Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater
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 th...
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MDPI AG
2021
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oai:doaj.org-article:126c789627d545b9bedd3ad1598148f82021-11-11T19:54:41ZGenome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater10.3390/w132130182073-4441https://doaj.org/article/126c789627d545b9bedd3ad1598148f82021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4441/13/21/3018https://doaj.org/toc/2073-4441Monitoring 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.Malte HeroldAymeric Fouquier d'HérouëlPatrick MayFrancesco DeloguAnke Wienecke-BaldacchinoJessica TappCécile WalczakPaul WilmesHenry-Michel CauchieGuillaume FournierLeslie OgorzalyMDPI AGarticleSARS-CoV-2high-throughput sequencingvariant of concernwastewatersignature mutationsshort-readsHydraulic engineeringTC1-978Water supply for domestic and industrial purposesTD201-500ENWater, Vol 13, Iss 3018, p 3018 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
SARS-CoV-2 high-throughput sequencing variant of concern wastewater signature mutations short-reads Hydraulic engineering TC1-978 Water supply for domestic and industrial purposes TD201-500 |
| spellingShingle |
SARS-CoV-2 high-throughput sequencing variant of concern wastewater signature mutations short-reads Hydraulic engineering TC1-978 Water supply for domestic and industrial purposes TD201-500 Malte Herold Aymeric Fouquier d'Hérouël Patrick May Francesco Delogu Anke Wienecke-Baldacchino Jessica Tapp Cécile Walczak Paul Wilmes Henry-Michel Cauchie Guillaume Fournier Leslie Ogorzaly Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater |
| description |
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. |
| format |
article |
| author |
Malte Herold Aymeric Fouquier d'Hérouël Patrick May Francesco Delogu Anke Wienecke-Baldacchino Jessica Tapp Cécile Walczak Paul Wilmes Henry-Michel Cauchie Guillaume Fournier Leslie Ogorzaly |
| author_facet |
Malte Herold Aymeric Fouquier d'Hérouël Patrick May Francesco Delogu Anke Wienecke-Baldacchino Jessica Tapp Cécile Walczak Paul Wilmes Henry-Michel Cauchie Guillaume Fournier Leslie Ogorzaly |
| author_sort |
Malte Herold |
| title |
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater |
| title_short |
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater |
| title_full |
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater |
| title_fullStr |
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater |
| title_full_unstemmed |
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater |
| title_sort |
genome sequencing of sars-cov-2 allows monitoring of variants of concern through wastewater |
| publisher |
MDPI AG |
| publishDate |
2021 |
| url |
https://doaj.org/article/126c789627d545b9bedd3ad1598148f8 |
| work_keys_str_mv |
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| _version_ |
1718431332186456064 |