A metatranscriptomic surveillance community in municipal sewage from the San Francisco Bay Area used to detect regionally prevalent SARS-CoV-2 variants during the COVID-19 pandemic. RNA was sequenced directly from sewage collected by municipal utility districts to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in sewage were identical to clinical genotypes, showing that wastewater metatranscriptomics can profile viral genetic diversity at the community scale.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| SARS-CoV-2 sewage population | NCBITaxon:2697049 | N/A | |
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Ecological Interactions
Taxon
Cross-feeding
Mutualism
Syntrophy
Competition
Commensalism
Niche partitioning
Colonization facilitation
Strain competition
Predation
Wastewater Genotype Matches Clinical Consensus
COMMENSALISMEvidence
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PMID:33468686 - SUPPORT (IN_VIVO)"The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical"
Metatranscriptomic Profiling of Viral Genetic Diversity
COMMENSALISMEvidence
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PMID:33468686 - SUPPORT (IN_VIVO)"metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities"
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication for the Bay Area sewage SARS-CoV-2 community
PubMed record for the Crits-Christoph et al. 2021 mBio paper. |
OTHER | PMID:33468686 |
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DOI landing page
DOI link to the mBio paper. |
OTHER | doi:10.1128/mBio.02703-20 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Sampling region | San Francisco Bay Area municipal utility districts | N/A |
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