Characterization of Tick-Borne Encephalitis Virus Isolates from Ixodes persulcatus Ticks Collected During 2020 in Selenge, Mongolia

Tick-borne encephalitis virus (TBEV) causes neurological disease in humans, with varied clinical severity influenced by the viral subtype. TBEV is endemic to Mongolia, where both Siberian and Far-Eastern subtypes are present. <i>Ixodes persulcatus</i> is considered the main vector of TBEV in Mongolia; although, the virus has also been detected in <i>Dermacentor</i> species. To further characterize the disease ecology of TBEV within the endemic Selenge province of Mongolia, 1300 <i>Ixodes persulcatus</i> ticks were collected in May 2020 from regions outside Ulaanbaatar. Pooled tick samples (n = 20-50) were homogenized and the supernatant was inoculated into Vero cells. Two RT-PCR assays were conducted on the cell supernatant following an observed cytopathic effect: one for TBEV detection and the second for viral subtyping. Lysed cell cultures were processed for next-generation sequencing (NGS) using Illumina technology. TBEV was detected in 10.7% of tick pools (3/28), and isolates were identified as the Siberian subtype. Phylogenetic analysis showed PQ479142 clustering within the Siberian subtype and sharing high similarity with published isolates collected in Selenge in 2012 from <i>Ixodes persulcatus</i>. Subtype analysis of circulating TBEV isolates and sequencing analytics to track viral evolution in ticks are vital to continued understanding of the risk to local populations.