Polymerase trapping as mechanism of H5 highly pathogenic avian influenza virus genesis

Highly pathogenic avian influenza viruses (HPAIVs) derive from H5 and H7
low pathogenic avian influenza viruses (LPAIVs). Although insertion of a
furin-cleavable multibasic cleavage site (MBCS) in the hemagglutinin gene
was identified decades ago as the genetic basis for the LPAIV-to-HPAIV
transition, the mechanisms underlying the occurrence of insertion are
unknown. Here, we show that transient H5 RNA structures predicted to trap
the influenza virus polymerase on purine-rich sequences drive nucleotide
insertions, providing the first strong empirical evidence of RNA structure
involvement in MBCS acquisition. Introduction of H5-like sequences and
structures into an H6 hemagglutinin resulted in MBCS-yielding insertions.
Our results show that nucleotide insertions that underlie H5 HPAIV
emergence result from a previously unknown RNA-structure-driven
diversity-generating mechanism, which could be shared with other RNA
viruses.