The 3' and 5'-terminal sequences of influenza A,B and C virus RNA segments are highly conserved and show partial inverted complementarity

The 3'- and 5'-terminal nucleotides of the genome segments of an influenza A, B, and C virus were identified by directly sequencing viral RNA using two different sequencing techniques. A high degree of conservation at the 3' ends as well as at the 5' ends was observed among the genome segments of each virus and among the segments of the three different virus types. A uridine-rich region was observed from positions 17 through 22 at the 5' end of each segment. Moreover, the conserved 3' and 5'-terminal sequences showed partial and inverted complementarity. This feature results in very similar sequences at the 3' ends of the plus and minus strand RNAs and may also enable single-strand RNAs of influenza virus to form “panhandle” structures. Inverted complementary repeats may play an important role in initiation of viral RNA replication.