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Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants

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Sun, 2020-12-20 08:32 — Jan Booher

Note: This contnt is from a pre-print that has not yet been certified by peer review.

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 near-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 (SNV) 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 US or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside of CA, 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.

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Country / Region Tags: 
US - SouthEast
General Topic Tags: 
COVID-19
Problem, Solution, SitRep, or ?: 
Solutions
Groups this Group Post belongs to: 
CFL RAC Orange Co Leadership Coordination Group
CFL RAC Sarasota Community Partners
- Private group -

Comments

Sun, 2020-12-20 09:09 — Dr Merritt

way cool.

They were doing this with colleges and universities earlier. It will be interesting to see if cross/repeat infections may be related to different strains, and whether some are more virulent or associated with certain organ systems more than others which might prioritize which communities get the vaccine vs others.
LM

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Yours in Unity&Health
Lisa Merritt MD
Sun, 2020-12-20 11:55 — Dr Hill

Interesting work.

Washington Clark Hill, M.D., FACOG
Obstetrics and Gynecology
Maternal-Fetal Medicine
CenterPlace Health
Cell-941-356-9099
Fax-941-922-2694
- Show quoted text -


way cool.

They were doing this with colleges and universities earlier. It will be interesting to see if cross/repeat infections may be related to different strains, and whether some are more virulent or associated with certain organ systems more than others which might prioritize which communities get the vaccine vs others.
LM

howdy folks