Opening up safely: public health system requirements for ongoing COVID-19 management based on evaluation of Australia’s surveillance system performance
Authors: Lokuge Kamalini , D’Onise Katina , Banks Emily , Street Tatum , Jantos Sydney , Baptista Mohana , Glass Kathryn 
Published: December 2021

Background

Ongoing management of COVID-19 requires an evidence-based understanding of the performance of public health measures to date, and application of this evidence to evolving response objectives. This paper aims to define system requirements for COVID-19 management under future transmission and response scenarios, based on surveillance system performance to date.

Methods

From 1st November 2020 to 30th June 2021 community transmission was eliminated in Australia, allowing investigation of system performance in detecting novel outbreaks, including against variants of concern (VoCs). We characterised surveillance systems in place from peer-reviewed and publicly available data, analysed the epidemiological characteristics of novel outbreaks over this period, and assessed surveillance system sensitivity and timeliness in outbreak detection. These findings were integrated with analysis of other critical COVID-19 public health measures to establish requirements for future COVID-19 management.

Findings

Australia reported 25 epidemiologically distinct outbreaks and 5 distinct clusters of cases in the study period, all linked through genomic sequencing to breaches in quarantine facilities housing international travellers. Most (21/30, 70%) were detected through testing of those with acute respiratory illness in the community, and 9 through quarantine screening. For the 21 detected in the community, the testing rate (percent of the total State population tested in the week preceding detection) was 2.07% on average, was higher for those detected while prior outbreaks were ongoing. For 17/30 with data, the delay from the primary case to detection of the index case was, on average 4.9 days, with 10 of the 17 outbreaks detected within 5 days and 3 detected after > 7days. One outbreak was preceded by an unexpected positive wastewater detection. Of the 24 outbreaks in 2021, 20 had publicly available sequencing data, all of which were VoCs. Surveillance for future VoCs using a similar strategy to that used for detecting SARS-CoV-2 to date would necessitate a 100-1,000-fold increase in capacity for genomic sequencing.

Interpretation

Australia’s surveillance systems performed well in detecting novel introduction of SARS-CoV-2 in a period when community transmission was eliminated, introductions were infrequent and case numbers were low. Detection relied on community surveillance in symptomatic members of the general population and quarantine screening, supported by comprehensive genomic sequencing. Once vaccine coverage is maximised, the priority for future COVID-19 control will shift to detection of SARS-CoV-2 Vos associated with increased severity of disease in the vaccinated and vaccine ineligible. This will require ongoing investment in maintaining surveillance systems and testing of all international arrivals, alongside greatly increased genomic sequencing capacity. Other essential requirements for managing voices are maintaining outbreak response capacity and developing capacity to rapidly engineer, manufacture, and distribute variant vaccines at scale. The most important factor in management of COVID-19 now and into the future will continue to be how effectively governments support all sectors of the community to engage in control measures.