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Lamsal A, Edgar KS, Jenkins A, Renssen H, Kjaer LJ, Alfsnes K, Bastakoti S, Dieseth M, Klitgaard K, Lindstedt HEH, Paulsen KM, Vikse R, Korslund L, Kjelland V, Stuen S, Kjellander P, Christensson M, Teräväinen M, Jensen LM, Regmi M, Giri D, Marsteen L, Bødker R, Soleng A, Andreassen ÅK. Prevalence of tick-borne encephalitis virus in questing Ixodes ricinus nymphs in southern Scandinavia and the possible influence of meteorological factors. Zoonoses Public Health 2023; 70:473-484. [PMID: 37248739 DOI: 10.1111/zph.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/25/2023] [Accepted: 05/06/2023] [Indexed: 05/31/2023]
Abstract
Ixodes ricinus ticks are Scandinavia's main vector for tick-borne encephalitis virus (TBEV), which infects many people annually. The aims of the present study were (i) to obtain information on the TBEV prevalence in host-seeking I. ricinus collected within the Øresund-Kattegat-Skagerrak (ØKS) region, which lies in southern Norway, southern Sweden and Denmark; (ii) to analyse whether there are potential spatial patterns in the TBEV prevalence; and (iii) to understand the relationship between TBEV prevalence and meteorological factors in southern Scandinavia. Tick nymphs were collected in 2016, in southern Scandinavia, and screened for TBEV, using pools of 10 nymphs, with RT real-time PCR, and positive samples were confirmed with pyrosequencing. Spatial autocorrelation and cluster analysis was performed with Global Moran's I and SatScan to test for spatial patterns and potential local clusters of the TBEV pool prevalence at each of the 50 sites. A climatic analysis was made to correlate parameters such as minimum, mean and maximum temperature, relative humidity and saturation deficit with TBEV pool prevalence. The climatic data were acquired from the nearest meteorological stations for 2015 and 2016. This study confirms the presence of TBEV in 12 out of 30 locations in Denmark, where six were from Jutland, three from Zealand and two from Bornholm and Falster counties. In total, five out of nine sites were positive from southern Sweden. TBEV prevalence of 0.7%, 0.5% and 0.5%, in nymphs, was found at three sites along the Oslofjord (two sites) and northern Skåne region (one site), indicating a potential concern for public health. We report an overall estimated TBEV prevalence of 0.1% in questing I. ricinus nymphs in southern Scandinavia with a region-specific prevalence of 0.1% in Denmark, 0.2% in southern Sweden and 0.1% in southeastern Norway. No evidence of a spatial pattern or local clusters was found in the study region. We found a strong correlation between TBEV prevalence in ticks and relative humidity in Sweden and Norway, which might suggest that humidity has a role in maintaining TBEV prevalence in ticks. TBEV is an emerging tick-borne pathogen in southern Scandinavia, and we recommend further studies to understand the TBEV transmission potential with changing climate in Scandinavia.
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Affiliation(s)
- Alaka Lamsal
- Department of Natural Science and Environmental Health, The University of South-Eastern Norway, Bø, Norway
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristin Skarsfjord Edgar
- Department of Pest Control, Norwegian Institute of Public Health, Oslo, Norway
- Department of Microbiology, Norwegian Veterinary Institute, Ås, Norway
| | - Andrew Jenkins
- Department of Natural Science and Environmental Health, The University of South-Eastern Norway, Bø, Norway
| | - Hans Renssen
- Department of Natural Science and Environmental Health, The University of South-Eastern Norway, Bø, Norway
| | - Lene Jung Kjaer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Kristian Alfsnes
- Department of Bacteriology, Norwegian Institute of Public Health, Oslo, Norway
| | - Srijana Bastakoti
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Malene Dieseth
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Kirstine Klitgaard
- Department for Diagnostics and Scientific Advice, National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Katrine M Paulsen
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Rose Vikse
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Lars Korslund
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - Vivian Kjelland
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
- Research Unit, Sørlandet Hospital Health Enterprise, Kristiansand, Norway
| | - Snorre Stuen
- Department of Production Animal Clinical Sciences, Section of Small Ruminant Research, Norwegian University of Life Sciences, Sandnes, Norway
| | - Petter Kjellander
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden
| | - Madeleine Christensson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden
| | - Malin Teräväinen
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden
| | - Laura Mark Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Manoj Regmi
- Department of Data Science, Kristiania University College, Oslo, Norway
| | - Dhiraj Giri
- School of Arts, Kathmandu University, Dhulikhel, Nepal
| | | | - René Bødker
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Arnulf Soleng
- Department of Pest Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Åshild Kristine Andreassen
- Department of Natural Science and Environmental Health, The University of South-Eastern Norway, Bø, Norway
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
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Esser HJ, Lim SM, de Vries A, Sprong H, Dekker DJ, Pascoe EL, Bakker JW, Suin V, Franz E, Martina BEE, Koenraadt CJM. Continued Circulation of Tick-Borne Encephalitis Virus Variants and Detection of Novel Transmission Foci, the Netherlands. Emerg Infect Dis 2022; 28:2416-2424. [PMID: 36288572 PMCID: PMC9707572 DOI: 10.3201/eid2812.220552] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is an emerging pathogen that was first detected in ticks and humans in the Netherlands in 2015 (ticks) and 2016 (humans). To learn more about its distribution and prevalence in the Netherlands, we conducted large-scale surveillance in ticks and rodents during August 2018-September 2020. We tested 320 wild rodents and >46,000 ticks from 48 locations considered to be at high risk for TBEV circulation. We found TBEV RNA in 3 rodents (0.9%) and 7 tick pools (minimum infection rate 0.02%) from 5 geographically distinct foci. Phylogenetic analyses indicated that 3 different variants of the TBEV-Eu subtype circulate in the Netherlands, suggesting multiple independent introductions. Combined with recent human cases outside known TBEV hotspots, our data demonstrate that the distribution of TBEV in the Netherlands is more widespread than previously thought.
