Article (Scientific journals)
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater
Herold, Malte; Fouquier d'herouël, Aymeric; May, Patrick et al.
2021In Water, 13 (21 3018)
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Keywords :
SARS-CoV-2; high-throughput sequencing; variant of concern; wastewater; signature mutations; short-reads
Abstract :
[en] 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.
Disciplines :
Microbiology
Author, co-author :
Herold, Malte
Fouquier d'herouël, Aymeric ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services
May, Patrick  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Delogu, Francesco ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Wienecke-Baldacchino, Anke
Tapp, Jessica
Walczak, Cécile
Wilmes, Paul ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Cauchie, Henry-Michel ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC)
Fournier, Guillaume
Ogorzaly, Leslie ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC)
External co-authors :
no
Language :
English
Title :
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater
Publication date :
27 October 2021
Journal title :
Water
ISSN :
2073-4441
Publisher :
MDPI, Basel, Switzerland
Volume :
13
Issue :
21 3018
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Systems Biomedicine
FnR Project :
FNR14806023 - The Value Of Sewage Surveillance To Provide New Insights On The Circulation Of Sars-cov-2 And To Reveal The True Extent Of The Coronavirus Pandemic At The National Scale, 2020 (01/06/2020-31/03/2021) - Leslie Ogorzaly
Funders :
Fonds National de la Recherche - FnR project 14806023 (CORONASTEP+), project 14744547 (Co-PhyloDyn) and project 14735280 (UCovis)
Available on ORBilu :
since 28 October 2021

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