Pathogen Detection - COVID-19 Wastewater Testing

People who have COVID-19 will excrete fragments of the SARS-CoV-2 virus through faecal waste or other bodily fluids into the wastewater stream through the sewerage system. A wastewater surveillance program therefore provides another mechanism through which community transmission can be monitored to complement clinical surveillance. The point of difference for wastewater surveillance is that it does not rely on clinical presentation by individuals. Wastewater surveillance will detect virus fragments from people who are weakly symptomatic or asymptomatic. The use of wastewater surveillance for detecting and quantifying the presence of SARS-CoV-2 virus fragments was expanded in 2022 to identify the variants of the virus circulating in the community in a manner that is independent of clinical presentation by individuals.

The aim was to provide a complementary source of information to analysis of variants detected from sequencing of clinical isolates. In South Australia, SA Water, SA Health and the SAGC ran a PCR-based screening wastewater surveillance program over the course of a year, whereby samples were collected from the major metropolitan wastewater treatment plants twice a week. These plants service about 65% of the SA population. PCR products from these samples were submitted to SAGC for sequencing. The resulting data produced was used by SA Health to assess changes in prevalence of variants and to monitor the appearance of new variants of concern (results are shown in the figure 1).