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.
In March of 2020, the need to address the newly recognized COVID-19 virus was paramount in the Western Upper Peninsula of Michigan, a remote, rural area (Figure 1). Testing was simply not available. Samples were being sent to Lansing, MI, 300 miles away, and some of those forwarded elsewhere. The turnaround time was up to two weeks. Members of Michigan’s state government approached Michigan Technological University’s Vice President for Government Relations and proposed the following: Michigan Technological University (MTU) would start a clinical testing lab specifically for COVID-19. Michigan Tech had the reputation, drive, expertise, and personnel, but realistically, would it be possible to build a clinical lab from the ground up and meet the necessary requirements to conduct patient testing?
Figure 1: Location of Michigan Technological University. Image courtesy of Karyn Fay.
Where to begin?
On March 26, 2020, a group of 19 individuals in multiple disciplines across campus conducted the first Zoom meeting regarding the feasibility of implementing a COVID-19 testing lab on campus. What these people had in common was the determination to help the residents of the Western Upper Peninsula. The Vice President of Research spearheaded the project. This was the first of countless Zoom meetings the team conducted. It should be noted that all these people already worked full-time at the University in some capacity, but were willing to meet this challenge, regardless.
What was available at that time were qualified and willing personnel and room for laboratory space. The first point of order was to identify the critical necessities required if this was going to come to fruition:
A way/place to safely receive and store samples
Identify an available Biological Safety Level 2 (BS2) facility for the testing
Determining if the PCRs (real time) on campus being used for research were available and adequate by CDC standards
Gaining access to a -80o freezer certified for sample storage, with a secondary probe to validate temperatures
Obtaining BS2 Biosafety hoods
Determining if the RNA Extraction methods used for research would be diagnostic grade approved
Appropriate Personal Protective Equipment (PPE), reagents, kits
A qualified Laboratory Director
Four days after these necessities were identified, on March 30, 2020, Cary Gottlieb, MD, was approached about the laboratory director position, and he said, “I’m your guy!” We had a Laboratory Director!
This completed, the next phase of planning began. A CLIA number was applied for and approved as well as the necessary Emergency Use Authorization (EUA) to run patient samples. Different platforms for the testing were considered and it was determined that the Qiagen RNA purification columns were the best option to get started.
By then classes had gone remote at MTU, and an on-campus teaching lab became available. It had the necessary BS2 designation with BSL2 Safety Cabinets (BSC) already in place, so it was ideal for the RNA extraction process. The BSC only needed to be upgraded to fit the centrifuges. The Biosafety Level 1 (BSL1) site for the post extraction PCR instrumentation necessary for the actual PCR analysis was identified in a research laboratory. What happened next was the conversion of both laboratories into clinical laboratories. It was important that only people with BSC experience would be utilized to work with patient samples.
What needed to be addressed next were day-to-day logistics. First was giving qualified people access to the laboratories. The issue of receiving patient samples and how they would be coded was resolved. A Zebra Printer for labeling samples was obtained and MTU’s billing department was brought into the conversation, working with the medical lab directors to discuss charges.
The medical providers needed access to Viral Transport Media (VTM). MTU’s resident Virologist (PhD) agreed to provide VTM that could be made in-house using CDC guidelines.
The last piece of the start up puzzle was to do trial runs and send the results to the Michigan State Lab for validation. The State was able to provide the required positive and negative samples to get things started, and as our own patient samples were analyzed, they were sent to the State Lab for further confirmation.
Personnel were also identified and trained on data security, HIPAA, and BSL2 equipment. These people were primarily made up of faculty volunteers and graduate students with expertise in PCR analysis. The undergraduates in the Medical Laboratory Science program were recruited as the laboratory assistants.
Our website became active for providers and samples started coming in on April 15, 2020—three weeks after our initial meeting.
Three local hospitals began submitting samples for testing samples: Aspirus Keweenaw in Laurium, Michigan; UP Health Portage in Hancock, Michigan; and Baraga County Memorial in L’Anse, Michigan. Shortly after, the Upper Great Lakes Family Health Center (UGL) initiated drive through sampling collection. The lab’s testing capacity was set at 50-100 samples per day to start.
In the first week, 50 samples were analyzed. During that week, it became evident that some tweaking needed to be done, and those issues addressed: RNA extraction capabilities needed to be increased so a vacuum manifold system was ordered to help alleviate tedious pipetting. A FAX machine in the lab was installed and the new PCR analyzer arrived. The certificate from CLIA arrived and COLA was contacted for certification approval. (Figure 2)
Figure 2: COLA Certification for the MTU COVID-19 Lab. Image courtesy of Karyn Fay.
Amazingly, the lab was now able to provide COVID-19 PCR testing for local patients having elective surgery. By the end of April, testing had scaled up to 120 samples per day.
By the beginning of May, due to great sample correlation with the State Health Lab, the “presumptive” verbiage from the results forms was able to be removed.
Our safety protocols were reinforced when a leaky sample arrived in the lab. Our “incident report” was used and the exposed staff were required to quarantine and be tested. It was reiterated to our providers how to safely package samples, and to the intake staff to carefully examine each sample before removing from the biohazard bag.
As May progressed, the Standard Operating Procedures (SOPs) were being updated and samples arrived from other hospitals in the Western Upper Peninsula. Sampling swabs and PPE were beginning to be in short supply. Michigan Tech is a university of engineers, and the possibility of 3-D printing of swabs and PPE shields was explored. By then COLA had been filed and assurance of compliance with the University’s Institutional Review Board (IRB) was obtained.
By the end of May, Houghton County had recorded five positive COVID-19 cases, with two of them reported through the MTU COVID-19 lab.
Stay tuned for Part II in this series.