Given the high similarity between strains within a sub-type, recombinant sequences in Tick-borne encephalitis virus species can probably only be detected between sub-types. Dating recombination events is challenging, due to high sequence similarity, low substation rate and condensed temporal sampling. In order to refine this analysis, additional full-length genomes of LIV strains are necessary. Now that the recombining fragment has been identified, it can readily be researched in LIV genomes. Finally, although sequencing the E-gene in order identify strains is a standard practice, the low substitution rate observed in this gene does not supply enough information for robust phylogenetic/ phylogeographic studies. We would therefore recommend to sequence, together with E, a faster evolving marker such as the Capsid-gene.