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Schilling M, Golding M, Jones BP, Mansfield KL, Gandy S, Medlock J, Johnson N. Sequences Related to Chimay Rhabdovirus Are Widely Distributed in Ixodes ricinus Ticks across England and Wales. Viruses 2024; 16:504. [PMID: 38675847 PMCID: PMC11054956 DOI: 10.3390/v16040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Ticks are the main arthropod vector of pathogens to humans and livestock in the British Isles. Despite their role as a vector of disease, many aspects of tick biology, ecology, and microbial association are poorly understood. To address this, we investigated the composition of the microbiome of adult and nymphal Ixodes ricinus ticks. The ticks were collected on a dairy farm in Southwest England and RNA extracted for whole genome sequencing. Sequences were detected from a range of microorganisms, particularly tick-associated viruses, bacteria, and nematodes. A majority of the viruses were attributed to phlebo-like and nairo-like virus groups, demonstrating a high degree of homology with the sequences present in I. ricinus from mainland Europe. A virus sharing a high sequence identity with Chimay rhabdovirus, previously identified in ticks from Belgium, was detected. Further investigations of I. ricinus ticks collected from additional sites in England and Wales also identified Chimay rhabdovirus viral RNA with varying prevalence in all tick populations. This suggests that Chimay rhabdovirus has a wide distribution and highlights the need for an extended exploration of the tick microbiome in the United Kingdom (UK).
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Affiliation(s)
- Mirjam Schilling
- Vector-Borne Diseases Workgroup, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, UK (N.J.)
| | - Megan Golding
- Rabies and Viral Zoonoses Workgroup, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, UK
| | - Ben P. Jones
- Vector-Borne Diseases Workgroup, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, UK (N.J.)
| | - Karen L. Mansfield
- Vector-Borne Diseases Workgroup, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, UK (N.J.)
| | - Sara Gandy
- Medical Entomology and Zoonoses Ecology, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Jolyon Medlock
- Medical Entomology and Zoonoses Ecology, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Nicholas Johnson
- Vector-Borne Diseases Workgroup, Animal and Plant Health Agency, Woodham Lane, Addlestone KT15 3NB, UK (N.J.)
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
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Ogola EO, Kopp A, Bastos ADS, Slothouwer I, Omoga DCA, Osalla J, Sang R, Torto B, Junglen S, Tchouassi DP. Phlebovirus diversity in ticks from livestock in arid ecologies in Kenya. Ticks Tick Borne Dis 2023; 14:102087. [PMID: 36459866 DOI: 10.1016/j.ttbdis.2022.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/11/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
Abstract
Phleboviruses are emerging pathogens of public health importance. However, their association with ticks is poorly described, particularly in Africa. Here, adult ticks infesting cattle, goats and sheep were collected in two dryland pastoralist ecosystems of Kenya (Baringo and Kajiado counties) and were screened for infection with phleboviruses. Ticks mainly belonged to the species Rhipicephalus appendiculatus, Hyalomma impeltatum, and Hyalomma rufipes. A fragment of the RNA-dependent RNA polymerase (RdRp) gene was identified in thirty of 671 tick pools, of which twenty-nine were from livestock sampled in Baringo county. Phylogenetic analyses revealed that twenty-five sequences were falling in three clades within the group of tick-associated phleboviruses. The sequences of the three clades showed nucleotide distances 8%, 19% and 22%, respectively, to previously known viruses suggesting that these sequence fragments may belong to three distinct viruses. Viruses of the group of tick-associated phleboviruses have been found in several countries and continents but so far have not been associated with disease in humans or animals. In addition, five sequences were found to group with the sandfly-associated phleboviruses Bogoria virus, Perkerra virus and Ntepes virus recently detected in the same region. Further studies are needed to investigate the transmission and maintenance cycles of these viruses, as well as to assess their potential to infect vertebrates.
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Affiliation(s)
- Edwin O Ogola
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya; Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria 0028, South Africa
| | - Anne Kopp
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Armanda D S Bastos
- Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria 0028, South Africa
| | - Inga Slothouwer
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Dorcus C A Omoga
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Josephine Osalla
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya; Department of Zoology and Entomology, University of Pretoria, Private Bag 20, Pretoria 0028, South Africa
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany.
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya.
