBE virus (TBEV) strains were isolated from the ticks and three mammals were positive for TBEV antibodies. The archipelago of Kotka is a newly emerged TBE focus of Siberian subtype TBEV circulating notably in I. ricinus. The patients had on average longer hospitalization than reported for the European subtype infection.
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Affiliation(s)
- Anu Jääskeläinen
- Department of Virology, University of Helsinki, P.O. Box 21, FI-00014 Helsinki, Finland.
| | - Elina Tonteri
- Department of Virology, University of Helsinki, P.O. Box 21, FI-00014 Helsinki, Finland.
| | | | - Tarja Sironen
- Department of Virology, University of Helsinki, P.O. Box 21, FI-00014 Helsinki, Finland.
| | - Liina Voutilainen
- Department of Virology, University of Helsinki, P.O. Box 21, FI-00014 Helsinki, Finland; Natural Resources Institute, Vantaa Unit, P.O. Box 18, FI-01301 Vantaa, Finland.
| | - Markku Kuusi
- Department of Infectious Diseases, National Institute for Health and Welfare, P.O. Box 30, FI-00271 Helsinki, Finland.
| | - Antti Vaheri
- Department of Virology, University of Helsinki, P.O. Box 21, FI-00014 Helsinki, Finland; Department of Virology and Immunology, HUSLAB, Helsinki University Hospital, P.O. Box 400, FI-00029 Helsinki, Finland.
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, P.O. Box 21, FI-00014 Helsinki, Finland; Department of Virology and Immunology, HUSLAB, Helsinki University Hospital, P.O. Box 400, FI-00029 Helsinki, Finland; Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66, FI-00014 Helsinki, Finland.
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28
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Kovalev SY, Mukhacheva TA. Tick-borne encephalitis virus subtypes emerged through rapid vector switches rather than gradual evolution. Ecol Evol 2014; 4:4307-16. [PMID: 25540692 PMCID: PMC4267869 DOI: 10.1002/ece3.1301] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/27/2014] [Accepted: 10/01/2014] [Indexed: 12/20/2022] Open
Abstract
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 exclusive hypotheses about the origin and distribution of TBEV subtypes, although they are based on the same assumption of gradual evolution. Recently, we have described the structure of TBEV populations in terms of a clusteron approach, a clusteron being a structural unit of viral population [Kovalev and Mukhacheva (2013) Infect. Genet. Evol., 14, 22–28]. This approach allowed us to investigate questions of TBEV evolution in a new way and to propose a hypothesis of quantum evolution due to a vector switch. We also consider a possible mechanism for this switch occurring in interspecific hybrids of ticks. It is necessarily accompanied by a rapid accumulation of mutations in the virus genome, which is contrary to the generally accepted view of gradual evolution in assessing the ages of TBEV populations. The proposed hypothesis could explain and predict not only the formation of new subtypes, but also the emergence of new vector-borne viruses.
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Affiliation(s)
- Sergey Y Kovalev
- Laboratory of Molecular Genetics, Department of Biology, Ural Federal University Lenin Avenue 51, Yekaterinburg, 620000, Russia
| | - Tatyana A Mukhacheva
- Laboratory of Molecular Genetics, Department of Biology, Ural Federal University Lenin Avenue 51, Yekaterinburg, 620000, Russia
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29
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Rieille N, Bressanelli S, Freire CCM, Arcioni S, Gern L, Péter O, Voordouw MJ. Prevalence and phylogenetic analysis of tick-borne encephalitis virus (TBEV) in field-collected ticks (Ixodes ricinus) in southern Switzerland. Parasit Vectors 2014; 7:443. [PMID: 25245773 PMCID: PMC4261884 DOI: 10.1186/1756-3305-7-443] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/13/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Tick-borne encephalitis is the most common tick-borne viral infection in Europe with 3,000 human cases reported each year. In Western Europe, the castor bean tick, Ixodes ricinus, is the principal vector of the tick-borne encephalitis virus (TBEV). TBEV appears to be spreading geographically and was recently detected for the first time in Canton Valais in the southern part of Switzerland. The purpose of the present study was to survey the I. ricinus tick populations of Canton Valais for TBEV. METHODS We collected a total of 19,331 I. ricinus ticks at 45 different sites in Canton Valais between 2010 and 2013. Ticks were processed in pools and tested for TBEV using reverse transcription quantitative PCR. The NS5 gene and the envelope gene of the TBEV isolates were partially sequenced for phylogenetic analysis. RESULTS TBEV was detected in tick populations at six of the 45 sites. These six sites were all located in a 33 km transect along the Rhône River. TBEV was detected in two sites for three of the four years of the study showing the temporal persistence of the pathogen. Prevalence of TBEV in the six positive sites ranged from 0.16% to 11.11%. Phylogenetic analysis found that all TBEV isolates from Canton Valais belonged to the European subtype. Genetic analysis found two distinct lineages of TBEV suggesting that Canton Valais experienced two independent colonization events. CONCLUSIONS TBEV appears to be well established at certain locations in Canton Valais.
