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

Nikolaos Pechlivanis,Evangelia Mouchtaropoulou,Agis Papadopoulos,Margaritis Kostoglou,Anastasis Togkousidis,Taxiarchis Chassalevris,Anagnostis Argiriou,Elisavet Vlachonikola,Stamatia Laidou,Nikolaos Papaioannou,Anastasia Chatzidimitriou,Chrysostomos I Dovas,Maria Christina Maniou,Fotis Psomopoulos,Serafeim C Chaintoutis,Maria Petala,Maria Tsagiopoulou,Thodoris Karapantsios

doi:10.1038/s41598-022-06625-6

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.

Highlights

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
In this work we propose a novel methodology called lineagespot, implemented as a software tool that can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS)
I.e. used water that goes through the drainage system to a treatment facility, is a way that researchers and surveillance systems can track pathogens, such as SARS-CoV-2, or biomarkers that are excreted in urine or feces

Summary

Introduction

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. 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). SARS-CoV-2 genotyping for epidemiological investigations/to understand its molecular epidemiology relies on PCR-based methods, affordable for most laboratories These methods are not scalable, especially in large urban areas, where a high number of individuals have to be tested to assess virus and variant spread among the population, or when new variant/mutation screening is needed, which can be attained only by sequencing methods. In this work we propose a novel methodology called lineagespot, implemented as a software tool that can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). The method is tested and validated across 14 municipal wastewater samples retrieved in Thessaloniki, Greece in 14 different time periods, and correlated with the mutations and lineages observed in patients from the same area time points. The methodology is proven to be effective in detecting the mutational load in the wastewater, with the inferred lineages being roughly aligned to the predominant lineages identified through targeted patient-derived genotypes

Methods

Results

Conclusion