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Bourdin A, Bord S, Durand J, Galon C, Moutailler S, Scherer-Lorenzen M, Jactel H. Forest Diversity Reduces the Prevalence of Pathogens Transmitted by the Tick Ixodes ricinus. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.891908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tick-borne diseases represent the majority of vector-borne human diseases in Europe, with Ixodes ricinus, mostly present in forests, as the main vector. Studies show that vertebrate hosts diversification would decrease the prevalence of these pathogens. However, it is not well known whether habitat diversity can have similar impact on ticks and their infection rates. We measured the presence and abundance of different stages of I. ricinus, and the prevalence of associated pathogens in a large-scale forest experiment in which we manipulated tree diversity and moisture level. We showed that larval abundance was influenced by tree species identity, with larvae being more present in pine plots than in oak plots, while nymph abundance increased with canopy tree density. The proportion of Borrelia burgdorferi s.l.-infected nymphs decreased with increasing tree diversity. Our findings suggest that tree overstorey composition, structure and diversity, can affect tick abundance and pathogen prevalence. They support the idea that forest habitats may have “diluting” or “amplifying” effects on tick-borne diseases with direct relevance for human health.
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Klimentov AS, Belova OA, Kholodilov IS, Butenko AM, Bespyatova LA, Bugmyrin SV, Chernetsov N, Ivannikova AY, Kovalchuk IV, Nafeev AA, Oorzhak ND, Pilikova OM, Polienko AE, Purmak KA, Romanenko EN, Romanova LI, Saryglar AA, Solomashchenko NI, Shamsutdinov AF, Vakalova EV, Lukashev AN, Karganova GG, Gmyl AP. Phlebovirus sequences detected in ticks collected in Russia: Novel phleboviruses, distinguishing criteria and high tick specificity. INFECTION GENETICS AND EVOLUTION 2020; 85:104524. [PMID: 32891876 DOI: 10.1016/j.meegid.2020.104524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 10/23/2022]
Abstract
Phlebovirus is an abundant and rather heterogeneous genus within the Phenuiviridae family (order Bunyavirales). The genus Phlebovirus is divided into two antigenic complexes, which also correspond to the main vector: sandflies/mosquitoes and ticks. Previously, only sandfly/mosquito-borne phleboviruses were associated with human disease, such as Rift Valley fever virus, Toscana virus, Sicilian and Naples Sandfly fever viruses and others. Until recently, tick-borne phleboviruses were not considered as human pathogens. After the discovery of severe fever with thrombocytopenia syndrome, interest to tick-borne phleboviruses has increased dramatically. In the last decade, many novel phleboviruses have been reported in different regions. Despite this, the diversity, ecology and pathogenicity of these viruses still remain obscure. The aim of this work was to study the diversity of phleboviruses in ticks collected in several regions of Russia. We used pan-phlebovirus RT-PCR assays based on multiple degenerate primers targeting the polymerase gene fragment. Arthropod specimens were collected from 2005 to 2018. A total of 5901 Ixodidae ticks combined into 1116 pools were screened. A total of 160 specific amplicons were produced. In three cases RT-PCR assays amplified two distinct viruses from same tick pools. Direct sequencing of amplicons and subsequent phylogenetic analysis revealed twelve representatives of divergent phlebovirus groups. Based on the distribution of pairwise nucleotide sequence identity values, a cut-off (88%) was suggested to distinguish tick-borne phleboviruses. According to this provisional criterion, two viruses found here could be termed novel, while ten viruses have been described in previous studies. Detected phleboviruses demonstrated almost perfect specificity to a tick species or, at least, a genus. The same pattern was observed for tick-borne phleboviruses found in different studies around the world. Viruses that grouped together on a phylogenetic tree and differed less than this sequence identity threshold suggested above were hosted by ticks from the same genus.
