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 , Part 2, Part 3, and Part 4.
All the careful planning paid off and the start of the new semester in January 2021 went well.
The Orchard LIS system was finally able to go live and the training was completed. The billing department needed to be involved with adjustments as necessary. The KingFisher was showing its value as the cost/sample was decreasing due to less labor needed/test. Even with an increase in reagent costs, the total costs were down.
January also ushered in vaccines. Laboratory workers were offered 1A status and a vaccine clinic was made available to those who opted to get vaccinated. MTU had the area’s only -800 freezer and so was the storage facility for the two weeks before the local hospitals obtained their own.
Antigen testing was also becoming more available. The Athletic department was using it for screening positives. All positive tests would still be analyzed by the lab for PCR confirmation. The question for the lab at this early stage was how to gauge what numbers would be coming into the lab. Antigen testing would be done three days a week for all outdoor sports and six days a week for all indoor sports. The positive samples would be dropped off in the morning and go straight to the lab for priority analysis and results sent back ASAP to the athletics department. The first two presumptive positive samples that were analyzed in the lab had 100% correlation.
The lab also found its first S-gene dropout variant and was in contact with the State Health Lab for sequencing. At this time, it was unknown what the variant indicated. This probably would not have been discovered without the switch to KingFisher. A second one was picked up in early February. The lab was waiting for directions from the State Health Department to develop a lab protocol to comply with the State’s direction. As more variants were discovered, a link was being sought out. Residents from a common site were asked to be voluntarily tested. A collection site was set up for the residents—600 people lived there, and the University was hoping to get 300 tested. The results would be sent to the health department.
Our TATs were evaluated using the last 1,500 tests. This was from sample collection to time of result. The median was 29 hours with the average being 35 hours. That is less than two days!
The question also came up as to “guidelines” vs “requirements.” Currently the State was using the guideline to test every student, but it was not a requirement. This was expected to remain the status quo. The three-day surge of baseline tests was completed, and surveillance testing would go into effect again.
The first proficiency samples arrived in the lab with a score of 100% on analysis.
By February the community samples had dropped to half of what they had been. This began the conversation of perhaps changing the shifts and personnel. The lab was on track to hit 30,000 samples and at that point had a 5% positivity rate for the history of the lab.
The district State Senator was on campus to tour our lab operation. He was very impressed by what the MTU COVID-19 Lab had accomplished in less than a year.
March showed a similar slowdown in sample numbers. The lab spent this time getting ready for the COLA visit. All the necessary paperwork was reviewed as well as environmental surveillance completed.
It was decided to decrease our twice-weekly Zoom calls to once per week, with the option to have an extra call if necessary.
After spring break the lab saw a slight uptick in testing again. Students had been travelling and there was also an increase in community tests. There were more S-gene dropouts as well.
By April the lab was operating one shift/day with about 70 samples. The community providers had begun doing testing in their own facilities and were using MTU as a back-up and not the primary testing site. The semester would be ending by the month's end and MTU would do surveillance testing through final exams and then demand testing and validation of positives from antigen testing.
At week 52 of lab operations, the lab had analyzed a total of 33,000 samples. April 22 marked one year. The State of Michigan gave Special Tribute to the MTU-COVID-19 Testing Lab (Figure 5) and interviews were being conducted with the local TV6 station and the Daily Mining Gazette, the local newspaper, to mark the anniversary. The Marquette Mining Journal carried the interview as well.
Figure 5: A Special Tribute from the State of Michigan
It was also the last week of doing pools for this semester which was described as a “quiet milestone.” On-demand testing was down to 15 to 20 samples.
Our Zoom calls would now be bi-weekly.
In May, with the end of the school year, things were quiet in the lab. It was time for validation studies of pipettes, the KingFisher, and annual sample validation with the Health Department. The slow time was helping with training employees in all areas.
The Western Michigan Health Department in Houghton was bringing up their own testing laboratory. MTU’s laboratory was providing samples for their validation studies. The Health Department Lab would have the capacity to do 100 tests per day.
Summer progressed with a minimum of tests to keep the lab operational. Housekeeping chores were completed during the down times. This opportunity also allowed for the calibration of the single channel pipettes.