a, Schematic showing different samples used for SHAPE-MaP analysis. b, Median SHAPE-MaP reactivities of different WSN viral RNA segments in virio. Medians were calculated over 50 nucleotide windows and plotted relative to the global median of a given segment. c, SHAPE-MaP reactivity distributions in different samples; ****P ≤ 2.2 × 10−16, two-sided Wilcoxon rank-sum test, n = 13,581 nucleotides per sample. In virio data is an average of three biologically independent samples, in vitro-transcribed RNA data is an average of two biologically independent samples and naked viral RNA data is from a single biological sample. d, Base-pairing probability distributions in different viral RNA samples, calculated using the SHAPE-MaP-informed partition function. e, Secondary RNA structure of the NS segment. The upper black arcs indicate the maximum expected accuracy (MEA) RNA structure; only interactions associated with >80% base-pairing probabilities are shown. The lower coloured arcs indicate base-pairing probabilities. f, RNA hairpin in the non-structural protein (NS) segment resistant to nucleoprotein (NP) indicated by the dashed rectangle in e. All sequence positions are annotated as 5′-3′ in viral RNA sense. PA, PB1 and PB2 represent three different polymerase (P) subunits. M, matrix protein; NA, neuraminidase; HA, hemagglutinin.