TBEV Subtyping in Terms of Genetic Distance

Abstract

Currently, the lowest formal taxon in virus classification is species; however, unofficial lower-level units are commonly used in everyday work. Tick-borne encephalitis virus (TBEV) is a species of mammalian tick-borne flaviviruses that may cause encephalitis. Many known representatives of TBEV are grouped into subtypes, mostly according to their phylogenetic relationship. However, the emergence of novel sequences could dissolve this phylogenetic grouping; in the absence of strict quantitative criterion, it may be hard to define the borders of the first TBEV taxonomic unit below the species level. In this study, the nucleotide/amino-acid space of all known TBEV sequences was analyzed. Amino-acid sequence p-distances could not reliably distinguish TBEV subtypes. Viruses that differed by less than 10% of nucleotides in the polyprotein-coding gene belonged to the same subtype. At the same time, more divergent viruses were representatives of different subtypes. According to this distance criterion, TBEV species may be divided into seven subtypes: TBEV-Eur, TBEV-Sib, TBEV-FE, TBEV-2871 (TBEV-Ob), TBEV-Him, TBEV-178-79 (TBEV-Bkl-1), and TBEV-886-84 (TBEV-Bkl-2).

Keywords: TBEV; pairwise genetic distance; subtypes; taxonomy.

Figure 1

Unrooted maximum likelihood tree for Tick-borne encephalitis virus (TBEV; E gene fragment—left panel, complete open reading frame (ORF)—right panel). Black circles indicate high-level nodes that were supported by UFBoot values over 95% [36]. The scale bar and branch lengths represent the expected number of substitutions per site.

Figure 2

Heatmap of concordance between nucleotide and amino-acid pairwise distances in E gene fragments (left panels) and ORF (right panels). First panel: all TBEV sequences. Second panel: all TBEV sequences except “2871” group viruses. Third panel: three major TBEV subtypes. The three bottom panels demonstrate the distribution of intrasubtype virus pairs for TBEV-Eur, TBEV-Sib, and TBEV-FE. Axes show uncorrected amino-acid and nucleotide sequence distances; dots correspond to distances between each possible pair of sequences in the dataset. Color indicates the density of dots according to the scale bar. The dotted line at 10% nucleotide difference indicates the proposed threshold for the division of TBEV species into subtypes.

Figure 3

Concordance between nucleotide and amino-acid pairwise distances for TBEV sequences in E gene fragment (left panel) and ORF (right panel). First panel: all TBEV sequences. Second panel: all TBEV sequences except “2871” group viruses. Axes show uncorrected amino-acid and nucleotide sequence distances; dots correspond to distances between each possible pair of sequences in the dataset. The dotted line at 10% nucleotide difference indicates the proposed threshold for segregation of TBEV species into subtypes. Virus pairs were divided into intrasubtype pairs (viruses from the same subtype, indicated by the red color) and intersubtype pairs (viruses from different subtypes, indicated by the blue color).