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.
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References and Notes
1
J. M. Gwaltney Jr., J. O. Hendley, G. Simon, W. S. Jordan Jr., N. Engl. J. Med.275, 1261 (1966).
2
S. L. Johnstonet al., Am. J. Respir. Crit. Care Med.154, 654 (1996).
3
K. G. Nicholson, J. Kent, D. C. Ireland, Br. Med. J.307, 982 (1993).
4
D. J. Jacksonet al., Am. J. Respir. Crit. Care Med.178, 667 (2008).
5
A. M. Fendrick, A. S. Monto, B. Nightengale, M. Sarnes, Arch. Intern. Med.163, 487 (2003).
6
K. B. Weiss, S. D. Sullivan, J. Allergy Clin. Immunol.107, 3 (2001).
7
M. Vlasaket al., J. Virol.79, 7389 (2005).
8
K. Andrieset al., J. Virol.64, 1117 (1990).
9
S. R. Dominguezet al., J. Clin. Virol.43, 219 (2008).
10
P. McErleanet al., PLoS ONE3, e1847 (2008).
11
S. K. Lauet al., J. Clin. Microbiol.45, 3655 (2007).
12
A. Djikenget al., BMC Genomics9, 5 (2008).
13
Materials and methods are available as supporting material on Science Online.
14
A. C. Palmenberg, J.-Y. Sgro, in Molecular Biology of Picornaviruses, B. L. Semler, E. Wimmer, Eds. (ASM Press, New York, 2001).
15
A. C. Palmenberg, J.-Y. Sgro, Semin. Virol.8, 231 (1997).
16
L. R. Martin, G. M. Duke, J. E. Osorio, D. J. Hall, A. C. Palmenberg, J. Virol.70, 2027 (1996).
17
R. J. Jackson, in Translational Control, W. B. Hershey, M. B. Mathews, N. Sonenberg, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1996).
18
K. Tamura, J. Dudley, M. Nei, S. Kumar, Mol. Biol. Evol.24, 1596 (2007).
19
On the basis of these data, the International Committee on Taxonomy of Viruses Picornavirus Study Group recently proposed to recognize them as a new species (29).
20
hrv-08 and hrv-95 are designated as two different serotypes by ATCC but differ by 67 nucleotides, perhaps indicating a misidentification in the repository.
21
R. M. Ledfordet al., J. Virol.78, 3663 (2004).
22
C. Savolainen, S. Blomqvist, M. N. Mulders, T. Hovi, J. Gen. Virol.83, 333 (2002).
23
A. L. Kistleret al., Virol. J.4, 40 (2007).
24
P. Simmonds, J. Virol.80, 11124 (2006).
25
D. Martin, E. Rybicki, Bioinformatics16, 562 (2000).
26
R. Fleischer, K. Laessig, Clin. Infect. Dis.37, 1722 (2003).
27
D. L. Barnard, Curr. Pharm. Des.12, 1379 (2006).
28
C. Savolainen, M. N. Mulders, T. Hovi, Virus Res.85, 41 (2002).
29
N. Knowles, personal communication.
30
Funded by the University of Maryland School of Medicine internal funds and by NIH grant U19-AI070503. We thank A. Wolf and J.-Y. Sgro for implementation of the tree topology tests. The accession numbers for the hrv strains are FJ445111 to FJ445190 (see table S1).
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Science
Volume 324 | Issue 5923
3 April 2009
3 April 2009
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American Association for the Advancement of Science.
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Submission history
Received: 5 September 2008
Accepted: 4 February 2009
Published in print: 3 April 2009
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Tables S1 to S5
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