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

Tick-borne encephalitis virus (TBEV) is primarily transmitted by <i>Ixodes</i> 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, <i>Ixodes persulcatus</i> 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>I. persulcatus</i> 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>I. persulcatus</i> 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.