Characterization of Tick-Borne Encephalitis Virus Isolates from 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. is considered the main vector of TBEV in Mongolia; although, the virus has also been detected in species. To further characterize the disease ecology of TBEV within the endemic Selenge province of Mongolia, 1300 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 . 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.