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.

Wave of COVID-19 outbreaks in Gold Coast residential aged care facilities after easing travel restrictions into Queensland.

Objective: This paper describes outbreaks of coronavirus disease 2019 (COVID-19) in Gold Coast residential aged care facilities (RACFs), in the two months following the easing of travel restrictions at Queensland's domestic border on 13 December 2021. Methods: This audit reviewed all RACF COVID-19 outbreaks notified to the Gold Coast Public Health Unit between 13 December 2021 and 12 February 2022. An outbreak was defined by the Communicable Diseases Network Australia guidelines current at the time. Results: There were 60 COVID-19 outbreaks across 57 RACFs during this period. In 44 outbreaks (73.3%), a staff member was identified as the primary or co-primary case. Transmission amongst residents occurred in 48 outbreaks (80.0%). The attack rates in staff and residents were 17.0% (n = 1,060) and 11.7% (n = 645) respectively. A higher number of males were hospitalised (n = 39: 57.4%) or died (n = 28: 66.7%) than were females (n = 29: 42.6%; n = 14: 33.3% respectively). Most resident cases (n = 565: 87.6%) had received two or more doses of a COVID-19 vaccine. In resident cases who were under-vaccinated (n = 76), twenty (26.3%) required hospitalisation and nine (11.8%) died. In resident cases who received two doses of vaccine (n = 484), forty-three (8.9%) were hospitalised and 27 (5.8%) died. In resident cases who had received three doses (n = 80), four (5.0%) were hospitalised and five (6.3%) died. Conclusions: COVID-19 caused significant morbidity and mortality in Gold Coast RACFs following the easing of border restrictions. Higher rates of hospitalisation and death occurred in males than in females, and in under-vaccinated resident cases than in those vaccinated with at least two doses of a COVID-19 vaccine. Implications for public health: These data support the need for up-to-date COVID-19 vaccination of residents in RACFs, continued surveillance and timely and appropriate implementation of public health guidelines to manage COVID-19 outbreaks in RACFs.

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.

A Discrete-Event, Simulated Social Agent-Based Network Transmission (DESSABNeT) model for communicable diseases: Method and validation using SARS-CoV-2 data in three large Australian cities.

IMPORTANCE: During pandemics Agent Based Models (ABMs) can model complex, fine-grained behavioural interactions occurring in social networks, that contribute to disease transmission by novel viruses such as SARS-CoV-2. OBJECTIVE: We present a new agent-based model (ABM) called the Discrete-Event, Simulated Social Agent based Network Transmission model (DESSABNeT) and demonstrate its ability to model the spread of COVID-19 in large cities like Sydney, Melbourne and Gold Coast. Our aim was to validate the model with its disease dynamics and underlying social network. DESIGN: DESSABNeT relies on disease transmission within simulated social networks. It employs an epidemiological SEIRD+M (Susceptible, exposed, infected, recovered, died and managed) structure. One hundred simulations were run for each city, with simulated social restrictions closely modelling real restrictions imposed in each location. MAIN OUTCOME(S) AND MEASURE(S): The mean predicted daily incidence of COVID-19 cases were compared to real case incidence data for each city. Reff and health service utilisation outputs were compared to the literature, or for the Gold Coast with daily incidence of hospitalisation. RESULTS: DESSABNeT modelled multiple physical distancing restrictions and predicted epidemiological outcomes of Sydney, Melbourne and the Gold Coast, validating this model for future simulation work. CONCLUSIONS AND RELEVANCE: DESSABNeT is a valid platform to model the spread of COVID-19 in large cities in Australia and potentially internationally. The platform is suitable to model different combinations of social restrictions, or to model contact tracing, predict, and plan for, the impact on hospital and ICU admissions, and deaths; and also the rollout of COVID-19 vaccines and optimal social restrictions during vaccination.

Epidemiology and clinical features of COVID-19 outbreaks in aged care facilities: A systematic review and meta-analysis.

BACKGROUND: COVID-19 outbreaks in aged care facilities (ACFs) often have devastating consequences. However, epidemiologically these outbreaks are not well defined. We aimed to define such outbreaks in ACFs by systematically reviewing literature published during the current COVID-19 pandemic. METHODS: We searched 11 bibliographic databases for literature published on COVID-19 in ACFs between December 2019 and September 2020. Original studies reporting extractable epidemiological data as part of outbreak investigations or non-outbreak surveillance of ACFs were included in this systematic review and meta-analysis. PROSPERO registration: CRD42020211424. FINDINGS: We identified 5,148 publications and selected 49 studies from four continents reporting data on 214,380 residents in 8,502 ACFs with 25,567 confirmed cases of COVID-19. Aged care residents form a distinct vulnerable population with single-facility attack rates of 45% [95% CI 32-58%] and case fatality rates of 23% [95% CI 18-28%]. Of the cases, 31% [95% CI 28-34%] were asymptomatic. The rate of hospitalization amongst residents was 37% [95% CI 35-39%]. Data from 21 outbreaks identified a resident as the index case in 58% of outbreaks and a staff member in 42%. Findings from the included studies were heterogeneous and of low to moderate quality in risk of bias assessment. INTERPRETATION: The clinical presentation of COVID-19 varies widely in ACFs residents, from asymptomatic to highly serious cases. Preventing the introduction of COVID-19 into ACFs is key, and both residents and staff are a priority group for COVID-19 vaccination. Rapid diagnosis, identification of primary and secondary cases and close contacts plus their isolation and quarantine are of paramount importance. FUNDING: Queensland Advancing Clinical Research Fellowship awarded to Prof. Gulam Khandaker by Queensland Health's Health Innovation, Investment and Research Office (HIRO), Office of the Director-General.

