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

Abstract

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. Ixodes persulcatus is considered the main vector of TBEV in Mongolia; although, the virus has also been detected in Dermacentor species. To further characterize the disease ecology of TBEV within the endemic Selenge province of Mongolia, 1300 Ixodes persulcatus 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 Ixodes persulcatus. 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.

Keywords: Ixodes persulcatus; Mongolia; Selenge; Siberian subtype; next-generation sequencing; tick-borne encephalitis virus.

Figure 1

Based on PCR results, white circles represent TBEV-negative tick pools and blue circles represent TBEV-positive tick pools. The red star represents the location of the capital, Ulaanbaatar.

Figure 2

Maximum likelihood (ML) phylogenies of full-genome TBEV isolates and consensus sequence. (A) ML tree inferred from 198 full-genome TBEV isolates plus our consensus sequence, with OHFV as the outgroup. Tip colors indicate subtype. PQ479142 (indicated by the arrow) clusters within the Siberian subtype clade. The best-fit evolutionary model was detected by the Bayesian information criterion (GTR+F+I+R3). Black circles at nodes indicate strong statistical support at branches determined by ultrafast bootstrap support values >90. (B) Phylogeny of Siberian clade. Tip color indicates geographic origin. Five Siberian subclades as defined by monophyletic clades with branch support > 90 are indicated. All isolates collected in Mongolia belong to Subclade IV. PQ479142 (indicated by the arrow) clusters with two isolates collected in Selenge, Mongolia in 2012 from I. persulcatus (LC017692.1 and LC017693.1).