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McErlean P, Shackelton LA, Andrews E, Webster DR, Lambert SB, Nissen MD, Sloots TP, Mackay IM. Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS One 2008; 3:e1847. [PMID: 18382652 PMCID: PMC2268738 DOI: 10.1371/journal.pone.0001847] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 02/21/2008] [Indexed: 11/26/2022] Open
Abstract
Background Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected. Methodology/Principle Findings Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe. Conclusions The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission.
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Affiliation(s)
- Peter McErlean
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Laura A. Shackelton
- Mueller Laboratory, Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Emily Andrews
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Dale R. Webster
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California, San Francisco, California, United States of America
| | - Stephen B. Lambert
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Michael D. Nissen
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Brisbane, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Brisbane, Queensland, Australia
| | - Theo P. Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Brisbane, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Brisbane, Queensland, Australia
| | - Ian M. Mackay
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Tormo J, Centeno NB, Fontana E, Bubendorfer T, Fita I, Blaas D. Docking of a human rhinovirus neutralizing antibody onto the viral capsid. Proteins 1995; 23:491-501. [PMID: 8749845 DOI: 10.1002/prot.340230404] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The structure of the complex between the Fab fragment of a human rhinovirus serotype 2 (HRV2) neutralizing antibody (8F5) and a cross-reactive synthetic peptide derived from the viral capsid protein VP2 has been recently determined by crystallographic methods. The conformation adopted by the peptide was very similar to and could be superimposed onto the corresponding region of the viral protein VP2 of human rhinovirus 1A (HRV1A) whose three-dimensional structure is known. The structure of the Fab fragment determined in the complex was docked onto the viral capsid using the superimposition transformation found for the peptide. In the resulting model the Fab protrudes almost radially to about 60 A from the surface of the virion without any major steric problem. The Fab fragment was then placed on each one of the 60 equivalent epitopes using the T = 1 icosahedral symmetry of the virus. The closest pairs of Fab fragments are related by viral 2-fold axes and run almost parallel to each other without clashing. These axes of symmetry from the viral particle could thus be coincident with the dyad axes of the antibodies. Furthermore, comparison of the three-dimensional structure of the Fab/peptide complex with the structure of the Fab fragment alone indicates that the flexibility of the antibody's elbow would facilitate bivalent attachment to the same viral particle. In accordance with the docking results, experimental determination of the stoichiometry of binding yielded a ratio of 30 IgG molecules per virion also suggesting bivalent attachment of antibody 8F5 onto the viral particle. The neutralization of viral infectivity, being neither aggregation (this paper) nor inhibition of receptor binding, might be mainly achieved by reducing viral spread from cell to cell and/or inhibition of uncoating.
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Affiliation(s)
- J Tormo
- Institute of Biochemistry, University of Vienna, Austria
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Abstract
Mutants of human rhinovirus serotype 14 (HRV14) with increased resistance to treatment at low pH were obtained by repeated cycles of exposure to pH 4.5 and propagation in HeLa cells. Whereas wild-type virus lost more than 5 logs of infectivity upon incubation at pH 4.3, the three isolates examined were essentially unaffected. Conformational change of the viral capsid upon exposure to low pH was assessed as an increase of hydrophobicity by partition between an aqueous phase and a Triton X-114 phase; the mutants required exposure to a much lower pH to accumulate in the Triton phase than wild-type HRV14. The sequence of the capsid region was determined for three isolates; two isolates were found to have the changes Thr17 to lie in VP2 and Asn 100 to lie in VP1. The third isolate also had the change Thr17 to Ile in VP2; however, in VP1, Asp101 was replaced by Glu. Separate introduction of the mutations into full length cDNA clones of the wild-type sequence of HRV14 showed that only the changes in VP1 were necessary for the increased stability at pH 4.5. The implications of the mutations for the three-dimensional structure of the viral capsid are discussed.