COVID-19 in Australia: our national response to the first cases of SARS-CoV-2 infection during the early biocontainment phase.

BACKGROUND: On 31 December 2019, the World Health Organization recognised clusters of pneumonia-like cases due to a novel coronavirus disease (COVID-19). COVID-19 became a pandemic 71 days later. AIM: To report the clinical and epidemiological features, laboratory data and outcomes of the first group of 11 returned travellers with COVID-19 in Australia. METHODS: This is a retrospective, multi-centre case series. All patients with confirmed COVID-19 infection were admitted to tertiary referral hospitals in New South Wales, Queensland, Victoria and South Australia. RESULTS: The median age of the patient cohort was 42 years (interquartile range (IQR), 24-53 years) with six men and five women. Eight (72.7%) patients had returned from Wuhan, one from Shenzhen, one from Japan and one from Europe. Possible human-to-human transmission from close family contacts in gatherings overseas occurred in two cases. Symptoms on admission were fever, cough and sore throat (n = 9, 81.8%). Co-morbidities included hypertension (n = 3, 27.3%) and hypercholesterolaemia (n = 2, 18.2%). No patients developed severe acute respiratory distress nor required intensive care unit admission or mechanical ventilation. After a median hospital stay of 14.5 days (IQR, 6.75-21), all patients were discharged. CONCLUSIONS: This is a historical record of the first COVID-19 cases in Australia during the early biocontainment phase of the national response. These findings were invaluable for establishing early inpatient and outpatient COVID-19 models of care and informing the management of COVID-19 over time as the outbreak evolved. Future research should extend this Australian case series to examine global epidemiological variation of this novel infection.

Hepatitis B immunization for indigenous adults, Australia.

OBJECTIVE: To quantify the disparity in incidence of hepatitis B between indigenous and non-indigenous people in Australia, and to estimate the potential impact of a hepatitis B immunization programme targeting non-immune indigenous adults. METHODS: Using national data on persons with newly acquired hepatitis B disease notified between 2005 and 2012, we estimated incident infection rates and rate ratios comparing indigenous and non-indigenous people, with adjustments for underreporting. The potential impact of a hepatitis B immunization programme targeting non-immune indigenous adults was projected using a Markov chain Monte Carlo simulation model. FINDINGS: Of the 54 522 persons with hepatitis B disease notified between 1 January 2005 and 31 December 2012, 1953  infections were newly acquired. Acute hepatitis B infection notification rates were significantly higher for indigenous than non-indigenous Australians. The rates per 100 000 population for all ages were 3.6 (156/4 368 511) and 1.1 (1797/168 449 302) for indigenous and non-indigenous people respectively. The rate ratio of age-standardized notifications was 4.0 (95% confidence interval: 3.7-4.3). If 50% of non-immune indigenous adults (20% of all indigenous adults) were vaccinated over a 10-year programme a projected 527-549 new cases of acute hepatitis B would be prevented. CONCLUSION: There continues to be significant health inequity between indigenous and non-indigenous Australians in relation to vaccine-preventable hepatitis B disease. An immunization programme targeting indigenous Australian adults could have considerable impact in terms of cases of acute hepatitis B prevented, with a relatively low number needed to vaccinate to prevent each case.

Monitoring the introduction of pneumococcal conjugate vaccines into West Africa: design and implementation of a population-based surveillance system.

Routine use of pneumococcal conjugate vaccines (PCVs) in developing countries is expected to lead to a significant reduction in childhood deaths. However, PCVs have been associated with replacement disease with non-vaccine serotypes. We established a population-based surveillance system to document the direct and indirect impact of PCVs on the incidence of invasive pneumococcal disease (IPD) and radiological pneumonia in those aged 2 months and older in The Gambia, and to monitor changes in serotype-specific IPD. Here we describe how this surveillance system was set up and is being operated as a partnership between the Medical Research Council Unit and the Gambian Government. This surveillance system is expected to provide crucial information for immunisation policy and serves as a potential model for those introducing routine PCV vaccination in diverse settings.