title: Pandemic clinical case definitions are non-specific: multiple respiratory viruses circulating in the early phases of the 2009 influenza pandemic in New South Wales, Australia.
abstract: BACKGROUND
  During the early phases of the 2009 pandemic, subjects with influenza-like illness only had laboratory testing specific for the new A(H1N1)pdm09 virus.
  
  
  RESULTS
  Between 25th May and 7th June 2009, during the pandemic CONTAIN phase, A(H1N1)pdm09 virus was detected using nucleic acid tests in only 56 of 1466 (3.8%) samples meeting the clinical case definition required for A(H1N1)pdm09 testing. Two hundred and fifty-five randomly selected A(H1N1)pdm09 virus-negative samples were tested for other respiratory viruses using a real-time multiplex PCR assay. Of the 255 samples tested, 113 (44.3%) had other respiratory viruses detected: rhinoviruses 63.7%, seasonal influenza A 17.6%, respiratory syncytial virus 7.9%, human metapneumovirus 5.3%, parainfluenzaviruses 4.4%, influenza B virus 4.4%, and enteroviruses 0.8%. Viral co-infections were present in 4.3% of samples.
  
  
  CONCLUSIONS
  In the very early stages of a new pandemic, limiting testing to only the novel virus will miss other clinically important co-circulating respiratory pathogens.
authors.forename: Vigneswary Mala
authors.initials: VM
authors.lastname: Ratnamohan
authors.forename: Janette
authors.initials: J
authors.lastname: Taylor
authors.forename: Frank
authors.initials: F
authors.lastname: Zeng
authors.forename: Kenneth
authors.initials: K
authors.lastname: McPhie
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Blyth
authors.forename: Sheena
authors.initials: S
authors.lastname: Adamson
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, Westmead Hospital, Westmead, New South Wales, Australia. dominic.dwyer@sydney.edu.au.
authors.forename: Dominic E
authors.initials: DE
authors.lastname: Dwyer
mesh_terms: D000293:Adolescent; D000328:Adult; D000818:Animals; D002648:Child; D002675:Child, Preschool; D060085:Coinfection / Q000175:diagnosis / Q000453:epidemiology / Q000821:virology; D005260:Female; D006801:Humans; D007251:Influenza, Human / Q000175:diagnosis* / Q000453:epidemiology* / Q000821:virology; D008297:Male; D009517:New South Wales / Q000453:epidemiology; D058873:Pandemics; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000453:epidemiology* / Q000821:virology; D014780:Viruses / Q000145:classification / Q000302:isolation & purification*