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Affiliation(s)
- Nadia Rieille
- />Central Institute of Valais Hospitals, Infectious diseases, Av Grand Champsec 86, Sion, Switzerland
- />Laboratory of Ecology and Evolution of Parasites, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Stéphane Bressanelli
- />Laboratoire de Virologie Moléculaire et Structurale, CNRS UPR3296, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
| | - Caio C M Freire
- />Inter-institutional Grad Program on Bioinformatics, University of Sao Paulo, Matao Street 1010, Sao Paulo, Brazil
| | - Séverine Arcioni
- />Central Institute of Valais Hospitals, Genetics, Av Grand Champsec 86, Sion, Switzerland
| | - Lise Gern
- />Laboratory of Eco-Epidemiology of Parasites, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Olivier Péter
- />Central Institute of Valais Hospitals, Infectious diseases, Av Grand Champsec 86, Sion, Switzerland
| | - Maarten J Voordouw
- />Laboratory of Ecology and Evolution of Parasites, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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30
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Kuivanen S, Hepojoki J, Vene S, Vaheri A, Vapalahti O. Identification of linear human B-cell epitopes of tick-borne encephalitis virus. Virol J 2014; 11:115. [PMID: 24946852 PMCID: PMC4078944 DOI: 10.1186/1743-422x-11-115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/13/2014] [Indexed: 12/30/2022] Open
Abstract
Background Tick-borne encephalitis (TBE) is a central nervous system infection transmitted to humans by ticks. The causative agent, tick-borne encephalitis virus (TBEV), belongs to the genus Flavivirus (family Flaviviridae), which includes globally important arthropod-borne viruses, such as dengue, Yellow fever, Japanese encephalitis and West Nile viruses. Flaviviruses are highly cross-reactive in serological tests that are currently based on viral envelope proteins. The envelope (E) protein is the major antigenic determinant and it is known to induce neutralizing antibody responses. Methods We synthesized the full-length TBEV proteome as overlapping synthetic 18-mer peptides to find dominant linear IgG epitopes. To distinguish natural TBEV infections from responses to TBE immunization or other flavivirus infections, the peptides were probed with sera of patients infected with TBEV, West Nile virus (WNV) or dengue virus (DENV), sera from TBE vaccinees and negative control sera by SPOT array technique. Results We identified novel linear TBEV IgG epitopes in the E protein and in the nonstructural protein 5 (NS5). Conclusions In this study, we screened TBEV structural and nonstructural proteins to find linear epitopes specific for TBEV. We found 11 such epitopes and characterized specifically two of them to be potential for differential diagnostics. This is the first report of identifying dominant linear human B-cell epitopes of the whole TBEV genome. The identified peptide epitopes have potential as antigens for diagnosing TBEV and to serologically distinguish flavivirus infections from each other.
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Affiliation(s)
- Suvi Kuivanen
- Department of Virology, Haartman Institute, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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31
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Pettersson JHO, Fiz-Palacios O. Dating the origin of the genus Flavivirus in the light of Beringian biogeography. J Gen Virol 2014; 95:1969-1982. [PMID: 24914065 DOI: 10.1099/vir.0.065227-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Flavivirus includes some of the most important human viral pathogens, and its members are found in all parts of the populated world. The temporal origin of diversification of the genus has long been debated due to the inherent problems with dating deep RNA virus evolution. A generally accepted hypothesis suggests that Flavivirus emerged within the last 10 000 years. However, it has been argued that the tick-borne Powassan flavivirus was introduced into North America some time between the opening and closing of the Beringian land bridge that connected Asia and North America 15 000-11 000 years ago, indicating an even older origin for Flavivirus. To determine the temporal origin of Flavivirus, we performed Bayesian relaxed molecular clock dating on a dataset with high coverage of the presently available Flavivirus diversity by combining tip date calibrations and internal node calibration, based on the Powassan virus and Beringian land bridge biogeographical event. Our analysis suggested that Flavivirus originated ~85 000 (64 000-110 000) or 120 000 (87 000-159 000) years ago, depending on the circumscription of the genus. This is significantly older than estimated previously. In light of our results, we propose that it is likely that modern humans came in contact with several members of the genus Flavivirus much earlier than suggested previously, and that it is possible that the spread of several flaviviruses coincided with, and was facilitated by, the migration and population expansion of modern humans out of Africa.
