Scripps Research & UCSD Scientists Use Genome Sequencing to Track Spread Of COVID-19

Local scientists received a $2.5 million contract from the Centers for Disease Control and Prevention to use genome sequencing to track the spread of COVID-19

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Scientists at UC San Diego and Scripps Research are using genome sequencing to track the spread of COVID-19 and identify the source of outbreaks in San Diego County and neighboring communities.

Scripps Research professor Kristian Andersen, Ph.D., is one of the leading scientists behind the project. His team of researchers received a $2.5 million contract from the Centers for Disease Control and Prevention to complete the study and has sampled 2,000 positive COVID-19 cases, according to Andersen.

Andersen's team uses leftover nasal swab samples from unidentified positive COVID-19 patients. As the virus spreads it slightly mutates, which helps scientists identify and track transmission. Andersen compared the virus mutations to a bar code.

“We can all piece it (virus samples) together as family trees. Essentially saying like, ‘this virus is related to that virus, but it's slightly more distantly related to that virus.'  What’s interesting here is the connectedness between San Diego and Baja and Imperial is pretty strong. So, it looks like one major epidemic, and less so if we’re talking about LA county and Orange county,” Andersen explained.

He said data proves cross-border transmission is moving equally in both directions between Mexico and San Diego. He also said the greatest source of transmission is superspreader events.  

“Eighty percent of the spreading that we see is probably due to some sort of superspreading events and that sounds scary, but it’s actually good news because superspreading events are something we can do a lot actively to prevent,” said Andersen.

The data confirms physical distancing, wearing a face mask and minimizing indoor activities are the best ways to slow the spread of the virus.

“We all need to work together with global, international, local, regional partners to get COVID under control and only by that can we be successful,” said Andersen.

Andersen said the CDC is funding the project for the next two years. He hopes to expand their sample size to several thousand. 

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