SARS-CoV-2 variant trends in Ireland: Wastewater based epidemiology and clinical surveillance

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Title: SARS-CoV-2 variant trends in Ireland: Wastewater based epidemiology and clinical surveillance
Authors: Reynolds, Liam J.Gonzalez, GabrielSala-Comorera, LauraMartin, Niamh A.Byrne, AlannahFennema, SanneHolohan, NiamhKuntamukkula, Sailusha RatnamSarwar, NatashaNolan, Tristan M.Stephens, Jayne H.Whitty, MeganBennett, CharleneLuu, QuynhMorley, UrsulaYandle, ZoeDean, JonathanJoyce, EadaoinO'Sullivan, J. J.Fletcher, Nicola F.Carr, Michael J.De Gascun, CillianMeijer, Wimet al.
Permanent link: http://hdl.handle.net/10197/13009
Date: 10-Sep-2022
Online since: 2022-07-19T08:43:34Z
Abstract: SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a community, accomplished to date by sequencing clinical samples. Quantifying variants in wastewater offers a cost-effective means to augment these sequencing efforts. In this study, SARS-CoV-2 N1 RNA concentrations and daily loadings were determined and compared to case-based data collected as part of a national surveillance programme to determine the validity of wastewater surveillance to monitor infection spread in the greater Dublin area. Further, sequencing of clinical samples was conducted to determine the primary SARS-CoV-2 lineages circulating in Dublin. Finally, digital PCR was employed to determine whether SARS-CoV-2 VOCs, Alpha and Delta, were quantifiable from wastewater. No lead or lag time was observed between SARS-CoV-2 wastewater and case-based data and SARS-CoV-2 trends in Dublin wastewater significantly correlated with the notification of confirmed cases through case-based surveillance preceding collection with a 5-day average. This demonstrates that viral RNA in Dublin's wastewater mirrors the spread of infection in the community. Clinical sequence data demonstrated that increased COVID-19 cases during Ireland's third wave coincided with the introduction of the Alpha variant, while the fourth wave coincided with increased prevalence of the Delta variant. Interestingly, the Alpha variant was detected in Dublin wastewater prior to the first genome being sequenced from clinical samples, while the Delta variant was identified at the same time in clinical and wastewater samples. This work demonstrates the validity of wastewater surveillance for monitoring SARS-CoV-2 infections and also highlights its effectiveness in identifying circulating variants which may prove useful when sequencing capacity is limited.
Funding Details: European Commission - European Regional Development Fund
Health Service Executive
Science Foundation Ireland
Funding Details: Ireland Wales Cooperation programme (Acclimatize)
Type of material: Journal Article
Publisher: Elsevier
Journal: The Science of the Total Environment
Volume: 838
Issue: 2
Start page: 1
End page: 8
Copyright (published version): 2022 The Authors
Keywords: Digital PCRGenomic surveillanceSARS-CoV-2VariantsWastewater surveillanceCOVID-19Coronavirus
DOI: 10.1016/j.scitotenv.2022.155828
Language: en
Status of Item: Peer reviewed
ISSN: 0048-9697
This item is made available under a Creative Commons License: https://creativecommons.org/licenses/by/3.0/ie/
Appears in Collections:Centre for Water Resources Research Collection
Biomolecular and Biomedical Science Research Collection
Medicine Research Collection
Civil Engineering Research Collection
Veterinary Medicine Research Collection

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