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

doi:10.1016/j.scitotenv.2022.158266

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

Sci Total Environ. 2022 Dec 10;851(Pt 2):158266. doi: 10.1016/j.scitotenv.2022.158266. Epub 2022 Aug 24.

Authors

Affiliations

¹ Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia, Australia. Electronic address: Avram.levy@health.wa.gov.au.
² Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia.
³ Public Health Emergency Operations Centre, Health Department of Western Australia, Western Australia, Australia.
⁴ Water Corporation, Western Australia, Australia.
⁵ Environmental Health Directorate, Health Department of Western Australia, Western Australia, Australia.
⁶ Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia; School of Medicine, University of Western Australia, Crawley, Western Australia, Australia.

Abstract

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.

Keywords: COVID-19; Genomic epidemiology; Public health microbiology; Wastewater surveillance.

MeSH terms

COVID-19* / epidemiology
Humans
Nucleotides
SARS-CoV-2* / genetics
Wastewater
Whole Genome Sequencing

Substances

Waste Water
Nucleotides