{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T06:36:10Z","timestamp":1769236570332,"version":"3.49.0"},"reference-count":42,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,22]],"date-time":"2025-09-22T00:00:00Z","timestamp":1758499200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Ticks are important parasites of economic and public health because of their ability to transmit zoonotic diseases. Tick-borne encephalitis virus (TBEV), now officially Orthoflavivirus encephalitidis, is a Flavivirus with five main subtypes of which three, the European (TBEV-EU), the Siberian (TBEV-Sib), and the Far-Eastern subtypes (TBEV-FE), are supposedly circulate in Latvia. Several hard tick species are involved in TBEV circulation and transmission in nature. This study set out to describe the genetic landscape of TBEV subtypes in Latvian tick populations. In 2019 and 2021 to 2023, a total of 3026 ticks were collected in three Latvian regions, with Ixodes ricinus as the dominant species (2822 specimens), followed by Ixodes persulcatus (200 specimens) and Dermacentor reticulatus (4 specimens). Ticks were morphologically identified, pooled, and screened for TBEV RNA by RT-qPCR. TBEV of positive tick pools were isolated and genetically characterized by genome sequencing. Our study demonstrates the prevalence of two TBEV subtypes in Latvia with specific spatial patterning. In the sympatric Vidzeme region, these subtypes display a preferential species association of TBEV-EU with Ixodes ricinus and TBEV-Sib with Ixodes persulcatus. Phylogeographic analysis suggests independent introductions of multiple genotypes from both subtypes. Further investigations are necessary to better understand the natural transmission and the medical importance of these TBEVs.<\/jats:p>","DOI":"10.3390\/pathogens14090950","type":"journal-article","created":{"date-parts":[[2025,9,22]],"date-time":"2025-09-22T13:04:44Z","timestamp":1758546284000},"page":"950","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Distribution and Genotypic Landscape of Tick-Borne Encephalitis Virus in Ticks from Latvia from 2019 to 2023"],"prefix":"10.3390","volume":"14","author":[{"given":"Lidia","family":"Chitimia-Dobler","sequence":"first","affiliation":[{"name":"Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Institute of Immunology, Infection and Pandemic Research IIP, 80799 Munich, Germany"},{"name":"Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7461-293X","authenticated-orcid":false,"given":"Gerhard","family":"Dobler","sequence":"additional","affiliation":[{"name":"Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany"},{"name":"Parasitology Unit, Institute of Zoology, University of Hohenheim, 70599 Stuttgart, Germany"},{"name":"Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of LMU, 80802 Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2166-0716","authenticated-orcid":false,"given":"Daniel","family":"Lang","sequence":"additional","affiliation":[{"name":"Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antra","family":"Bormane","sequence":"additional","affiliation":[{"name":"Unit Epidemiology, Centre for Disease Prevention and Control of Latvia, Infectious Diseases Surveillance and Immunization, 1005 Riga, Latvia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renate","family":"Ranka","sequence":"additional","affiliation":[{"name":"Latvian Biomedical Research and Study Centre, 1067 Riga, Latvia"},{"name":"Faculty of Pharmacy, Riga Stradins University, 1007 Riga, Latvia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabine","family":"Schaper","sequence":"additional","affiliation":[{"name":"Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zane","family":"Freimane","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Riga Stradins University, 1007 Riga, Latvia"},{"name":"Children\u2019s Clinical University Hospital, 1004 Riga, Latvia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4892-3763","authenticated-orcid":false,"given":"Dace","family":"Zavadska","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Riga Stradins University, 1007 Riga, Latvia"},{"name":"Children\u2019s Clinical University Hospital, 1004 Riga, Latvia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1007\/s00705-023-05835-1","article-title":"Renaming of the genus Flavivirus to Orthoflavivirus and extension of binomial species names within the family Flaviviridae","volume":"168","author":"Postler","year":"2023","journal-title":"Arch. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1002\/jmv.21765","article-title":"Genotyping and characterization of the geographical distribution of tick-borne encephalitis virus variants with a set of molecular probes","volume":"82","author":"Demina","year":"2010","journal-title":"J. Med. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41426-018-0081-6","article-title":"A new subtype of eastern tick-borne encephalitis virus discovered in Qinghai-Tibet Plateau, China","volume":"7","author":"Dai","year":"2018","journal-title":"Emerg. Microbes Infect."