title: Molecular characterization of a variant rhinovirus from an outbreak associated with uncommonly high mortality.
abstract: BACKGROUND
  Human rhinoviruses (HRVs) are the most frequent cause of acute upper respiratory tract infection, however, they are also known to replicate in the lower respiratory tract and associate with more severe respiratory illnesses. An outbreak of HRV occurred in a long-term facility in Santa Cruz, California with unusually high morbidity and mortality.
  
  
  OBJECTIVE
  To identify viral characteristics associated with this unique outbreak, genetic relationships between these clinical isolates (SCRVs) and prototype strains of rhinovirus were investigated.
  
  
  METHODS
  Sequence homology and phylogenetic analyses of the SCRV VP4/VP2 region were performed in conjunction with all HRV prototypes. Due to the importance of the 5'noncoding region (NCR) and the structural genes to viral replication and host immune responses, respectively, we focused on a segment of the HRV genome which includes these regions. Molecular models of SCRV were also assessed.
  
  
  RESULTS
  SCRV showed closest similarity to HRV82 with some divergence from the prototype. Amino acid differences were concentrated within predicted neutralization epitopes within VP2, VP3 and VP1.
  
  
  CONCLUSIONS
  Sequence analyses and differences in cell culture growth characteristics suggest that this virus is a variant of HRV which has distinctive properties from its respective prototype strain.
authors.affiliation: Viral and Rickettsial Disease Laboratories, California State Department of Health Services, 850 Marina Bay Parkway, Richmond, CA 94804, USA. dkiang@dhs.ca.gov
authors.forename: David
authors.initials: D
authors.lastname: Kiang
authors.forename: Shigeo
authors.initials: S
authors.lastname: Yagi
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Kantardjieff
authors.forename: Euna J
authors.initials: EJ
authors.lastname: Kim
authors.forename: Janice K
authors.initials: JK
authors.lastname: Louie
authors.forename: David P
authors.initials: DP
authors.lastname: Schnurr
mesh_terms: D000595:Amino Acid Sequence; D002140:California / Q000453:epidemiology; D036022:Capsid Proteins / Q000235:genetics; D004196:Disease Outbreaks; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000453:epidemiology* / Q000401:mortality / Q000821:virology*; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000401:mortality / Q000821:virology*; D012229:Rhinovirus / Q000235:genetics* / Q000302:isolation & purification; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics
chemical_list: D036022:Capsid Proteins; C442544:VP2 protein, Rhinovirus; D014764:Viral Proteins; C074995:viral protein 1, rhinovirus