Estimating the incidence of COVID-19, influenza and respiratory syncytial virus infection in three regions of Queensland, Australia, winter 2022: findings from a novel longitudinal testing-based sentinel surveillance programme

OBJECTIVE

The 2022 Australian winter was the first time that COVID-19, influenza and respiratory syncytial virus (RSV) were circulating in the population together, after two winters of physical distancing, quarantine and borders closed to international travellers. We developed a novel surveillance system to estimate the incidence of COVID-19, influenza and RSV in three regions of Queensland, Australia.

DESIGN

We implemented a longitudinal testing-based sentinel surveillance programme. Participants were provided with self-collection nasal swabs to be dropped off at a safe location at their workplace each week. Swabs were tested for SARS-CoV-2 by PCR. Symptomatic participants attended COVID-19 respiratory clinics to be tested by multiplex PCR for SARS-CoV-2, influenza A and B and RSV. Rapid antigen test (RAT) results reported by participants were included in the analysis.

SETTING AND PARTICIPANTS

Between 4 April 2022 and 3 October 2022, 578 adults were recruited via their workplace. Due to rolling recruitment, withdrawals and completion due to positive COVID-19 results, the maximum number enrolled in any week was 423 people.

RESULTS

A total of 4290 tests were included. Participation rates varied across the period ranging from 25.9% to 72.1% of enrolled participants. The total positivity of COVID-19 was 3.3%, with few influenza or RSV cases detected. Widespread use of RAT may have resulted in few symptomatic participants attending respiratory clinics. The weekly positivity rate of SARS-CoV-2 detected during the programme correlated with the incidence of notified cases in the corresponding communities.

CONCLUSION

This testing-based surveillance programme could estimate disease trends and be a useful tool in settings where testing is less common or accessible. Difficulties with recruitment meant the study was underpowered. The frontline sentinel nature of workplaces meant participants were not representative of the general population but were high-risk groups providing early warning of disease.

Protocol for a winter sentinel surveillance program of notifiable respiratory viruses in Queensland

BACKGROUND

With the reduction in access to polymerase chain reaction (PCR) testing and changes in testing guidelines in Australia, a reduced number of people are seeking testing for coronavirus disease (COVID-19), limiting the opportunity to monitor disease transmission. Knowledge of community transmission of COVID-19 and other respiratory viruses is essential to better predict subsequent surges in cases during the pandemic to alert health services, protect vulnerable populations and enhance public health measures. We describe a methodology for a testing-based sentinel surveillance program to monitor disease in the community for early signal detection of SARS-CoV-2 and other respiratory viruses.

METHODS/DESIGN

A longitudinal active testing-based sentinel surveillance program for respiratory viruses (including SARS-CoV-2, influenza A, influenza B and Respiratory Syncytial Virus) will be implemented in some regions of Queensland. Adults will be eligible for enrolment if they are part of specific community groups at increased risk of exposure and have not had a COVID-19 infection in the last 13 weeks. Recruitment via workplaces will occur in-person, via email and through online advertisement. Asymptomatic participants will be tested via PCR for SARS-CoV-2 infection by weekly self-collected nasal swabs. In addition, symptomatic participants will be asked to seek SARS-CoV-2 and additional respiratory virus PCR testing at nominated COVID-19 testing sites. SARS-CoV-2 and respiratory virus prevalence data will be analysed weekly and at the end of the study period.

DISCUSSION

Once implemented, this surveillance program will determine the weekly prevalence of COVID-19 and other respiratory viruses in the broader community by testing a representative sample of adults, with an aim to detect early changes in the baseline positivity rate. This information is essential to define the epidemiology of SARS-CoV-2 in the community in near-real time to inform public health control measures and prepare health services and other stakeholders for a rise in service demand.

Defining the peak: Point prevalence of SARS-CoV-2 using randomised sampling

Since Queensland eased border restrictions to the rest of Australia on 13 December 2021, notified cases of Coronavirus disease 2019 (COVID-19) dramatically increased, with the SARS-CoV-2 Omicron variant now the most widespread variant of concern: 145,881 cases and 13 deaths were recorded in Queensland in the month following the opening of the border. For an effective public health response to a highly transmissible disease, it is important to know the prevalence in the community, but the exponential increase in cases meant that many with symptoms had difficulty getting tested. We implemented a surveillance program on the Gold Coast that used a modified randomised household cluster survey method to estimate the point prevalence of individuals with SARS-CoV-2 detected by polymerase chain reaction (PCR). The estimated point prevalence of SARS-CoV-2 detected by PCR on self-collected swabs was 17.2% on the first visit to households (22 January 2022). This subsequently decreased to 5.2% (5 February 2022) and finally to 1.1% (19 February 2022). Out of 1,379 specimens tested over five weeks, 63 had detected SARS-CoV-2 and 35 (55.6%) were sequenced. All were SARS-CoV-2 variant: B.1.1.529 (i.e. Omicron). This surveillance program could be scaled up or reproduced in other jurisdictions to estimate the prevalence of COVID-19 in the community.

Since Queensland eased border restrictions to the rest of Australia on 13 December 2021, notified cases of Coronavirus disease 2019 (COVID-19) dramatically increased, with the SARS-CoV-2 Omicron variant now the most widespread variant of concern: 145,881 cases and 13 deaths were recorded in Queensland in the month following the opening of the border. For an effective public health response to a highly transmissible disease, it is important to know the prevalence in the community, but the exponential increase in cases meant that many with symptoms had difficulty getting tested. We implemented a surveillance program on the Gold Coast that used a modified randomised household cluster survey method to estimate the point prevalence of individuals with SARS-CoV-2 detected by polymerase chain reaction (PCR). The estimated point prevalence of SARS-CoV-2 detected by PCR on self-collected swabs was 17.2% on the first visit to households (22 January 2022). This subsequently decreased to 5.2% (5 February 2022) and finally to 1.1% (19 February 2022). Out of 1,379 specimens tested over five weeks, 63 had detected SARS-CoV-2 and 35 (55.6%) were sequenced. All were SARS-CoV-2 variant: B.1.1.529 (i.e. Omicron). This surveillance program could be scaled up or reproduced in other jurisdictions to estimate the prevalence of COVID-19 in the community.