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Coronavirus

How genetic sequencing is helping solve the mystery of coronavirus’ spread through Colorado nursing homes

A research team at Colorado State University analyzed dozens of samples to figure out whether the virus is being transmitted within the facilities or spread primarily from outside them

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As infections from the novel coronavirus earlier this year overwhelmed nursing homes across Colorado, those trying to stop the virus were presented with a mystery: How, exactly, was it getting into and spreading through facilities that were off-limits to outsiders and subject to rigorous infection-control rules?

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Now, a research team at Colorado State University has found a clue by analyzing the virus’ genetic fingerprints. The team is among the first in the state to attempt to track the spread of the coronavirus by conducting genomic sequencing — the painstaking process of reading the virus’ genetic code. By looking for slight mutations in the code, researchers can create something of a family tree, showing which cases are closely related and which are more distantly separated.

And, though they still have plenty of work to do, the researchers’ data — gathered from dozens of samples from infected workers at nursing homes and other long-term care facilities — are showing a clear trend.

“They suggest that viruses sampled from within the same facility are more closely related genetically to each other than they are to viruses that are sampled from other facilities,” said Greg Ebel, the CSU professor who is leading the study.

That means that each outbreak in a facility likely starts from a single introduction of the virus that is then passed around and not from multiple introductions. The conclusion provides needed insight to health officials as they seek to control outbreaks within the facilities and it provides important context for the state’s decision to launch a massive campaign to regularly test all workers at the facilities.

Streets near Frasier Meadows, left, a campus of senior apartments and skilled nursing care in Boulder, are marked for the safety of older residents in the neighborhood. The doors at the complex are closed to visitors because of fears about the coronavirus. During a COVID-19 outbreak at the facility, three cases of the illness were confirmed among residents, and eight cases were confirmed or suspected among staff. No deaths were reported at the facility. (Dana Coffield, The Colorado Sun)

Ebel and his team’s research was published last month as a “preprint” paper on the website medRxiv, which is a place for health scientists to publish preliminary studies that have not yet gone through peer review.

As of last week, there have been COVID-19 outbreaks at nearly 170 nursing homes, independent-living facilities and other long-term care centers, according to the Colorado Department of Public Health and Environment. Those outbreaks have resulted in more than 3,000 confirmed or suspected cases among residents and nearly 2,500 confirmed or suspected cases among staff. More than 900 residents of the facilities and six staff members have died with confirmed or probable cases of COVID-19, according to CDPHE.

TODAY’S UNDERWRITER

In recent weeks, as testing of workers at the facilities has ramped up, the number of new cases and deaths at nursing homes has slowed. As of last week, more than half of the outbreaks are considered resolved by CDPHE.

Greg Ebel, associate professor of Microbiology Immunology and Pathology at Colorado State University. (Provided by CSU)

Ebel and his team have previously shown one reason why it has proven so difficult to stop outbreaks at nursing homes. After conducting tests on workers at five Vivage Senior Living facilities in Colorado, researchers found an alarmingly high rate of workers who were infected — and many were both asymptomatic and also shedding viral particles capable of starting new infections in others.

“We never dreamed that we would walk into a facility and 20% of the people working there would be positive, but that’s what we found,” Ebel said.

The team decided to take the research a step further by conducting the genomic sequencing.

Nicole Sexton, a postdoctoral fellow in Ebel’s lab, did much of the tedious work. Overall, she said, there wasn’t much variation between any of the samples. That’s to be expected because coronaviruses contain proofreading mechanisms to limit the natural mutations that occur as the virus replicates.

But what little variation there was showed a distinct pattern.

“What we saw is within facilities a lot of the same sequence, whereas within different facilities, they had a different sequence,” she said. “It does look like, with the data we have so far, that they really are clustering within the same facility.”

Sexton said it’s not entirely certain that this means the outbreaks are the result of a single introduction of the virus that is passed around within a facility. Her samples don’t contain any taken from residents. If coworkers gathered somewhere in their off hours, it’s possible they could share the virus then, rather than at work. And the team still has work to do to learn about what strains of the virus are circulating within the state as a whole.

But Ebel said the most likely scenario is that the viral transmission is happening within the facilities, as the result of an introduction through an infected staff member. As researchers tested more workers at the facilities — and the infected ones were told to isolate at home — Ebel said the prevalence of infections within the facilities declined, further strengthening the case that stopping outbreaks within the facilities requires better testing of workers.

“We’re taking infected people out of the workplace,” he said, “and we think that really is having an impact.”


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