title: Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia.
abstract: Human rhinoviruses (HRV) cause a wide spectrum of disease, ranging from a mild influenza-like illness (ILI) to severe respiratory infection. Molecular epidemiological data are limited for HRV circulating in the Southern Hemisphere.
  
  
  
  To identify the species and genotypes of HRV from clinical samples collected in Sydney, Australia, from 2006 to 2009.
  
  
  
  Combined nose and throat swabs or nasopharyngeal aspirates collected from individuals with ILI were tested for HRV using real-time reverse-transcriptase polymerase chain reaction (RT-PCR). Sequencing data of 5'UTR and VP4/VP2 coding regions on RT-PCR-positive specimens were analysed.
  
  
  
  Human rhinoviruses were detected by real-time PCR in 20.9% (116/555) of samples tested. Phylogenetic analysis of 5'UTR and VP4/VP2 on HRV-positive samples was concordant in the grouping of HRV A and B species but not HRV C species. Eighty per cent (16/20) of sequences that grouped as HRV C in the VP4/VP2 tree clustered as HRV A, alongside some previously described C strains as subspecies C/A. Discordant branching was seen within HRV A group: two sequences clustering as A in the VP4/VP2 tree branched within the C/A subspecies in the 5'UTR tree, and one sequence showed identity to different HRV A strains in the two genes. The prevalence of HRV C and C/A species was greater in paediatric compared to adult patients (47.9% vs 25.5%, P = .032).
  
  
  
  Human rhinoviruses are a common cause of respiratory infections, and HRV C is present in the Southern Hemisphere. Sequencing of multiple HRV regions may be necessary to determine exact phylogenetic relationships.
authors.affiliation: Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.
authors.forename: Vigneswary M
authors.initials: VM
authors.lastname: Ratnamohan
authors.affiliation: Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.
authors.forename: Frank
authors.initials: F
authors.lastname: Zeng
authors.affiliation: Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.
authors.forename: Linda
authors.initials: L
authors.lastname: Donovan
authors.affiliation: School of Public Health and Community Medicine, University of New South Wales, Kensington, NSW, Australia.
authors.forename: Chandini R
authors.initials: CR
authors.lastname: MacIntyre
authors.affiliation: Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia. jen.kok@health.nsw.gov.au.|Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Hospital, University of Sydney, Westmead, NSW, Australia. jen.kok@health.nsw.gov.au.|Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, NSW, Australia. jen.kok@health.nsw.gov.au.
authors.forename: Jen
authors.initials: J
authors.lastname: Kok
authors.affiliation: Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Pathology West, Westmead Hospital, Westmead, NSW, Australia.|Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead Hospital, University of Sydney, Westmead, NSW, Australia.|Centre for Research Excellence in Critical Infections, Westmead Hospital, University of Sydney, Westmead, NSW, Australia.
authors.forename: Dominic E
authors.initials: DE
authors.lastname: Dwyer
mesh_terms: D000328:Adult; D001315:Australia / Q000453:epidemiology; D002648:Child; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008297:Male; D058889:Molecular Typing / Q000379:methods; D009305:Nasopharynx / Q000821:virology; D009666:Nose / Q000821:virology; D010614:Pharynx / Q000821:virology; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000453:epidemiology* / Q000821:virology; D015995:Prevalence; D012367:RNA, Viral / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000821:virology; D012229:Rhinovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D012367:RNA, Viral
keywords: human rhinovirus; influenza-like illness; molecular typing; phylogeny