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Background  Tick-borne encephalitis is the most common tick-borne viral infection in Europe with 3,000 human cases reported each year. In Western Europe, the castor bean tick,  Ixodes ricinus , is the principal vector of the tick-borne encephalitis virus (TBEV). TBEV appears to be spreading geographically and was recently detected for the first time in Canton Valais in the southern part of Switzerland. The purpose of the present study was to survey the  I. ricinus  tick populations of Canton Valais for TBEV.    Methods  We collected a total of 19,331  I. ricinus  ticks at 45 different sites in Canton Valais between 2010 and 2013. Ticks were processed in pools and tested for TBEV using reverse transcription quantitative PCR. The  NS5  gene and the  envelope  gene of the TBEV isolates were partially sequenced for phylogenetic analysis.    Results  TBEV was detected in tick populations at six of the 45 sites. These six sites were all located in a 33 km transect along the Rhône River. TBEV was detected in two sites for three of the four years of the study showing the temporal persistence of the pathogen. Prevalence of TBEV in the six positive sites ranged from 0.16% to 11.11%. Phylogenetic analysis found that all TBEV isolates from Canton Valais belonged to the European subtype. Genetic analysis found two distinct lineages of TBEV suggesting that Canton Valais experienced two independent colonization events.    Conclusions  TBEV appears to be well established at certain locations in Canton Valais.    Electronic supplementary material  The online version of this article (doi:10.1186/1756-3305-7-443) contains supplementary material, which is available to authorized users.

Prevalence and phylogenetic analysis of tick-borne encephalitis virus (TBEV) in field-collected ticks (Ixodes ricinus) in southern Switzerland