Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
17 02 2022
17 02 2022
Historique:
received:
02
07
2021
accepted:
28
01
2022
entrez:
18
2
2022
pubmed:
19
2
2022
medline:
26
2
2022
Statut:
epublish
Résumé
The COVID-19 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot, for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). Our proposed method was tested and evaluated using NGS data produced by the sequencing of 14 wastewater samples from the municipality of Thessaloniki, Greece, covering a 6-month period. The results showed the presence of SARS-CoV-2 variants in wastewater data. lineagespot was able to record the evolution and rapid domination of the Alpha variant (B.1.1.7) in the community, and allowed the correlation between the mutations evident through our approach and the mutations observed in patients from the same area and time periods. lineagespot is an open-source tool, implemented in R, and is freely available on GitHub and registered on bio.tools.
Identifiants
pubmed: 35177697
doi: 10.1038/s41598-022-06625-6
pii: 10.1038/s41598-022-06625-6
pmc: PMC8854625
doi:
Substances chimiques
Waste Water
0
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Validation Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
2659Informations de copyright
© 2022. The Author(s).
Références
Mol Cell Probes. 2019 Aug;46:101412
pubmed: 31201852
Pathogens. 2021 Aug 10;10(8):
pubmed: 34451472
Viruses. 2020 Oct 09;12(10):
pubmed: 33050264
Emerg Infect Dis. 2021 May;27(5):1405-1415
pubmed: 33900177
mBio. 2021 Jan 19;12(1):
pubmed: 33468686
Front Genet. 2012 Mar 15;3:35
pubmed: 22435069
Sci Total Environ. 2021 Dec 20;801:149757
pubmed: 34467932
Sci Rep. 2021 Sep 16;11(1):18456
pubmed: 34531412
Cell Rep Med. 2020 Sep 22;1(6):100098
pubmed: 32904687
Viruses. 2021 Sep 10;13(9):
pubmed: 34578384
Sci Total Environ. 2021 Jan 10;751:141750
pubmed: 32861187
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Sci Total Environ. 2021 Feb 10;755(Pt 1):142855
pubmed: 33199018
Virus Evol. 2021 Jul 30;7(2):veab064
pubmed: 34527285
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genome Biol. 2019 Jan 8;20(1):8
pubmed: 30621750
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Water Res. 2021 Sep 1;202:117400
pubmed: 34274898