COVID-19 Wastewater Monitoring: Tracking SARS-CoV-2 Infection Dynamics Through Genome Sequencing

COVID-19 Wastewater Monitoring: Tracking SARS-CoV-2 Infection Dynamics Through Genome Sequencing

About the Webinar:

The COVID-19 pandemic has revealed the imminent need for rapid surveillance at the community level to track potential outbreak clusters ahead of clinical diagnosis, particularly considering the important role of asymptomatic infection in transmission. Wastewater monitoring has been used as a surrogate to track the extent and spread of SARS-CoV-2, the virus that causes COVID-19, in communities, particularly when diagnostic testing is limited. This presentation will describe large scale wastewater surveillance at the UC San Diego campus level, as well as the San Diego county level. Learners will also explore how high throughput wastewater SARS-CoV-2 genome sequencing helped uncover early and cryptic transmission of SARS-CoV-2 variants of concern in the county.

Learning Objectives

  1. Describe the high-resolution wastewater surveillance and clinical sequencing system deployed in San Diego by UCSD Technical Solutions
  2. Discuss the role of high throughput wastewater SARS-CoV-2 genome sequencing in identifying transmission of SARS-CoV-2 variants of concern
  3. Apply computational methods as a solution to implementing wastewater surveillance at scale

Instructor: Smruthi Karthikeyan, PhD

Smruthi Karthikeyan obtained her Masters in Earth and Environmental Engineering in 2014 from Columbia University, New York and a PhD in Environmental Engineering from Georgia Institute of Technology, specializing in environmental microbial genomics, working at the interface of microbial ecology, computational biology, and engineering. Smruthi is interested in using multi-omics approaches to provide a holistic view of environmental systems. As a part of her postdoctoral research at Rob Knight’s lab in UC San Diego, she is developing integrated wet-lab and computational biology based techniques to study how environmental systems could serve as biomarkers for health and disease. Currently, she is working on developing high throughput approached for monitoring SARSs-CoV-2 signatures in wastewater at the campus and county level.


Rob Knight is the Director of the Center for Microbiome Innovation at UC San Diego, where he is a Professor of Pediatrics, Bioengineering, and Computer Science & Engineering. He co-founded the Earth Microbiome Project, and the American Gut Project, which is among the largest crowdfunded science projects of any kind to date. He has spoken at TED, written three books and over 700 scientific articles, and in 2017 he won the Massry Prize, often considered a predictor of the Nobel. He was honored with the 2019 NIH Director’s Pioneer Award for his microbiome research. His work combines microbiology, DNA sequencing, ecology and computer science to understand the vast numbers of microbes that inhabit our bodies and our planet.