| Summary: | Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3<inline-formula> <math display="inline"> <semantics> <msup> <mrow></mrow> <mo>′</mo> </msup> </semantics> </math> </inline-formula>UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3<inline-formula> <math display="inline"> <semantics> <msup> <mrow></mrow> <mo>′</mo> </msup> </semantics> </math> </inline-formula>UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.
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