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

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

doi:10.1016/j.scitotenv.2022.158266

Cited by 3 publications

(2 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our study encountered specific challenges, notably during the week ending 19 February 2023, when all wastewater samples failed GS due to SARS-CoV-2 genome coverage below 60%, attributed to low SARS-CoV-2 wastewater concentrations. However, these instances were relatively rare, mitigated by our testing protocols designed for low viral concentrations in response to stringent border controls in WA [44] and the need to detect and characterize virus importation events [26]. Collaboration with the Australian WBE consortium (ColoSSoS, WaterRA) enabled the selection of a qPCR kit resistant to common wastewater inhibitors, enhancing the reliability of SARS-CoV-2 RNA quantification.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia

Gazeley,

Lee,

Knight

et al. 2024

Environments

Self Cite

View full text Add to dashboard Cite

Wastewater-based epidemiology (WBE) has emerged as a key method for the continuous monitoring of COVID-19 prevalence including circulating SARS-CoV-2 lineages. WBE addresses the limitations of traditional clinical COVID-19 surveillance such as clinical test availability, fluctuating testing rates, and increased reliance on rapid antigen tests. Our study in Perth, Western Australia found a significant positive correlation between SARS-CoV-2 concentrations in wastewater and clinical PCR positivity rates (rs = 0.772; p < 0.001) over an 18-month period that included four successive COVID-19 waves. A strong positive correlation was apparent between the proportions of SARS-CoV-2 lineages in wastewater and clinical cases within the same region (rs = 0.728, p < 0.001), including earlier detection of Omicron and recombinant lineages in wastewater before clinical case confirmation. The successful integration of WBE with healthcare data underscores its critical role in enhancing public health decision-making and pandemic management. This approach not only demonstrates the value of WBE in current global health surveillance efforts but also highlights the potential of WBE to address future public health challenges, as a comprehensive disease monitoring and response approach.

show abstract

Section: Discussionmentioning

confidence: 99%

“…Each wastewater sample was pre-treated, concentrated, and nucleic-acid-purified using 50 mL aliquots, as per a previously described procedure [26]. Briefly, sample aliquots were pre-treated with MgCl 2 and centrifuged to remove solids.…”

Section: Wastewater Concentration and Extractionmentioning

confidence: 99%

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia

Gazeley,

Lee,

Knight

et al. 2024

Environments

Self Cite

View full text Add to dashboard Cite

show abstract

Definition of a concentration and RNA extraction protocol for optimal whole genome sequencing of SARS-CoV-2 in wastewater (ANRS0160)

Chaqroun,

El Soufi,

Gerber

et al. 2024

Science of The Total Environment

View full text Add to dashboard Cite

Identifying factors that influence the use of pathogen genomics in Australia and New Zealand: a protocol

Ong,

Zulfiqar,

Glass

et al. 2024

Front. Public Health

View full text Add to dashboard Cite

IntroductionPathogen genomics, where whole genome sequencing technologies are used to produce complete genomic sequences of pathogens, is being increasingly used for infectious disease surveillance and outbreak response. Although proof-of-concept studies have highlighted the viability of using pathogen genomics in public health, few studies have investigated how end-users utilize pathogen genomics in public health. We describe a protocol for a study that aims to identify key factors that influence the use of pathogen genomics to inform public health responses against infectious diseases in Australia and New Zealand.MethodsWe will use qualitative comparative analysis (QCA), a case-oriented methodology that systematically compares and analyses multiple cases (or ‘units of analysis’), to identify multiple pathways leading to the use of pathogen genomics results in public health actions. As part of the process, we will develop a rubric to identify and define the use of pathogen genomics and individual factors affecting this process. Simultaneously, we will identify cases where pathogen genomics has been used in public health across Australia and New Zealand. Data for these cases will be collected from document review of publicly available and confidential documents and semi-structured interviews with technicians and end-users and summarized in a case report. These case reports will form the basis for scoring each case on the extent of the use of pathogen genomics data and the presence or absence of specific factors such as the ease of extracting essential information from pathogen genomics reports and perceptions toward pathogen genomics. Using the scores, cases will be analyzed using QCA techniques to identify pathways leading to the use of pathogen genomics data. These pathways will be interpreted alongside the cases to provide rich explanations of the use of pathogen genomics in public health.DiscussionThis study will improve our understanding of the key factors that facilitate or hinder the use of pathogen genomics to inform public health authorities and end-users. These findings may inform ways to enhance the use of pathogen genomics data in public health.

show abstract

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

Cited by 3 publications

References 25 publications

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia

Correlating Quantitative and Genomic SARS-CoV-2 Wastewater Data with Clinical Metrics in Metropolitan Perth, Western Australia

Definition of a concentration and RNA extraction protocol for optimal whole genome sequencing of SARS-CoV-2 in wastewater (ANRS0160)

Identifying factors that influence the use of pathogen genomics in Australia and New Zealand: a protocol

Contact Info

Product

Resources

About