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Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece.
Pechlivanis, Nikolaos; Tsagiopoulou, Maria; Maniou, Maria Christina; Togkousidis, Anastasis; Mouchtaropoulou, Evangelia; Chassalevris, Taxiarchis; Chaintoutis, Serafeim C; Petala, Maria; Kostoglou, Margaritis; Karapantsios, Thodoris; Laidou, Stamatia; Vlachonikola, Elisavet; Chatzidimitriou, Anastasia; Papadopoulos, Agis; Papaioannou, Nikolaos; Dovas, Chrysostomos I; Argiriou, Anagnostis; Psomopoulos, Fotis.
  • Pechlivanis N; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Tsagiopoulou M; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Maniou MC; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Togkousidis A; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Mouchtaropoulou E; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Chassalevris T; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Chaintoutis SC; School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Petala M; School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Kostoglou M; Department of Civil Engineering, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Karapantsios T; Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Laidou S; Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Vlachonikola E; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Chatzidimitriou A; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Papadopoulos A; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Papaioannou N; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
  • Dovas CI; Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece.
  • Argiriou A; EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A., 54636, Thessaloníki, Greece.
  • Psomopoulos F; School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloníki, Greece.
Sci Rep ; 12(1): 2659, 2022 02 17.
Article in English | MEDLINE | ID: covidwho-1900621
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Wastewater / SARS-CoV-2 / Mutation Type of study: Experimental Studies / Observational study Topics: Variants Limits: Humans Language: English Journal: Sci Rep Year: 2022 Document Type: Article Affiliation country: S41598-022-06625-6

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Software / Wastewater / SARS-CoV-2 / Mutation Type of study: Experimental Studies / Observational study Topics: Variants Limits: Humans Language: English Journal: Sci Rep Year: 2022 Document Type: Article Affiliation country: S41598-022-06625-6