Wastewater surveillance for SARS-CoV-2 has proven effective in supporting COVID control efforts globally, allowing detection of novel infection clusters, supporting assessment of community transmission risk, and providing an important reminder to the public to remain vigilant in adhering to social distancing and other public health policies. Surveillance is achieved through the application of highly sensitive molecular diagnostic tools. In such applications, the diagnostic markers employed for wastewater surveillance can be improved, but more genetic information is needed. Whole genome sequencing (WGS) provides the most conclusive and robust approach to providing more genomic material for analysis.

This project addresses a recent priority research call from WaterRA for programs to extend capacity for wastewater testing for SARS-CoV-2. This includes the evaluation and implementation WGS methods for SARS-CoV-2 in wastewater and seek to overcome current limitations in detection sensitivity that have prevented their use in Australia to date.

This project formed the Mekong node of the Collaboration on Sewage Surveillance for SARS-CoV-2 “ColoSSoS” project after Water Research Australia and the Australian Water Association identified that technology transfer within Australia’s broader region was a logical extension of the local project.

This project transferred leading Australian innovation in the environmental surveillance of SARS-CoV-2 to support the Governments of five countries in the Mekong River Delta (including Vietnam, Cambodia, Laos, Myanmar, and Thailand) to prepare, respond and recover from the COVID-19 pandemic. It established partnerships between Australia and these five countries and transferred SARS-CoV-2 environmental surveillance methods established in Australia by WaterRA and partners. The transfer of these methods has supported each Government’s efforts to monitor SARS-CoV-2 prevalence in water environments (primarily sewage and stormwater), to inform COVID-19 control strategies of the Governments and add to their COVID-19 resilience toolbox. Through developing the set-up for potential cost-effective earlier warning detection systems for COVID-19 outbreaks in each country, the project has supported the long-term strengthening of health security, systems, stability, social cohesion and economic recovery across the Mekong region.

Following on from the successes of the Mekong node of the ColoSSoS program, WaterRA entered into another project with the Australian Water Association to provide knowledge transfer and capacity building services to the Water Authority of Fiji. The techniques developed in Australia have now been trialed in both low prevalence case settings as well as during the height of the Australian outbreaks and can be confidently adapted and applied in these scenarios in Suva, Fiji.

The project has been structured in a similar way to ColoSSoS Mekong, with SA Water providing both utility and laboratory expertise to developed tailored sampling and analysis protocols. Australian health departments will also be engaged in a formal capacity to provide tailored advice to Fijian counterparts.

The international work to date has seen the application of SARS-CoV-2 detection and analysis practices outside of Australia in the Mekong region, through the sharing of tools, protocols, and best practice skills, and knowledge. These wastewater monitoring techniques will remain relevant if new strains of the SARS-CoV-2 virus emerge globally, and current global and Australian research efforts focus on the identification of new strains in the community and ports of entry, as well as the quantification of proportions of these variants within community populations. Its use in Fiji will provide the heath agency with valuable information to make critical decisions to protect the community.

WaterRA’s continued involvement in these projects has provided our Australian Members an opportunity to elevate their international profile through DFAT-funded collaborations under the umbrella of the Australian Water Partnership. Furthermore, this sharing of Australian knowledge and skills supports Australia’s regional response to the ever-evolving Covid-19 situation, providing tools and strategies to help protect communities both in Australia and the Asia-Pacific region.

The Collaboration on Sewage Surveillance of SARS-CoV-2 (ColoSSoS) project combined the expertise of more than 50 Australian organisations in R&D activities that have enabled health departments across the country to integrate quantitative measurements of SARS-CoV-2 virus detected in sewage with human clinical PCR test data for COVID-19. This subproject trialled a series of molecular tests to identify the best laboratory protocols for the reliable retrieval of SARS-CoV-2 virus from sewage samples, extraction of the viral RNA and the amplification of viral sequences that can distinguish between SARS-CoV-2 and other closely related types of viruses. Laboratory test control and validation methods were also established. These methods have been implemented in the Victorian state wastewater monitoring programme and are also the foundation for the ongoing development of genome sequencing methods which will be applied to detect and identify emerging variants in the future.

Water Research Australia led an innovative, and collaborative Australia-wide investigation that developed novel methods for the detection of SARS-CoV-2 in wastewater. This work enabled health departments across Australia to integrate reliable detections of the SARS-CoV-2 virus in sewage with clinical health data for COVID-19.