Conserved secondary structures predicted within the 5′ packaging signal region of influenza A virus PB2 segment

Infectious particles of influenza A virus (IAV) typically contain eight unique negative-strand viral RNA (vRNA) segments. It has been suggested that the selective packaging of IAV segments occurs through RNA-RNA interactions between different vRNA segments, and that local secondary structures formed within vRNA segments are involved in such interactions. PB2 segment plays a critical role in the viral packaging process and 80-150 bases at the 5′ end of PB2 vRNA sequence are thought to contain packaging signals. Here we show that the 5′ packaging signal region of PB2 segment forms a stem-loop structure specifically in the negative-strand RNA in > 97% of 1703 IAV strains analyzed. This stem-loop structure is located at the nucleotide positions where synonymous mutations and partial deletions have been shown to markedly reduce the packaging efficiency of PB2 segment. These observations suggest that the stem-loop structure predicted in the present study is a component of packaging signal in PB2 segment.