BioE Graduate Seminars

Event Introduction

Wastewater surveillance for SARS-CoV-2 in the Bay Area

Abstract

Wastewater based epidemiology has shown promise as a means to track the COVID-19 pandemic. At UC Berkeley, we have developed a fast, efficient method for RNA extraction from sewage; used high-throughput sequencing to resolve single nucleotide variations in SARS-CoV-2 genomes from sewage; and set up a regional wastewater monitoring program for the San Francisco Bay Area.

The (“4S”) method—Sewage, Salt, Silica, and SARS-CoV-2—for RNA extraction relies on salt and heat for viral lysis, followed by silica column-based purification. We compared this method against ultrafiltration, and found that it recovered more virus, took less time, and allowed for safer handling of wastewater samples. We used probe-capture enrichment coupled with high-throughput sequencing to recover genomes for SARS-CoV-2 from wastewater samples.

We then analyzed the relative abundance of single nucleotide variants (SNVs) across the consensus genome, and compared this information to SNVs found in genomes from clinical samples. Lastly, we have recently started a regional wastewater monitoring program to connect public health officials, wastewater agencies and our wastewater monitoring laboratory.

Rose will touch on each of these aspects of the project in her seminar.

About the speaker

Rose Kantor is a postdoctoral scholar with Kara Nelson at UC Berkeley. Currently she leads research in wastewater-based epidemiology (WBE) for SARS-CoV-2 applied to the San Francisco Bay Area.

Prior to the pandemic, she studied the microbial communities in water for potable reuse using meta-omics techniques. She is interested in changes to the drinking water distribution system microbial community with the introduction of advanced treated wastewater.

More broadly, she is interested in the microbiology of engineered environments and microbial biotechnologies that improve environmental and human health. Rose earned her B.A. in Biology from Carleton College (2010), and her Ph.D. in Microbiology (2016) in the lab of Professor Jill Banfield at UC Berkeley.