Whole genome sequencing of SARS-CoV-2 from wastewater links to individual cases in catchments

Avram Levy, Jake Gazeley, Terence Lee, Andrew Jardine, Cameron Gordon, Natalie Cooper, Richard Theobald, Clare Huppatz, Sandra Sjollema, Meredith Hodge, David Speers

Research output: Contribution to journalArticlepeer-review


After a limited first wave of community transmission in March 2020 and until 2022, Western Australia was largely free of COVID-19, with cases restricted to hotel quarantine, commercial vessels, and small, infrequent community clusters. Despite the low case load setting, sequencing of wastewater samples from large municipal treatment plants produced SARS-CoV-2 genomes with coverage up to 99.7 % and depth to 4000×, which was sufficient to link wastewater sequences to those of active cases in the catchment at the time. This study demonstrates that ≤5 positive individuals can be enough to produce high genomic coverage (>90 %) assemblies even in catchments of up to a quarter of a million people. Genomic analysis of wastewater contemporaneous with clinical cases can also be used to rule out transmission between cases in different catchments, when their SARS-CoV-2 genomes have distinguishing nucleotide polymorphisms. These findings reveal a greater potential of wastewater WGS to inform outbreak management and disease surveillance than previously recognized.
Original languageEnglish
Article number158266
JournalScience of the Total Environment
Publication statusPublished - 10 Dec 2022


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