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Zakotnik S, Knap N, Bogovič P, Zorec TM, Poljak M, Strle F, Avšič-Županc T, Korva M. Complete Genome Sequencing of Tick-Borne Encephalitis Virus Directly from Clinical Samples: Comparison of Shotgun Metagenomic and Targeted Amplicon-Based Sequencing. Viruses 2022; 14:v14061267. [PMID: 35746738 PMCID: PMC9231111 DOI: 10.3390/v14061267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/30/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
The clinical presentation of tick-borne encephalitis virus (TBEV) infection varies from asymptomatic to severe meningoencephalitis or meningoencephalomyelitis. The TBEV subtype has been suggested as one of the most important risk factors for disease severity, but TBEV genetic characterization is difficult. Infection is usually diagnosed in the post-viremic phase, and so relevant clinical samples of TBEV are extremely rare and, when present, are associated with low viral loads. To date, only two complete TBEV genomes sequenced directly from patient clinical samples are publicly available. The aim of this study was to develop novel protocols for the direct sequencing of the TBEV genome, enabling studies of viral genetic determinants that influence disease severity. We developed a novel oligonucleotide primer scheme for amplification of the complete TBEV genome. The primer set was tested on 21 clinical samples with various viral loads and collected over a 15-year period using the two most common sequencing platforms. The amplicon-based strategy was compared to direct shotgun sequencing. Using the novel primer set, we successfully obtained nearly complete TBEV genomes (>90% of genome) from all clinical samples, including those with extremely low viral loads. Comparison of consensus sequences of the TBEV genome generated using the novel amplicon-based strategy and shotgun sequencing showed no difference. We conclude that the novel primer set is a powerful tool for future studies on genetic determinants of TBEV that influence disease severity and will lead to a better understanding of TBE pathogenesis.
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Affiliation(s)
- Samo Zakotnik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Petra Bogovič
- Department of Infectious Diseases, Ljubljana University Medical Center, SI-1000 Ljubljana, Slovenia; (P.B.); (F.S.)
| | - Tomaž Mark Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Franc Strle
- Department of Infectious Diseases, Ljubljana University Medical Center, SI-1000 Ljubljana, Slovenia; (P.B.); (F.S.)
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (S.Z.); (N.K.); (T.M.Z.); (M.P.); (T.A.-Ž.)
- Correspondence:
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Mohamed WMA, Moustafa MAM, Kelava S, Barker D, Matsuno K, Nonaka N, Shao R, Mans BJ, Barker SC, Nakao R. Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification. Ticks Tick Borne Dis 2021; 13:101832. [PMID: 34607157 DOI: 10.1016/j.ttbdis.2021.101832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/02/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022]
Abstract
High-throughput sequencing (HTS) technology has profoundly been involved in sequencing whole genomes of several organisms in a fast and cost-effective manner. Although HTS provides an alternative biomonitoring method to the time-consuming and taxonomy-expertise dependent morphological approach, still we cannot rule out the possibility of the impediment and misidentification biases. In this article we aim to retrieve whole mitochondrial genome (mitogenome) sequences from publicly available raw sequencing data for phylogenetic comparison of Ixodes persulcatus. For this comparison, we sequenced whole mitogenomes of four I. persulcatus ticks from Japan and constructed mitogenomes from raw sequencing data of 74 I. persulcatus ticks from China. Bayesian phylogenetic trees were inferred by the concatenated fifteen mitochondrial genes. We further tested our results by the phylogenetic analysis of cytochrome c oxidase subunit 1 (cox1) gene and internal transcribed spacer 2 (ITS2) sequences. Our findings showed that 70 constructed mitogenomes from China were clustered with the sequenced four mitogenomes of I. persulcatus from Japan. We also revealed that mitogenome sequences retrieved from two data sets CRR142297 and CRR142298 were clustered with Ixodes nipponensis. Moreover, other two mitogenome sequences from CRR142310 and CRR142311 formed a clade with Ixodes pavlovskyi. The phylogenetic analysis of cox1 gene and ITS2 sequences confirmed the identification errors of these four samples. The overall phylogenetics in our study concluded that accurate morphological identification is necessary before implementing HTS to avoid any misidentification biases.
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Affiliation(s)
- Wessam Mohamed Ahmed Mohamed
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Japan; Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Hokkaido 001-0020, Japan
| | - Mohamed Abdallah Mohamed Moustafa
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Japan; Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt.
| | - Samuel Kelava
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dayana Barker
- School of Veterinary Science, University of Queensland, Gatton Qld, 4343, Australia
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan; One Health Research Center, Hokkaido University, Sapporo 060-0818, Japan
| | - Nariaki Nonaka
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Japan
| | - Renfu Shao
- School of Science, Technology and Engineering, GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland 4558, Australia
| | - Ben J Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council-Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa; Department of Life and Consumer Sciences, University of South Africa, South Africa; Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria 0110, South Africa
| | - Stephen C Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Japan.
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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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