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Affiliation(s)
- Alexander S Klimentov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Gamaleya Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow 123098, Russia.
| | - Oxana A Belova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Ivan S Kholodilov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Alexander M Butenko
- Gamaleya Research Center for Epidemiology and Microbiology of the Ministry of Health of the Russian Federation, Moscow 123098, Russia
| | - Liubov A Bespyatova
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk 185910, Russia
| | - Sergey V Bugmyrin
- Institute of Biology, Karelian Research Centre of RAS, Petrozavodsk 185910, Russia
| | - Nikita Chernetsov
- Zoological Institute of RAS, St. Petersburg 199034, Russia; Dept. Vertebrate Zoology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Anna Y Ivannikova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Irina V Kovalchuk
- Office of Rospotrebnadzor in the Stavropol Territory, Stavropol 355008, Russia; Stavropol State Medical University, Stavropol 355017, Russia
| | - Alexander A Nafeev
- Center for Hygiene and Epidemiology in the Ulyanovsk Region, Ulyanovsk 432005, Russia
| | | | - Olga M Pilikova
- Black Sea Anti-Plague Station of Rospotrebnadzor, Novorossiysk 353919, Russia
| | - Alexandra E Polienko
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
| | - Kristina A Purmak
- Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Evgeniya N Romanenko
- Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Lidiya Iu Romanova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Institute for Translational Medicine and Biotechnology, Sechenov University, Moscow 119991, Russia
| | | | - Nataliya I Solomashchenko
- Stavropol State Medical University, Stavropol 355017, Russia; Center for Hygiene and Epidemiology in the Stavropol Kray, Stavropol 355008, Russia
| | - Anton F Shamsutdinov
- Kazan Scientific Research Institute of Epidemiology and Microbiology of Rospotrebnadzor, Kazan 420015, Russia
| | - Elena V Vakalova
- Astrakhan Anti-Plague Station of Rospotrebnadzor, Astrakhan 414000, Russia
| | - Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow 119435, Russia
| | - Galina G Karganova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia; Institute for Translational Medicine and Biotechnology, Sechenov University, Moscow 119991, Russia
| | - Anatoly P Gmyl
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, Moscow 108819, Russia
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5
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Novel Tick Phlebovirus Genotypes Lacking Evidence for Vertebrate Infections in Anatolia and Thrace, Turkey. Viruses 2019; 11:v11080703. [PMID: 31374842 PMCID: PMC6723390 DOI: 10.3390/v11080703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 01/23/2023] Open
Abstract
We screened ticks and human clinical specimens to detect and characterize tick phleboviruses and pathogenicity in vertebrates. Ticks were collected at locations in Istanbul (Northwest Anatolia, Thrace), Edirne, Kırklareli, and Tekirdağ (Thrace), Mersin (Mediterranean Anatolia), Adiyaman and Şanlıurfa (Southeastern Anatolia) provinces from 2013-2018 and were analyzed following morphological identification and pooling. Specimens from individuals with febrile disease or meningoencephalitic symptoms of an unknown etiology were also evaluated. The pools were screened via generic tick phlebovirus amplification assays and products were sequenced. Selected pools were used for cell culture and suckling mice inoculations and next generation sequencing (NGS). A total of 7492 ticks were screened in 609 pools where 4.2% were positive. A phylogenetic sequence clustering according to tick species was observed. No human samples were positive. NGS provided near-complete viral replicase coding sequences in three pools. A comprehensive analysis revealed three distinct, monophyletic virus genotypes, comprised of previously-described viruses from Anatolia and the Balkans, with unique fingerprints in conserved amino acid motifs in viral replicase. A novel tick phlebovirus group was discovered circulating in the Balkans and Turkey, with at least three genotypes or species. No evidence for replication in vertebrates or infections in clinical cases could be demonstrated.
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Petersen A, Rosenstierne MW, Rasmussen M, Fuursted K, Nielsen HV, O'Brien Andersen L, Bødker R, Fomsgaard A. Field samplings of Ixodes ricinus ticks from a tick-borne encephalitis virus micro-focus in Northern Zealand, Denmark. Ticks Tick Borne Dis 2019; 10:1028-1032. [PMID: 31151922 DOI: 10.1016/j.ttbdis.2019.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/25/2019] [Accepted: 05/17/2019] [Indexed: 12/01/2022]
Abstract
In 2008-2009 a tick-borne encephalitis virus (TBEV) micro-focus was detected in Northern Zealand, Denmark. No new cases of TBE with an epidemiological link to Northern Zealand has been reported since. Here we undertook to investigate Ixodes ricinus ticks from this endemic micro-focus in 2016 and 2017. In addition to TBEV, I. ricinus ticks may host other pathogens that include Borrelia spp., Babesia spp., Rickettsia spp. and Neoehrlichia mikurensis, together with various endosymbiont microorganisms. To detect multiple organisms we used a metagenomics PanVirus microarray and next-generation sequencing to examine the persistence and evolution of other emerging viruses, bacteria and parasites. Here we report the rise and fall of the Danish TBEV micro-focus in Northern Zealand. However, we identify for the first time in Danish I. ricinus ticks the presence of Uukuniemi virus in addition to a tick-borne phlebovirus and a range of bacteria.
