Reference : Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wast...
Scientific journals : Article
Life sciences : Microbiology
Systems Biomedicine
http://hdl.handle.net/10993/48456
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater
English
Herold, Malte [> >]
Fouquier d'herouël, Aymeric mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Scientific Central Services >]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core]
Delogu, Francesco mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >]
Wienecke-Baldacchino, Anke [> >]
Tapp, Jessica [> >]
Walczak, Cécile [> >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology]
Cauchie, Henry-Michel mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) >]
Fournier, Guillaume [> >]
Ogorzaly, Leslie mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) >]
27-Oct-2021
Water
13
21 3018
Yes (verified by ORBilu)
International
2073-4441
[en] SARS-CoV-2 ; high-throughput sequencing ; variant of concern ; wastewater ; signature mutations ; short-reads
[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.
Fonds National de la Recherche - FnR project 14806023 (CORONASTEP+), project 14744547 (Co-PhyloDyn) and project 14735280 (UCovis)
Researchers ; Professionals ; Students ; General public
http://hdl.handle.net/10993/48456
10.3390/w13213018
https://www.mdpi.com/2073-4441/13/21/3018
FnR ; FNR14806023 > Leslie Ogorzaly > CORONASTEP+ > 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 > 01/06/2020 > 31/03/2021 > 2020

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