Identification of conserved RNA secondary structures in human respiratory syncytial virus A (hRSV A)

Respiratory Syncytial Virus Type A (RSV A), a major cause of lower respiratory tract infections in vulnerable populations, is a nonsegmented, negative-sense RNA virus with a 15-kilobase genome encoding eleven proteins. RNA secondary structures may be critical for RSV processes like transcription, translation, and genome packaging. This study used a variety of computational tools, including ScanFold and RNAfold, to identify 123 thermodynamically stable RNA structures in the positive-sense antigenome and 113 in the negative-sense genome. Of these 103 and 98 showing structural conservation, respectively. Analysis revealed differential t _i/t _v ratios between stems and loops, suggesting RNA structural constraints on RSV evolution. Key structures were found in the L (RdRp), Fusion (F), Nonstructural 1 and 2, Matrix 2 (M2), Matrix (M) genes, and the 3' UTR (155 nt Trailer sequence). These findings highlight potentially functional RNA structures that may regulate viral replication, offering novel targets for antiviral drug development.