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. 2022 Mar 1:211:118007.
doi: 10.1016/j.watres.2021.118007. Epub 2021 Dec 24.

Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater

Alba Pérez-Cataluña  1 , Álvaro Chiner-Oms  2 , Enric Cuevas-Ferrando  3 , Azahara Díaz-Reolid  3 , Irene Falcó  3 , Walter Randazzo  3 , Inés Girón-Guzmán  3 , Ana Allende  4 , María A Bracho  5 , Iñaki Comas  6 , Gloria Sánchez  3
Affiliations

Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater

Alba Pérez-Cataluña et al. Water Res. .

Abstract

Wastewater-based epidemiology (WBE) has proven to be an effective tool for epidemiological surveillance of SARS-CoV-2 during the current COVID-19 pandemic. Furthermore, combining WBE together with high-throughput sequencing techniques can be useful for the analysis of SARS-CoV-2 viral diversity present in a given sample. The present study focuses on the genomic analysis of SARS-CoV-2 in 76 sewage samples collected during the three epidemiological waves that occurred in Spain from 14 wastewater treatment plants distributed throughout the country. The results obtained demonstrate that the metagenomic analysis of SARS-CoV-2 in wastewater allows the detection of mutations that define the B.1.1.7 lineage and the ability of the technique to anticipate the detection of certain mutations before they are detected in clinical samples. The study proves the usefulness of sewage sequencing to track Variants of Concern that can complement clinical testing to help in decision-making and in the analysis of the evolution of the pandemic.

Keywords: Genome sequencing; SARS-CoV-2; Spike mutations; Variants of concern; Variants of interest; Wastewater.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Representation of the number of samples that covered each nucleotide of the SARS-CoV-2 isolate Wuhan-Hu-1 genome (MN908947.3) with coverage values higher than 20X.
Fig. 2
Fig. 2
Frequency of the different nucleotide substitutions and deletions obtained for samples of each epidemiological wave grouped by genomic region. A, first and second waves; B, third wave.
Fig. 3
Fig. 3
Frequency of nucleotide substitutions and deletions related with B.1.1.7 linage according to the sampling week. *Clinical frequency based on data obtained from the Spanish Ministry of Health according to the results obtained by S-gene target failure (SGTF) marker or detection of N501Y mutation.
See this image and copyright information in PMC

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Supplementary concepts