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.
Vasin, A. V., Petrova, A. V., Egorov, V. V., Plotnikova, M. A., Klotchenko, S. A., Karpenko, M. N., & Kiselev, O. I. (2016). The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure. BMC Research Notes, 9(1). https://doi.org/10.1186/s13104-016-2083-6