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, and Part 3.
Part IV: Six Month Anniversary
October of 2020 marked the six month anniversary of the MTU COVID-19 lab. In those six months the lab had analyzed 13,000 samples. The positivity rate for Michigan Tech students and employees was at 1%. The many issues that cropped up were able to be resolved. The resulting was more efficient, more personnel were being added as needed, and the website had been updated. There was a lot less stress, but it was said the MTU lab was the “Gold Standard Lab” for the State of Michigan.
The analyzer was being readied to put into operation and a support tech was scheduled to set it up. It was advised that once this was done, it could not be moved to another room as it is outlet-dependent for validation. The instrument would help with the bottleneck of RNA extraction. Before putting it into operation, parallel studies with samples provided by the State were completed.
The LIS system needed a separate interface built in for a State Export File to report our results to the State Health Lab.
The month ended with a Safety Inspection of the Lab, which was successful. An FDA update was received that would allow the continuation of running our individual and pooled samples, as we had been doing, according to our protocol.
As always, planning was a key component. Thanksgiving scheduling and communication with all the providers was necessary to see what would be most beneficial to all involved. The week after Thanksgiving break would be busy with MTU and community samples.
Immediately following Thanksgiving is final exam week, and the end of the semester. Plans were being formulated to anticipate sample volumes with the return of the students in January.
With winter on the horizon, an inclement weather plan had to be devised, especially if the University closed. It was communicated to the providers to always call first before sending out the couriers.
November arrived and the sample numbers continued to increase. More than 17,000 tests in total had been completed: 10,000 from the community, and 7,000 from MTU. The lab was still maxed out with 1,000 per week. The new goal was to be able to double the capacity with a 50/50 split with MTU samples and the community. It was anticipated that this would be possible, with the analyzer system, by the end of the month.
The lab was seeing not only an increase in samples from the community but a lot of positives with high viral loads. The pooled positivity rates from the University remained stable. If that started to increase as well, it was determined that the lab would switch to individual testing.
The increase in positive samples was causing some contamination, forcing re-runs with the vacuum system of RNA extraction. This was resolved by decontaminating the entire process. All CT values >30 would still be repeated.
The increase in volume was starting to impact the courier drop-off center at MTU, where all biohazard materials entered the University. A schedule for drop off was devised which included specific times for community (hospital and nursing home) samples and MTU samples. During this time an extra person would be at the drop off center devoted to COVID-19 sample check-in.
Communication was also at the forefront as new staff were being added in receiving and reporting. Meetings were scheduled to avoid any pre- or post-analytical errors and to impress the importance of “getting it right.”
The lab supervisor completed training on the Orchard LIS system while the Information Technology (IT) department at MTU was busy getting the scanner and testing accounts set up and validated. The live date would be four to six weeks out.
A COLA compliance meeting was attended by key personnel to assure compliance and proficiency. Proficiency testing also became commercially available for enrollment. It was decided to go through the Wisconsin State Lab of Hygiene (WSLH).
Future plans were still at the forefront. It was expected that when students returned from Thanksgiving break, the lab could expect about 175 samples/day with the on-demand collection schedule. In addition, the current athletes could contribute an additional 30/day. It was noted that the athletic department was transitioning to rapid testing.
December started where November left off, with more planning of holiday operations and the beginning of the new semester. The courier system over the holiday break would change as the normal drop off center would be closed. The samples would be delivered directly to the testing lab. Information and signage for providers would be done in advance. (Figure 3)
Figure 3: Holiday Break Drop off at the Great Lakes Research Center
The University was faced with the possibility of having to test all students upon their return to campus. The school start date was pushed back a week by the Governor to January 18. The big push would be Martin Luther King weekend. Residence Hall move in would be during that time as well.
This would mean a surge that would affect community testing capability. No outside providers would be accepted for those three days, so the providers were busy making alternate testing plans. The lab was anticipating 5,000 samples between January 6 and January 20. The maximum number the lab was analyzing was 1,000/day in pooled samples, but the plan was to up that to 1,100/day for those three days.
The neighboring Finlandia University students would also be returning to the area. We were expecting 40 samples between January 8 and 13, and 400 samples between January 14 and 20.
The lab was readying for this increase. Logging and reporting would also increase so an extra label maker was obtained. The lab hours would increase, as would personnel. Our supplies would be ordered as early as possible, and a three-week supply would be always on hand. We had supplies stocked up for 10,000 tests. We also added a new refrigerator which increased the storage capacity 33%.
By that time, 20,000 samples had been completed with a positivity rate of 8-10% with the community samples higher than the MTU samples.
The KingFisher was ready to run at a 25% capacity after comparison with the Qiagen System. Personnel training was ongoing, and things were going well. The TAT with KingFisher would decrease to 12 to 24 hours, which was a game changer. Side-by-side testing with the two instruments would be done annually per requirements.
At this time, the University got the approval for State funding that was applied for in September. The lab received a grant for startup costs and equipment.
As the employee numbers grew, a lunchroom was set up with a microwave, food, and drink. Their efforts and professionalism were very much appreciated.
2020 ended with the Medical Director, Dr. Cary Gottlieb, MD, being recognized by the Michigan Technological University Board of Trustees with appreciation and a plaque for his volunteer service to the MTU COVID-19 Laboratory. (Figure 4)
Figure 4: Appreciation Plaque from the MTU Board of Trustees
The lab had processed 21,000 samples as the unknown challenges of 2021 were being anticipated. 2020 was not without problems that popped up, but with perseverance, expertise and “grit,” the lab was able to circumvent these issues, never compromising any patient results in the process.