Phylogenetic relationships and molecular adaptation dynamics of human rhinoviruses

Molecular Biology and Evolution

Volumn 26, Issue 5, 2009, Pages 969-981

  Lewis Rogers, Nicole ^a   Bendall, Matthew L ^a   Crandall, Keith A ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

Adaptive evolution; Enterovirus; Human rhinovirus; Recombination; Selection

Indexed keywords

CAPSID PROTEIN;

ARTICLE; GENE EXPRESSION; GENE STRUCTURE; GENETIC CODE; GENETIC RECOMBINATION; GENETIC VARIABILITY; MOLECULAR DYNAMICS; NONHUMAN; PHENOTYPE; PHYLOGENY; PROTEIN STRUCTURE; RHINOVIRUS; SEROTYPE; VIRUS GENE;

ADAPTATION, BIOLOGICAL; AMINO ACID SEQUENCE; CAPSID PROTEINS; EVOLUTION, MOLECULAR; GENOME, VIRAL; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RECOMBINATION, GENETIC; RHINOVIRUS; RNA, VIRAL; SELECTION (GENETICS); VIRAL NONSTRUCTURAL PROTEINS;

ENTEROVIRUS; HUMAN RHINOVIRUS SP.; MIRIDAE;

EID: 65349186618     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp009     Document Type: Article

References (66)

1. Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 21: 2104-2105.
2. Akaike H. 1974. The new look at the statistical model identification. IEEE Trans Autom Contr. 19:716-723.
3. Andersson P, Edman K, Lindberg AM. 2002. Molecular analysis of the echovirus 18 prototype: evidence of interserotypic recombination with echovirus 9. Virus Res. 85:71-83.
4. Appleby TC, Luecke H, Shim JH, Wu JZ, Cheney W, Zhong W, Vogeley L, Hong Z, Yao N. 2005. Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer. J Virol. 79:277-288.
5. Appleyard G, Russell SM, Clarke BE, Speller SA, Trowbridge M, Vadolas J. 1990. Neutralization epitopes of human rhinovirus type 2. J Gen Virol. 71:1275-1282.
6. Baranowski E, Ruiz-Jarabo CM, Domingo E. 2001. Evolution of cell recognition by viruses. Science. 292:1102-1105.
7. Binford SL, Maldonado MA, Brothers MA, Weady PT, Zalman LS, Meador JW, Matthews DA, Patick AK. 2005. Conservation of amino acids in human rhinovirus 3C protease correlates with broad-spectrum antiviral activity of rupintrivir, a novel human rhinovirus 3C protease inhibitor. Antimicrob Agents Chemother. 49:619-626.
8. Bjorndahl TC, Andrew LC, Semenchenko V, Wishart DS. 2007. NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (serotype 14): structural and dynamic comparison. Biochemistry. 46:12945-12958.
9. Cho MW, Richards OC, Dmitrieva TM, Vadim A, Ehrenfeld E. 1993. RNA duplex unwinding activity of poliovirus RNA-dependent RNA polymerase 3Dpol. J Virol. 67:3010-3018.
10. Cooney MR, Fox JP, Kenny GE. 1982. Antigenic groupings of 90 rhinovirus serotypes. Infect Immun. 37:642-647.
11. Crandall KA, Kelsey CR, Imamichi H, Lane HC, Salzman NP. 1999. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol Biol Evol. 16:372-382.
12. Cuervo NS, Guillot S, Romanenkova N, Comiescu M, Aubert-Combiescu A, Seghier M, Caro V, Crainic R, Delpeyroux F. 2001. Genomic features of intertypic recombinant Sabin poliovirus strains excreted by primary vaccinees. J Virol. 75: 5740-5751.
13. Edgar RC. 2004. MUCSLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
14. Gromeier M, Wimmer E, Gorbalenya AE. 1999. Genetics, pathogenesis and evolution of picornaviruses. In: Domingo E, Webster R, Holland J, editors. Origin and evolution of viruses. San Diego (CA): Academic Press. p. 287-344.
15. Gruenberger M, Wandl R, Nimpf J, Hiesberger T, Schneider WJ, Kuechler E, Blaas D. 1995. Avian homologs of the mammalian low-density lipoprotein receptor family bind minor receptor group human rhinovirus. J Virol. 69: 7244-7247.
16. Guindon S, Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
17. Hamparian VV, Colonno RJ, Cooney MR, et al. (15 co-authors). 1982. A collaborative report: rhinovirus - extension of the numbering system from 89 to 100. Virology. 159:191-192.
18. Heath L, van der Walt E, Varsani A, Martin DP. 2006. Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol. 80:11827-11832.
19. Hewat EA, Neumann E, Conway JF, Moser R, Ronacher B, Marlovits TC, Blass D. 2000. The cellular receptor to human rhinovirus 2 binds around the 5-fold axis and not in the canyon: a structural view. EMBO J. 19:6317-6325.
20. Hofer F, Gruenberger M, Kowalski H, Machat H, Huettinger M, Kuechler E, Blaas D. 1994. Members of the low density lipoprotein receptor family mediate cell entry of a minor-group common cold virus. Proc Natl Acad Sci USA. 91:1839-1842.
21. Humphrey W, Dalke A, Schulten K. 1996. VMD: visual molecular dynamics. J Mol Graphics. 14:33-38.
22. Kim KH, Willingmann P, Gong ZX , et al. (13 co-authors). 1993. A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A. J Mol Biol. 230:206-227.
23. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
24. Kirchberger S, Majdic O, Stöckl J. 2007. Modulation of the immune system by human rhinovirus. Int Arch Allergy Immunol. 142:1-10.
25. Kishino H, Miyata T, Hasegawa M. 1990. Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol. 30:151-160.
26. Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. 2007. Genome-wide diversity and selective pressure in the human rhinovirus. Virol J. 4:40, doi: 10.1186/1743-422X-4-40.
27. Kolatkar PR, Bella J, Olson NH, Bator CM, Baker TS, Rossmann MG. 1999. Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor. EMBO J. 18:6249-6259.
28. Kuiken CL, Foley B, Guzman E, Korber BTM. 1999. Determinants of HIV-1 protein evolution. In: Crandall KA, editor. The evolution of HIV. Baltimore (MD): The John Hopkins University Press. p. 432-468.
29. Laine P, Blomqvist S, Savolainen C, Andries K, Hovi T. 2006. Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains. J Gen Virol. 87:129-138.
30. Laine P, Savolainen C, Blomqvist S, Hovi T. 2005. Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses. J Gen Virol. 86: 697-706.
31. Ledford RM, Patel NR, Demenszuk TM, Watanyar A, Herbertz T, Collett MS, Pevear DC. 2004. VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds. J Virol. 78:3663-3674.
