Portal de Periódicos da CAPES

Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece

2022; Nature Portfolio; Volume: 12; Issue: 1 Linguagem: Inglês

10.1038/s41598-022-06625-6

2045-2322

Nikolaos Pechlivanis, Maria Tsagiopoulou, Μαρία Μανιού, Anastasis Togkousidis, Evangelia Mouchtaropoulou, Taxiarchis Chassalevris, Serafeim C. Chaintoutis, Maria Petala, Margaritis Kostoglou, Thodoris D. Karapantsios, Stamatia Laidou, Elisavet Vlachonikola, Anastasia Chatzidimitriou, Agis M. Papadopoulos, Nikolaos Papaioannou, Chrysostomos Ι. Dovas, Anagnostis Argiriou, Fotis Psomopoulos,

SARS-CoV-2 and COVID-19 Research

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.