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Article

Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater

1
Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), L-4422 Belvaux, Luxembourg
2
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
3
Laboratoire National de Santé, Department of Microbiology, 1 Rue Louis Rech, L-3555 Dudelange, Luxembourg
4
Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de l’Université, L-4362 Esch-sur-Alzette, Luxembourg
*
Author to whom correspondence should be addressed.
Academic Editors: Silvia Monteiro and Alba Pérez-Cataluña
Water 2021, 13(21), 3018; https://doi.org/10.3390/w13213018
Received: 27 September 2021 / Revised: 21 October 2021 / Accepted: 22 October 2021 / Published: 27 October 2021
(This article belongs to the Special Issue SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals)
Monitoring SARS-CoV-2 in wastewater has shown to be an effective tool for epidemiological surveillance. More specifically, RNA levels determined with RT-qPCR have been shown to track with the infection dynamics within the population. However, the surveillance of individual lineages circulating in the population based on genomic sequencing of wastewater samples is challenging, as the genetic material constitutes a mixture of different viral haplotypes. Here, we identify specific signature mutations from individual SARS-CoV-2 lineages in wastewater samples to estimate lineages circulating in Luxembourg. We compare circulating lineages and mutations to those detected in clinical samples amongst infected individuals. We show that especially for dominant lineages, the allele frequencies of signature mutations correspond to the occurrence of particular lineages in the population. In addition, we provide evidence that regional clusters can also be discerned. We focused on the time period between November 2020 and March 2021 in which several variants of concern emerged and specifically traced the lineage B.1.1.7, which became dominant in Luxembourg during that time. During the subsequent time points, we were able to reconstruct short haplotypes, highlighting the co-occurrence of several signature mutations. Our results highlight the potential of genomic surveillance in wastewater samples based on amplicon short-read data. By extension, our work provides the basis for the early detection of novel SARS-CoV-2 variants. View Full-Text
Keywords: SARS-CoV-2; high-throughput sequencing; variant of concern; wastewater; signature mutations; short-reads SARS-CoV-2; high-throughput sequencing; variant of concern; wastewater; signature mutations; short-reads
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MDPI and ACS Style

Herold, M.; d'Hérouël, A.F.; May, P.; Delogu, F.; Wienecke-Baldacchino, A.; Tapp, J.; Walczak, C.; Wilmes, P.; Cauchie, H.-M.; Fournier, G.; Ogorzaly, L. Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater. Water 2021, 13, 3018. https://doi.org/10.3390/w13213018

AMA Style

Herold M, d'Hérouël AF, May P, Delogu F, Wienecke-Baldacchino A, Tapp J, Walczak C, Wilmes P, Cauchie H-M, Fournier G, Ogorzaly L. Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater. Water. 2021; 13(21):3018. https://doi.org/10.3390/w13213018

Chicago/Turabian Style

Herold, Malte, Aymeric Fouquier d'Hérouël, Patrick May, Francesco Delogu, Anke Wienecke-Baldacchino, Jessica Tapp, Cécile Walczak, Paul Wilmes, Henry-Michel Cauchie, Guillaume Fournier, and Leslie Ogorzaly. 2021. "Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater" Water 13, no. 21: 3018. https://doi.org/10.3390/w13213018

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