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.

SummaryObjectivesThe aim of this study was to investigate the genetic diversity in the stem-loop (SL) IV sub-domain of the human rhinovirus (HRV) internal ribosomal entry site (IRES), which plays key roles in the initiation of viral translation by host protein interaction.MethodsThe primary SL-IV sequences of 194 HRVs, consisting of 97 reference strains and 97 clinical isolates, including the IRES sub-domains SL-IVa, SL-IVb, SL-IVc, and SL-IVd, were analyzed using Lasergene, MEGA 4, and WebLogo. Additionally, secondary structures of SL-IV were predicted and classified by RNAfold and CentroidHomfold-LAST.ResultsThe predicted secondary structures of SL-IV showed variations in the position of bulbs, size of the loop, and length of stems. SL-IVc had the most highly conserved nucleotide sequence, with structures classified into two groups by the location of the poly(C) loop. Of the SL-IV sequences analyzed, 74 (79.56%) were classified in the major group and 19 (20.44%) in the minor group. Thirteen compensatory substitution pairs of SL-IVc contributed to maintaining the stem structure.ConclusionsThis study showed that the IRES secondary structures of a large number of reference and clinical HRVs were highly conserved, with several compensatory substitutions. It is expected that these results will facilitate investigations into HRV function based on IRES secondary structures.