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Affiliation(s)
- T Skern
- Institute of Biochemistry, University of Vienna, Austria
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Kim SS, Smith TJ, Chapman MS, Rossmann MC, Pevear DC, Dutko FJ, Felock PJ, Diana GD, McKinlay MA. Crystal structure of human rhinovirus serotype 1A (HRV1A). J Mol Biol 1989; 210:91-111. [PMID: 2555523 DOI: 10.1016/0022-2836(89)90293-3] [Citation(s) in RCA: 165] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The structure of human rhinovirus 1A (HRV1A) has been determined to 3.2 A resolution using phase refinement and extension by symmetry averaging starting with phases at 5 A resolution calculated from the known human rhinovirus 14 (HRV14) structure. The polypeptide backbone structures of HRV1A and HRV14 are similar, but the exposed surfaces are rather different. Differential charge distribution of amino acid residues in the "canyon", the putative receptor binding site, provides a possible explanation for the difference in minor versus major receptor group specificities, represented by HRV1A and HRV14, respectively. The hydrophobic pocket in VP1, into which antiviral compounds bind, is in an "open" conformation similar to that observed in drug-bound HRV14. Drug binding in HRV1A does not induce extensive conformational changes, in contrast to the case of HRV14.
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Affiliation(s)
- S S Kim
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
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Kowalski H, Maurer-Fogy I, Vriend G, Casari G, Beyer A, Blaas D. Trypsin sensitivity of several human rhinovirus serotypes in their low pH-induced conformation. Virology 1989; 171:611-4. [PMID: 2548332 DOI: 10.1016/0042-6822(89)90632-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Five serotypes of human rhinovirus (HRV) were examined for sensitivity to trypsin at physiological pH, HRV1A, HRV2, and HRV14 were found to be resistant whereas in serotypes HRV49 and HRV89 degradation of VP2 was observed. However, exposure to low pH followed by neutralization, a treatment which causes irreversible conformational changes in the capsid, led to rapid cleavage by trypsin of VP1 in HRV1A, HRV2, and HRV49 at defined sites followed by degradation of VP2. In the case of HRV2, the cleavage site in VP1 was determined by direct protein sequencing and was shown to occur between Arg260 and Thr261, close to the C-terminus. HRV49 behaves similarly to HRV2 as expected from extensive sequence similarity in this region, whereas VP1 in HRV1A is most probably cleaved at a site closer to the C-terminus than that in HRV2. Although HRV14 contains the same amino acid pair present in HRV2 and HRV49, it was not cleaved under these conditions. HRV89, which lacks a basic residue at the corresponding position, was also insensitive. Examination of the cleavage site on the three-dimensional structural map of native HRV2 reveals that it is most probably buried inside the capsid and thus not accessible. Structural rearrangements of the viral capsid are thus necessary to account for the cleavage observed after low pH treatment.
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Affiliation(s)
- H Kowalski
- Institut für Biochemie, University of Vienna, Wien, Austria
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Baxt B, Vakharia V, Moore DM, Franke AJ, Morgan DO. Analysis of neutralizing antigenic sites on the surface of type A12 foot-and-mouth disease virus. J Virol 1989; 63:2143-51. [PMID: 2467993 PMCID: PMC250631 DOI: 10.1128/jvi.63.5.2143-2151.1989] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A series of seven neutralizing monoclonal antibodies (nMAbs) directed against type A12 foot-and-mouth disease virus was used to generate neutralization-resistant variants. Both plaque reduction neutralization and microneutralization assays showed that the variants were no longer neutralized by the nMAbs used to generate them, although some of the variants still reacted with the nMAbs at high antibody concentrations. Results of cross-neutralization studies by both plaque reduction neutralization and microneutralization assays suggested the presence of at least one immunodominant antigenic site on the surface of type A12 foot-and-mouth disease virus, along with evidence of a second antigenic site on the viral surface. Two of the variants had reduced virulence in tissue culture as evidenced by their inability to inhibit cellular protein synthesis and a marked reduction in virus-induced cellular morphological alterations. Nucleotide sequencing of the variant genomes placed three epitopes of the major antigenic site on VP1 and the fourth epitope on VP3 and VP1. The one epitope of the minor site appears to reside only on VP1.
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Affiliation(s)
- B Baxt
- Department of Molecular Biology, Plum Island Animal Disease Center, Greenport, New York 11944-0848
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