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 — ontology label: Severe acute respiratory syndrome coronavirus 2 | NCBITaxon:2697049 · TaxonMech · TraitMech | N/A | |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Wastewater Minor SARS-CoV-2 Allele Profiling
Computational SNV analysis of sampled wastewater RNA identified sub-consensus SARS-CoV-2 alleles. Minor variants describe a mixed population; they are not all resolved strain haplotypes. Concordant allele frequencies can support linkage of particular variants but do not prove complete donor genomes or infectivity.
Evidence
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PMID:33468686 - SUPPORT (COMPUTATIONAL)"Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater"
Regional Clinical Genotype Concordance
Major wastewater SARS-CoV-2 consensus genotypes matched clinical genomes sampled in the same region. This is sequence concordance between sampled populations, not proof of specific transmission events, complete coverage of local infections or viral activity within sewage.
Evidence
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PMID:33468686 - SUPPORT (COMPUTATIONAL)"The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical"
Preclinical Local Lineage-Introduction Signal
PARTIAL - four recurrent wastewater variants absent from the available California clinical genomes but seen elsewhere supported the authors' inference of possible recent lineage introductions. The inference depends on clinical sampling and sequence detection; it is not confirmed transmission, a dated introduction or demonstrated infectivity.
Evidence
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PMID:33468686 - PARTIAL (COMPUTATIONAL)"wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Can denser clinical sampling and linked genomes distinguish recent introductions from unsampled local diversity?
Metatranscriptomic sequencing and consensus assembly are analytical methods, so their two workflow nodes were removed. No previously removed workflow arrow is restored. The retained nodes describe sequence observations and inference, not biological replication or infectivity. Whole main text/captions read; images, supplementary sequences and code remain unread.
Attaches to: ecological_interactions#Wastewater Minor SARS-CoV-2 Allele Profiling, ecological_interactions#Regional Clinical Genotype Concordance, ecological_interactions#Preclinical Local Lineage-Introduction Signal
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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