NSW Health continually reviews the methods used to monitor respiratory virus activity in New South Wales. This is due to the changes in testing, notification patterns and levels of respiratory infections, including COVID-19, in the community. These changes affect the usefulness of notifications for monitoring activity and community transmission over time. The Public Health, Rapid, Emergency and Syndromic Surveillance (PHREDSS) data, COVID-19 sewage surveillance program, whole genome sequencing (WGS) data, sentinel laboratory respiratory virus test results and all-cause mortality are currently of most value for monitoring the activity and impact of COVID-19 and other respiratory infections of importance in the community.

Significant changes to COVID-19 monitoring in NSW in 2023:

  • PCR testing at public COVID-19 test clinics ceased on 14 May 2023. PCR tests could only be undertaken via a referral from a medical practitioner.
  • Registration of positive COVID-19 rapid antigen tests (RAT) in NSW ceased on 30 September 2023. From then, notifications predominantly reflect cases referred by a doctor for PCR.

The frequency of production of the Respiratory Surveillance Report is weekly during the winter respiratory season and fortnightly at other times of the year.

Case notifications

Information related to notifications of COVID-19, influenza and respiratory syncytial virus (RSV) are collected in the NSW Notifiable Conditions Information Management System (NCIMS) and stored for analysis in Notifiable Conditions Records for Epidemiology and Surveillance (NCRES). These data assets are managed by Health Protection NSW. Notification data reported in the weekly report are sourced from NCRES. Data is updated as additional information becomes available, therefore data cannot be compared to previous published reports. Notifications are included if they are for a resident of NSW and meet national guidelines for case definitions. Notification rates per 100,000 population by age and Local Health Districts are calculated using the NSW annual estimated resident population sourced by NSW Health from the Australian Bureau of Statistics.


If a person dies in NSW, their death must be registered under the Births, Deaths and Marriages Registration Act 1995 (Part 7). NSW Health receives a secure feed from the NSW Registry of Births, Deaths and Marriages (BDM) on a daily basis under the Public Health Act 2010 (Part 129A). Deaths reported to a coroner will be registered with the BDM, however cause of death information may be delayed as it is not recorded until there is a coronial determination.

A comprehensive way to estimate the total impact of the COVID-19, and other prolonged and significant health threats, on deaths is to measure changes in the overall number of deaths in a community (regardless of cause), using an indicator called all-cause mortality.

Method for the weekly all-cause mortality graph

This analysis includes all deaths registered in NSW, including overseas and interstate visitors, sourced from the BDM. We report mortality up to 4 weeks prior to the date of analysis. Not all deaths are registered in this time (in 2023, 95% of deaths were registered within 6 weeks), therefore death rates are corrected to reflect delays in the most recent weeks. A time series of weekly counts of deaths from January 2017 to 2024 year-to-date are presented. The date of death is used to count deaths in a week ending Sunday. Mortality rates are calculated using 2022 NSW Department of Planning and Environment population projections. The seasonal baseline is estimated by modelling all-cause mortality rates using seasonally adjusted robust regression. In 2024, deaths from 2017-2023 (excluding 2020 and 2022) are used to fit the model and forecast the seasonal baseline for 2024. The usual variation limits are estimated as 1.96 standard errors above and below the seasonal baseline (95% confidence interval).

This analysis is undertaken as part the surveillance of all-cause mortality in NSW, which examines mortality in the presence of ongoing SARS-CoV-2 and respiratory virus transmission, with resulting impacts including COVID-19, influenza and RSV infection. This is not the same approach as that used by the Australian Bureau of Statistics or by the Actuaries Institute to examine excess mortality associated with COVID-19 during the pandemic period.

COVID-19 Sewage Surveillance Program

The NSW Sewage Surveillance Program tests untreated sewage for fragments of the SARS-CoV-2 virus that causes COVID-19. Gene copy numbers are influenced by many factors including virus shedding by people (which varies individually and over the course of the infection), dilution of virus within sewage – such as during rain, the period over which the sewage sample is collected, and the presence of chemicals and microorganisms in the sewage that affects how well the testing can detect SARS-CoV-2 virus fragments. Gene concentrations are normalised to 1,000 people per catchment and adjusted for sewer discharge flows. Time-series of these normalised gene concentrations are averaged by week (ending Saturday) then smoothed with exponential moving averages with a backward window length of four weeks. These time series are presented for the three Sydney metro sites (Bondi, Liverpool and Quaker’s Hill) and a Newcastle site (Hunter - Burwood Beach). Trends should be interpreted over an extended period and fluctuations considered in the context of environmental conditions.

