SARS-CoV-2 Genomics for COVID-19 wastewater tracking

This project aims to develop SARS-CoV-2 genomics tools to apply to the tracking of COVID-19 in municipal wastewater. Detection of SARS-CoV-2 genetic material in wastewater has been used to estimate prevalence of the virus in the corresponding community. This has the potential to be a relatively inexpensive early warning system that is complementary to testing in the clinic. However, genome sequencing to differentiate between lineages or genetic variants, which could be used to track origin of outbreaks, has not yet been applied to wastewater. There are still a number of technical challenges that must be solved in processing the wastewater samples such that the viral genetic material is suitable for sequencing, There are also bioinformatics challenges to solve, related to extraction of meaningful genome sequence information from complex mixtures of microbial communities, and mixtures of different SARS-CoV-2 genetic variants. The two interns will therefore directly address these two challenges, with one of them focusing on genome sequencing, and the other on bioinformatics.

Faculty Supervisor:

Jozef Nissimov;Trevor Charles


Danielle Rose;Isaac Ellmen


Metagenom Bio Inc.




Professional, scientific and technical services


University of Waterloo



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