Influenza (flu) and other respiratory virus surveillance

Over a number of years, ESR has developed acute respiratory illness surveillance systems in selected clinical settings across New Zealand to provide a robust understanding of the burden of disease due to these viruses in New Zealand in near real-time.

Surveillance for acute respiratory illness that encompasses viral testing allows for tracking of influenza (flu) as well as other viruses that cause similar symptoms including those that could be newly emerging. Reports on influenza and other respiratory viruses can be found here – current week(external link)historical(external link), and laboratory-based virologic surveillance.
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Surveillance Systems

The sentinel (in selected sites around the country) surveillance systems that ESR coordinate to monitor respiratory viruses in the population are described below.

  1. Hospital and Intensive Care Unit (ICU) – Sentinel hospital-based surveillance for influenza is conducted on patients admitted overnight with severe acute respiratory infections (SARI), defined by the World Health Organisation (WHO) as the acute onset of cough and fever in the previous 10 days (external link)requiring hospitalisation(external link). This system was established during 2012 in the four public hospitals in central, east and south Auckland (population 906,000) as part of the Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance Project(external link)(SHIVERS), funded by the United States Centers for Disease Control and Prevention. All patients defined as SARI are tested for influenza and a panel of other respiratory viruses. Intensive care unit admissions and deaths among SARI patients are also monitored. ESR do not routinely report on seasonal mortality.  It is difficult to determine the exact numbers of deaths each season which are due to influenza because influenza virus infection may be one of many factors contributing to a person’s death. Previously published modelling(external link) work has estimated that there are around 500 influenza related deaths in New Zealand each year.
  2. Emergency room– Starting in 2018, emergency department (ED) visits in the Capital and Coast District health Board (Wellington region) that are flagged as acute respiratory illnesses based International Classification of Disease (ICD) codes, are tracked. Additional EDs from around New Zealand are being approached for inclusion in this system. This surveillance is entirely syndromic, and therefore, does not include virologic testing. Such syndromic monitoring (external link)is now commonly used internationally as part of influenza surveillance. ED data will be presented on the dashboard in the coming weeks.
  3. HealthStat, general practice surveillance – This sentinel surveillance system is managed by CBG Health Research Limited. This system extracts ILI data from a random sample of around 300 General Practices via practice management system (PMS) software, and sends data weekly to ESR.  More information on HealthStat is available here(external link).
  4. Community virological surveillance is currently being established for 2020. Respiratory samples for influenza and non-influenza respiratory virus testing will be collected from patients who visit general practice with ILI symptoms based on a defined sampling scheme.
  5. HealthLine – Calls made to the Healthline, the free, national, 24 hour telephone health advice service funded by the Ministry of Health, are triaged using electronic clinical decision support software. Calls coded as Cold/Flu; Cough; Croup; Fever (symptom); General Aches; Headache; Sore Throat are counted as influenza-like illness (ILI). Non-symptomatic calls (30% of Healthline calls) are excluded.
  6. FluTracking is on online health surveillance system that was launched in New Zealand in 2018. Over 60,000 registered New Zealand volunteers complete a weekly survey to record the presence of typical flu-like symptoms such as fever and cough. More information on FluTracking is available here(external link)

Viral Identification and Characterisation Methods

Nasopharyngeal samples are collected on consenting patients. Swabs collected through sentinel general practice Influenza-like Illness (ILI) surveillance and samples collected at sentinel hospitals by surveillance nurses are forwarded to the Institute for Environmental Science and Research (ESR) for testing. These samples are tested for Influenza and certain other respiratory viruses (respiratory syncytial virus, parainfluenza virus 1–3, human metapneumovirus, rhinovirus and adenovirus) using the United States Centers of Disease Control and Prevention (US CDC) real-time RT–PCR protocol. Samples forwarded to ESR that are found to be Influenza positive undergo antigenic, genetic and antiviral characterization either at ESR or the WHO collaborating centres in Melbourne.

