At the beginning of the COVID-19 pandemic, Michigan Technological University in Houghton, Michigan, was tasked by the State of Michigan to develop a clinical laboratory capable of providing RT-PCR testing for the Western Upper Peninsula of Michigan. Using the resources and expertise available, the clinical laboratory was developed, and over the course of 20 months was able to meet the ever-changing demands associated with the pandemic. The following narrative describes the evolution of the testing lab from inception to closure. Read Part I and Part 2.
Part III: PPE Problems and Improved Infrastructure
In early September 2020, the lab was getting maxed out again. On the first day of student testing, 140 students were invited individually to participate, 100 of those made reservations, and 92 showed up to be swabbed. As time went on, the pooled samples from surveillance testing on campus were increasing. There was also a rise in community samples. It should be noted that concurrent testing (not in MTU’s COVID-19 lab) wastewater sampling from the dorms was being tested for COVID-19 as part of epidemiological monitoring.
Hiring more employees helped alleviate the sample burden. A receiving supervisor who worked night shift at a local hospital laboratory was recruited to help part time on day shift at the MTU COVID-19 Lab. A full-time general supervisor, with many years of clinical laboratory expertise, was obtained. These two individuals added an extra layer of clinical expertise to the growing laboratory. By mid-September, the sample numbers were at capacity, less positives were being identified and the lab no longer felt overwhelmed.
With the rise in numbers, the infrastructure of the lab was also being improved. A potential LIS system was being evaluated and a new autoclave was being installed. A new fax machine was also installed to help expedite reporting. The Vacuum Manifold System, on the other hand, was giving problems with contamination and a lot of time was spent re-extracting, re-analyzing, and trouble shooting.
As September moved forward, the sample numbers again started increasing, and the lab was processing 300 per day. It was time to triage so it was decided that the routine testing would be prioritized as first the athletes followed by surveillance testing. The community samples would be analyzed as they were received. An area nursing home was showing a COVID-19 outbreak, and those samples were increasing the load as well.
Planning ahead still had to be a priority as the holidays loomed. Lab scheduling and staffing between Christmas and New Year needed to be addressed as many of our student volunteers and employees would be off campus during that time. There would also be back -to-school testing with the new semester in January. Another upcoming event that had to be considered was the Nordic Ski Competition scheduled on the MTU Cross Country Ski Trails.
Supplies and staffing were a priority in these plans. An evening cleaning crew would be starting and needed HIPAA and biosafety training.
The projections at this point were for 1,000 samples per week, consisting of 100 pooled samples per day and 80 community samples per day.
It was also evident that the surveillance testing schedule needed to be revamped as the lab was getting overloaded with samples on Fridays. The logging, reporting, and faxing were overwhelming and although the positive results were reported in a timely manner, the negatives were taking too long to result. It was decided that the MTU surveillance samples would be minimized for Friday testing. The lab ran much more efficiently when the sample volumes were front loaded during the week.
PPE was again becoming an issue. Using reusable, battery operated, decontaminated PAPR masks was being investigated. As it turned out, they were too bulky to use under the safety hoods, too hard to maneuver in the laboratory due to mobility and visibility issues, and answering the telephone was a problem as well. It was a good idea for masking safely, but not appropriate for our lab.
At end of September, the University applied for a grant from the Michigan State Health Lab to cover the COVID-19 lab’s startup costs.
There was a fear in the community that MTU would have an impact on increasing COVID-19 infections. However, the positivity numbers demonstrated <2% for 300 MTU Surveillance sample pools with community symptomatic samples at 13%. That fear was fortunately not being borne out. The roar enhanced by social media started to calm down.
The community samples were primarily submitted by Baraga Hospital, Portage Health and Upper Great Lakes. By this time Aspirus Hospital was sending its samples to their home headquarters in Wausau, WI. Inquiries were coming in from senior communities to screen all their residents, but the lab capacity only allowed for employee screenings and symptomatic residents. The lab was processing the expected 1,000 samples per week and was maxed out.
With the continuing demand and increase in specimens, more infrastructure issues needed to be addressed. The lab needed more sample storage space, so an additional refrigerator was purchased. The Orchard LIS system needed to be organized. And finally, we added a Thermo-Fisher KingFisher RNA extraction instrument and began the validation process to get it operational as soon as possible.
As September concluded, the University was surprised by the Governor’s mandate for school closure and TV6 out of Marquette, MI was coming to film our lab.