SARS-CoV-2 Nextstrain build

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Nextstrain is an open source project using genomic epidemiology to perform real-time tracking of pathogen evolution. The goal is to improve epidemiological understanding and outbreak response using openly shared data from research groups around the world.


This build, which incorporates data from the Ebel lab and which is based on the work of Cole Jensen and Anderson Brito of the Grubaugh Lab (Yale School of Public Health), uses genetic data and metadata of SARS-CoV-2 that has been openly shared by many research groups.

Ebel lab undergraduate research assistant Parker Cline was instrumental to this collaboration. See his contribution below, as well as a link to the Nextstrain project main page.

https://nextstrain.org/community/parkercline/CSU-SARS-CoV-2/ncovupdate

http://grubaughlab.com/nextstrain/

DISCLAIMER: These builds use preliminary data.

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

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The Ebel lab’s COVID-19 surveillance work was again featured in the Colorado Sun. The project, a collaboration with Nicole Ehrhart and CSU’s Healthy Aging Center, is beginning to reveal clues about how SARS-CoV-2 spreads within skilled nursing facilities across the state. From the article:

“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.”

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)

 

“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.'”

With thanks to Colorado Sun reporter John Ingold!

Colorado will test for coronavirus at every nursing home every week for 8 weeks

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The Ebel lab’s SARS-CoV-2 collaboration with CSU’s Healthy Aging Center was recently featured on CPR. With support from the Colorado Department of Public Health & Environment (CDPHE), the coronavirus surveillance testing effort will soon expand rapidly to long-term care facilities around the state. From the article:

“The new study will help paint a picture of how COVID-19 spreads in complex facilities like residential nursing homes. Both state officials and researchers hope that the testing could mark a turning point in controlling COVID-19 in the beleaguered facilities.

Through this new effort, CDPHE and CSU will administer around 45,000 nose swab tests. These will be performed on staff members and some residents that are permitted to leave the facility during the lockdown for essential health appointments.

“The idea is to catch people as they become positive and then isolate them,” Erhart said.”

With thanks to CPR reporter Lindsay Fendt!

Dr. Emily Gallichotte featured on CBS Denver

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Dr. Emily Gallichotte was featured recently on CBS Denver’s “Good Question” segment. A listener asked whether SARS-CoV-2 could be transmitted through mosquito bites, and CBS Denver reached out to Dr. Gallichotte for more information. From the interview:

“In science we want to be very cautious. All of the evidence from WHO and CDC and every expert in the field says it is essentially no,” says post-doctoral research scientist Emily Gallichotte.

“Mosquitoes aren’t just syringes that transfer blood possibly with virus from one person to another. It takes that blood, it gets into their gut and then it has to survive seven days at least to make its way and replicate through the mosquito’s body and end up in the saliva to then be transferred to that next person.”

Find the full segment and more information on the CBS Denver website. With big thanks to Alan Gionet for giving our lab an opportunity to answer such timely questions!

 

CSU team finds dozens of asymptomatic nursing home workers infected with coronavirus

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The Ebel lab’s SARS-CoV-2 surveillance work in Colorado long-term care facilities has been featured in the ColoradoanFrom the article:

“The facilities, used to taking precautions against things like seasonal flu outbreaks, seemed to be doing everything right. No visitors were allowed in. Employees of the five Denver metro area living communities were screened for coronavirus symptoms each day they reported to work. Management was following guidance from the state and Centers for Disease Control and Prevention.

But as the test results came back, it became clear that dozens of infected workers were showing no symptoms at all. Of 462 employees tested in the first two months of the Colorado State University project, 57 people (about 12.3%) were coronavirus-positive but had no symptoms. The positive rate at the five facilities ranged between 1% and 23%.

“Most people in our study who are virus positive are not sick,” said Ebel, a CSU professor in the Department of Microbiology, Immunology and Pathology whose lab processed the tests. “And they’re really virus-positive. They’re not just kind of, a little bit positive. There is no doubt that they’re very positive and capable of transmitting.””

