title: Diversity of the population of Tick-borne encephalitis virus infecting Ixodes ricinus ticks in an endemic area of central Switzerland (Canton Bern).
abstract: Tick-borne encephalitis virus (TBEV), a member of the genus Flavivirus, has a positive-strand RNA genome containing a single open reading frame flanked by non-coding regions (NCRs). Ixodes ricinus ticks (n = 307) were collected from vegetation in a natural TBEV focus in Belp, Switzerland. The presence and identity of the virus were determined by nested RT-PCR followed by sequencing of the 5'-terminal region that comprises the 5' NCR and the capsid-encoding region (C). The presence of the western European TBEV subtype (W-TBEV) genome was detected in 14.3 % of the ticks. Nucleotide sequence analysis revealed a high variability of 55.5 %. In particular, four DNA fragments (CS 'A', CS 'B', the folding-stem structure and the start codon) showed substantial heterogeneity, which has the potential of compromising replication, translation and packaging of the viral genome. This variability may reflect a viral strategy to select the fittest RNA molecule to produce a viral infection in the different vertebrate hosts that may be encountered by the ticks. It may also indicate a possible ancient introduction of TBEV to the Belp site. In addition, it may contribute to explaining the annual low incidence of tick-borne encephalitis in the natural focus of Belp, despite the high prevalence of TBEV genomes in ticks.
authors.affiliation: Istituto Cantonale di Microbiologia, Via Mirasole 22A, 6500 Bellinzona, Switzerland.
authors.forename: Simona
authors.initials: S
authors.lastname: Casati
authors.affiliation: Institut de Parasitologie, Université de Neuchâtel, Rue Emile Argand, 2000 Neuchâtel, Switzerland.
authors.forename: Lise
authors.initials: L
authors.lastname: Gern
authors.affiliation: Istituto Cantonale di Microbiologia, Via Mirasole 22A, 6500 Bellinzona, Switzerland.
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Piffaretti
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics; D004669:Encephalitis Viruses, Tick-Borne / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D014644:Genetic Variation; D018884:Ixodes / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017354:Point Mutation; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013557:Switzerland
chemical_list: D020121:5' Untranslated Regions; D036022:Capsid Proteins; D012367:RNA, Viral