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Updated: Mar 20, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure
A V Vasin1,2, A V Petrova3,4, V V Egorov3
1Research Institute of Influenza, 197376, St-Petersburg, Russia. vasin@influenza.spb.ru.
Background:
Influenza A virus (IAV) is a segmented negative-sense RNA virus that causes seasonal epidemics and periodic pandemics in humans. Two regions (nucleotide positions 82-148 and 497-564) in the positive-sense RNA of the NS segment fold into a multi-branch loop or hairpin structures.
Results:
We studied 25,384 NS segment positive-sense RNA unique sequences of human and non-human IAVs in order to predict secondary RNA structures of the 82-148 and 497-564 regions using RNAfold software, and determined their host- and lineage-specific distributions. Hairpins prevailed in avian and avian-origin human IAVs, including H1N1pdm1918 and H5N1. In human and swine IAV hairpins distribution varied between evolutionary lineages.
Conclusions:
These results suggest a possible functional role for these RNA secondary structures and the need for experimental evaluation of these structures in the influenza life cycle.
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