National-scale surveillance of emerging SARS-CoV-2 variants in wastewater

Amman, Fabian; Markt, Rudolf; Endler, Lukas; Hupfauf, Sebastian; Agerer, Benedikt; Schedl, Anna; Richter, Lukas; Zechmeister, Melanie; Bicher, Martin; Heiler, Georg; Tříska, Petr; Thornton, Matthew; Penz, Thomas; Senekowitsch, Martin; Laine, Jan; Keszei, Zsofia; Daleiden, Beatrice; Steinlechner, Martin; Niederstaetter, Harald; Scheffknecht, Christoph; Vogl, Gunther; Weichlinger, Guenther; Wagner, Andreas Otto; Slipko, Katarzyna; Masseron, Amandine; Radu, Elena; Allerberger, Franz; Popper, Niki; Bock, Christoph; Schmid, Daniela; Oberacher, Herbert; Kreuzinger, Norbert; Insam, Heribert; Bergthaler, Andréas

doi:10.1101/2022.01.14.21267633

Cited by 9 publications

(22 citation statements)

References 90 publications

(95 reference statements)

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“…Here, we report a high-resolution approach to study community virus transmission using wastewater genomic surveillance, leveraging several technical advances in wastewater virus concentration and nucleic acid sequencing, and a computational tool for resolving multiple SARS-CoV-2 lineages in short-read sequence data from a mixed sample (lineage deconvolution). We obtained near 95% genome coverage even for samples with low viral load, compared with 40% or below from previous studies [11][12][13] , a key advance that allowed us to build a robust pipeline to monitor virus lineage prevalence in community wastewater. Because places of communal living, such as university campuses, are considered key sites for virus spread and represent well-controlled and relatively isolated environments, they are ideal for comparing the relative utility of clinical and wastewater genomic surveillance 16 .…”

mentioning

confidence: 93%

“…However, wastewater genomic surveillance is technically challenging 10 . Low viral loads, heavily fragmented RNA, and PCR inhibitors in complex environmental samples lead to poor sequencing coverage 12,13 . Obtaining high quality sequences from samples with low viral load and elevated levels of PCR inhibitors remains an outstanding technical challenge in implementation of wastewater genomic surveillance at scale.…”

Section: Introductionmentioning

confidence: 99%

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Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

Karthikeyan

Levy

Hoff

et al. 2021

Preprint

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As SARS-CoV-2 becomes an endemic pathogen, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

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confidence: 93%

Section: Introductionmentioning

confidence: 99%

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

Karthikeyan

Levy

Hoff

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…Wastewater monitoring has been an effective method of pathogen surveillance during the SARS-CoV-2 pandemic. In countries with developed wastewater treatment infrastructure, wastewater monitoring can provide sensitive and large-scale pathogen monitoring on the population level [1]. Genome sequencing of the SARS-CoV-2 virus in wastewater allows for reliable quantification of variants detected in the wastewater sample and even detection of novel mutations.…”

Section: Introductionmentioning

confidence: 99%

“…We can illustrate this with the example of initial spread of BA.1 variant in Austria in December 2021. While the BA.1 variant was not reliably detected (frequency > 10%) in wastewater in Austria until 19 th December 2021, the characteristic Spike mutation S:E484A was detected at a high frequency more than two weeks earlier in sample from Leoben (Figure 1, from raw data included in [1]). WAVES dashboard works as a web application.…”

Section: Introductionmentioning

confidence: 99%

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WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) – a web application for visualization of wastewater pathogen sequencing results

Tříska

Amman

Endler

et al. 2022

Preprint

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Environmental monitoring of pathogens provides an accurate and timely source of information for public health authorities and policymakers. In the last two years, wastewater sequencing proved to be an effective way of detection and quantification of SARS-CoV-2 variants circulating in population. Wastewater sequencing produces substantial amounts of geographical and genomic data. Proper visualization of spatial and temporal patterns in this data is crucial for the assessment of the epidemiological situation and forecasting. Here, we present a web-based dashboard application for visualization and analysis of data obtained from sequencing of environmental samples. The dashboard provides multi-layered visualization of geographical and genomic data. It allows to display frequencies of detected pathogen variants as well as individual mutation frequencies. The features of WAVES for early tracking and detection of novel variants in the wastewater are demonstrated in an example of BA.1 variant and the signature Spike mutation S:E484A. WAVES dashboard is easily customized through the editable configuration file and can be used for different types of pathogens and environmental samples.

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Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

et al. 2022

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The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level. We devised a bioinformatics method named COJAC (Co-Occurrence adJusted Analysis and Calling) that uses read pairs carrying multiple variant-specific signature mutations as a robust indicator of low-frequency variants. Application of COJAC revealed that a local outbreak of the Alpha variant in two Swiss cities was observable in wastewater up to 13 d before being first reported in clinical samples. We further confirmed the ability of COJAC to detect emerging variants early for the Delta variant by analysing an additional 1,339 wastewater samples. While sequencing data of single wastewater samples provide limited precision for the quantification of relative prevalence of a variant, we show that replicate and close-meshed longitudinal sequencing allow for robust estimation not only of the local prevalence but also of the transmission fitness advantage of any variant. We conclude that genomic sequencing and our computational analysis can provide population-level estimates of prevalence and fitness of emerging variants from wastewater samples earlier and on the basis of substantially fewer samples than from clinical samples. Our framework is being routinely used in large national projects in Switzerland and the UK.

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National-scale surveillance of emerging SARS-CoV-2 variants in wastewater

Cited by 9 publications

References 90 publications

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) – a web application for visualization of wastewater pathogen sequencing results

Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

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