COVID-19 Australia: Epidemiology Report 57: Reporting period ending 16 January 2022

Ibrahim A.F., Li A., Hao B., Schlegel C., Hood G.M., Agnew M., Kirk M.D., Jordan K., Kelly P.M., Gould P.

Abstract Background Years of life lost (YLL) is a measure of fatal burden, quantifying the toll associated with premature death. YLL is an important and useful metric for assessing the mortality impacts of the COVID-19 pandemic. In this study, we calculated the fatal burden associated with COVID-19 and other causes of death in Australia from 2019 to 2022. Methods The analysis was conducted using demographic and death data contained within the Person Level Integrated Data Asset. The study population included all deaths which occurred between 2019 to 2022 in Australia that were received and registered by the Australian Bureau of Statistic (ABS) by 31 March 2023. We calculated YLL using the 2019–2021 Australian life tables published by the ABS, which provided more contemporary single-age and gender breakdowns of aspirational life expectancy than standard reference life tables found in the Global Burden of Disease studies. Results Between 2019 and 2022, the fatal burden in Australia increased from an age-standardised YLL of 74.14 per 1,000 population in 2019 to 80.88 per 1,000 population in 2022, an increase of 9.1%. However, this increase was not linear, with a slight decrease observed in 2020, followed by a rise to baseline in 2021 and a continued increase in 2022. Throughout the four-year period, the YLL per 1,000 population in males was consistently around 1.5 times that observed for females, though females experienced a higher proportional increase in total fatal burden between 2019 and 2022 (10.1% in females compared to 8.8% in males). Fatal burden from COVID-19 increased considerably between 2020 to 2022. In 2022, based on age-standardised YLL per death, COVID-19 was the third leading cause of fatal burden in Australia, following cerebrovascular diseases and ‘other cardiac conditions’ (cardiac disease that is not coronary artery disease). The only conditions which showed a reduction in fatal burden in 2022 compared to 2019 were influenza and pneumonia and chronic lower respiratory diseases. Conclusions Our findings contribute to improving our understanding of the mortality impacts of the COVID-19 pandemic in Australia and how these have evolved over time. The results highlight areas of health where COVID-19 has had a disproportionate impact, which can support the implementation of more targeted and nuanced public health measures.

Wang Y., Ni G., Tian W., Wang H., Li J., Thai P., Choi P.M., Jackson G., Hu S., Yang B., Guo J.

The ongoing evolution of SARS-CoV-2 is a significant concern, especially with the decrease in clinical sequencing efforts, which impedes the ability of public health sectors to prepare for the emergence of new variants and potential COVID-19 outbreaks. Wastewater-based epidemiology (WBE) has been proposed as a surveillance program to detect and monitor the SARS-CoV-2 variants being transmitted in communities. However, research is limited in evaluating the effectiveness of wastewater collection at sentinel sites for monitoring disease prevalence and variant dynamics, especially in terms of inferring the epidemic patterns on a broader scale, such as at the state/province level. This study utilized a multiplexed tiling amplicon-based sequencing (ATOPlex) to track the longitudinal dynamics of variant of concern (VOC) in wastewater collected from municipalities in Queensland, Australia, spanning from 2020 to 2022. We demonstrated that wastewater epidemiology measured by ATOPlex exhibited a strong and consistent correlation with the number of daily confirmed cases. The VOC dynamics observed in wastewater closely aligned with the dynamic profile reported by clinical sequencing. Wastewater sequencing has the potential to provide early warning information for emerging variants. These findings suggest that WBE at sentinel sites, coupled with sensitive sequencing methods, provides a reliable and long-term disease surveillance strategy.

Inacio M.C., Davies L., Jorissen R., Air T., Eshetie T., Mittinty M., Caughey G., Miller C., Wesselingh S.

Abstract Background To date, the excess mortality experienced by residential aged care facility (RACF) residents related to COVID-19 has not been estimated in Australia. This study examined (i) the historical mortality trends (2008–09 to 2021–22) and (ii) the excess mortality (2019–20 to 2021–22) of Australian RACF residents. Methods A retrospective population-based study was conducted using the Australian Institute of Health and Welfare’s GEN website data (publicly available aged care services information). Non-Aboriginal, older (≥65 years old) RACF residents between 2008–09 and 2021–22 were evaluated. The observed mortality rate was estimated from RACF exits compared with the RACF cohort yearly. Direct standardization was employed to estimate age-standardized mortality rates and 95% CIs. Excess mortality and 95% prediction intervals (PIs) for 2019–20 to 2021–22 were estimated using four negative binomial (NB) and NB generalized additive models and compared. Results The age-standardized mortality rate in 2018–19 was 23 061/100 000 residents (95% CI, 22 711–23 412). This rate remained similar in 2019–20 (23 023/100 000; 95% CI, 22 674–23 372), decreased in 2020–21 (22 559/100 000; 95% CI, 22 210–22 909) and increased in 2021–22 (24 885/100 000; 95% CI, 24 543–25 227). The mortality rate increase between 2020–21 and 2021–22 was observed in all age and sex groups. All models yielded excess mortality in 2021–22. Using the best-performing model (NB), the excess mortality for 2019–20 was –160 (95% PI, –418 to 98), –958 (95% PI, –1279 to –637) for 2020–21 and 4896 (95% PI, 4503–5288) for 2021–22. Conclusions In 2021–22, RACF residents, who represented <1% of the population, experienced 21% of the Australian national excess mortality (4896/22 886). As Australia adjusts to COVID-19, RACF residents remain a population vulnerable to COVID-19.

