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 VoCs 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 VoCs 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.