Baltic Group Tick-Borne Encephalitis Virus Phylogeography: Systemic Inconsistency Pattern between Genetic and Geographic Distances

Abstract

Tick-Borne Encephalitis Virus (TBEV) is a dangerous arbovirus widely distributed in Northern Eurasia. The area of this pathogen changes over time. At the beginning of the 2000s, the Ixodes tick populations in Karelia increased. At the same time, the area of I. persulcatus, the main vector of the Siberian TBEV subtype, also expanded. Herein, we sequenced 10 viruses isolated from ticks collected in three locations from the Karelia region in 2008–2018. PCR positive samples were passaged in suckling mice or pig embryo kidney cells (PEK). After the second passage in suckling, mice viral RNA was isolated and E-gene fragment was sequenced. Viral sequences were expected to be similar or nearly identical. Instead, there was up to a 4.8% difference in nucleotide sequence, comparable with the most diverse viruses belonging to the Baltic subgroup in Siberian TBEV subtype (Baltic TBEV-Sib). To reveal whether this was systemic or incidental, a comprehensive phylogeographical analysis was conducted. Interestingly, viruses within each geographic region demonstrated comparable diversity to the whole Baltic TBEV-Sib. Moreover, Baltic TBEV-Sib has a distribution area limited by three ecological regions. This means that active virus mixing occurs in the vast geographic area forming one common virus pool. The most plausible explanation is the involvement of flying animals in the TBEV spread.

Differences in Genetic Diversity of Mammalian Tick-Borne Flaviviruses

“…There have been a few studies characterizing the genetic diversity of different members of the MTBF group [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ], but only a fraction of those used in deep sequencing techniques [ 14 , 15 , 16 , 17 ]. Overall, most studies have focused on TBEV and AHFV [ 9 , 18 , 19 , 20 , 21 , 22 ], whereas other members of the complex, such as OHFV, KFDV, LGTV, and POWV, have been poorly characterized. This paper reports on the genetic diversity of many members of the MTBF group using Next Generation Sequencing (NGS), and shows that there are differences between the viruses within the group.…”

Evaluating the Impact of Anthropogenic Factors on the Dissemination of Contemporary Cosmopolitan, Arctic, and Arctic-like Rabies Viruses

“…Unlike phylogenetic trees, gene-geo plots do not establish the relationship between individual groups of viruses but show the fingerprint of the geographic and evolutionary distances correspondence. The distribution of dots in this plot may indicate isolated virus transfers or general phylogeographical patterns in the evolution of a virus group as a whole [25].…”