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. 2022 Sep 10;838(Pt 2):155828.
doi: 10.1016/j.scitotenv.2022.155828. Epub 2022 May 16.

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

Liam J Reynolds  1 , Gabriel Gonzalez  2 , Laura Sala-Comorera  1 , Niamh A Martin  1 , Alannah Byrne  1 , Sanne Fennema  1 , Niamh Holohan  1 , Sailusha Ratnam Kuntamukkula  1 , Natasha Sarwar  1 , Tristan M Nolan  1 , Jayne H Stephens  1 , Megan Whitty  1 , Charlene Bennett  3 , Quynh Luu  3 , Ursula Morley  3 , Zoe Yandle  3 , Jonathan Dean  3 , Eadaoin Joyce  4 , John J O'Sullivan  5 , John M Cuddihy  6 , Angeline M McIntyre  6 , Eve P Robinson  6 , Darren Dahly  7 , Nicola F Fletcher  8 , Michael Carr  2 , Cillian De Gascun  3 , Wim G Meijer  9
Affiliations

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

Liam J Reynolds et al. Sci Total Environ. .

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.

Keywords: Digital PCR; Genomic surveillance; SARS-CoV-2; Variants; Wastewater surveillance.

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Conflict of interest statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Unlabelled Image
Graphical abstract
Fig. 1
Fig. 1
Daily SARS-CoV-2 loading in wastewater and number of SARS-CoV-2 positive cases. A) The new daily cases in Dublin (incident cases) are represented by gray bars. The 5-day average of new cases preceding wastewater sampling are indicated as black dots on the graph. The Ringsend geo-coded cases for the NWSP are indicated by the red line. B) The daily loadings of the SARS-CoV-2 N1 gene (gc/day) through the Ringsend wastewater treatment plant are illustrated as black dots. The black line depicts the generalised additive model smoothing of the SARS-CoV-2 N1 daily loading data.
Fig. 2
Fig. 2
Phylogenetic and temporal relationships among SARS-CoV-2 genome sequences. A) Phylogenetic tree of SARS-CoV-2 complete genome sequences from clinical samples in Dublin (n = 505) rooted with the reference genome. The horizontal axis corresponds to the length of the branches and represents the number of nucleotide mutations per site. Tips are coloured according to the corresponding PANGOLIN lineage grouped by variant/super lineage on the right of the fig. B) Scatterplot reflecting the phylogenetic position of the tree tips against the collection date of the respective samples in the horizontal axis.
Fig. 3
Fig. 3
Circulating lineages and Quantification of SARS-CoV-2 Alpha and Delta Variants in Ringsend Wastewater. A) The date of wastewater sample collection is indicated on the X-axis. The left Y-axis indicates the daily loading of the SARS-CoV-2 N1 gene. The right Y-axis illustrates the daily loadings of both variants. The dashed black line is the smoothed curve depicting fluctuations in SARS-CoV-2 N1. The red and green lines depict the loadings of the Alpha (N501Y) and Delta (L452R) variants in the Ringsend wastewater treatment plant. B) Over the same period, percentages of Dublin cases per super-lineage during the sampling period are shown. Sequences are grouped biweekly, and the vertical axis represents the percentage of cases in each super lineage considering all available sequence data (n = 9187).
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