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Affiliation(s)
- John H-O Pettersson
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Omar Fiz-Palacios
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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32
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The three subtypes of tick-borne encephalitis virus induce encephalitis in a natural host, the bank vole (Myodes glareolus). PLoS One 2013; 8:e81214. [PMID: 24349041 PMCID: PMC3862475 DOI: 10.1371/journal.pone.0081214] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/09/2013] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) infects bank voles (Myodes glareolus) in nature, but the relevance of rodents for TBEV transmission and maintenance is unclear. We infected colonized bank voles subcutaneously to study and compare the infection kinetics, acute infection, and potential viral persistence of the three known TBEV subtypes: European (TBEV-Eur), Siberian (TBEV-Sib) and Far Eastern (TBEV-FE). All strains representing the three subtypes were infective and highly neurotropic. They induced (meningo)encephalitis in some of the animals, however most of the cases did not present with apparent clinical symptoms. TBEV-RNA was cleared significantly slower from the brain as compared to other organs studied. Supporting our earlier findings in natural rodent populations, TBEV-RNA could be detected in the brain for up to 168 days post infection, but we could not demonstrate infectivity by cell culture isolation. Throughout all time points post infection, RNA of the TBEV-FE was detected significantly more often than RNA of the other two strains in all organs studied. TBEV-FE also induced prolonged viremia, indicating distinctive kinetics in rodents in comparison to the other two subtypes. This study shows that bank voles can develop a neuroinvasive TBEV infection with persistence of viral RNA in brain, and mount an anti-TBEV IgG response. The findings also provide further evidence that bank voles can serve as sentinels for TBEV endemicity.
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Karan LS, Ciccozzi M, Yakimenko VV, Presti AL, Cella E, Zehender G, Rezza G, Platonov AE. The deduced evolution history of Omsk hemorrhagic fever virus. J Med Virol 2013; 86:1181-7. [DOI: 10.1002/jmv.23856] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2013] [Indexed: 02/03/2023]
Affiliation(s)
| | - Massimo Ciccozzi
- Department of Infectious; Parasitic and Immunomediated Diseases; National Institute of Health; Rome Italy
| | | | - Alessandra Lo Presti
- Department of Infectious; Parasitic and Immunomediated Diseases; National Institute of Health; Rome Italy
| | - Eleonora Cella
- Department of Infectious; Parasitic and Immunomediated Diseases; National Institute of Health; Rome Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences; L. Sacco Hospital; University of Milan; Milan Italy
| | - Giovanni Rezza
- Department of Infectious; Parasitic and Immunomediated Diseases; National Institute of Health; Rome Italy
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Ytrehus B, Vainio K, Dudman SG, Gilray J, Willoughby K. Tick-borne encephalitis virus and louping-ill virus may co-circulate in Southern Norway. Vector Borne Zoonotic Dis 2013; 13:762-8. [PMID: 23808981 DOI: 10.1089/vbz.2012.1023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The European subtype of tick-borne encephalitis virus (TBEV-Eu) and louping-ill virus (LIV) are two closely related tick-borne flaviviruses. However, whereas the first is the cause of one of Europe's most important zoonoses, the latter most often only causes disease in sheep and grouse. TBEV-Eu is typically found in the forests of central and northeastern Europe, and LIV typically is found in sheep pastures in the British Isles. In the 1980s, however, LIV was isolated from sheep with encephalomyelitis in Norway. In the 1990s, the first cases of human TBEV were also detected in this country, but while Louping-ill in sheep is very rare, the number of human TBEV cases is increasing. No larger investigations of TBEV and/or LIV seroprevalence and distribution in Norway have been published. However, before such studies are initiated, it is pertinent to know if LIV and TBEV are potentially co-circulating. In the current study, we examined if antibodies against LIV and TBEV were found in wild cervids in one location (Farsund) in southern and one location (Molde) in northwestern Norway using a commercially available enzyme-linked immunosorbent assay for detection of anti-TBEV immunoglobulin G (IgG) and a hemagglutination inhibition test for anti-LIV IgG. Positive results were confirmed by serum neutralization tests. In Farsund, 22 of 54 cervids had antibodies against TBEV and 8 antibodies against LIV. In Molde, 1 of 64 cervids was confirmed positive for TBEV, whereas none were positive for LIV. This shows that TBEV and LIV may co-circulate in southern Norway and that virus(es) antigenetically very similar to TBEV may be found in northwestern Norway. The latter is intriguing, because the climatic conditions typical of TBEV locations should not be expected this far north.
