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

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.

Prevalence and circulation patterns of SARS-CoV-2 variants in European sewage mirror clinical data of 54 European cities

“…High coverage is important to avoid loss of information about the mutations detected in wastewater because mutation profiles serve as the backbone to determine the variants present in wastewater samples. For example, some previous studies used detected mutations to determine variants ( Fontenele et al, 2021 ; Pérez-Cataluña et al, 2022 ). The data presented in this study clearly shows that it is possible to obtain high coverage SARS-CoV-2 genomes, irrespective of variability in the composition of wastewater and the concentration of the SARS-CoV-2 RNA in the wastewater from different locations (Table S1).…”

“… Crits-Christoph et al, (2021) used the Illumina Respiratory Virus Oligo Panel generating 2×75 bp paired-end reads and achieved a SARS-CoV-2 genome coverage of >99% for 7 out of 22 samples. Some studies performed Illumina sequencing on amplicons generated using the ARCTIC Network Protocol, Hillary et al, (2021) recovered between 25 and 75% of the SARS-CoV-2 genome, whereas, Pérez-Cataluña et al, (2022) recovered a genome coverage higher than 90% for 11 out of 76 samples. Agrawal et al, (2021) used the Ion AmpliSeq SARS-CoV-2 research panel together with the Ion Torrent platform and achieved >90% SARS-CoV-2 genome coverage.…”

Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future

“…To further complicate things, new variants usually start to occur in a small group of people, which necessitates the development of sensitive and reliable bioinformatics approaches to discover the emerging low-frequency variants in wastewater. Metagenomic shotgun sequencing of either untargeted ( Crits-Christoph et al, 2021 ) or targeted amplicons ( Bar-Or et al, 2021 ; Fontenele et al, 2021 ; Nemudryi et al, 2020 ; Pérez-Cataluña et al, 2022 ; Swift et al, 2021 ) enables the discovery of viral genetic mutations to infer variants that are circulating in the sewershed. Reliable lineage assignment from viral metagenomic dataset remains putative ( Fontenele et al, 2021 ) though methodological improvements have been made ( Karthikeyan et al, 2021 ).…”

“pySewage”: a hybrid approach to predict the number of SARS-CoV-2-infected people from wastewater in Brazil

“…This is probably part of the reason that although several studies have been conducted to monitor SARS-CoV-2, and estimate the number of infected people from wastewater samples, they are mostly used by a small group of researchers (Sanches-Neto et al 2021 ). Therefore, in addition to studies of SARS-CoV-2 monitoring by experimental techniques such as RT-qPCR and genomic sequencing, it is extremely important to develop web applications to automate the SARS-CoV-2 detection combined with COVID-19 monitoring (Pérez-Cataluña et al 2022 ). Moreover, the use of our web application can provide early prediction in wastewater, potentially identifying new variants for recurrent outbreaks (Peterson et al 2022 ; Wurtzer et al 2022 ).…”