title: Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution.
abstract: Infection by human rhinovirus (HRV) is a major cause of upper and lower respiratory tract disease worldwide and displays considerable phenotypic variation. We examined diversity by completing the genome sequences for all known serotypes (n = 99). Superimposition of capsid crystal structure and optimal-energy RNA configurations established alignments and phylogeny. These revealed conserved motifs; clade-specific diversity, including a potential newly identified species (HRV-D); mutations in field isolates; and recombination. In analogy with poliovirus, a hypervariable 5' untranslated region tract may affect virulence. A configuration consistent with nonscanning internal ribosome entry was found in all HRVs and may account for rapid translation. The data density from complete sequences of the reference HRVs provided high resolution for this degree of modeling and serves as a platform for full genome-based epidemiologic studies and antiviral or vaccine development.
authors.affiliation: Institute for Molecular Virology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Ann C
authors.initials: AC
authors.lastname: Palmenberg
authors.forename: David
authors.initials: D
authors.lastname: Spiro
authors.forename: Ryan
authors.initials: R
authors.lastname: Kuzmickas
authors.forename: Shiliang
authors.initials: S
authors.lastname: Wang
authors.forename: Appolinaire
authors.initials: A
authors.lastname: Djikeng
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Rathe
authors.forename: Claire M
authors.initials: CM
authors.lastname: Fraser-Liggett
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Liggett
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D001482:Base Composition; D001483:Base Sequence; D018388:Codon, Terminator; D019143:Evolution, Molecular; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000821:virology; D020815:Polyproteins / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D011995:Recombination, Genetic; D012141:Respiratory Tract Infections / Q000821:virology; D012229:Rhinovirus / Q000145:classification / Q000235:genetics* / Q000648:ultrastructure; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012703:Serotyping; D014764:Viral Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D018388:Codon, Terminator; D020815:Polyproteins; D012367:RNA, Viral; D014764:Viral Proteins