The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure

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Abstract

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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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

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