title: Codon conservation in the influenza A virus genome defines RNA packaging signals.
abstract: Genome segmentation facilitates reassortment and rapid evolution of influenza A virus. However, segmentation complicates particle assembly as virions must contain all eight vRNA species to be infectious. Specific packaging signals exist that extend into the coding regions of most if not all segments, but these RNA motifs are poorly defined. We measured codon variability in a large dataset of sequences to identify areas of low nucleotide sequence variation independent of amino acid conservation in each segment. Most clusters of codons showing very little synonymous variation were located at segment termini, consistent with previous experimental data mapping packaging signals. Certain internal regions of conservation, most notably in the PA gene, may however signify previously unidentified functions in the virus genome. To experimentally test the bioinformatics analysis, we introduced synonymous mutations into conserved codons within known packaging signals and measured incorporation of the mutant segment into virus particles. Surprisingly, in most cases, single nucleotide changes dramatically reduced segment packaging. Thus our analysis identifies cis-acting sequences in the influenza virus genome at the nucleotide level. Furthermore, we propose that strain-specific differences exist in certain packaging signals, most notably the haemagglutinin gene; this finding has major implications for the evolution of pandemic viruses.
authors.affiliation: DAMTP, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK.
authors.forename: Julia R
authors.initials: JR
authors.lastname: Gog
authors.forename: Emmanuel Dos Santos
authors.initials: Edos S
authors.lastname: Afonso
authors.forename: Rosa M
authors.initials: RM
authors.lastname: Dalton
authors.forename: India
authors.initials: I
authors.lastname: Leclercq
authors.forename: Laurence
authors.initials: L
authors.lastname: Tiley
authors.forename: Debra
authors.initials: D
authors.lastname: Elton
authors.forename: Johann C
authors.initials: JC
authors.lastname: von Kirchbach
authors.forename: Nadia
authors.initials: N
authors.lastname: Naffakh
authors.forename: Nicolas
authors.initials: N
authors.lastname: Escriou
authors.forename: Paul
authors.initials: P
authors.lastname: Digard
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D003062:Codon / Q000737:chemistry*; D017124:Conserved Sequence; D016679:Genome, Viral; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D009980:Influenza A virus / Q000235:genetics* / Q000502:physiology; D009154:Mutation; D016366:Open Reading Frames; D012367:RNA, Viral / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D019065:Virus Assembly / Q000235:genetics*
chemical_list: D003062:Codon; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D012367:RNA, Viral; D038621:Regulatory Sequences, Ribonucleic Acid