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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 here.
Part II: Advanced Planning
It became clear that it was necessary to be proactive, not reactive, and constantly plan ahead. The concerns for the students returning to campus in the fall were addressed. A testing plan for fall semester was implemented which would involve surveillance testing for the residence halls, off campus housing, and MTU staff. This would be done in addition to the community testing.
It also became clear there was a need for a permanent home for the testing labs, as the space being used would need to be returned to the original purpose for teaching and research. Other labs in the Upper Peninsula had reached out to MTU to be a “back up” as COVID-19 testing in their institutions and long-term-care facilities were being implemented.
After conferring with the campus epidemiologist, it was determined the lab would need to be operational 10 hours per day to meet a projected goal of performing 200 samples per day. The community testing demand was increasing, and the student athletes would be arriving on campus.
The 3D swabs were being printed on campus and checked for human factor safety, before being sterilized and stockpiled. At this time, how to best sample for COIVD-19 was still in debate: nasal swabs or nasopharyngeal.
Pooled testing was now being discussed for surveillance testing. If the pooled sample was positive, everyone in the pool would subsequently be tested. After initial testing runs, it was determined that five samples in the pool was the optimal number. Pooling would start mid-August when the students would be moving into the residence halls.
Looking at the plan, it became obvious that additional personnel to meet the increased workload would have to be brought on board.
Space became available in the Great Lakes Research Center (GLRC) and it would become the permanent home for the MTU COVID-19 Testing Laboratories. The goal was to have the new space operational by the second week of July. Retrofitting the allotted space to accommodate the equipment, instrumentation, and new safety cabinets was needed, and was completed by the facilities management staff in a timely manner.
By the end of June, the numbers had increased, the uptick due to nursing home samples. Of the 1,700 samples processed to date, there were 10 positives with four being from a specific nursing home. By July 1, the lab had hit 2,000 samples, averaging 92 per day.
“Move into the GLRC Day” was scheduled for Sunday, July 12. The validation studies on a new Step One PCR analyzer were complete and the new Biological Safety Cabinets were certified. A new autoclave was also ordered, with the ability to continue use of the one in the previous lab, until the new autoclave arrived.
The intake of samples and output of results was also enhanced. A fifth computer was added with the possibility of a sixth if necessary. A Slack Channel was added to the computer system to improve lab communications. It was determined the lab phone number would remain the same.
Keeping up with increased sample numbers
The samples numbers had a sudden increase. A third shift was added to avoid backlogs. With the additional shift, the sample processing capability increased to 250 per day. However, PPE had become in short supply and difficult to obtain, especially lab coats. Additional vendors were sought for the short-supplied items. With the increase in samples, refrigerator and freezer space became an issue and a second one was ordered.
The State of Michigan requested we report our sample results to them twice a day, including all negatives, to both the local Western Upper Peninsula Health Department as well as the State Health Department. At that time reporting was being done once a day.
The lab was fortunate to receive a grant from the Portage Health Foundation in Hancock, Michigan, to obtain a new Laboratory Information System (LIS) computer system. This would help automate the process that was currently being done manually. The College of Science and Arts also contributed funds for the costs. At this point, in July, the lab had identified 17 positive samples.
Being proactive and planning ahead for the August student move-in for Fall Semester was important as a high demand in testing was anticipated.
The Upper Great Lakes (UGL) collection center was given the OK to utilize oral pharyngeal (OP) swabs rather than nasal pharyngeal (NP) swabs. UGL would continue to send 25% of the community samples collected to the MTU COVID-19 Lab with the remaining 75% being sent to Quest Diagnostics. The MTU COVID-19 Lab would process the symptomatic patients or those people with new exposures.
All student testing would be performed by the MTU COVID-19 Lab. Pooled samples would be done for surveillance testing only.
Community testing would continue on demand. A drive through sample clinic was being started by the Tribal Health Center in Watersmeet, Michigan. By July’s end, the Emergency Use Authorization (EUA) was still in queue for review. However, the EUA requirements for reporting negative student results in pooled testing samples, as “presumptive negative, no additional testing needed” was implemented.
August began as busy as anticipated. The Portage Health Foundation was at this point using MTUs COVID-19 Lab for surveillance testing in Keweenaw, Ontonagon, and Baraga counties.
Supplies and PPE for the increased testing were being stockpiled as N95 respirators were getting hard to obtain.
An additional instrument for RNA extraction was necessary and the Portage Health Foundation also agreed to help with the costs of this instrument.
The neighboring university in Hancock, Michigan, Finlandia University (FU), would be using the MTU COVID-19 Lab for their athletics testing. MTU’s own students would be arriving back to campus and tent sample collection had to be arranged.
By mid-August the initial students arrived on campus, including student athletes, resident assistants (RAs), and orientation team leaders (OTLs). This allowed the “testing” of the tent sampling and pooling procedures. Initially 60 athletes and 100 RAs and OTLs were tested. The collection process was being handled by Emergency Medical Services (EMS) students and the Finlandia University nursing students. Both groups were trained to collect OP swabs. The process went very well.
The general testing plan was that all MTU students will be able to be tested voluntarily, on top of surveillance samples with employee asymptomatic testing twice a semester. Of the first 350 pools completed, there were four positive pools. Each pool contained one positive sample.
At this time, the State Health Department arrived on campus for a site visit and tour which went well.
The lab’s part time volunteers were moving back to their full-time responsibilities with the new school year. A full-time general supervisor was needed as the current General Supervisor was returning to her full-time position in the Medical Lab Science program as the Clinical Practicum Coordinator and Instructor. Training for two new operators in the PCR lab had also begun.
By the end of August 2020, the community needs were beginning to shift. Aspirus Hospital in Laurium, MI was sending their testing to their home hospital in Wausau, WI. However, Upper Great Lakes was asking MTU’s COVID-19 Lab to do more than was initially anticipated. Also, the billing was getting complicated, but MTU’s billing department did a wonderful job keeping abreast of the constant changes.
At the month's end, our baseline surveillance was completed with 1784 tests with seven positive samples, 0.39%. The overall MTU and FU positivity rates were at 0.25%.