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Affiliation(s)
- Andreas Petersen
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Solna, Sweden; Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnosis, Statens Serum Institut, Copenhagen, Denmark; Bacteria, Parasites and Fungi, Infection Preparedness, Statens Serum Institut, Copenhagen, Denmark.
| | - Maiken Worsøe Rosenstierne
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnosis, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnosis, Statens Serum Institut, Copenhagen, Denmark
| | - Kurt Fuursted
- Bacteria, Parasites and Fungi, Infection Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Vedel Nielsen
- Bacteria, Parasites and Fungi, Infection Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Lee O'Brien Andersen
- Bacteria, Parasites and Fungi, Infection Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - René Bødker
- DTU National Veterinary Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnosis, Statens Serum Institut, Copenhagen, Denmark; Infectious Disease Research Unit, Clinical Institute, University of Southern Denmark, Odense, Denmark
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7
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Pimentel V, Afonso R, Nunes M, Vieira ML, Bravo-Barriga D, Frontera E, Martinez M, Pereira A, Maia C, Paiva-Cardoso MDN, Freitas FB, Abecasis AB, Parreira R. Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences. Ticks Tick Borne Dis 2019; 10:942-948. [PMID: 31078467 DOI: 10.1016/j.ttbdis.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 11/27/2022]
Abstract
The large diversity of new tick-borne phleboviruses, and the negative impacts of the virulent viruses on human/animal health have led to a growing interest in their analysis. In this report, new insights are brought out into the diversity of putative phleboviruses circulating in Portugal (both the continental territory and the islands of São Miguel, in the Azores, and Madeira), as well as in the Spanish western regions of Extremadura and Castilla and León. Phlebovirus sequences were frequently detected (L-segment) from both questing and feeding ticks, but especially in Rhipicephalus sanguineus sensu lato (s.l.) specimens. These sequences were detected in adult ticks, as well as nymphs and eggs, supporting the hypothesis of viral maintenance by vertical transmission. Though multiple genetic groups could be identified in phylogenetic trees (AnLuc, KarMa, RiPar virus 1, and Spanish group 1 and 2), all the sequences from Portugal and Spain shared common ancestry with other viral sequence obtained from samples collected over a large geographic coverage. Spatiotemporal analysis placed Middle-East as the geographic origin of the most recent common ancestor (MRCA) of all phleboviruses analysed in the present study. More recent viral transitions might include migrations from Spain to continental Portugal, and from there to the Portuguese Islands. Our findings suggest that the time of the MRCA of phleboviruses was dated around 225 years ago [95% HPD: 124-387 year before the last sampling date].
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Affiliation(s)
- Victor Pimentel
- Unidade de Saúde Pública Internacional e Bioestatística, Instituto de Higiene e Medicina Tropical (IHTM)/Universidade Nova de Lisboa (UNL), and Global Health and Tropical Medicine (GHTM) research center, Lisboa, Portugal
| | - Rita Afonso
- Unidade de Microbiologia Médica, (IHMT/UNL, and GHTM), Oeiras, Portugal
| | - Mónica Nunes
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | | | - Daniel Bravo-Barriga
- Parasitology and Parasitic Diseases, Animal Health Department, Veterinary Faculty, University of Extremadura, Cáceres, Spain
| | - Eva Frontera
- Parasitology and Parasitic Diseases, Animal Health Department, Veterinary Faculty, University of Extremadura, Cáceres, Spain
| | - Manuel Martinez
- Parasitology and Parasitic Diseases, Animal Health Department, Veterinary Faculty, University of Extremadura, Cáceres, Spain
| | - André Pereira
- Unidade de Parasitologia Médica (IHMT/UNL, and GHTM), Lisboa, Portugal
| | - Carla Maia
- Unidade de Parasitologia Médica (IHMT/UNL, and GHTM), Lisboa, Portugal
| | - Maria das Neves Paiva-Cardoso
- Departmento de Ciências Veterinárias, Universidade de Trás-os-Montes e Alto Douro (UTAD) and Centro de Investigação e Tecnologias Agroambientais e Biológicas (CITAB), Vila Real, Portugal
| | | | - Ana B Abecasis
- Unidade de Saúde Pública Internacional e Bioestatística, Instituto de Higiene e Medicina Tropical (IHTM)/Universidade Nova de Lisboa (UNL), and Global Health and Tropical Medicine (GHTM) research center, Lisboa, Portugal
| | - Ricardo Parreira
- Unidade de Microbiologia Médica, (IHMT/UNL, and GHTM), Oeiras, Portugal.