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1089\/vbz.2016.2094","article-title":"Partial Characterization of Tick-Borne Encephalitis Virus Isolates from Ticks of Southern Ukraine","volume":"17","author":"Yurchenko","year":"2017","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"334","DOI":"10.4103\/0972-9062.172836","article-title":"Detection of Far-Eastern subtype of tick-borne encephalitis viral RNA in ticks collected in the Republic of Moldova","volume":"52","author":"Ponomareva","year":"2015","journal-title":"J. Vector Borne Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1002\/(SICI)1096-9071(200002)60:2<216::AID-JMV18>3.0.CO;2-Z","article-title":"Characterization of tick-borne encephalitis virus from Latvia","volume":"60","author":"Mavtchoutko","year":"2000","journal-title":"J. Med. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.tmaid.2018.07.001","article-title":"Slovakia reports highest occurrence of alimentary tick-borne encephalitis in Europe: Analysis of tick-borne encephalitis outbreaks in Slovakia during 2007\u20132016","volume":"26","author":"Kerlik","year":"2018","journal-title":"Travel. Med. Infect. Dis."},{"key":"ref_8","first-page":"2200543","article-title":"Spatiotemporal spread of tick-borne encephalitis in the EU\/EEA, 2012 to 2020","volume":"28","author":"Beaute","year":"2023","journal-title":"Euro Surveill."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.ttbdis.2009.11.002","article-title":"Isolation and molecular characterization of a tick-borne encephalitis virus strain from a new tick-borne encephalitis focus with severe cases in Bavaria, Germany","volume":"1","author":"Kupca","year":"2010","journal-title":"Ticks Tick. Borne Dis."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Bestehorn, M., Weigold, S., Kern, W.V., Chitimia-Dobler, L., Mackenstedt, U., Dobler, G., and Borde, J.P. (2018). Phylogenetics of tick-borne encephalitis virus in endemic foci in the upper Rhine region in France and Germany. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0204790"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Zavadska, D., Odzelevica, Z., Karelis, G., Liepina, L., Litauniece, Z.A., Bormane, A., Lucenko, I., Perevoscikovs, J., Bridina, L., and Veide, L. (2018). Tick-borne encephalitis: A 43-year summary of epidemiological and clinical data from Latvia (1973 to 2016). PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0204844"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Freimane, Z., Karelis, G., Zolovs, M., and Zavadska, D. (2024). Tick-borne encephalitis infections without CNS involvement: An observational study in Latvia, 2007\u20132022. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0305120"},{"key":"ref_13","first-page":"31","article-title":"The relationship between the tick-borne encephalitis virus and the ticks and mammals of the Tribec mountain range","volume":"36","author":"Nosek","year":"1967","journal-title":"Bull. World Health Organ."},{"key":"ref_14","first-page":"275","article-title":"The ecological approach to the study of tick-borne encephalitis","volume":"14","author":"Blaskovic","year":"1972","journal-title":"Prog. Med. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1089\/153036602321653789","article-title":"Quantitative ecology of ticks as a basis for transmission models of tick-borne pathogens","volume":"2","author":"Randolph","year":"2002","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2059","DOI":"10.1017\/S0950268815000485","article-title":"Factors affecting the ecology of tick-borne encephalitis in Slovenia","volume":"143","author":"Knap","year":"2015","journal-title":"Epidemiol. Infect."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Bago, J., Bjedov, L., Vucelja, M., Tomljanovic, K., Cetinic Balent, N., Zember, S., Margaletic, J., and Dakovic Rode, O. (2025). The Influence of Biogeographic Diversity, Climate and Wildlife on the Incidence of Tick-Borne Encephalitis in Croatia. Viruses, 17.","DOI":"10.3390\/v17020266"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Nygren, T.M., Pilic, A., Bohmer, M.M., Wagner-Wiening, C., Wichmann, O., Harder, T., and Hellenbrand, W. (2022). Tick-Borne Encephalitis Risk Increases with Dog Ownership, Frequent Walks, and Gardening: A Case-Control Study in Germany 2018\u20132020. Microorganisms, 10.","DOI":"10.3390\/microorganisms10040690"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1002\/jmv.2097","article-title":"Characterization of tick-borne encephalitis virus from Latvia: Evidence for co-circulation of three distinct subtypes","volume":"65","author":"Lundkvist","year":"2001","journal-title":"J. Med. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1186\/s13071-020-04219-7","article-title":"Large-scale countrywide screening for tick-borne pathogens in field-collected ticks in Latvia during 2017\u20132019","volume":"13","author":"Capligina","year":"2020","journal-title":"Parasit. Vectors"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.ttbdis.2014.11.011","article-title":"Detection of tick-borne encephalitis virus in I. ricinus ticks collected from autumn migratory birds in Latvia","volume":"6","author":"Kazarina","year":"2015","journal-title":"Ticks Tick. Borne Dis."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Krol, N., Chitimia-Dobler, L., Dobler, G., Kiewra, D., Czulowska, A., Obiegala, A., Zajkowska, J., Juretzek, T., and Pfeffer, M. (2024). Identification of New Microfoci and Genetic Characterization of Tick-Borne Encephalitis Virus Isolates from Eastern Germany and Western Poland. Viruses, 16.","DOI":"10.3390\/v16040637"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/S1386-6532(02)00168-3","article-title":"Development of a quantitative real-time RT-PCR assay with internal control for the laboratory detection of tick borne encephalitis virus (TBEV) RNA","volume":"27","author":"Schwaiger","year":"2003","journal-title":"J. Clin. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Lang, D., Chitimia-Dobler, L., Bestehorn-Willmann, M., Lindau, A., Drehmann, M., Stroppel, G., Hengge, H., Mackenstedt, U., Kaier, K., and Dobler, G. (2022). The Emergence and Dynamics of Tick-Borne Encephalitis Virus in a New Endemic Region in Southern Germany. Microorganisms, 10.","DOI":"10.3390\/microorganisms10112125"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Letcher, B., Hunt, M., and Iqbal, Z. (2021). Gramtools enables multiscale variation analysis with genome graphs. Genome Biology, 22.","DOI":"10.1186\/s13059-021-02474-0"},{"key":"ref_26","unstructured":"Garrison, E., and Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Poon, A.F.Y., Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2\u2014Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2490","DOI":"10.1093\/bioinformatics\/bty121","article-title":"Parallelization of MAFFT for large-scale multiple sequence alignments","volume":"34","author":"Nakamura","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.virol.2006.12.013","article-title":"Microevolution of tick-borne encephalitis virus in course of host alternation","volume":"362","author":"Romanova","year":"2007","journal-title":"Virology"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1111\/jvec.12219","article-title":"Genetic diversity ofIxodes ricinus(Ixodida: Ixodidae) ticks in sympatric and allopatric zones in Baltic countries","volume":"41","author":"Paulauskas","year":"2016","journal-title":"J. Vector Ecol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/j.ttbdis.2015.05.007","article-title":"New localities of Dermacentor reticulatus ticks in the Baltic countries","volume":"6","author":"Paulauskas","year":"2015","journal-title":"Ticks Tick-Borne Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Brandenburg, P.J., Obiegala, A., Schmuck, H.M., Dobler, G., Chitimia-Dobler, L., and Pfeffer, M. (2023). Seroprevalence of Tick-Borne Encephalitis (TBE) Virus Antibodies in Wild Rodents from Two Natural TBE Foci in Bavaria, Germany. Pathogens, 12.","DOI":"10.3390\/pathogens12020185"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1016\/j.ttbdis.2015.10.013","article-title":"Siberian subtype tick-borne encephalitis virus in Ixodes ricinus in a newly emerged focus, Finland","volume":"7","author":"Jaaskelainen","year":"2016","journal-title":"Ticks Tick. Borne Dis."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1002\/jmv.23732","article-title":"Clusterons as a tool for monitoring populations of tick-borne encephalitis virus","volume":"86","author":"Kovalev","year":"2014","journal-title":"J. Med. Virol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1186\/s13071-019-3346-6","article-title":"Repeated isolation of tick-borne encephalitis virus from adult Dermacentor reticulatus ticks in an endemic area in Germany","volume":"12","author":"Lemhofer","year":"2019","journal-title":"Parasit. Vectors"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4307","DOI":"10.1002\/ece3.1301","article-title":"Tick-borne encephalitis virus subtypes emerged through rapid vector switches rather than gradual evolution","volume":"4","author":"Kovalev","year":"2014","journal-title":"Ecol. Evol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"100508","DOI":"10.1016\/j.onehlt.2023.100508","article-title":"Geographical distribution of Ixodes persulcatus and associated pathogens: Analysis of integrated data from a China field survey and global published data","volume":"16","author":"Wang","year":"2023","journal-title":"One Health"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Sukhorukov, G.A., Paramonov, A.I., Lisak, O.V., Kozlova, I.V., Bazykin, G.A., Neverov, A.D., and Karan, L.S. (2023). The Baikal subtype of tick-borne encephalitis virus is evident of recombination between Siberian and Far-Eastern subtypes. PLoS Negl. Trop. Dis., 17.","DOI":"10.1371\/journal.pntd.0011141"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2884","DOI":"10.1099\/vir.0.012419-0","article-title":"Origin and distribution of tick-borne encephalitis virus strains of the Siberian subtype in the Middle Urals, the north-west of Russia and the Baltic countries","volume":"90","author":"Kovalev","year":"2009","journal-title":"J. Gen. Virol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.meegid.2017.09.014","article-title":"Reconsidering the classification of tick-borne encephalitis virus within the Siberian subtype gives new insights into its evolutionary history","volume":"55","author":"Kovalev","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"101327","DOI":"10.1016\/j.ttbdis.2019.101327","article-title":"Genetic diversity and geographical distribution of the Siberian subtype of the tick-borne encephalitis virus","volume":"11","author":"Tkachev","year":"2020","journal-title":"Ticks Tick. Borne Dis."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/9\/950\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:46:50Z","timestamp":1760035610000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/9\/950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,22]]},"references-count":42,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["pathogens14090950"],"URL":"https:\/\/doi.org\/10.3390\/pathogens14090950","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,22]]}}}