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Affiliation(s)
- Bjørnar Ytrehus
- 1 Norwegian Veterinary Institute , Section for Pathology, Oslo, Norway
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Weidmann M, Frey S, Freire CCM, Essbauer S, Růžek D, Klempa B, Zubrikova D, Vögerl M, Pfeffer M, Hufert FT, Zanotto PM, Dobler G. Molecular phylogeography of tick-borne encephalitis virus in central Europe. J Gen Virol 2013; 94:2129-2139. [PMID: 23784447 DOI: 10.1099/vir.0.054478-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to obtain a better understanding of tick-borne encephalitis virus (TBEV) strain movements in central Europe the E gene sequences of 102 TBEV strains collected from 1953 to 2011 at 38 sites in the Czech Republic, Slovakia, Austria and Germany were determined. Bayesian analysis suggests a 350-year history of evolution and spread in central Europe of two main lineages, A and B. In contrast to the east to west spread at the Eurasian continent level, local central European spreading patterns suggest historic west to east spread followed by more recent east to west spread. The phylogenetic and network analyses indicate TBEV ingressions from the Czech Republic and Slovakia into Germany via landscape features (Danube river system), biogenic factors (birds, red deer) and anthropogenic factors. The identification of endemic foci showing local genetic diversity is of paramount importance to the field as these will be a prerequisite for in-depth analysis of focal TBEV maintenance and long-distance TBEV spread.
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Affiliation(s)
- Manfred Weidmann
- Department of Virology, University Medical Center, 37075 Göttingen, Germany
| | - Stefan Frey
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany
| | - Caio C M Freire
- Department of Microbiology, Biomedical Sciences Institute - ICB II University of São Paulo, 05508-000 São Paulo, Brazil
| | | | - Daniel Růžek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic.,Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Boris Klempa
- Institute of Virology Charité University Hospital, Berlin, Germany.,Institute of Virology, Slovak Academy of Science, Dubravska cesta 9, 84505 Bratislava, Slovakia
| | - Dana Zubrikova
- Institute of Parasitology, Slovak Academy of Science, Kosice, Slovakia
| | - Maria Vögerl
- Comparative Tropical Medicine and Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Martin Pfeffer
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Frank T Hufert
- Department of Virology, University Medical Center, 37075 Göttingen, Germany
| | - Paolo M Zanotto
- Department of Microbiology, Biomedical Sciences Institute - ICB II University of São Paulo, 05508-000 São Paulo, Brazil
| | - Gerhard Dobler
- Bundeswehr Institute of Microbiology, 80937 Munich, Germany
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Norberg P, Roth A, Bergström T. Genetic recombination of tick-borne flaviviruses among wild-type strains. Virology 2013; 440:105-16. [PMID: 23510672 DOI: 10.1016/j.virol.2013.02.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 12/28/2012] [Accepted: 02/20/2013] [Indexed: 11/19/2022]
Abstract
Genetic recombination has been suggested to occur in mosquito-borne flaviviruses. In contrast, tick-borne flaviviruses have been thought to evolve in a clonal manner, although recent studies suggest that recombination occurs also for these viruses. We re-analyzed the data and found that previous conclusions on wild type recombination were probably falsely drawn due to misalignments of nucleotide sequences, ambiguities in GenBank sequences, or different laboratory culture histories suggestive of recombination events in laboratory. To evaluate if reliable predictions of wild type recombination of tick-borne flaviviruses can be made, we analyzed viral strains sequenced exclusively for this study, and other flavivirus sequences retrieved from GenBank. We detected genetic signals supporting recombination between viruses within the three clades of TBEV-Eu, TBEV-Sib and TBEV-Fe, respectively. Our results suggest that the tick-borne encephalitis viruses may undergo recombination under natural conditions, but that geographic barriers restrict most recombination events to involve only closely genetically related viruses.
