Molecular characterization of a variant rhinovirus from an outbreak associated with uncommonly high mortality

Journal of Clinical Virology

Volumn 38, Issue 3, 2007, Pages 227-237

  Kiang, David ^a   Yagi, Shigeo ^a   Kantardjieff, Katherine A ^b   Kim, Euna J ^b   Louie, Janice K ^a   Schnurr, David P ^a  

^a VIRAL AND RICKETTSIAL DISEASE LABORATORY   (United States)

^b CALIFORNIA STATE UNIVERSITY   (United States)

Author keywords

Molecular modeling; Mortality; Neutralization immunogens; Outbreak; Phylogenetic analysis; Rhinovirus; Variant

Indexed keywords

EPITOPE; PROTEIN VP1; PROTEIN VP2; PROTEIN VP4; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ARTICLE; DISEASE SEVERITY; EPIDEMIC; HUMAN; HUMAN CELL; HUMAN RHINOVIRUS; IMMUNE RESPONSE; MOLECULAR MODEL; MORBIDITY; MORTALITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RHINOVIRUS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURAL GENE; UNITED STATES; UPPER RESPIRATORY TRACT INFECTION; VIROGENESIS; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS ISOLATION; VIRUS NEUTRALIZATION; VIRUS REPLICATION; VIRUS STRAIN;

AMINO ACID SEQUENCE; CALIFORNIA; CAPSID PROTEINS; DISEASE OUTBREAKS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PICORNAVIRIDAE INFECTIONS; RESPIRATORY TRACT INFECTIONS; RHINOVIRUS; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL PROTEINS;

EID: 33847048268     PISSN: 13866532     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jcv.2006.12.016     Document Type: Article

References (61)

