FEATURE
Colorado ’ s state laboratory division has also implemented wastewater surveillance . “ Before the pandemic , we were doing sequence analysis for foodborne pathogens . We capitalized on that knowledge to quickly pivot to doing [ WGS ] on clinical samples for COVID- 19 ,” said Emily Travanty , PhD , laboratory director of the
Colorado Department of Public Health and Environment . “ And then the wastewater surveillance piece came into play , so we added capacity for that type of digital droplet PCR .”
With the clinical sequencing workflow already set up , the state laboratory was able to easily “ slide the water samples that were positive for COVID-19 into those same sorts of pathways ,” Travanty explained .
“ I ’ m certain that it is going to go a long way ,” she continued . “ It is a pillar of our ongoing surveillance that we ’ re going to continue in Colorado to ensure that we understand the ongoing impact that COVID-19 has in our state , as well as use the same samples and the same network of samples to expand what we ’ re testing for in wastewater .”
Learning About Congregate Settings
Colorado also learned how to test in congregate settings , but one unique to the US West : fire camps . August 2020 was the start of the worst fire season in Colorado history . Because of the magnitude of the fires , fire crews poured in from other states and lived together in camps , creating “ ripe conditions ” for COVID-19 spread , Travanty said .
At the time , PCR test results were not quick enough to learn who was infectious and who should quarantine . But the laboratory did track the data to see how COVID-19 moved through the camps . The Cameron Peak Fires lasted for five months , and fire crews from multiple states were deployed every two weeks . Firefighters were tested before they arrived and encouraged to practice social distancing .
On-site tests showed 78 firefighters tested positive for COVID-19 . WGS was performed on 42 positive cases , identifying five sequence types . The types were not in clusters , which suggests COVID-19 spread among the crews .
On-site tests showed 78 firefighters tested positive for COVID-19 . WGS was performed on 42 positive cases , identifying five sequence types . The types were not in clusters , which suggests COVID-19 spread among the crews , according to the APHL 2021 poster abstract “ The Use of Whole Genome Sequencing ( WGS ) to Investigate the Spread of COVID-19 in Fire Camps During the Cameron Peak Fires ( August 2020 ) in Larimer County , Colorado .”
In addition , individuals may not have suspected they had COVID-19 because of the bad air quality — if someone is coughing is that because of the smoke or COVID-19 ? In future fire seasons , Travanty said , it will be important to have stronger fire camp guidelines for testing , including additional use of over-the-counter rapid tests ( which were not widely available during previous fire seasons ), quarantining , social distancing and use of personal protective equipment .
“ If we have fires this summer , we will definitely be able to deploy ,” she said . “ We have teams that can deploy rapid tests , as well as teams that can go into the field now and respond and swab people for PCR testing .”
For congregate settings in Hawaii , laboratory workers learned it was necessary and possible to quickly create training materials . When point-of-care tests were distributed to congregate facilities in 2020 , it was apparent that staff , such as those at prisons and nursing homes , needed test-specific training .
Seabourn quickly created a couple of slide presentations teaching people how to administer the tests , complete with
embedded videos of Seabourn showing the step-by-step process . She shot the videos using only her iPhone with the help of a postdoctoral fellow .
“ Everyone was just hitting the ground running , considering the pandemic ,” she said . “ I basically took two weeks to get updated on the literature , made sure I was very familiar with the protocol and all the different specifications , and then I just quickly made the videos .”
Creating a professionally shot and edited video would have taken longer and cost more . “ I think sometimes you have to ask yourself , ‘ What is the need ?’ And if it ’ s something that you can just quickly do , it ’ s better to just have it out in the public and ready for everyone .”
Photo : Minnesota Public Health Laboratory Division
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Summer 2022 LAB MATTERS 7 |