Your browser doesn't support javascript.
Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants.
Crits-Christoph, Alexander; Kantor, Rose S; Olm, Matthew R; Whitney, Oscar N; Al-Shayeb, Basem; Lou, Yue Clare; Flamholz, Avi; Kennedy, Lauren C; Greenwald, Hannah; Hinkle, Adrian; Hetzel, Jonathan; Spitzer, Sara; Koble, Jeffery; Tan, Asako; Hyde, Fred; Schroth, Gary; Kuersten, Scott; Banfield, Jillian F; Nelson, Kara L.
  • Crits-Christoph A; Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
  • Kantor RS; Innovative Genomics Institute, Berkeley, California, USA.
  • Olm MR; Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA.
  • Whitney ON; Department of Microbiology and Immunology, Stanford University, Stanford, California, USA.
  • Al-Shayeb B; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
  • Lou YC; Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
  • Flamholz A; Innovative Genomics Institute, Berkeley, California, USA.
  • Kennedy LC; Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
  • Greenwald H; Innovative Genomics Institute, Berkeley, California, USA.
  • Hinkle A; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
  • Hetzel J; Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA.
  • Spitzer S; Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA.
  • Koble J; Department of Civil and Environmental Engineering, University of California, Berkeley, California, USA.
  • Tan A; Illumina, San Diego, California, USA.
  • Hyde F; Illumina, San Diego, California, USA.
  • Schroth G; Illumina, San Diego, California, USA.
  • Kuersten S; Illumina, San Diego, California, USA.
  • Banfield JF; Illumina, Madison, Wisconsin, USA.
  • Nelson KL; Illumina, San Diego, California, USA.
mBio ; 12(1)2021 01 19.
Article in English | MEDLINE | ID: covidwho-1066817
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
Semantic information from SemMedBD (by NLM)
1. genome sequencing DIAGNOSES 2019 novel coronavirus
Subject
genome sequencing
Predicate
DIAGNOSES
Object
2019 novel coronavirus
2. 2019 novel coronavirus COEXISTS_WITH COVID-19
Subject
2019 novel coronavirus
Predicate
COEXISTS_WITH
Object
COVID-19
3. Infected PROCESS_OF Community
Subject
Infected
Predicate
PROCESS_OF
Object
Community
4. Alleles PART_OF 2019 novel coronavirus
Subject
Alleles
Predicate
PART_OF
Object
2019 novel coronavirus
5. Metagenome COEXISTS_WITH Alleles
Subject
Metagenome
Predicate
COEXISTS_WITH
Object
Alleles
6. Patients LOCATION_OF Genome
Subject
Patients
Predicate
LOCATION_OF
Object
Genome
7. genome sequencing DIAGNOSES 2019 novel coronavirus
Subject
genome sequencing
Predicate
DIAGNOSES
Object
2019 novel coronavirus
8. 2019 novel coronavirus COEXISTS_WITH COVID-19
Subject
2019 novel coronavirus
Predicate
COEXISTS_WITH
Object
COVID-19
9. Infected PROCESS_OF Community
Subject
Infected
Predicate
PROCESS_OF
Object
Community
10. Alleles PART_OF 2019 novel coronavirus
Subject
Alleles
Predicate
PART_OF
Object
2019 novel coronavirus
11. Metagenome COEXISTS_WITH Alleles
Subject
Metagenome
Predicate
COEXISTS_WITH
Object
Alleles
12. Patients LOCATION_OF Genome
Subject
Patients
Predicate
LOCATION_OF
Object
Genome
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.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Sewage / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Year: 2021 Document Type: Article Affiliation country: MBio.02703-20

Similar

MEDLINE

...
LILACS

LIS


Full text: Available Collection: International databases Database: MEDLINE Main subject: Sewage / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study Topics: Variants Limits: Humans Country/Region as subject: North America Language: English Year: 2021 Document Type: Article Affiliation country: MBio.02703-20