Impact of RNA structures on H5 hemagglutinin cleavage site insertions

Highly pathogenic avian influenza viruses (HPAIVs) cause severe disease and high fatality in poultry. HPAIVs spontaneously emerge from low pathogenic avian influenza viruses (LPAIV). Although insertion of a furin-cleavable multibasic cleavage site in the hemagglutinin (HA) gene was identified decades ago as the genetic basis for LPAIV-to-HPAIV transition, the exact mechanisms underlying said insertion have remained unknown. We have suggested previously that these insertions are driven by RNA structures forming around the influenza polymerase as it replicates this region. Here we performed circular sequencing of the cleavage site in WT HAs and HAs in which putative polymerase-trapping RNA structures were altered by nucleotide subsitutions in the region flanking the cleavage site. Uploaded reads are single merged reads after paired-end sequencing. Merged reads are unprocessed beyond removal of contaminant sequences as stated in the Methods section of the associated article.