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Updated: May 18, 2026
High-throughput Detection Method for Influenza Virus
Published on: February 4, 2012
Sequence-based identification and characterization of nosocomial influenza A(H1N1)pdm09 virus infections
M Jonges1, J Rahamat-Langendoen, A Meijer
1National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands. marcel.jonges@rivm.nl
Background:
Highly transmissible viruses such as influenza are a potential source of nosocomial infections and thereby cause increased patient morbidity and mortality.
Aim:
To assess whether influenza virus sequence data can be used to link nosocomial influenza transmission between individuals.
Methods:
Dutch A(H1N1)pdm09-positive specimens from one hospital (N = 107) were compared with samples from community cases (N = 685). Gene fragments of haemagglutinin, neuraminidase and PB2 were sequenced and subsequently clustered to detect patients infected with identical influenza viruses. The probability of detecting a second patient was calculated for each hospital cluster against the background diversity observed in hospital and community strains. All clusters were further analysed for possible links between patients.
Findings:
Seventeen A(H1N1)pdm09 hospital clusters were detected of which eight had a low probability of occurrence compared with background diversity (P < 0.01). Epidemiological analysis confirmed a total of eight nosocomial infections in four of these eight clusters, and a mother-child combination in a fifth cluster. The nine clusters with a high probability of occurrence involved community cases of influenza without a known epidemiological link.
Conclusion:
If a background sequence dataset is available, the detection of hospital sequence clusters that differ from dominant community strains can be used to select clusters requiring further investigation by hospital hygienists before a nosocomial influenza outbreak is epidemiologically suspected.