Li R., Liu H., Fairley C.K., Ong J.J., Guo Y., Lu P., Zou Z., Xie L., Zhuang G., Li Y., Shen M., Zhang L.

Australia implemented an mRNA-based booster vaccination strategy against the COVID-19 Omicron variant in November 2021. We aimed to evaluate the effectiveness and cost-effectiveness of the booster strategy over 180 days.We developed a decision-analytic Markov model of COVID-19 to evaluate the cost-effectiveness of a booster strategy (administered 3 months after 2nd dose) in those aged ≥ 16 years, from a healthcare system perspective. The willingness-to-pay threshold was chosen as A$ 50,000.Compared with 2-doses of COVID-19 vaccines without a booster, Australia's booster strategy would incur an additional cost of A$0.88 billion but save A$1.28 billion in direct medical cost and gain 670 quality-adjusted life years (QALYs) in 180 days of its implementation. This suggested the booster strategy is cost-saving, corresponding to a benefit-cost ratio of 1.45 and a net monetary benefit of A$0.43 billion. The strategy would prevent 1.32 million new infections, 65,170 hospitalisations, 6,927 ICU admissions and 1,348 deaths from COVID-19 in 180 days. Further, a universal booster strategy of having all individuals vaccinated with the booster shot immediately once their eligibility is met would have resulted in a gain of 1,599 QALYs, a net monetary benefit of A$1.46 billion and a benefit-cost ratio of 1.95 in 180 days.The COVID-19 booster strategy implemented in Australia is likely to be effective and cost-effective for the Omicron epidemic. Universal booster vaccination would have further improved its effectiveness and cost-effectiveness.

Hall R., Jones A., Crean E., Marriott V., Pingault N., Marmor A., Sloan-Gardner T., Kennedy K., Coleman K., Johnston V., Schwessinger B.

SummaryThe Australian Capital Territory rapidly responded to an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant on 12 August 2021 with several public health interventions, including a territory-wide lockdown and genomic sequencing. Prior to this date, SARS-CoV-2 had been eliminated locally since July 7, 2020. Sequencing of >75% of cases identified at least 13 independent incursions with onwards spread in the community during the study period, between 12 August and 11 November 2021. Two incursions resulted in the majority of community transmission during this period, with persistent transmission in vulnerable sections of the community. Ultimately, both major incursions were successfully mitigated through public health interventions, including COVID-19 vaccines. In this study we explore the demographic factors that contributed to the spread of these incursions. The high rates of SARS-CoV-2 sequencing in the Australian Capital Territory and the relatively small population size facilitated detailed investigations of the patterns of virus transmission. Genomic sequencing was critical to disentangling complex transmission chains to target interventions appropriately.Despite a strict lockdown and interstate travel restrictions, the Australian Capital Territory experienced at least 13 incursions of SARS-CoV-2 Delta (B.1.617.2) with onwards spread in the community between 12 August and 11 November 2021.This level of detail was only accessible because of the high rate of SARS-CoV-2 sequencing, with sequencing attempted on 1438/1793 (80%) of cases.Transmission chains varied in size and duration, with two dominant incursions (ACT.19 and ACT.20) comprising 35% and 53% of all sequenced cases during the study period, respectively.The ACT.20 outbreak persisted longer, due to specific challenges with implementing public health interventions in the affected populations.Both major incursions were successfully curbed through stringent public health measures, including the widespread acceptance of COVID-19 vaccines (>95% of the eligible population by the end of the study period).

Li R., Liu H., Fairley C.K., Ong J.J., Guo Y., Zou Z., Xie L., Zhuang G., Li Y., Shen M., Zhang L.

AbstractBackgroundAustralia implemented an mRNA-based booster vaccination strategy against the COVID-19 Omicron variant in November 2021. We aimed to evaluate the effectiveness and cost-effectiveness of the booster strategy over 180 days.MethodsWe developed a decision-analytic Markov model of COVID-19 to evaluate the cost-effectiveness of a booster strategy (administered 3 months after 2nd dose) in those aged ≥16 years in Australia from a healthcare system perspective. The willingness-to-pay threshold was chosen as A$ 50,000.FindingsCompared with 2-doses of COVID-19 vaccines without a booster, Australia’s booster strategy would incur an additional cost of A$0.88 billion but save A$1.28 billion in direct medical cost and gain 670 quality-adjusted life years (QALYs) in 180 days of its implementation. This suggested the booster strategy is cost-saving, corresponding to a benefit-cost ratio of 1.45 and a net monetary benefit of A$0.43 billion. The strategy would prevent 1.32 million new infections, 65,170 hospitalisations, 6,927 ICU admissions and 1,348 deaths from COVID-19 in 180 days. Further, a universal booster strategy of having all individuals vaccinated with the booster shot immediately once their eligibility is met would have resulted in a gain of 1,599 QALYs, a net monetary benefit of A$1.46 billion and a benefit-cost ratio of 1.95 in 180 days.InterpretationThe COVID-19 booster strategy implemented in Australia is likely to be effective and cost-effective for the Omicron epidemic. Universal booster vaccination would have further improved its effectiveness and cost-effectiveness.FundingNational Natural Science Foundation of China. Bill and Melinda Gates Foundation