1. Abagyan R., Batalov S., Cardozo T., Totrov M., Webber J., and Zhou Y. Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search. Proteins Suppl. 1 (1997) 29-37
2. Abagyan R., Totrov M., and Kuznetsov D. ICM: a new method for protein modeling and design. Applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15 (1994) 488-506 Ref Type: Journal (Full)
3. Arola M., Ziegler T., Ruuskanen O., Mertsola J., Nanto-Salonen K., and Halonen P. Rhinovirus in acute otitis media. J Pediatr 113 (1988) 693-695
4. Balfour-Lynn I.M., Valman H.B., Stanway G., and Khan M. Use of polymerase chain reaction to detect rhinovirus in wheezy infants. Arch Dis Child 67 (1992) 760
5. Bella J., and Rossmann M.G. ICAM-1 receptors and cold viruses. Pharm Acta Helv 74 (2000) 291-297
6. Casas I., Powell L., Klapper P.E., and Cleator G.M. New method for the extraction of viral RNA and DNA from cerebrospinal fluid for use in the polymerase chain reaction assay. J Virol Methods 53 (1995) 25-36
7. Domingo E., Escarmis C., Sevilla N., Moya A., Elena S.F., Quer J., et al. Basic concepts in RNA virus evolution. FASEB J 10 (1996) 859-864
8. Drinka P.J., Gravenstein S., Langer E., Krause P., and Shult P. Mortality following isolation of various respiratory viruses in nursing home residents. Infect Control Hosp Epidemiol 20 (1999) 812-815
9. Duechler M., Skern T., Sommergruber W., Neubauer C., Gruendler P., Fogy I., et al. Evolutionary relationships within the human rhinovirus genus: comparison of serotypes 89, 2, and 14. Proc Natl Acad Sci USA 84 (1987) 2605-2609
10. Engh R.A., and Huber R. Accurate bond and angle parameters for X-ray structure refinement. Acta Cryst A47 (1991) 392-400
11. Falsey A.R., McCann R.M., Hall W.J., Criddle M.M., Formica M.A., Wycoff D., et al. The "common cold" in frail older persons: impact of rhinovirus and coronavirus in a senior daycare center. J Am Geriatr Soc 45 (1997) 706-711
12. Falsey A.R., Treanor J.J., Betts R.F., and Walsh E.E. Viral respiratory infections in the institutionalized elderly: clinical and epidemiologic findings. J Am Geriatr Soc 40 (1992) 115-119
13. Falsey A.R., Walsh E.E., and Hayden F.G. Rhinovirus and coronavirus infection-associated hospitalizations among older adults. J Infect Dis 185 (2002) 1338-1341
14. Friedlander S.L., and Busse W.W. The role of rhinovirus in asthma exacerbations. J Allergy Clin Immunol 116 (2005) 267-273
15. Gern J.E., and Busse W.W. Association of rhinovirus infections with asthma. Clin Microbiol Rev 12 (1999) 9-18
16. Graat J.M., Schouten E.G., Heijnen M.L., Kok F.J., Pallast E.G., de Greeff S.C., et al. A prospective, community-based study on virologic assessment among elderly people with and without symptoms of acute respiratory infection. J Clin Epidemiol 56 (2003) 1218-1223
17. Greenberg S.B. Respiratory consequences of rhinovirus infection. Arch Intern Med 163 (2003) 278-284
18. Hadfield A.T., Lee W., Zhao R., Oliveira M.A., Minor I., Rueckert R.R., et al. The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle. Structure 5 (1997) 427-441
19. Halfon P., Roubicek C., Gerolami V., Quentin Y., Khiri H., Pepe G., et al. Use of phylogenetic analysis of hepatitis C virus (HCV) hypervariable region 1 sequences to trace an outbreak of HCV in an autodialysis unit. J Clin Microbiol 40 (2002) 1541-1545
20. Hayden F.G. Rhinovirus and the lower respiratory tract. Rev Med Virol 14 (2004) 17-31
21. Heymann P.W., Carper H.T., Murphy D.D., Platts-Mills T.A., Patrie J., McLaughlin A.P., et al. Viral infections in relation to age, atopy, and season of admission among children hospitalized for wheezing. J Allergy Clin Immunol 114 (2004) 239-247
22. Hicks L.A., Shepard C.W., Britz P.H., Erdman D.D., Fischer M., Flannery B.L., et al. Two outbreaks of severe respiratory disease in nursing homes associated with rhinovirus. J Am Geriatr Soc 54 (2006) 284-289
23. Hooft R.W., Vriend G., Sander C., and Abola E.E. Errors in protein structures. Nature 381 (1996) 272
24. Horsnell C., Gama R.E., Hughes P.J., and Stanway G. Molecular relationships between 21 human rhinovirus serotypes. J Gen Virol 76 Pt 10 (1995) 2549-2555
25. Imakita M., Shiraki K., Yutani C., and Ishibashi-Ueda H. Pneumonia caused by rhinovirus. Clin Infect Dis 30 (2000) 611-612
26. Ison M.G., Hayden F.G., Kaiser L., Corey L., and Boeckh M. Rhinovirus infections in hematopoietic stem cell transplant recipients with pneumonia. Clin Infect Dis 36 (2003) 1139-1143
27. Kantardjieff K.A., Hochtl P., Segelke B.W., Tao F.M., and Rupp B. Concanavalin A in a dimeric crystal form: revisiting structural accuracy and molecular flexibility. Acta Crystallogr D Biol Crystallogr 58 (2002) 735-743
28. Kleywegt G.J., and Jones T.A. Phi/psi-chology: Ramachandran revisited. Structure 4 (1996) 1395-1400
29. Laine P., Blomqvist S., Savolainen C., Andries K., and Hovi T. Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains. J Gen Virol 87 (2006) 129-138
30. Las H.J., and Swanson V.L. Sudden death of an infant with rhinovirus infection complicating bronchial asthma: case report. Pediatr Pathol 1 (1983) 319-323
31. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26 (1993) 283-291
32. Ledford R.M., Patel N.R., Demenczuk T.M., Watanyar A., Herbertz T., Collett M.S., et al. VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds. J Virol 78 (2004) 3663-3674