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Ohlendorf V, Marklewitz M, Kopp A, Yordanov S, Drosten C, Junglen S. Huge diversity of phleboviruses in ticks from Strandja Nature Park, Bulgaria. Ticks Tick Borne Dis 2019; 10:697-703. [DOI: 10.1016/j.ttbdis.2019.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 10/27/2022]
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9
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Qiu Y, Abe T, Nakao R, Satoh K, Sugimoto C. Viral population analysis of the taiga tick, Ixodes persulcatus, by using Batch Learning Self-Organizing Maps and BLAST search. J Vet Med Sci 2019; 81:401-410. [PMID: 30674747 PMCID: PMC6451905 DOI: 10.1292/jvms.18-0483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ticks transmit a wide range of viral, bacterial, and protozoal pathogens, which are often zoonotic. Several novel tick-borne viral pathogens have been reported during the past few years.
The aim of this study was to investigate a diversity of tick viral populations, which may contain as-yet unidentified viruses, using a combination of high throughput pyrosequencing and Batch
Learning Self-Organizing Map (BLSOM) program, which enables phylogenetic estimation based on the similarity of oligonucleotide frequencies. DNA/cDNA prepared from virus-enriched fractions
obtained from Ixodes persulcatus ticks was pyrosequenced. After de novo assembly, contigs were cataloged by the BLSOM program. In total 41 different viral
families and order including those previously associated with human and animal diseases such as Bunyavirales, Flaviviridae, and Reoviridae,
were detected. Therefore, our strategy is applicable for viral population analysis of other arthropods of medical and veterinary importance, such as mosquitos and lice. The results lead to
the contribution to the prediction of emerging tick-borne viral diseases. A sufficient understanding of tick viral populations will also empower to analyze and understand tick biology
including vector competency and interactions with other pathogens.
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Affiliation(s)
- Yongjin Qiu
- Division of Collaboration and Education, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020 Japan.,Hokudai Center for Zoonosis Control in Zambia, the University of Zambia, Lusaka, 10101 Zambia
| | - Takashi Abe
- Graduate School of Science and Technology, Niigata University, Ikarashi 2 no-cho 8050, Nishi-ku, Niigata, Niigata 950-2181 Japan
| | - Ryo Nakao
- Unit of Risk Analysis and Management, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020 Japan.,Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido 060-0818 Japan
| | - Kenro Satoh
- Graduate School of Science and Technology, Niigata University, Ikarashi 2 no-cho 8050, Nishi-ku, Niigata, Niigata 950-2181 Japan
| | - Chihiro Sugimoto
- Division of Collaboration and Education, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020 Japan.,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0020 Japan
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10
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Torii S, Matsuno K, Qiu Y, Mori-Kajihara A, Kajihara M, Nakao R, Nao N, Okazaki K, Sashika M, Hiono T, Okamatsu M, Sakoda Y, Ebihara H, Takada A, Sawa H. Infection of newly identified phleboviruses in ticks and wild animals in Hokkaido, Japan indicating tick-borne life cycles. Ticks Tick Borne Dis 2018; 10:328-335. [PMID: 30478009 DOI: 10.1016/j.ttbdis.2018.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/31/2018] [Accepted: 11/12/2018] [Indexed: 11/25/2022]
Abstract
Recent discoveries of tick-borne pathogens have raised public health concerns on tick-borne infectious diseases and emphasize the need to assess potential risks of unrecognized tick-borne pathogens. First, to determine the existence of tick-borne phleboviruses (TBPVs), genetic surveillance of phleboviruses in ticks was conducted mainly in Hokkaido, the northernmost island in Japan from 2013 to 2015. Genes of two TBPVs, previously reported as Mukawa virus (MKWV) and a newly identified relative of MKWV, Kuriyama virus (KURV), were detected and the viruses were isolated from Ixodes persulcatus collected in Hokkaido, but not in I. persulcatus collected from other areas of Japan. These viruses were phylogenetically and antigenically similar to each other. Next, to investigate the infection of MKWV in mammals, serum samples from wildlife captured in Hokkaido from 2007 to 2011 were used for serological screening. Neutralizing antibodies against MKWV were detected in both Yezo-deer (Cervus nippon yesoensis) (2/50) and raccoons (Procyon lotor) (16/64). However, no infectious MKWV was recovered from laboratory mice in experimental infections, though viral RNAs were detected in their tissues. Thus, MKWV and KURV may maintain tick-mammalian life cycles in Hokkaido, suggesting their potential as causative agents of tick-borne diseases in mammals.
