title: The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure.
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.
authors.affiliation: Research Institute of Influenza, 197376, St-Petersburg, Russia. vasin@influenza.spb.ru.|Peter the Great St-Petersburg Polytechnic University, 195251, St-Petersburg, Russia. vasin@influenza.spb.ru.
authors.forename: A V
authors.initials: AV
authors.lastname: Vasin
authors.affiliation: Research Institute of Influenza, 197376, St-Petersburg, Russia.|Peter the Great St-Petersburg Polytechnic University, 195251, St-Petersburg, Russia.
authors.forename: A V
authors.initials: AV
authors.lastname: Petrova
authors.affiliation: Research Institute of Influenza, 197376, St-Petersburg, Russia.
authors.forename: V V
authors.initials: VV
authors.lastname: Egorov
authors.affiliation: Research Institute of Influenza, 197376, St-Petersburg, Russia.
authors.forename: M A
authors.initials: MA
authors.lastname: Plotnikova
authors.affiliation: Research Institute of Influenza, 197376, St-Petersburg, Russia.
authors.forename: S A
authors.initials: SA
authors.lastname: Klotchenko
authors.affiliation: Peter the Great St-Petersburg Polytechnic University, 195251, St-Petersburg, Russia.
authors.forename: M N
authors.initials: MN
authors.lastname: Karpenko
authors.affiliation: Research Institute of Influenza, 197376, St-Petersburg, Russia.
authors.forename: O I
authors.initials: OI
authors.lastname: Kiselev
mesh_terms: D000818:Animals; D016679:Genome, Viral; D006801:Humans; D009980:Influenza A virus / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D017361:Viral Nonstructural Proteins / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D017361:Viral Nonstructural Proteins
keywords: Evolution; Influenza A virus; NS gene; Pathogenicity; RNA hairpin; RNA secondary structure