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

Reviewers: Pei-ying Hong (King Abdullah University of Science and Technology) | 📒📒📒◻️◻️ • Blake Wiedenheft (Montana State University Bozeman), Anna Nemudraia, Artem Nemudryy | 📘📘📘📘📘

Published onJan 24, 2021
Reviews of "Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants"
key-enterThis Pub is a Review of
Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants
Description

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.

Since our solicitation of reviews, this preprint has been published in mBio journal and the link to the published manuscript can be found here.

To read the original manuscript, click the link above.

Summary of Reviews: This preprint offers a successful demonstration of WGS-based detection of emerging SARS-CoV-2 variants in wastewater samples. Reviewers deemed major claims reliable, but experimental methodology and justification should be described in further detail.

Reviewer 1 (Pei-ying Hong) | 📒📒📒 ◻️◻️

Reviewer 2 (Blake Wiedenheft, Anna Nemudraia, Artem Nemudryy) | 📘📘📘📘📘

RR:C19 Strength of Evidence Scale Key

📕 ◻️◻️◻️◻️ = Misleading

📙📙 ◻️◻️◻️ = Not Informative

📒📒📒 ◻️◻️ = Potentially Informative

📗📗📗📗◻️ = Reliable

📘📘📘📘📘 = Strong

To read the reviews, click the links below.


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