Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
Top Cited Papers
Open Access
- 23 February 2021
- journal article
- research article
- Published by American Society for Microbiology in mBio
- Vol. 12 (1)
- https://doi.org/10.1128/mbio.02703-20
Abstract
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.Keywords
Funding Information
- Innovative Genomics Institute
- Center for Information Technology Research in the Interest of Society
This publication has 40 references indexed in Scilit:
- Frequent Detection and Genetic Diversity of Human Bocavirus in Urban Sewage SamplesFood and Environmental Virology, 2016
- Sambamba: fast processing of NGS alignment formatsBioinformatics, 2015
- Detection of human coronaviruses in simultaneously collected stool samples and nasopharyngeal swabs from hospitalized children with acute gastroenteritisVirology Journal, 2013
- Identification of Viral Pathogen Diversity in Sewage Sludge by Metagenome AnalysisEnvironmental Science & Technology, 2013
- High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated SewageJournal of Virology, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Raw Sewage Harbors Diverse Viral PopulationsmBio, 2011
- Frequent Detection of Highly Diverse Variants of Cardiovirus , Cosavirus , Bocavirus , and Circovirus in Sewage Samples Collected in the United StatesJournal of Clinical Microbiology, 2009
- Corrigendum to “Concentration and detection of SARS coronavirus in sewage from Xiao Tang Shan Hospital and the 309th Hospital” [J. Virol. Methods 128 (2005) 156–161]Journal of Virological Methods, 2005
- Concentration and detection of SARS coronavirus in sewage from Xiao Tang Shan Hospital and the 309th HospitalJournal of Virological Methods, 2005