32. Lewis-Rogers N, McClellan DA, Crandall KA. 2008. The evolution of foot-and-mouth disease virus: impacts of recombination and selection. Infect Genet Evol. 8:786-798.
33. Lloyd RE, Grubman MJ, Enrenfeld E. 1988. Relationship of p220 cleavage during picornavirus infection to 2A sequences. J Virol. 62:4216-4233.
34. Love RA, Maegley KA, Yu X, Ferre RA, Lingardo LK, Diehl W, Parge HE, Dragovich PS, Fuhrman SA. 2004. The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy. Structure. 12:1533-1544.
35. Mallia P, Johnston SL. 2005. Mechanisms and experimental models of chronic obstructive pulmonary disease exacerbations. Proc Am Thor Soc. 2:361-366.
36. Martin DP, Williamson C, Posada D. 2005. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics. 21:260-262.
37. Matthews DA, Dragovich PS, Webber SE, et al. 1999. Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. ProcNatl Acad Sci USA. 96:11000-11007.
38. Maynard Smith J. 1992. Analyzing the mosaic structure of genes. J Mol Evol. 34:126-129.
39. McClellan DA, McCracken KG. 2001. Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domain. Mol Biol Evol. 18:917-925.
40. McClellan DA, Palfreyman EJ, Smith MJ, Moss JL, Christensen RG, Sailsbery JK. 2005. Physiochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. Mol Biol Evol. 22:437-455.
41. McClellan DA, Woolley S. 2004. AlignmentHelper ver.1.0. Provo (UT): Brigham Young University, Department of Integrative Biology.
42. Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247:536-540.
43. Nylander JAA. 2004. MrModeltest v2 Program. Evolutionary Biology Centre, Uppsala University. Distributed by the author
44. Oberste MS, Maher K, Pallansch MA. 2004. Evidence for frequent recombination within species Human Enterovirus B based on complete genomic sequences of all thirty-seven serotypes. J Virol. 78:855-867.
45. Olson NH, Kolatkar PR, Oliverira MA, Cheng RH, Greve JM, McClelland A, Baker TS, Rossmann MG. 1993. Structure of a human rhinovirus complexed with its receptor molecule. ProcNatl Acad Sci USAof America. 90:507-511.
46. Padidam M, Sawyer S, Fauquet CM. 1999. Possible emergence of new geminiviruses by frequent recombination. Virology. 265:218-225.
47. Paul AV. 2002. Possible unifying mechanisms of picornavirus genome replication. In: Semler BL, Wimmer E, editors. Molecular biology of picornaviruses. Washington (DC): ASM Press. p. 227-246.
48. Petersen JFW, Cherney MM, Liebig H-D, Skern T, Kuechler E, James MNG. 1999. The structure of the 2A proteinase from a common cold virus: a proteinase responsible for the shut-off of host-cell protein synthesis. EMBO J. 18:5463-5475.
49. Pitkäranta A, Hayden FG. 1998. Rhinoviruses: important respiratory pathogens. Ann Med. 30:529-537.
50. Posada D. 2002. Evaluation of methods for detecting recombination from DNA sequences: Real data. Mol Biol Evol. 19:708-717.
51. Posada D, Crandall KA. 2001. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA. 98:13757-13762.
52. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817-818.
53. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572-1574.
54. Savolainen C, Laine P, Mulders MN, Hovi T. 2004. Sequence analysis of human rhinovirus in the RNA-dependent RNA polymerase coding region reveals large within-species variation. J Gen Virol. 85:2271-2277.
55. Sherry B, Mosser AG, Colonno RJ, Rueckert RR. 1986. Use of monoclonal antibodies to identify four neutralization immunogens on a common cold picornavirus, human rhinovirus 14. J Virol. 57:246-257.
56. Shimodaira H, Hasegawa M. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol Biol Evol. 16:1114-1116.
57. Simmonds P, Welch J. 2006. Frequency and dynamics of recombination within different species of human enteroviruses. J Virol. 80:483-493.
58. Smith TJ. 2002. Antibody interactions with Rhinovirus. In: Semler B, Wimmer E, editors. Molecular biology of picornaviruses. Washington (DC): ASM Press. p. 39-49.
59. Swofford DL. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sunderland (MA): Sinauer.
60. Tapparel C, Junier T, Gerlach D, Cordey S, Van Belle S, Perrin L, Zdobnov EM, Kaiser L. 2007. New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. BMC Genomics. 8:227, doi: 10.1186/1471-2164-8-224.
61. van de Stolpe A, van der Saag PT. 1996. Intercellular adhesion molecule-1. J Mol Med. 74:13-33.
62. Walker PA, Leong LE-C, Porter AG. 1995. Sequence and structural determinants of the interaction between the 5′-noncoding region of picornavirus RNA and rhinovirus protease 3C. J Biol Chem. 270:14510-14516.
63. Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA. 2003. TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics. 19:671-672.
64. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics. 13:555-556.
65. Yang Z. 2007. Paml 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
66. Yang Z, Wong WSW, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22:1107-1118.