Table 1 Surveillance system requirements based on scenarios for COVID-19 epidemiology

A. While COVID-19 vaccination programme being rolled out

Risk of substantial morbidity and mortality requires maintaining current community-based surveillance for disease and screening protocols for returned overseas travellers and staff in quarantine facilities, supported by genomic sequencing.

As per current requirements, i.e. as current surveillance system requirements are influenced by community acute respiratory illness level rather than SARS-CoV-2 rates [35], capacity requirements will be dictated by levels of ARI in the community.

Nil to maintain performance. However, if performance was improved, this is likely to make control of outbreaks, especially due to novel variants, easier to control.

Performance could be further improved through improving testing rates (currently <50%) and timeliness in the symptomatic, particularly in communities at risk of low engagement in health interventions, and in high-risk occupations (e.g. healthcare workers).

B (1) current vaccination programme completed; herd immunity achieved; current variants circulating

Even if importations increase, transmission will be self-limiting in the general population, as the reproductive number will remain below 1 overall.

If herd immunity or even close to herd immunity is achieved through vaccination, SARS-CoV-2 levels will remain low, and community surveillance capacity will continue to be related to non-SARS-CoV-2 ARI rates.

Surveillance capacity will continue depending on background ARI rates (e.g. 4–6% of the population per week during the study period [25], likely to increase once social and mobility restrictions are fully lifted).

Focus will need to include communities at risk of low uptake of health interventions, which may experience increased disease circulation and morbidity and mortality of both vaccine coverage and testing uptake are low.

B (2) current vaccination programme is completed; herd immunity not achieved, current variants of concern circulating

If herd immunity is not achieved through vaccination, and a decision is made not to utilise non-pharmaceutical interventions to a level that would eliminate transmission, this will mean endemic circulation of SARS-CoV-2, with the level of circulation dependent on the impact of the public health measures left in place.

It is likely that SARS-CoV-2 levels will eventually reach levels similar to other acute respiratory illnesses. If SARS-CoV-2 displaces other respiratory viruses [36], overall ARI levels will remain constant, and therefore also surveillance requirements. If COVID-19 infections are additive to the existing ARI burden, an increase in community surveillance capacity will be required.

If surveillance capacity needs to increase substantially, alternatives to PCR will be needed. For example, rapid antigen tests are already in widespread use in developed high-burden settings such as the UK and USA [37]. Although of lower sensitivity [37], overall performance will be similar or better than PCR if they facilitate more widespread and frequent screening. Prior analysis has shown that at a population prevalence of 3%, a test with 80% sensitivity that can test all the population exhaustively will miss 24% of cases, whereas test with 99.9% sensitivity, but which can only test a third of the population under surveillance, will miss 66% of cases in the population overall [35].

C. Emergence of new variants of concern

Given the characteristics of the virus to date, there is potential for new variants of concern to emerge that result in increased severity of disease, including in the vaccinated, as long as transmission is widespread globally [38].

The first level of surveillance for variants of concern relies on detecting SARS-CoV-2, and therefore the requirements outlined in the sections above apply. In addition, testing would need to include a greatly increased number of international arrivals.

The second level of surveillance for early and effective detection of variants will rely on genomic sequencing of either all or an adequate proportion of all detected SARS-CoV-2 in the community and in international arrivals.

To achieve similar performance in detecting variants of concern as current capacity to detect SARS-CoV-2, sequencing capacity will need to be similar to current PCR-testing capacity, i.e. 1–2% of the population

This equates to 200,000–400,000 samples per week nationally, given Australia’s population of ~21million. This is a >1000-fold increase from current sequencing levels.