Secondary structure conservation of the stem loop-IV sub-domain of internal ribosomal entry sites in human rhinovirus clinical isolates.

•We analyzed human rhinovirus internal ribosomal entry site (IRES) sequences from 194 reference and clinical samples.•The nucleotide sequence of the stem-loop IVc (SL-IVc) sub-domain is highly conserved.•Among the SL-IV sub-domains, SL–IVc had the most conserved secondary RNA structure.•The SL-IVc sub-domain has a high rate of compensatory substitutions.•Two groups of SL-IVc secondary structure are based on the poly(C) loop location.