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Volume 15
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10.3390/pathogens15040378
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Article

Two Coding-Complete Genomes of Tick-Borne Encephalitis Virus Sequenced from Ixodes persulcatus Collected in Bulgan, Mongolia

by
Nora G. Cleary
1,2,
Nyamdelger Tsevelmaa
3,
Julia E. Paoli
1,2,
Micah Hoylman
4,
Doniddemberel Altantogtokh
3,5,
Michael R. Wiley
4,6,
Jessica D. Wiley
6,
Juan G. Perez Jimenez
2,7,
Adam Salyer
8,
Irina V. Etobayeva
8,
Nergui Davaasuren
3,
Buyandelger Bolorchimeg
5,
Bandikhuu Amgalanbayar
5,
Carla Mavian
2,9,
Andrew G. Letizia
8,
Bazartseren Boldbaatar
3,* and
Michael E. von Fricken
1,2,*
1
Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
2
Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
3
School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar 17029, Mongolia
4
Department of Pathology, Microbiology, and Immunology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
5
National Center for Zoonotic Diseases, Ulaanbaatar 18131, Mongolia
6
PathoSeq Bio, Omaha, NE 68101, USA
7
Genetics and Genomics Institute, University of Florida, Gainesville, FL 32610, USA
8
Naval Medical Research Unit INDO PACIFIC (NAMRU-IP), Singapore 759657, Singapore
9
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
*
Authors to whom correspondence should be addressed.
Pathogens 2026, 15(4), 378; https://doi.org/10.3390/pathogens15040378
Submission received: 4 March 2026 / Revised: 23 March 2026 / Accepted: 25 March 2026 / Published: 1 April 2026
(This article belongs to the Special Issue Tick-Borne Encephalitis Virus: 2nd Edition)
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Abstract

Tick-borne encephalitis virus (TBEV) is primarily transmitted by Ixodes spp. and poses significant health risks, leading to morbidity and mortality in humans. Two of the five subtypes, Siberian and Far Eastern are known to circulate in Mongolia. In 2021, Ixodes persulcatus ticks were collected from Bulgan aimag (province) using flagging and dragging methods and subsequently screened for TBEV using PCR. Positive samples underwent sequencing using an Oxford Nanopore Technologies-based hybrid capture approach, resulting in two coding-complete TBEV genomes from separate tick pools. Phylogenetic analysis classified both genomes within the Siberian subtype, grouping them with other Mongolian sequences from I. persulcatus collected in 2014, 2020, 2021, and 2023. The study sequences, PX654173 and PX654174, showed high genetic similarity (99.9% and 99.8%, respectively) to the sequence PQ479142, obtained from I. persulcatus ticks in Selenge, Mongolia, in 2021. The estimated time to most recent common ancestor (TMRCA) of the Siberian genotype was approximately 981 CE (95% HPD: 646–1347) with the emergence of a distinct Mongolian clade of TBEV around 1888 CE (95% HPD: 1834–1934). These findings highlight the value of expanded whole-genome sequencing to improve our understanding of TBEV’s genetic diversity and evolutionary history in Central Asia.
Keywords: tick-borne encephalitis virus; hybrid capture sequencing; Mongolia tick-borne encephalitis virus; hybrid capture sequencing; Mongolia

Share and Cite

MDPI and ACS Style

Cleary, N.G.; Tsevelmaa, N.; Paoli, J.E.; Hoylman, M.; Altantogtokh, D.; Wiley, M.R.; Wiley, J.D.; Perez Jimenez, J.G.; Salyer, A.; Etobayeva, I.V.; et al. Two Coding-Complete Genomes of Tick-Borne Encephalitis Virus Sequenced from Ixodes persulcatus Collected in Bulgan, Mongolia. Pathogens 2026, 15, 378. https://doi.org/10.3390/pathogens15040378

AMA Style

Cleary NG, Tsevelmaa N, Paoli JE, Hoylman M, Altantogtokh D, Wiley MR, Wiley JD, Perez Jimenez JG, Salyer A, Etobayeva IV, et al. Two Coding-Complete Genomes of Tick-Borne Encephalitis Virus Sequenced from Ixodes persulcatus Collected in Bulgan, Mongolia. Pathogens. 2026; 15(4):378. https://doi.org/10.3390/pathogens15040378

Chicago/Turabian Style

Cleary, Nora G., Nyamdelger Tsevelmaa, Julia E. Paoli, Micah Hoylman, Doniddemberel Altantogtokh, Michael R. Wiley, Jessica D. Wiley, Juan G. Perez Jimenez, Adam Salyer, Irina V. Etobayeva, and et al. 2026. "Two Coding-Complete Genomes of Tick-Borne Encephalitis Virus Sequenced from Ixodes persulcatus Collected in Bulgan, Mongolia" Pathogens 15, no. 4: 378. https://doi.org/10.3390/pathogens15040378

APA Style

Cleary, N. G., Tsevelmaa, N., Paoli, J. E., Hoylman, M., Altantogtokh, D., Wiley, M. R., Wiley, J. D., Perez Jimenez, J. G., Salyer, A., Etobayeva, I. V., Davaasuren, N., Bolorchimeg, B., Amgalanbayar, B., Mavian, C., Letizia, A. G., Boldbaatar, B., & von Fricken, M. E. (2026). Two Coding-Complete Genomes of Tick-Borne Encephalitis Virus Sequenced from Ixodes persulcatus Collected in Bulgan, Mongolia. Pathogens, 15(4), 378. https://doi.org/10.3390/pathogens15040378

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