Public Health Rapid, Emergency, Disease and Syndromic Surveillance

The NSW Public Health Rapid, Emergency, Disease and Syndromic Surveillance (PHREDSS) system provides daily monitoring of most unplanned presentations to NSW public hospital emergency departments (EDs) and all emergency Triple Zero (000) calls to NSW Ambulance. Emergency hospital presentations and ambulance calls are grouped into related acute illness and injury categories. The number of presentations and calls in each category is monitored over time to quickly identify unusual patterns of illness. Unusual patterns could signify an emerging outbreak of disease or issue of public health importance in the population. PHREDSS is also useful for monitoring the impact of seasonal and known disease outbreaks, such as seasonal influenza or gastroenteritis, on the NSW population. The 88 NSW public hospital EDs used in PHREDSS surveillance account for 95% of all ED activity in NSW public hospitals in 2020-2021, including most major metropolitan public hospitals (99%) and rural public hospitals (89%).

PHREDSS ED diagnosis-based surveillance syndromes include clinician applied provisional diagnoses (ICD9, ICD-10AM or SNOMED-CT codes):

  • Bronchiolitis (0-4 years): associated with the clinical syndrome of viral bronchiolitis in infants and is usually caused by RSV or other common respiratory viruses.
  • COVID-19: coronavirus infections SARS-CoV-2 and other coronaviruses, or clinical condition of Severe Acute Respiratory Syndrome (SARS). Although the surveillance syndrome includes a range of coronavirus diagnoses, current activity reflects disease associated with circulating SARS-CoV-2.
  • ILI (influenza-like illness): influenza-like illness (ILI), influenza, including pneumonia with influenza and avian and other new influenza viruses.

The PHREDDS graphs published in the report reflect the number of ED presentations for the specific syndrome and the number and proportion of presentations to the ED requiring an admission. The latter data are an indicator of disease severity.

COVID-19 Whole Genomic Sequencing

Whole genome sequencing (WGS) is a laboratory procedure that identifies the genetic profile of an organism. WGS can help understand how a virus transmits, responds to vaccination, and the severity of disease it may cause. It can also help to monitor the spread of the virus by identifying specimens that are genomically similar. WGS has been used in NSW since the start of the COVID-19 pandemic to inform epidemiological investigations, and to monitor for and analyse the behaviour of new SARS-CoV-2 variants circulating in the community. WGS is conducted at three NSW reference laboratories.

Community samples are sourced from cases who test via PCR at community pathology services and may not necessarily reflect the distribution in all cases across NSW. NSW continues to monitor results from cases who are admitted to ICU to monitor for increased disease severity and from cases who return from overseas to monitor for new variants introduced into NSW. As COVID-19 cases decline, data should be interpreted with caution.


FluTracking is an online health surveillance system used to detect epidemics of influenza across Australia and New Zealand. Participants complete an online survey each week to provide community level influenza-like illness surveillance, consistent surveillance of influenza activity across all jurisdictions over time, and year to year comparisons of the timing, attack rates and seriousness of influenza in the community. Participants are given the option of not continuing to report over the summer season. For more information and ways to be involved visit FluTracking.

NSW sentinel laboratory network

The NSW sentinel laboratory network comprises 13 public and private laboratories throughout NSW who provide additional data on positive and negative test results for common respiratory viruses. These include COVID-19 (4 laboratories only), influenza, RSV, parainfluenza, adenovirus, rhinovirus, human metapneumovirus and enterovirus. These data enable the determination of test positivity, that is among the people who have been tested, how many test positive. A high positivity suggests high transmission in the community. The number of laboratories that report vary each week; updated data may not be published if the number of reports is insufficient for meaningful interpretation.

Current as at: Thursday 21 March 2024
Contact page owner: Health Protection NSW