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Affiliation(s)
- Peter Norberg
- Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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Clusteron structure of tick-borne encephalitis virus populations. INFECTION GENETICS AND EVOLUTION 2013. [DOI: 10.1016/j.meegid.2012.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Fajs L, Durmiši E, Knap N, Strle F, Avšič-Županc T. Phylogeographic characterization of tick-borne encephalitis virus from patients, rodents and ticks in Slovenia. PLoS One 2012. [PMID: 23185257 PMCID: PMC3502456 DOI: 10.1371/journal.pone.0048420] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is the most important arboviral agent causing infections of the central nervous system in central Europe. Previous studies have shown that TBEV exhibits pronounced genetic variability, which is often correlated to the geographical origin of TBEV. Genetic variability of TBEV has previously been studied predominantly in rodents and ticks, while information about the variability in patients is scarce. In order to understand the molecular relationships of TBEV between natural hosts, vectors and humans, as well as correlation between phylogenetic and geographical clustering, sequences of TBEV E and NS5 protein genes, were obtained by direct sequencing of RT-PCR products from TBE-confirmed patients as well as from rodents and ticks collected from TBE-endemic regions in Slovenia. A total of 27 partial E protein gene sequences representing 15 human, 4 rodent and 8 tick samples and 30 partial NS5 protein gene sequences representing 17 human, 5 rodent and 8 tick samples were obtained. The complete genome sequence of TBEV strain Ljubljana I was simultaneously obtained. Phylogenetic analysis of the E and NS5 protein gene sequences revealed a high degree of TBEV variability in patients, ticks and rodents. Furthermore, an evident correlation between geographical and phylogenetic clustering was shown that was independent of the TBEV host. Moreover, we show the presence of a possible recombination event in the TBEV genome obtained from a patient sample, which was supported with multiple recombination event detection methods. This is the first study that simultaneously analyzed the genetic relationships of directly sequenced TBEV samples from patients, ticks and rodents and provides the largest set of patient-derived TBEV sequences up to date. In addition, we have confirmed the geographical clustering of TBEV sequences in Slovenia and have provided evidence of a possible recombination event in the TBEV genome, obtained from a patient.
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Affiliation(s)
- Luka Fajs
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Emina Durmiši
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Franc Strle
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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Revisiting the clinal concept of evolution and dispersal for the tick-borne flaviviruses by using phylogenetic and biogeographic analyses. J Virol 2012; 86:8663-71. [PMID: 22674986 DOI: 10.1128/jvi.01013-12] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tick-borne flaviviruses (TBF) are widely dispersed across Africa, Europe, Asia, Oceania, and North America, and some present a significant threat to human health. Seminal studies on tick-borne encephalitis viruses (TBEV), based on partial envelope gene sequences, predicted a westward clinal pattern of evolution and dispersal across northern Eurasia, terminating in the British Isles. We tested this hypothesis using all available full-length open reading frame (ORF) TBF sequences. Phylogenetic analysis was consistent with current reports. However, linear and nonlinear regression analysis of genetic versus geographic distance combined with BEAST analysis identified two separate clines, suggesting that TBEV spread both east and west from a central point. In addition, BEAST analysis suggested that TBF emerged and dispersed more than 16,000 years ago, significantly earlier than previously predicted. Thus, climatic and ecological changes may have played a greater role in TBF dispersal than humans.
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40
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Complete genomic characterization of two tick-borne encephalitis viruses isolated from China. Virus Res 2012; 167:310-3. [PMID: 22659297 DOI: 10.1016/j.virusres.2012.05.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 05/20/2012] [Accepted: 05/22/2012] [Indexed: 10/28/2022]
Abstract
Tick-borne encephalitis (TBEV) is prevalent over a wide area of the Eurasian continent. TBE viruses cause severe encephalitis in humans, with serious sequelae, and have a significant impact on public health in these endemic regions. To gain insight into genetic evolution of tick-borne encephalitis virus (TBEV) in China, the complete genomic sequences of two TBEV strains Senzhang and MDJ01, which were isolated in 1953 and 2001 respectively, were characterized. The complete genome sequences of two strains were all consist 10,784 nucleotides and there are 364 nucleotides deletion in the 3' nontranslated region. Compared with other TBEV strains, homology range from 85.2% (Zausaev) to 99.6% (MDJ02 and MDJ03) on the level of nucleotide. Phylogenetic trees based on the complete genome, open reading frame and E gene nucleotide sequences all showed that the strains Senzhang and MDJ01 belong to Far-Eastern subtype and cluster with other Chinese TBEV strains. All these implied that TBEVs prevalent in China were highly conservative, other measurement should be taken to improve protective efficacy of present vaccine.
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