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

Ticks are important parasites of economic and public health because of their ability to transmit zoonotic diseases. Tick-borne encephalitis virus (TBEV), now officially <i>Orthoflavivirus encephalitidis</i>, 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 <i>Ixodes ricinus</i> as the dominant species (2822 specimens), followed by <i>Ixodes persulcatus</i> (200 specimens) and <i>Dermacentor reticulatus</i> (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 <i>Ixodes ricinus</i> and TBEV-Sib with <i>Ixodes persulcatus</i>. 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.