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Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

Our take —

This study used sewage samples from Alameda and Marin Counties in California, USA, to demonstrate that population-level wastewater sampling can be used to identify SARS-CoV-2 variants circulating in the local population. The authors presented a methodology that can be used to generate genomic data from wastewater samples and showed that the majority of variants detected were also available in publicly available sequences from clinical patient samples. These findings suggest that wastewater sampling may be an effective tool for detecting circulating SARS-CoV-2 variants even in the absence of, or prior to, sequencing of patient-derived samples.

Study design


Study population and setting

This study included data from 27 samples from wastewater treatment facilities from Alameda and Marin Counties in Northern California, USA. These samples, all 24-hour 1-liter composite samples of raw sewage (meaning sewage samples were collected every 15 minutes over the course of 24 hours and then combined), were collected between May 19 and July 15, 2020. The goal of the study was not only to detect SARS-CoV-2 in wastewater, but to assemble whole SARS-CoV-2 virus genomes and to compare observed variants to those found in publicly available sequences from clinical patient samples in California.

Summary of Main Findings

The authors found multiple SARS-CoV-2 genotypes in sewage known to be present in local communities. Assembled whole genomes from wastewater samples matched published genomes from clinical samples. In addition, the majority of individual variants (even those at low frequencies) detected within wastewater samples were also observed in patient-derived genomes from California, and that variants found in two or more samples were 2.3 times more likely to be observed in California or US patient-derived genomes than variants observed only once. This suggests that the variation observed in wastewater samples is representative of the SARS-CoV-2 variation circulating in the sampled population — individuals in Alameda and Marin counties, California. The authors also found evidence of new variants not yet found in patient-derived samples from California and suggested that these variants may be detected in clinical patient samples in the near future. On a technical side, the authors addressed the difficulties inherent to isolating virus in wastewater samples, and reported that both the RNA extraction method and the initial concentration of SARS-CoV-2 in the sample have a significant effect on genome recovery and coverage.

Study Strengths

This study demonstrated that wastewater samples can be used not only to detect the presence of SARS-CoV-2 in the community, but also to detect distinct genotypes circulating in the local population. The authors presented a comparison of RNA extraction and sequencing methods that may help to inform future wastewater sequencing studies, and their findings suggest that wastewater sampling may be an effective tool for surveying SARS-CoV-2 variants at a population scale.


The authors provided some evidence that common variants occur at similar frequencies in wastewater samples but, in the absence of phylogenetic context or additional technical replicates, it is difficult to evaluate if variant frequencies in wastewater samples can be used to track the spread and abundance of particular viral lineages.

Value added

This study demonstrated that sequencing of wastewater samples can detect SARS-CoV-2 and identify multiple genotypes known to be circulating in local communities.

This review was posted on: 19 February 2021