Deviatkin et al.
TBEV subtyping in terms of genetic distance.
Viruses. 2020; 12(11): 1240; doi:10.3390/v12111240
There is no universal system to classify viruses below the species level. For TBE virus, the term „subtype“ has been used for decades (for other viruses, terms like lineage, clade, group, serotype etc. are used), and is based on its primary geographical distribution.
All available TBE virus glycoprotein E sequences as of July 2020 (n=987), and all available complete open reading frames (n=236), were phylogenetically analyzed. TBE virus subtypes could perfectly be distinguished by nucleotide sequences, but not so well by amino acid sequences (there is a higher rate of synonymous substitutions). The protein E gene is historically the most common sequenced genome fragment, and there were remarkable conservations in amino acid sequences, even between distinct subtypes.
Whenever the ORF of two viruses differed by less than 10% nucleotide sequence, these viruses belonged to the same subtype – seven in total. The subtype abbreviations were unified as follows: the European subtype (TBEV-Eur), the Siberian subtype (TBEV-Sib), the Far Eastern subtype (TBEV-FE), the Baikalian subtype TBEV-Bkl-1 (for strain 178-179), the Baikalian subtype TBEV-Bkl-2 (for strain 886-84), TBEV-Ob for the Obskaya lineage (strain 2871) and TBEV-Him for the Himalayan subtype.