Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveal Structure and Evolution
Ann C. Palmenberg,1*
David Spiro,2*
Ryan Kuzmickas,2
Shiliang Wang,2
Appolinaire Djikeng,2
Jennifer A. Rathe,3
Claire M. Fraser-Liggett,4
Stephen B. Liggett3
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.
2 J. Craig Venter Institute, Rockville, MD 20850, USA.
3 Cardiopulmonary Genomics Program, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
4 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
* These authors contributed equally to this work.
To whom correspondence should be addressed. E-mail: sligg001{at}umaryland.edu