Greg Ebel, left, and Nicole Ehrhart, right, are collaborating on a Colorado State University project to test asymptomatic employees of skilled nursing facilities for coronavirus.

Greg Ebel, left, and Nicole Ehrhart, right, are collaborating on a Colorado State University project to test asymptomatic employees of skilled nursing facilities for coronavirus. (Photo: Courtesy of Colorado State University)

 

With thanks to Coloradoan City Government Reporter Jacy Marmaduke!

SARS-CoV-2 surveillance testing featured in the Colorado Sun

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The Ebel lab’s SARS-CoV-2 surveillance work in Colorado long-term care facilities has been featured in the Colorado Sun. From the article:

“A brainstorming call sparked the connection. Soon, Ehrhart and Ebel had a plan in place with Lakewood-based Vivage Senior Living to test workers at five Vivage facilities in Colorado. And, most importantly, they were going to test the workers over and over again.

“What is unique about this testing versus pretty much anything we’ve seen so far is we are testing people weekly,” Ehrhart said.

That would give the researchers insight into the virus’s spread and how long workers remain infected. It would give the facilities an early warning that a worker was sick and a precise idea when the worker could come back to work. Most importantly, it would help keep the facilities’ residents safe — and their staff.

“Health care workers are this really critical, finite resource that needs to be protected,” Ebel said.”

Research at CSU shows why testing only symptomatic people won’t stop coronavirus in Colorado

With big thanks to John Ingold!

Ebel lab’s SARS-CoV-2 surveillance efforts featured in the Dallas Morning News

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The Ebel lab’s SARS-CoV-2 surveillance work in Colorado long-term care facilities has been featured in the Dallas Morning News. From the article:

“In Colorado, Connecticut and Washington such efforts have been underway, identifying asymptomatic carriers and isolating them so they will not spread the disease to coworkers or residents.

Over the last two months, a lab run by Colorado State University microbiology professor Greg Ebel tested 462 nursing home workers in Colorado to gauge whether workers without symptoms were silently carrying the virus. The lab identified 57 people who tested positive but had no symptoms.

“This kind of surveillance is extraordinarily valuable to these vulnerable communities to help reduce risks,” Ebel said.”

With thanks to  and .

Minimizing transmission: Testing asymptomatic healthcare workers to find silent COVID-19 carriers

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The following article appeared in Colorado State University’s SOURCE, a central hub for news about the university. The Ebel lab is grateful to Mary Guiden for the write up about our recent efforts!


Minimizing transmission: Testing asymptomatic healthcare workers to find silent COVID-19 carriers

A team of researchers at Colorado State University is leading an effort to help the most vulnerable people in our communities –residents in long-term care communities – during the coronavirus pandemic.

Over the last two months, a lab run by Greg Ebel, professor in the Department of Microbiology, Immunology and Pathology, tested samples from 462 healthcare workers in Colorado to determine if workers without symptoms were silently carrying the virus. The tests identified 57 people who tested positive for COVID-19 but had no symptoms.

Ebel is partnering on this project with Dr. Nicole Ehrhart, director of the Columbine Health Systems Center for Healthy Aging at CSU.

Ehrhart introduced the concept for the groundbreaking project during a conference call with Colorado Gov. Jared Polis and state healthcare leaders, including Dr. Greg Gahm, a geriatrician and corporate medical director of Vivage, which owns a range of skilled nursing communities in Colorado and Missouri. Following the call, he tracked down Ehrhart and asked, “How can we work together?”

The purpose of the research, Ehrhart explained, is to enact an early warning system in long-term care facilities that would allow them to temporarily remove asymptomatic but COVID-19 positive caregivers from the workforce until they were no longer shedding the virus. This would minimize the chance that these workers could unwittingly infect vulnerable residents.

