TY - JOUR
T1 - Whole genome sequencing of SARS-CoV-2 from wastewater links to individual cases in catchments
AU - Levy, Avram
AU - Gazeley, Jake
AU - Lee, Terence
AU - Jardine, Andrew
AU - Gordon, Cameron
AU - Cooper, Natalie
AU - Theobald, Richard
AU - Huppatz, Clare
AU - Sjollema, Sandra
AU - Hodge, Meredith
AU - Speers, David
N1 - Funding Information:
We appreciate the advice on cell culture and virus isolation methods provided by Dr. Chisha Sikazwe and thank the WGS scientists and COVID wastewater team at PathWest. This work was funded by WA Department of Health and PathWest Laboratory Medicine WA .
Publisher Copyright:
© 2022 Elsevier B.V.
PY - 2022/12/10
Y1 - 2022/12/10
N2 - 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.
AB - 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.
KW - COVID-19
KW - Genomic epidemiology
KW - Public health microbiology
KW - Wastewater surveillance
UR - http://www.scopus.com/inward/record.url?scp=85138442484&partnerID=8YFLogxK
U2 - 10.1016/j.scitotenv.2022.158266
DO - 10.1016/j.scitotenv.2022.158266
M3 - Article
C2 - 36028041
AN - SCOPUS:85138442484
SN - 0048-9697
VL - 851
JO - Science of the Total Environment
JF - Science of the Total Environment
M1 - 158266
ER -
