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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

Vigneswary Mala Ratnamohan1, Janette Taylor2, Frank Zeng1, Kenneth McPhie1, Christopher C Blyth34, Sheena Adamson5, Jen Kok167 and Dominic E Dwyer1267*

Author Affiliations

1 Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia

2 Centre for Virus Research, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales, Australia

3 School of Paediatrics and Child Health, University of Western Australia, Crawley, Western Australia, Australia

4 Department of Paediatrics and Adolescent Medicine and PathWest Laboratory Medicine WA, Princess Margaret Hospital, Subiaco, Western Australia, Australia

5 Communicable Diseases Branch, Health Protection New South Wales, New South Wales Health, North Sydney, New South Wales, Australia

6 Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia

7 Centre for Research Excellence in Critical Infections, University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia

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Virology Journal 2014, 11:113  doi:10.1186/1743-422X-11-113

Published: 18 June 2014



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.


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.


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.

Influenza; A(H1N1)pdm09; Pandemic; Respiratory viruses