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Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
- Source :
- mBio, mBio, Vol 12, Iss 1 (2021), mBio, vol 12, iss 1
- Publication Year :
- 2021
- Publisher :
- American Society for Microbiology, 2021.
-
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.<br />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.
- Subjects :
- viruses
coronavirus
Sewage
010501 environmental sciences
01 natural sciences
Genome
California
Clinical Science and Epidemiology
Genotype
Environmental Microbiology
2.1 Biological and endogenous factors
Viral
Aetiology
skin and connective tissue diseases
Lung
Genetics
0303 health sciences
Single Nucleotide
respiratory system
QR1-502
Infectious Diseases
environmental microbiology
RNA, Viral
Infection
Research Article
Genomics
Context (language use)
Genome, Viral
Biology
Real-Time Polymerase Chain Reaction
Polymorphism, Single Nucleotide
Microbiology
DNA sequencing
Vaccine Related
03 medical and health sciences
Biodefense
Virology
genomics
Humans
Polymorphism
Allele
030304 developmental biology
0105 earth and related environmental sciences
metagenomics
Genetic diversity
Base Sequence
SARS-CoV-2
business.industry
Prevention
Human Genome
fungi
COVID-19
Pneumonia
body regions
Emerging Infectious Diseases
Good Health and Well Being
Metagenomics
RNA
Metagenome
Transcriptome
business
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- mBio, mBio, Vol 12, Iss 1 (2021), mBio, vol 12, iss 1
- Accession number :
- edsair.doi.dedup.....6ed0f3675441a6cb76f9ad81146fdc1c