Wastewater surveillance of SARS-CoV-2 in Victoria, Australia

We have developed a duplex hemi-nested PCR method that, coupled with short amplicon sequencing, allows simultaneous typing of two of the most highly variable and informative regions of the SARS-CoV-2 Spike gene: the N-terminal domain (NTD) and the receptor binding motif (RBM). Using this method, we identified the first known incursion of Omicron BA.1 into Victoria, Australia and demonstrated how sensitive amplicon sequencing methods can be combined with wastewater surveillance as a relatively low-cost solution for early warning of SARS-CoV-2 variant incursion and spread.