Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing.
alpha variant,beta variant
coronaviruses
gamma variant
variants-of-concern
Journal
The Lancet regional health. Europe
ISSN: 2666-7762
Titre abrégé: Lancet Reg Health Eur
Pays: England
ID NLM: 101777707
Informations de publication
Date de publication:
Nov 2021
Nov 2021
Historique:
pubmed:
24
8
2021
medline:
24
8
2021
entrez:
23
8
2021
Statut:
ppublish
Résumé
Wastewater surveillance was proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater surveillance projects were based on qPCR measurement of virus titers and did not address the mutational spectrum of SARS-CoV-2 circulating in the population. We have implemented a nanopore RNA sequencing monitoring system in the city of Nice (France, 550,000 inhabitants). Between October 2020 and March 2021, we monthly analyzed the SARS-CoV-2 variants in 113 wastewater samples collected in the main wastewater treatment plant and 20 neighborhoods. We initially detected the lineages predominant in Europe at the end of 2020 (B.1.160, B.1.177, B.1.367, B.1.474, and B.1.221). In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. It rapidly spread and became dominant all over the city. Other variants of concern (B.1.351, P.1) were also detected in some neighborhoods, but at low frequency. Comparison with individual clinical samples collected during the same week showed that wastewater sequencing correctly identified the same lineages as those found in COVID-19 patients. Wastewater sequencing allowed to document the diversity of SARS-CoV-2 sequences within the different neighborhoods of the city of Nice. Our results illustrate how sequencing of sewage samples can be used to track pathogen sequence diversity in the current pandemics and in future infectious disease outbreaks. For the French translation of the abstract see Supplementary Materials section.
Sections du résumé
BACKGROUND
BACKGROUND
Wastewater surveillance was proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater surveillance projects were based on qPCR measurement of virus titers and did not address the mutational spectrum of SARS-CoV-2 circulating in the population.
METHODS
METHODS
We have implemented a nanopore RNA sequencing monitoring system in the city of Nice (France, 550,000 inhabitants). Between October 2020 and March 2021, we monthly analyzed the SARS-CoV-2 variants in 113 wastewater samples collected in the main wastewater treatment plant and 20 neighborhoods.
FINDINGS
RESULTS
We initially detected the lineages predominant in Europe at the end of 2020 (B.1.160, B.1.177, B.1.367, B.1.474, and B.1.221). In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. It rapidly spread and became dominant all over the city. Other variants of concern (B.1.351, P.1) were also detected in some neighborhoods, but at low frequency. Comparison with individual clinical samples collected during the same week showed that wastewater sequencing correctly identified the same lineages as those found in COVID-19 patients.
INTERPRETATION
CONCLUSIONS
Wastewater sequencing allowed to document the diversity of SARS-CoV-2 sequences within the different neighborhoods of the city of Nice. Our results illustrate how sequencing of sewage samples can be used to track pathogen sequence diversity in the current pandemics and in future infectious disease outbreaks.
TRANSLATION
UNASSIGNED
For the French translation of the abstract see Supplementary Materials section.
Identifiants
pubmed: 34423327
doi: 10.1016/j.lanepe.2021.100202
pii: S2666-7762(21)00179-4
pmc: PMC8372489
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100202Informations de copyright
© 2021 The Author(s).
Déclaration de conflit d'intérêts
The authors have read the journal's policy and have the following competing interests: VL is employed by LBM Bioesterel, a Biogroup company. AL, ES and SL are employed by VEOLIA. There are no patents, products in development or marketed products associated with this research to declare.
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