“The scientific community is putting their heads down, working around the clock, and sharing data across cultural belief systems and across borders that are closed right now. It’s an incredible moment of humanity and it’s the greatest interdisciplinary scientific effort that’s ever happened on Earth,” Ehrhart said.

 

Disease surveillance

The concept behind the research is a basic principle in disease surveillance, especially during a pandemic, said Ehrhart, a veterinarian and professor of surgical oncology at CSU.

Ehrhart said the team will sequence the virus genomes from these samples, which will provide information about how the virus is being spread. This will help them determine whether it’s due to a common source within the facility or if it’s being brought into the facility from the community.“We don’t know when people become infectious with COVID-19,” she said. “It’s possible that they could be infectious prior to the onset of symptoms. It’s important that when there’s an at-risk community, like seniors, that we think about how to minimize the potential for transmission.”

Graduate student volunteers – trained and certified to transport pathogens –  are serving as couriers, picking up swabs at facilities and delivering them to Ebel’s lab.

Gahm said that there are numerous reasons why his organization would like to know if asymptomatic workers test positive for COVID-19.

“It allows us to identify those people to say: you’re positive, even though you’ve been wearing a mask and following other safety protocols,” he said. “The Centers for Disease Control and Prevention and the health department is saying you need to go home at this time.”

 

Existing virus tracking methods

The tests being conducted in Ebel’s lab are similar in principle to the tests his team has used for West Nile virus surveillance in northern Colorado since 2014.

“We’re using equipment, approaches and efficiencies we developed from doing this type of work every summer, to try and protect the health of Fort Collins, Loveland and Berthoud residents from West Nile virus,” he said.

Ebel said what’s currently needed in response to the pandemic is a public health approach, and rapid testing.

“The crisis in test availability was bewildering,” he said. “A physician in a clinic wants an ironclad diagnosis. We provide something slightly different: rapid information on infection among people who aren’t showing symptoms.”

Ebel said the team first tests to see if there is any evidence at all that these healthcare workers have the RNA of the virus in a swab taken from the back of the nose.

“When we get a sample that is positive, we test it with two additional assays for confirmation,” he explained. “If an individual’s sample is positive using three different assays, there is very little doubt the person is infected with coronavirus.”

The Veterinary Diagnostic Lab at CSU – recently certified to conduct lab testing on human samples – is confirming the positive tests.

 

Helping the research community

Despite the trying times, Ebel says he’s in a perfect position to help scientists and the broader public health community learn more about COVID-19.

“For anybody who has been a virologist or infectious disease researcher, this is what we’ve been training for,” he said. “It feels good to do some small thing to help try and make things better.”

Ehrhart said that it’s been exciting to watch CSU’s scientific community collaborate in a way she’s never seen before.

“In order to do the screening tests, we need graduate students who have biosafety training to pick up test kits,” she said. “We are working with researchers who are computer modelers, because they are interested in looking at the data. All of these people are working as volunteers, and we see examples of this kind of collaboration happening all around the world.”

 

This research project is currently supported by startup funds through Ehrhart’s work at the Columbine Health Systems Center for Healthy Aging at CSU and Ebel’s lab. Additional support comes from the Office of the Vice President for Research at CSU, College of Health and Human Sciences, College of Natural Sciences, College of Veterinary Medicine and Biomedical Sciences and Walter Scott, Jr. College of Engineering.


With thanks to the team at Colorado State University’s SOURCE.

Bekah McMinn featured by CSU’s Office of the Vice President for Research

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Ph.D. Candidate Bekah McMinn was featured in a recent video from CSU’s Office of the Vice President for Research.

In the video, she discusses her work on xenosurveillance in Guatemala and its implications for global disease surveillance. “Being able to sample blood from humans and animals in mosquitoes is a huge sample source that we can utilize for a number of different things… the number of applications is kind of limitless.”

With a shout-out to Dr. Anna Fagre and our partners in the Kading laboratory!