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Affiliation(s)
- Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Keita Matsuno
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan.
| | - Yongjin Qiu
- Division of Collaboration and Education, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Akina Mori-Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Naganori Nao
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Katsunori Okazaki
- Laboratory of Microbiology and Immunology, Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Mariko Sashika
- Laboratory of Wildlife Biology and Medicine, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Takahiro Hiono
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan; Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ayato Takada
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan; Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan; Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia; Global Virus Network, Baltimore, USA
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11
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Ehrmann S, Ruyts SC, Scherer-Lorenzen M, Bauhus J, Brunet J, Cousins SAO, Deconchat M, Decocq G, De Frenne P, De Smedt P, Diekmann M, Gallet-Moron E, Gärtner S, Hansen K, Kolb A, Lenoir J, Lindgren J, Naaf T, Paal T, Panning M, Prinz M, Valdés A, Verheyen K, Wulf M, Liira J. Habitat properties are key drivers of Borrelia burgdorferi (s.l.) prevalence in Ixodes ricinus populations of deciduous forest fragments. Parasit Vectors 2018; 11:23. [PMID: 29310722 PMCID: PMC5759830 DOI: 10.1186/s13071-017-2590-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/13/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The tick Ixodes ricinus has considerable impact on the health of humans and other terrestrial animals because it transmits several tick-borne pathogens (TBPs) such as B. burgdorferi (sensu lato), which causes Lyme borreliosis (LB). Small forest patches of agricultural landscapes provide many ecosystem services and also the disservice of LB risk. Biotic interactions and environmental filtering shape tick host communities distinctively between specific regions of Europe, which makes evaluating the dilution effect hypothesis and its influence across various scales challenging. Latitude, macroclimate, landscape and habitat properties drive both hosts and ticks and are comparable metrics across Europe. Therefore, we instead assess these environmental drivers as indicators and determine their respective roles for the prevalence of B. burgdorferi in I. ricinus. METHODS We sampled I. ricinus and measured environmental properties of macroclimate, landscape and habitat quality of forest patches in agricultural landscapes along a European macroclimatic gradient. We used linear mixed models to determine significant drivers and their relative importance for nymphal and adult B. burgdorferi prevalence. We suggest a new prevalence index, which is pool-size independent. RESULTS During summer months, our prevalence index varied between 0 and 0.4 per forest patch, indicating a low to moderate disservice. Habitat properties exerted a fourfold larger influence on B. burgdorferi prevalence than macroclimate and landscape properties combined. Increasingly available ecotone habitat of focal forest patches diluted and edge density at landscape scale amplified B. burgdorferi prevalence. Indicators of habitat attractiveness for tick hosts (food resources and shelter) were the most important predictors within habitat patches. More diverse and abundant macro- and microhabitat had a diluting effect, as it presumably diversifies the niches for tick-hosts and decreases the probability of contact between ticks and their hosts and hence the transmission likelihood. CONCLUSIONS Diluting effects of more diverse habitat patches would pose another reason to maintain or restore high biodiversity in forest patches of rural landscapes. We suggest classifying habitat patches by their regulating services as dilution and amplification habitat, which predominantly either decrease or increase B. burgdorferi prevalence at local and landscape scale and hence LB risk. Particular emphasis on promoting LB-diluting properties should be put on the management of those habitats that are frequently used by humans. In the light of these findings, climate change may be of little concern for LB risk at local scales, but this should be evaluated further.
