2CIMPL	dual crosslinking, immunoprecipitation and proximity ligation
ASO	antisense oligonucleotides
Cryo-EM	cryo electron microscopy
DMS-MaPseq	dimethyl-sulfate mutational profiling with sequencing
DREEM	detection of RNA folding ensembles using expectation-maximization
G4	g-quadruplex
GORS	genome-scale ordered RNA structure
HTS	high-throughput screening
IAV	influenza A virus
IRES	internal ribosome entry sites
MaP	mutational profiling
MD	molecular dynamics
MM-GBSA	MD dynamics and molecular mechanics generalized born surface area
NGS	next generation sequencing
NMR	nuclear magnetic resonance
NS	non-structural protein
PA	polymerase acidic protein
PARIS	psoralen analysis of RNA interactions and structures
PB1	polymerase basic 1 protein
PKS	pseudoknot stem
PQS	potential quadruplex-forming sequence
RING-MaP	RNA interaction groups by mutational profiling
SARS-CoV-2	severe acute respiratory syndrome coronavirus 2
SCFGs	stochastic context-free grammars
sgRNA	subgenomic RNA
SHAPE	selective 2′-hydroxyl acylation analyzed by primer extension
SPLASH	sequencing of psoralen-crosslinked, ligated and selected hybrids
vHTS	virtual high-throughput screening
vPAR-CL	viral photoactivatable ribonucleoside crosslinking
vRNA	viral RNA
ZIKV	Zika virus