The laboratories serving the sentinel hospitals conducting severe acute respiratory infection (SARI), test samples taken from patients based on clinicians’ orders using existing laboratory protocols. Results from these tests for SARI patients are forwarded to ESR for integration into surveillance measures.

Analytic Methods

Rate Calculations

Population data used to calculate rates of hospitalisations, Healthline calls, Emergency Department visits, and immunisation coverage are derived from mid-year population estimates published by Statistics New Zealand. General practice visit rates are calculated using registered patient populations provided by general practices participating in sentinel surveillance. Registered patient counts are limited further to participating clinicians, if not all practice clinicians are contributing to surveillance.

Presented rates are unadjusted.

MEM Thresholds

MEM is a standardised method of reporting influenza activity adopted by the European Centre for Disease Prevention and Control that allows intra- and inter- country comparisons. MEM defines the baseline influenza activity in historical data and establishes an epidemic threshold above which the weekly rates are considered to be in the epidemic period. Based on the historical data, influenza activity intensity is then also described according to categories as follows: (i) baseline: weekly rate is below or at the baseline epidemic threshold; (ii) low: weekly rate is above the baseline threshold and below the medium threshold; (iii) medium: weekly rate is between the medium and high intensity thresholds (iv) high: weekly rate is between the high and very high intensity thresholds; (v) very high: weekly rate is above the very high intensity threshold.

The historical data used to calculate the MEM thresholds for the GP ILI surveillance graph has been collected by ESR over the years 2000 to 2017, excluding the pandemic year 2009.  The thresholds are set at the 40%, 90%, and 97.5% confidence intervals, and labelled "Low seasonal level", "Moderate Seasonal Level", and "High Seasonal Level".  The level at which the season is defined as having started is labelled "Baseline Seasonal Level".


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Heim A, et al. Rapid and quantitative detection of human adenovirus DNA by real-time PCR. Journal of Medical Virology. 2003;70:228–39. doi: 10.1002/jmv.10382.

Lu X, et al. Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses. Journal of Clinical Microbiology. 2008;46:533–9. doi: 10.1128/JCM.01739-07.

WHO Global Influenza Surveillance Network. Manual for the laboratory diagnosis and virological surveillance of influenza. Geneva: World Health Organization; 2011. 153 pp.

Vega T Lozano JE, Meerhoff T, Snacken R, Mott J, Ortiz de Lejarazu R. Influenza surveillance in Europe: establishing epidemic thresholds by the moving epidemic method.   Influenza Other Respi Viruses. 2013;7(4):546-58. DOI: 10.1111/j.1750-2659.2012.00422.x PMID: 22897919

 Green HK, Charlett A, Moran-Gilad J, Fleming D, Durnall H, Thomas DR. Harmonizing influenza primary-care surveillance in the United Kingdom: piloting two methods to assess the timing and intensity of the seasonal epidemic across several general practice-based surveillance schemes.   Epidemiol Infect. 2015;143(1):1-12. DOI: 10.1017/S0950268814001757 PMID: 25023603

Vega T Lozano JE, Meerhoff T, Snacken R, Beauté J, Jorgensen P. Influenza surveillance in Europe: comparing intensity levels calculated using the moving epidemic method.   Influenza Other Respi Viruses. 2015;9(5):234-46. DOI: 10.1111/irv.12330 PMID: 26031655

Lozano Alonso JE. Mem: Moving Epidemics Method, R Package v. 2.11; 2017. Available from:

Laboratory-based virologic surveillance

ESR's virology laboratory carries out year-round laboratory-based surveillance of influenza and other viruses, together with four regional laboratories. These laboratories report all virus diagnoses made, largely from hospital in-patients and outpatients, to ESR. This data is reported nationally in the ESR Virology Weekly Reports on the New Zealand Public Health Surveillance website(external link)

Previous Influenza Intelligence Reports

 2018 New Zealand influenza intelligence reports(external link)