Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology

Abstract

Tick-borne encephalitis virus (TBEV) is the etiological agent of tick-borne encephalitis, an infectious disease of the central nervous system that is often associated with severe sequelae in humans. While TBEV is typically classified into three subtypes, recent evidence suggests a more varied range of TBEV subtypes and lineages that differ substantially in their 3’UTR architecture. Building on comparative genomics approaches and thermodynamic modelling, we characterize the TBEV 3’UTR structureome diversity and propose a unified picture of pervasive non-coding RNA (ncRNA) structure conservation. Moreover, we provide an updated phylogeny of TBEV, building on more than 220 publicly available complete genomes, and investigate the molecular epidemiology and phylodynamics with Nextstrain, a web-based visualization framework for real-time pathogen evolution.

Identification of Host Factors Differentially Induced by Clinically Diverse Strains of Tick-Borne Encephalitis Virus

“…Three closely related groups of TBEV exist, namely, European (TBEV-Eur), Far Eastern (TBEV-FE), and Siberian (TBEV-Sib), although more recent sequence-based analysis suggests further distinct subdivisions ( 10 ). Increased sampling in recent decades has further expanded the TBEV landscape with strains isolated in Eastern Siberia designated “Baikalean” isolates (genotype 4 [TBEV-Bkl-1] and genotype 5 [TBEV-Bkl-2]) ( 11 to 13 ), encompassing strain 886-84 and related East Siberian isolates ( 11 , 14 ). All TBEV strains show high similarity at the nucleotide level (~84%), but the clinical outcome of infection is variable, ranging from asymptomatic in ~80 to 98% of cases to encephalitis of various severity ( 2 to 4 , 15 ).…”