In lieu of wide-spread vaccination, efforts to limit the impact of the COVID pandemic, caused by the SARS-CoV-2 virus, rely heavily on improved frontline treatment, social distancing policies and robust case detection and active contact tracing. In Australia, where the public has largely adhered well to social distancing programs and COVID cases are among the lowest per capita in the world, early case detection and contact tracing has moved to the forefront of the public health response. This latter arm rests on a classical foundation of broad-scale clinical testing, quarantine and active tracking of close contacts of infected individuals. However, the COVID pandemic has also seen the emergence of environmental-based surveillance, particularly the detection of SARS-CoV-2 viruses shed into distributed sewage (‘wastewater’) networks in metropolitan and regional populations. Although wastewater detection has played an important role in polio eradication programs for decades, these current programs represent implementation at an unprecedented scale and speed, and their first use in a pandemic.
My team has played a key role in the Victorian component of the national ColoSSoS (Collaboration on Sewage Surveillance of SARS-CoV-2) program. Development and implementation of this program required extensive collaboration across health, water and diagnostic industries and government authorities, as well as the shared research expertise of numerous academic groups across the state and around the country. In addition, the program had to overcome significant technical challenges including the identification of diagnostic methods that could detect SARS-CoV-2 in complex environmental samples at absolute trace levels, the development of novel approaches to verify the accuracy of these detections, and the policy understanding on how to make use of this information in a public health response. Here, I will touch on the operation, scale and unique challenges of the Victorian ColoSSoS program, focusing on the molecular diagnostic methods underpinning it. I will also discuss the next steps in development of this program, including efforts to identify methods that allow rapid detection of high-risk SARS-CoV-2 variants in wastewater, and the use of whole genomic sequencing to improve capacity to link these environmental detections with their community source.