UC Santa Cruz Genomics Institute | January 28, 2021

The virus that causes COVID-19 is mutating. 

Over time, mutations add up to become a trail of breadcrumbs showing where a virus has been and where it is headed. The breadcrumb trail reveals itself when we sequence a virus sample’s genome, and then use a powerful digital microscope called a genome browser to help with analysis.  

We know some of those genetic variations make the virus extra contagious. And we know that those variants are here in the Bay Area. 

We also know that sequencing test samples can help us identify super-contagious variants and contain their outbreaks. This approach to containing the spread, referred to as genomic surveillance, is known to be effective but hasn’t been tried here — yet. 

“We know how to do this,” said Beth Shapiro, UCSC Professor, Ecology and Evolutionary Biology, and HHMI Investigator.  “Sequencing the genome of the virus is no different than sequencing a mammoth genome. We have established and validated protocols and experienced hands. We are ready to help,” she explained.

“We absolutely need to increase our surveillance of what the virus is doing and how it is being transmitted,” said David Haussler, Professor of Biomolecular Engineering at UCSC, Scientific Director of the Genomics Institute and HHMI Investigator. “We must keep track of how the virus is taking advantage of us.” 

The UK has sequenced about 10% of all its infections to date, and can process 5,000 samples a week. This capacity increases the opportunity to detect new variants and spotlights where interventions such as quarantining might stop a surge.

By comparison, the U.S. has sequenced 0.3% of its cases.  Australia and New Zealand lead the ranking, each with half or more of their COVID-19 samples sequenced.

“What we desperately need is more sequencing in the U.S.,” said Institute affiliate Russ Corbett-Detig.  

There is some good news: UC Santa Cruz already had the leading genome browser in the world before the pandemic. Now, we have a SARS-CoV-2 version of that browser with all the latest virus data available in that browser; plus, we have an expanded Covid testing lab on campus. 

While the U.S. is off to a slower start as compared to other countries, more virus genome sequencing data is coming online all the time. “My impression is that we’re about to get a ton more data from across the U.S. and many other countries too,” Corbett-Detig added.

Locally, UCSC, SC County Health, and Salud Para la Gente have joined forces to sequence area test samples. Sequencing test data will help us see how the contagion is occurring. We’ll need more resources to scale up, to share that data, and increase our impact. But, UCSC is ready — and we are coming for you, coronavirus!