title: Tick-borne encephalitis virus sequenced directly from questing and blood-feeding ticks reveals quasispecies variance.
abstract: The increased distribution of the tick-borne encephalitis virus (TBEV) in Scandinavia highlights the importance of characterizing novel sequences within the natural foci. In this study, two TBEV strains: the Norwegian Mandal 2009 (questing nymphs pool) and the Swedish Saringe 2009 (blood-fed nymph) were sequenced and phylogenetically characterized. Interestingly, the sequence of Mandal 2009 revealed the shorter form of the TBEV genome, similar to the highly virulent Hypr strain, within the 3' non-coding region (3'NCR). A different genomic structure was found in the 3'NCR of Saringe 2009, as in-depth analysis demonstrated TBEV variants with different lengths within the poly(A) tract. This shows that TBEV quasispecies exists in nature and indicates a putative shift in the quasispecies pool when the virus switches between invertebrate and vertebrate environments. This prompted us to further sequence and analyze the 3'NCRs of additional Scandinavian TBEV strains and control strains, Hypr and Neudoerfl. Toro 2003 and Habo 2011 contained mainly a short (A)3C(A)6 poly(A) tract. A similar pattern was observed for the human TBEV isolates 1993/783 and 1991/4944; however, one clone of 1991/4944 contained an (A)3C(A)11 poly(A) sequence, demonstrating that quasispecies with longer poly(A) could be present in human isolates. Neudoerfl has previously been reported to contain a poly(A) region, but to our surprise the re-sequenced genome contained two major quasispecies variants, both lacking the poly(A) tract. We speculate that the observed differences are important factors for the understanding of virulence, spread, and control of the TBEV.
authors: School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden.
authors: Naveed
authors: N
authors: Asghar
authors: Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
authors: Pontus
authors: P
authors: Lindblom
authors: School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden.
authors: Wessam
authors: W
authors: Melik
authors: Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden.
authors: Richard
authors: R
authors: Lindqvist
authors: Department of Infectious Diseases, County Hospital, Kalmar, Sweden.
authors: Mats
authors: M
authors: Haglund
authors: Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Clinic of Infectious Diseases, Linköping University Hospital, Linköping, Sweden.
authors: Pia
authors: P
authors: Forsberg
authors: Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden.
authors: Anna K
authors: AK
authors: Överby
authors: Division of Infectious Disease Control, Department of Virology, Norwegian Institute of Public Health, Oslo, Norway.
authors: Åshild
authors: Å
authors: Andreassen
authors: Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden; Division of Medical Services, Department of Microbiology, County Hospital Ryhov, Jönköping, Sweden.
authors: Per-Eric
authors: PE
authors: Lindgren
authors: School of Natural Science, Technology & Environmental Studies, Södertörn University, Huddinge, Sweden; School of Medicine, Örebro University, Örebro, Sweden; iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
authors: Magnus
authors: M
authors: Johansson
mesh_terms: D000368:Aged; D000818:Animals; D001483:Base Sequence; D002648:Child; D004669:Encephalitis Viruses, Tick-Borne / Q000145:classification* / Q000235:genetics*; D004675:Encephalitis, Tick-Borne / Q000097:blood / Q000821:virology*; D014644:Genetic Variation; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009758:Nymph; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D013987:Ticks / Q000821:virology*
chemical_list: D012367:RNA, Viral