In order to obtain a better understanding of tick-borne encephalitis virus 
(TBEV) strain movements in central Europe the E gene sequences of 102 TBEV 
strains collected from 1953 to 2011 at 38 sites in the Czech Republic, Slovakia, 
Austria and Germany were determined. Bayesian analysis suggests a 350-year 
history of evolution and spread in central Europe of two main lineages, A and B. 
In contrast to the east to west spread at the Eurasian continent level, local 
central European spreading patterns suggest historic west to east spread 
followed by more recent east to west spread. The phylogenetic and network 
analyses indicate TBEV ingressions from the Czech Republic and Slovakia into 
Germany via landscape features (Danube river system), biogenic factors (birds, 
red deer) and anthropogenic factors. The identification of endemic foci showing 
local genetic diversity is of paramount importance to the field as these will be 
a prerequisite for in-depth analysis of focal TBEV maintenance and long-distance 
TBEV spread.