Surveillance key to dealing with novel SARS-CoV-2 variants of concern

In a recent study published on the medRxiv* preprint server, a team of researchers critically evaluated the performance of public health surveillance systems in detecting coronavirus disease 2019 (COVID-19) community outbreaks in Australia while simultaneously characterizing the epidemiology of the novel outbreaks between November 1, 2020, to June 30, 2021.

Australia successfully eliminated local community transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by June 2021. Continuing this success would require ongoing investment in maintaining surveillance systems and testing all international arrivals, alongside increasing genomic sequencing capacity.

Study: Opening up safely: public health system requirements for ongoing COVID-19 management based on evaluation of Australia's surveillance system performance. Image Credit: DesignPrax / Shutterstock.com

About the study

The researchers of the present study characterized existing surveillance systems using peer-reviewed and publicly available data, studied the epidemiological characteristics of new outbreaks during the study period, and determined the sensitivity and timeliness of surveillance systems in outbreak detection. They integrated these findings with studies of other critical COVID-19 public health measures to assess future COVID-19 management requirements.

Sensitivity measures the number of new outbreaks divided by the total number of new outbreaks in the study period. Comparatively, timeliness measures the delay between the primary case and reporting date of the index case.

Epidemiological data were obtained from State/Federal government websites and media sources, whereas information related to the data system characteristics, per capita testing rates, and wastewater surveillance sites in operation, was acquired through the characterization of surveillance systems. In addition, the outbreaks were analyzed quantitatively and characterized to gather data of index cases, first diagnosed cases, total cases at the time of identification of the first case, and other important case detection factors.

Study findings

The surveillance system detected outbreaks due to the SARS-CoV-2 Delta variant through community-based surveillance for symptomatic disease. The remaining cases were detected through screening of overseas travelers and staff of quarantine facilities.

Interestingly, all outbreaks in 2021 were due to novel SARS-CoV-2 variants of concern (VOCs). COVID-19 outbreaks were detected, on average, within five days of detection of the primary case.

The study results confirmed that wastewater surveillance was of limited utility due to its low sensitivity and specificity. However, in the period following the study from July-August 2021, two outbreaks were preceded by unexpected positive wastewater surveillance results. This suggests that wastewater detection may be more sensitive when variants with a higher viral load, such as the SARS-CoV-2 Delta variant, are responsible for them. Wastewater surveillance may also be of some value in areas adjacent to outbreaks that have not reported community transmission cases.

The researchers identified 25 epidemiologically distinct COVID-19 outbreaks in Australia with five clusters of cases. All these outbreaks were a result of breaches in quarantine facilities housing international travelers, as revealed by genomic sequencing studies.

Of these, 21 cases occurred in the community at a testing rate of an average of 2.07%. The testing rate was higher for individuals in whom COVID-19 was detected when outbreaks were ongoing.

Out of 30 cases, nine were detected through quarantine screening. The data showed that in 17 of these 30 cases, there was a delay of 4.9 days, on average, from detection of the primary case to the index case, with 10 cases detected within five days and three cases after more than seven days.

Discussion and conclusions

During the study period, when local SARS-CoV-2 transmission cases were eliminated and novel introductions through overseas arrivals were limited, community-based surveillance and routine screening of residents and staff in overseas quarantine facilities led to early and comprehensive detection of new outbreaks in the community.

The study results suggest that while epidemiological investigation and comprehensive genomic sequencing effectively helped in identifying transmission sources and outbreak clusters, more effective strategies and concerted efforts would be needed to continue doing so in the future. A surveillance strategy for future SARS-CoV-2 VOCs would require a 100-1,000-fold increase in capacity for genomic sequencing to show similar performance in detecting variants as Australia had in detecting novel outbreaks of SARS-CoV-2.

After vaccination coverage is optimized, the priority for surveillance will need to be shifted to detect novel SARS-CoV-2 VOCs associated with increased severity of disease in those who are vaccinated and vaccine ineligible. However, the most crucial factor that will affect the prevention of current and future SARS-CoV-2 transmission and Australia's capacity to reopen society safely will be government support across all community sectors.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Neha Mathur

Neha Mathur has a Master’s degree in Biotechnology and extensive experience in digital marketing. She is passionate about reading and music. When she is not working, Neha likes to cook and travel.