Tick-borne encephalitis virus (TBEV) is a flavivirus with major impact on global 
health. The geographical TBEV distribution is expanding, thus making it pivotal 
to further characterize the natural virus populations. In this study, we 
completed the earlier partial sequencing of a TBEV pulled out of a pool of RNA 
extracted from 115 ticks collected on Torö in the Stockholm archipelago. The 
total RNA was sufficient for all sequencing of a TBEV genome (Torö-2003), 
without conventional enrichment procedures such as cell culturing or suckling 
mice amplification. To our knowledge, this is the first time that the genome of 
TBEV has been sequenced directly from an arthropod reservoir. The Torö-2003 
sequence has been characterized and compared with other TBE viruses. In silico 
analyses of secondary RNA structures formed by the two untranslated regions 
revealed a temperature-sensitive structural shift between a closed replicative 
form and an open AUG accessible form, analogous to a recently described 
bacterial thermoswitch. Additionally, novel phylogenetic conserved structures 
were identified in the variable part of the 3'-untranslated region, and their 
sequence and structure similarity when compared with earlier identified 
structures suggests an enhancing function on virus replication and translation. 
We propose that the thermo-switch mechanism may explain the low TBEV prevalence 
often observed in environmentally sampled ticks. Finally, we were able to detect 
variations that help in the understanding of virus adaptations to varied 
environmental temperatures and mammalian hosts through a comparative approach 
that compares RNA folding dynamics between strains with different mammalian cell 
passage histories.