33. Lee B.E., Robinson J.L., Khurana V., Pang X.L., Preiksaitis J.K., and Fox J.D. Enhanced identification of viral and atypical bacterial pathogens in lower respiratory tract samples with nucleic acid amplification tests. J Med Virol 78 (2006) 702-710
34. Lemanske Jr. R.F., Jackson D.J., Gangnon R.E., Evans M.D., Li Z., Shult P.A., et al. Rhinovirus illnesses during infancy predict subsequent childhood wheezing. J Allergy Clin Immunol 116 (2005) 571-577
35. Louie J.K., Hacker J.K., Gonzales R., Mark J., Maselli J.H., Yagi S., et al. Characterization of viral agents causing acute respiratory infection in a San Francisco University Medical Center Clinic during the influenza season. Clin Infect Dis 41 (2005) 822-828
36. Louie J.K., Yagi S., Nelson F.A., Kiang D., Glaser C.A., Rosenberg J., et al. Rhinovirus outbreak in a long term care facility for elderly persons associated with unusually high mortality. Clin Infect Dis 41 (2005) 262-265
37. Maiorov V., and Abagyan R. Energy strain in three-dimensional protein structures. Fold Des 3 (1998) 259-269
38. Minor P.D., John A., Ferguson M., and Icenogle J.P. Antigenic and molecular evolution of the vaccine strain of type 3 poliovirus during the period of excretion by a primary vaccinee. J Gen Virol 67 Pt 4 (1986) 693-706
39. Neumann E., Moser R., Snyers L., Blaas D., and Hewat E.A. A cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid. J Virol 77 (2003) 8504-8511
40. NIAID Factsheet. The common cold. NIAID 2001.
41. Nicholson K.G., Kent J., Hammersley V., and Cancio E. Risk factors for lower respiratory complications of rhinovirus infections in elderly people living in the community: prospective cohort study. BMJ 313 (1996) 1119-1123
42. Nicolle L.E., Strausbaugh L.J., and Garibaldi R.A. Infections and antibiotic resistance in nursing homes. Clin Microbiol Rev 9 (1996) 1-17
43. Nizet S., Wruss J., Landstetter N., Snyers L., and Blaas D. A mutation in the first ligand-binding repeat of the human very-low-density lipoprotein receptor results in high-affinity binding of the single V1 module to human rhinovirus 2. J Virol 79 (2005) 14730-14736
44. Nokso-Koivisto J., Raty R., Blomqvist S., Kleemola M., Syrjanen R., Pitkaranta A., et al. Presence of specific viruses in the middle ear fluids and respiratory secretions of young children with acute otitis media. J Med Virol 72 (2004) 241-248
45. Osur S.L. Viral respiratory infections in association with asthma and sinusitis: a review. Ann Allergy Asthma Immunol 89 (2002) 553-560
46. Papadopoulos N.G., Bates P.J., Bardin P.G., Papi A., Leir S.H., Fraenkel D.J., et al. Rhinoviruses infect the lower airways. J Infect Dis 181 (2000) 1875-1884
47. Papadopoulos N.G., Moustaki M., Tsolia M., Bossios A., Astra E., Prezerakou A., et al. Association of rhinovirus infection with increased disease severity in acute bronchiolitis. Am J Respir Crit Care Med 165 (2002) 1285-1289
48. Papadopoulos N.G., Papi A., Psarras S., and Johnston S.L. Mechanisms of rhinovirus-induced asthma. Paediatr Respir Rev 5 (2004) 255-260
49. Papadopoulos N.G., Sanderson G., Hunter J., and Johnston S.L. Rhinoviruses replicate effectively at lower airway temperatures. J Med Virol 58 (1999) 100-104
50. Pitkaranta A., Starck M., Savolainen S., Poyry T., Suomalainen I., Hyypia T., et al. Rhinovirus RNA in the maxillary sinus epithelium of adult patients with acute sinusitis. Clin Infect Dis 33 (2001) 909-911
51. Pitkaranta A., Virolainen A., Jero J., Arruda E., and Hayden F.G. Detection of rhinovirus, respiratory syncytial virus, and coronavirus infections in acute otitis media by reverse transcriptase polymerase chain reaction. Pediatrics 102 (1998) 291-295
52. Puro V., Minosse C., Cappiello G., Lauria F.N., and Capobianchi M.R. Rhinovirus and lower respiratory tract infection in adults. Clin Infect Dis 40 (2005) 1068-1069
53. Rossmann M.G. The canyon hypothesis. Viral Immunol 2 (1989) 143-161
54. Rossmann M.G. Viral cell recognition and entry. Protein Sci 3 (1994) 1712-1725
55. Rossmann M.G., Arnold E., Erickson J.W., Frankenberger E.A., Griffith J.P., Hecht H.J., et al. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317 (1985) 145-153
56. Rueckert R.R. Picornaviridae: the viruses and their replication. In: Knipe B.N., Howley D.M., Chanock P.M., Melnick J.L., Monath T.P., Roizman B., and Straus S.E. (Eds). Fields Virology (1996), Lippincott-Raven Publishers, Philadelphia, PA 609-654
57. Savolainen C., Blomqvist S., Mulders M.N., and Hovi T. Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70. J Gen Virol 83 (2002) 333-340
58. Sherry B., Mosser A.G., Colonno R.J., and Rueckert R.R. Use of monoclonal antibodies to identify four neutralization immunogens on a common cold picornavirus, human rhinovirus 14. J Virol 57 (1986) 246-257
59. Strausbaugh L.J., Sukumar S.R., and Joseph C.L. Infectious disease outbreaks in nursing homes: an unappreciated hazard for frail elderly persons. Clin Infect Dis 36 (2003) 870-876
60. The National Nursing Home Survey: 1999 Summary. National Center for Health Statistics.
61. Wald T.G., Shult P., Krause P., Miller B.A., Drinka P., and Gravenstein S. A rhinovirus outbreak among residents of a long-term care facility. Ann Intern Med 123 (1995) 588-593