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Affiliation(s)
- Steffen Ehrmann
- Geobotany, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Sanne C. Ruyts
- Forest & Nature Lab, Ghent University, Geraardsbergsesteenweg 267, B-9090 Melle-Gontrode, Belgium
| | | | - Jürgen Bauhus
- Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacherstr. 4, 79106 Freiburg, Germany
| | - Jörg Brunet
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Box 49, SE-230 53 Alnarp, Sweden
| | - Sara A. O. Cousins
- Landscape Ecology, Department of Geography and Quaternary Geology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc Deconchat
- DYNAFOR, Université de Toulouse, INRA, INPT, Chemin de Borde Rouge, CS 52627, F-31326 Castanet, France
| | - Guillaume Decocq
- UR “Ecologie et Dynamique des Systèmes Anthropisés” (EDYSAN, FRE 3498 CNRS-UPJV), Jules Verne University of Picardie, 1 rue des Louvels, F-80037 Amiens Cedex 1, France
- UF PRiMAX, Clinical Pharmacology Department, CHU Amiens-Picardie, Amiens, France
| | - Pieter De Frenne
- Forest & Nature Lab, Ghent University, Geraardsbergsesteenweg 267, B-9090 Melle-Gontrode, Belgium
- Department of Plant Production, Ghent University, Proefhoevestraat 22, BE-9090 Melle, Belgium
| | - Pallieter De Smedt
- Forest & Nature Lab, Ghent University, Geraardsbergsesteenweg 267, B-9090 Melle-Gontrode, Belgium
| | - Martin Diekmann
- Faculty of Biology/Chemistry (FB 02), Institute of Ecology, Vegetation Ecology and Conservation Biology, University of Bremen, Leobener Str. 5, 28359 Bremen, Germany
| | - Emilie Gallet-Moron
- UR “Ecologie et Dynamique des Systèmes Anthropisés” (EDYSAN, FRE 3498 CNRS-UPJV), Jules Verne University of Picardie, 1 rue des Louvels, F-80037 Amiens Cedex 1, France
| | - Stefanie Gärtner
- Faculty of Environment and Natural Resources, University of Freiburg, Tennenbacherstr. 4, 79106 Freiburg, Germany
- Black Forest National Park, Kniebisstraße 67, 77740 Bad Peterstal-Griesbach, Germany
| | - Karin Hansen
- Natural Resources & Environmental Effects, IVL Swedish Environmental Research Institute, Box 210 60, SE-100 31 Stockholm, Sweden
| | - Annette Kolb
- Faculty of Biology/Chemistry (FB 02), Institute of Ecology, Vegetation Ecology and Conservation Biology, University of Bremen, Leobener Str. 5, 28359 Bremen, Germany
| | - Jonathan Lenoir
- UR “Ecologie et Dynamique des Systèmes Anthropisés” (EDYSAN, FRE 3498 CNRS-UPJV), Jules Verne University of Picardie, 1 rue des Louvels, F-80037 Amiens Cedex 1, France
| | - Jessica Lindgren
- Landscape Ecology, Department of Geography and Quaternary Geology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Tobias Naaf
- Institute of Land Use Systems, Leibniz-ZALF (e.V.), Eberswalder Str. 84, 15374 Müncheberg, Germany
| | - Taavi Paal
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
| | - Marcus Panning
- Institute of Virology, University Medical Center Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Maren Prinz
- Institute of Virology, University Medical Center Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany
| | - Alicia Valdés
- UR “Ecologie et Dynamique des Systèmes Anthropisés” (EDYSAN, FRE 3498 CNRS-UPJV), Jules Verne University of Picardie, 1 rue des Louvels, F-80037 Amiens Cedex 1, France
| | - Kris Verheyen
- Forest & Nature Lab, Ghent University, Geraardsbergsesteenweg 267, B-9090 Melle-Gontrode, Belgium
| | - Monika Wulf
- Institute of Land Use Systems, Leibniz-ZALF (e.V.), Eberswalder Str. 84, 15374 Müncheberg, Germany
| | - Jaan Liira
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, EE-51005 Tartu, Estonia
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