Molecular phylogeography of tick-borne encephalitis virus in central Europe

Abstract

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 indepth analysis of focal TBEV maintenance and long-distance TBEV spread.

Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses

“…To test whether the weak molecular clock in the LIV dataset was characteristic for TBFV in general, we estimated a molecular clock and performed date randomisation tests for TBEV-Eu, a close relative of LIV. The clock rate obtained was 3.3×10 -5 subs/site/yr (95% HPD: 2×10 -5 -5×10 -5 substitutions/site/year) which is consistent with previous estimates based on sub genomic datasets (19, 31). Rates estimated for two of the date randomised runs overlapped with the rate estimated from the observed dataset (Fig 6B).…”

“…BEAST analysis produced a molecular clock rate of 1.9×10 -5 substitutions/site/year (95% HPD: 5.7×10 -6 -3.9×10 -5 substitutions/site/year). This clock rate is about an order of magnitude slower than the estimated molecular clock rate of TBEV-Eu (19,30,31) and for LIV based on E gene data only (17) but similar to the rate estimated for Far-Eastern POWV strains (66,72,73). The estimated TMRCA was 3077 years ago (95% HPD: 909-5616) which an order of magnitude older than the TMRCA estimated by previous studies which have utilised only E gene sequences (17).…”

“…Phylogenies are essential for determining the epidemiological and evolutionary history of viruses, and, by calibrating trees with a molecular clock, to place their history into a temporal context (29). Previous phylogenetic studies have reported clock rates and time calibrated trees for both TBEV and LIV; however, only in the case of TBEV were estimates based on full genomes (19,30,31). In contrast, rates for LIV were derived from glycoprotein sequences, resulting in considerable uncertainty with respect to phylogenetic relationships and divergence times (17).…”

Complete Genome Sequence of Tick-Borne Encephalitis Virus Strain A104 Isolated from a Yellow-Necked Mouse ( Apodemus flavicollis ) in Austria

“…Interestingly, strain A104 showed a closer phylogenetic relationship with the German strain AS33 than with the geographically closer Austrian strain Neudoerfl. The latter finding is concordant with data from neighboring Slovenia, Slovakia, and Germany showing that geographically close does not necessarily mean phylogenetically close (11, 12; Frey et al, submitted). Although this would be expected in a rodent-associated tick-borne virus, other factors will likewise drive geographical distribution of TBEV (11, 12).…”

A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors

“…Another important feature of JMTV epidemiology is the presence of long distance dispersals. As it is unlikely for ticks themselves to move over long distance, the most plausible route is human-mediated transportation of infected cattle and sheep, or the migration of wild animals (17,18).…”