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Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

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Wed, 2021-01-27 16:42 — mike kraft
Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants 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. mBio

Mutated versions of SARS-CoV-2, the virus that causes COVID-19, have been popping up across the globe. One called B.1.1.7, first reported in the United Kingdom in December, has already made appearances in 24 U.S. states . Another new variant called CAL.20C has emerged from Southern California and coincides with a surge of cases in the area, raising concerns that some mutations to the virus could allow it to spread more easily.

Because of the spread of these variants and the concerns they raise, public health officials want to track the variants’ spread, which relies on deciphering the genetic code of the virus. But collecting samples from human patients can be invasive and takes time, making it impractical to detect variants. Another tactic could be checking wastewater for the variants, researchers recently reported in mBio.

Analysis of sewage samples taken last summer from the San Francisco Bay Area detected not only the presence of SARS-CoV-2 in communities, the team found, but also the appearance of distinct mutations of different viral variants. One detected mutation, called D614G, emerged after the pandemic began and led to more contagious variants that quickly became the dominant versions of the virus around the world. The wastewater testing method even detected variants not yet picked up in clinical samples. This information could help researchers track the transmission of variants and assess any impacts on vaccines and treatments. 

 

 

Country / Region Tags: 
United States
US - West
General Topic Tags: 
COVID-19
Data
Disease
Pandemics
Research
Waste
Problem, Solution, SitRep, or ?: 
Analysis
Situation Report
Groups this Group Post belongs to: 
Water
- Private group -

Comments

Thu, 2021-01-28 03:49 — mdmcdonald

Dear RAC Environmental Testing work group members and associates, 


It may be that the RAC’s efforts to move widespread COVID-19 testing upstream and hyper-local around the country has shifted from being valuable in controlling local outbreaks to being of strategic importance to our nation’s fight against the pandemic.  What are your thoughts on the article below and our current national efforts to engage early identification and responses to control COV-2 variants, especially those that are “immunity escaping.” 


You may want to raise questions to Rear Admiral Paul Reed (DASH, DHHS OASH) and Tom WIlkinson (Chief, Medical Information Officer, CWMD, DHS) in today’s RAC Convocation about these issues.  Let me know and I may be about to work with Ahmed Calvo to cue up these types of questions today.  

Mike

Michael D. McDonald, Dr.P.H. 

Coordinator
Resilient American Communities (RAC) Initiative 

Executive Director
Health Initiatives Foundation, Inc.

Cell: 202-468-7899


Begin forwarded message:


Subject: [cfl_dri_sanitation_sewer_systems][1 other group] Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
Date: January 27, 2021 at 4:42:47 PM EST
Reply-To: CFL DRI - Sanitation - Sewer Systems <cfl_dri_sanitation_sewer_systems@m.resiliencesystem.org>, Water <water@m.resiliencesystem.org>


Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 VariantsViral 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.mBio

Mutated versions of SARS-CoV-2, the virus that causes COVID-19, have been popping up across the globe. One called B.1.1.7, first reported in the United Kingdom in December, has already made appearances in 24 U.S. states . Another new variant called CAL.20C has emerged from Southern California and coincides with a surge of cases in the area, raising concerns that some mutations to the virus could allow it to spread more easily.

Because of the spread of these variants and the concerns they raise, public health officials want to track the variants’ spread, which relies on deciphering the genetic code of the virus. But collecting samples from human patients can be invasive and takes time, making it impractical to detect variants. Another tactic could be checking wastewater for the variants, researchers recently reported in mBio.

Analysis of sewage samples taken last summer from the San Francisco Bay Area detected not only the presence of SARS-CoV-2 in communities, the team found, but also the appearance of distinct mutations of different viral variants. One detected mutation, called D614G, emerged after the pandemic began and led to more contagious variants that quickly became the dominant versions of the virus around the world. The wastewater testing method even detected variants not yet picked up in clinical samples. This information could help researchers track the transmission of variants and assess any impacts on vaccines and treatments. 

 
 

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