The Influenza virus pseudoknot is an RNA pseudoknot structure formed in one of the non-structural coding segments (NS) of influenza virus genome.

[1] Pseudoknots are commonly found in viral genomes, especially RNA viruses, where they incorporate an RNA splice site and can have a wide range of functions.

A unique point mutation occurring in the strains of influenza A virus subtype H5N1 after 2001 has been suggested to result in RNA conformational shift,[5] favouring an alternative hairpin structure instead of the pseudoknot.

[1] Another pseudoknot occurs at the Influenza A Segment 7 Splice Site, which is used to produce the important viral M2 ion channel protein.

[6][7] Both pseudoknots have the possibility of alternating between hairpin loop and pseudoknot conformations, which place splicing regulatory motifs in different structural contexts.