Australian and New Zealand Laboratory Experience and Proposed Future Direction of Wastewater Pathogen Genomic Surveillance

Wastewater pathogen surveillance was rapidly implemented across Australia and New Zealand as a public health tool during the COVID-19 pandemic. To assess method consistency and identify opportunities for harmonization, we surveyed all Australian and New Zealand Laboratories conducting government-funded wastewater pathogen surveillance. The survey demonstrated alignment of some method choices, particularly municipal wastewater treatment plant (WWTP) sampling and the use of electromagnetic membrane filtration followed by RT-qPCR. However, key differences were observed in the wastewater sample volumes; nucleic acid purification methods; validation approaches; and sequencing, analysis, and reporting methods for SARS-CoV-2 lineages. A lack of consensus on best-practice methods was evident, highlighting the need for interlaboratory sample and data exchanges to support validation and comparability. Following the pandemic period, several jurisdictional programs were discontinued despite the mounting international evidence for the utility of wastewater-based epidemiology for a range of pathogens. Subsequently, a nationally funded program was announced in Australia, necessitating the re-establishment of laboratory capacity for some jurisdictions and expansion of target pathogens for other centers. The results of this survey are intended to inform the re-establishment and enhancement of regional capacity and to provide a foundation for best-practice knowledge sharing and approach harmonization.