What Bug's In You?

Winter 2021

SARS-CoV-2 genomes continue to diversify. Here, isolates from Louisiana are color-coded and compared to other samples from around the world over time.

Say an elementary school has an outbreak of COVID-19, with three confirmed cases in one week. Although quarantining and contact tracing are the best tools we have for ending lines of transmission, those tools can’t always tell you where each of those kids got the virus in the first place. 

And for the school, weighing its options on what to do next, the million-dollar question is: Did these families get the bug on campus or someplace else? 

There’s a good way to answer that, says Vaughn Cooper, Pitt professor of microbiology and molecular genetics. His lab is taking positive COVID-19 tests and sequencing the entire genome of each virus found therein—all 29,000 nucleotides of it. And, using techniques Cooper and his team developed, they’re turning it all around in 72 hours or less. 

Viruses propagate by copying themselves, a less-than-perfect process. In SARS-CoV-2, there’s a new mistake, or mutation, in a given viral lineage about once every two weeks. Because of this, the genomes of the viruses found in cases around the globe have enormous variety—many thousands of distinct flavors. 

When the team sequences a virus, they can compare it “with literally every other sequence ever decoded on the planet,” Cooper said recently on Washington Post Live.  

Take our hypothetical elementary school: If the three virus genomes are identical, “then that’s likely a spreading event, and that might be support for a closure”—to deep clean, test folks en masse and hunt for the culprit within. If the genomes are all different, though, that’s more in line with random infections coming from elsewhere in the community. “You would just isolate those cases and their families, and you could probably keep the facility open,” he says.

Cooper has partnered with the Louisiana Department of Health and Louisiana State University to help quash SARS-CoV-2 outbreaks in that state’s nursing homes, jails and agricultural work sites. And here at home, he’s been using these microbial genome sequencing techniques for years to sleuth out bacterial pathogens within UPMC hospitals in real time. “We were kind of primed to do this when COVID hit,” he says.  

And Cooper’s thoughts on B.1.1.7, the new variant that first turned up in the UK in December?

The reason we know about it, he says, is because the UK had the foresight to invest in sequencing simply for the purposes of monitoring this pathogen. "This shows how important it is that our country try to rebuild and reinvest in infrastructure like this.
 
He adds: “All of the primary ways of controlling this virus still matter. And we think that the vaccine is going to work just fine against it." 
 
—Elaine Vitone
 

Vaughn Cooper talks about predicting evolution and tracking the novel coronavirus in our Pitt Medcast, “Evolving Situation.” 

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Image: LSU Health Shreveport Emerging Viral Threat Laboratory and GISAID. Built by Freitas et al with Auspice and Augur. Data made available through GISAID EpiCoV.