Distribution and Genotypic Landscape of Tick-Borne Encephalitis Virus in Ticks from Latvia from 2019 to 2023

Abstract

Ticks are important parasites of economic and public health because of their ability to transmit zoonotic diseases. Tick-borne encephalitis virus (TBEV), now officially Orthoflavivirus encephalitidis, is a Flavivirus with five main subtypes of which three, the European (TBEV-EU), the Siberian (TBEV-Sib), and the Far-Eastern subtypes (TBEV-FE), are supposedly circulate in Latvia. Several hard tick species are involved in TBEV circulation and transmission in nature. This study set out to describe the genetic landscape of TBEV subtypes in Latvian tick populations. In 2019 and 2021 to 2023, a total of 3026 ticks were collected in three Latvian regions, with Ixodes ricinus as the dominant species (2822 specimens), followed by Ixodes persulcatus (200 specimens) and Dermacentor reticulatus (4 specimens). Ticks were morphologically identified, pooled, and screened for TBEV RNA by RT-qPCR. TBEV of positive tick pools were isolated and genetically characterized by genome sequencing. Our study demonstrates the prevalence of two TBEV subtypes in Latvia with specific spatial patterning. In the sympatric Vidzeme region, these subtypes display a preferential species association of TBEV-EU with Ixodes ricinus and TBEV-Sib with Ixodes persulcatus. Phylogeographic analysis suggests independent introductions of multiple genotypes from both subtypes. Further investigations are necessary to better understand the natural transmission and the medical importance of these TBEVs.

Keywords: Latvia; emergence; geographic distribution; phylogeny; tick-borne encephalitis.

Figure 1

Distribution, genotypic landscape, and origins of tick-borne encephalitis viruses in Latvia. (a) Large-scale sampling of Latvian tick species with TBEV potential. Map depicting the three monitored Latvian regions: Kurzeme (light orange), Zemgale (light red), and Vidzeme (light green). Color-coded, dated boxes represent localization and timing of flagging-based sampling of three tick species: D. reticulatus (bright red), I. ricinus (dark red), and I. persulcatus. Box sizes are scaled according to the number of sampled ticks. TBEV-positive tick pools are emphasized by adding “TBEV” in bold font. If a full or partial genome could be sequenced, the respective TBEV subtype is displayed in bold font. Lower-case characters d-g near a dated box point to the subfigure displaying the phylogeny that comprises the respective TBEV isolate. Three pie charts depict the relative fraction of each tick species with respect to the total number of ticks sampled in each of the three Latvian regions. (b) Relative and absolute abundances of the juvenile and adult forms of the three tick species in the three Latvian regions. Stacked bar chart displaying the distribution of developmental stage or sex among the three sampled tick species in the three regions. (c) Example photographs of the sampled D. reticulatus (male), I. persulcatus (female), and I. ricinus (female) ticks. (d–g) Phylograms displaying the phylogenetic context of the Latvian TBEV isolates. Latvian isolates are highlighted with a tip point. The seven Latvian TBEV isolates sequenced in this study are displayed in bold font. Host taxon origins (tick species or non-tick origin) of the tips and inferred ancestral states are color-coded as depicted in the legend at the bottom right corner.

Figure 2

Disjunct periods of nymph activity of the two Ixodes species in sympatric locations in Vidzeme. Loess-smoothed curves of conditional means (colored lines) with confidence intervals (gray areas) of number of ticks per monitored developmental stage sampled between months of April and July between 2019 and 2023 at Vidzeme locations where both Ixodes species were found at least once.