We have all suffered through a steep learning curve about SARS-CoV-2, the virus responsible for causing the COVID-19 disease, in the past few months. Accordingly, there has been an unprecedented response from the medical and scientific communities consolidating their efforts to combat the spread and crippling effects of this disease. On January 10, 2020—a mere week after the SARS-CoV-2 virus was isolated from a patient’s bronchoalveolar lavage (BAL) in Wuhan, China—a viral genome sequence was released on an open platform online (virological.org). This set the stage for diagnostic companies to begin developing primers and probes for the detection of viral presence. We saw the first case of COVID-19 in the United States on January 20th. If you were like me, at that time you were not thinking strongly about the need to be able to test for SARS-CoV-2 in your lab.
Set Clear Communications Standards
Based in Norfolk, Virginia, Sentara Healthcare is an integrated not-for-profit system of 12 hospitals, over 300 sites of care, and 28,000 employees in Virginia and North Carolina. By late January, it was clear that we needed a coordinated, health-system-wide response effort to what was quickly becoming a crisis. Our administrators spearheaded the initiative to set up incident command centers throughout the system, at each hospital, and including the laboratory. Our lab command center is staffed by laboratory directors from across our region and members of the laboratory quality team. This enabled rapid and standardized communication throughout our organization and provided a structure and escalation process for, among other things, the issues and questions facing laboratory management. As part of the laboratory command center, our team began meeting daily to discuss testing, supply inventory, and process changes.
Rapid Regulatory Change
At the beginning, we were relying on public health and CDC laboratories to provide testing, as was the case in most places. This involved strict criteria regarding which patients would be tested in order to prioritize resources for those that needed them most. On February 4th, the FDA announced that COVID-19 was officially a public health crisis, thereby allowing SARS-CoV-2 testing to fall under the emergency use authorization (EUA) program. Subsequently, we saw the major reference laboratories quickly respond by offering COVID-19 testing. However, given the explosive growth rate of the virus, it became readily apparent that despite these efforts, a centralized, outsourced testing process was not going to be able to accommodate the TAT we needed to address our patient needs and an expectedly large surge in testing volume. Almost immediately, our health system alone was sending out 400 COVID tests per day. At that point, we knew we needed to enable in-house testing.
Diversification is Key
On one hand, we were receiving emails daily about new EUA assays from numerous molecular microbiology diagnostic companies, but the announcement of a new assay availability often was followed by information that reagent or instrumentation stock was depleted or already gone, and that any remaining stock was being prioritized for the hardest hit areas of the country. Given the wide-spread nature of this crisis, we realized we would not be able to source supplies from a single company and be able to provide the level of service our health system demands. To address this, we began developing and utilizing a strategy to diversify our supply chain and insource reagents from numerous vendors. This strategy was utilized for both collection devices and reagents for testing.
We began contracting and sourcing material from numerous different diagnostic and collection device sources. Although we had the benefit of a wide variety of existing platforms within our molecular diagnostics laboratory, we still needed to insource two additional pieces of equipment: an additional multiplexed molecular testing platform and a real-time PCR instrument (the GenMark DX ePlex System and the Abbott M2000 RealTime PCR, respectively).
We worked directly with reagent and instrument vendor representatives for quotes and found most to match national pricing that is standardized and did not allow for negotiation or require volume commitments. Thus, our materials management team was quick to process these contracts and purchase orders so we could get in line to acquire reagents and instruments.
Assembling the Puzzle Pieces
The first SARS-CoV-2 kit with an EUA that we were able to secure was the Quidel Lyra SARS-CoV-2 assay, which required nucleic acid extraction (originally performed on a Roche MagNa Pure 96) and amplification on the ABI 7500 Fast Real-Time PCR system. This was possible for us because our molecular diagnostics laboratory operates both pre- and post-amplification rooms. These rooms maintain separation between primary specimens and amplicon to decrease contamination risks. The pre-lab maintains positive pressure and negative pressure is maintained in the post-amplification room. We also already had the ABI 7500 Fast RT-PCR and the Roche MagNa Pure 96 necessary for rapid insourcing of the Quidel Lyra assay.
An important first step was to quickly verify the assay yet ensure CAP and CLIA standards were met. Essential to this process was CAP’s clarification that EUA assays are not considered laboratory developed tests, and therefore require verification of the package insert claims but not a traditional validation.
The verification for the first assay was performed on residual viral transport media (VTMs) we had remaining from patients that had a Flu or Respiratory Pathogen Panel test performed in house and a COVID test sent out. The Sentara IT team helped us quickly build the test into our laboratory information system so specimens could route to the appropriate laboratory based on patient class (inpatient vs outpatient) and our providers could easily find results. This action also allowed us to be able to report our data directly to the Virginia public health office through our existing interface.
The diagnostic companies we worked with pointed us toward vendors that could supply standards for SARS-CoV-2 at known concentrations that can be used to verify the assay’s limit of detection (LoD) as claimed by the manufacturer (eg, SeraCare and Exact Diagnostics). We utilized patient samples (3 positive and 3 negative), quality control samples from the kit (positive and negative), and standards in triplicate to assess the assay limit of detection (1X and 3X LoD) for accuracy, precision, and reportable range. Notably, this simplified verification process helped to conserve reagents for patient testing and we were able to go live with the first assay on March 25th.
Due to the overwhelming volume of test requests and the limited number of companies providing nucleic acid extraction kits, a limiting factor was established for the number of tests we could provide. To make do, we performed additional verifications as we received alternate extraction kits for our secondary automated nucleic acid extraction platform (in this case, the ProMega Maxwell RSC Instrument). While having only one method that required extraction and amplification, we were able to perform roughly 150 tests per day (with staff covering the lab 24/7). While this proved sufficient for our inpatient volume, it was not enough to cover our emergency department or outpatient volumes.
Scaling up Operations
While we were able to incorporate the Quidel Lyra assay for inpatients, we were still working to bring in more automated methods (on the Abbott M2000 RT-PCR and the Roche cobas 6800), as well as additional, lower throughput (but faster) methods (ie, the GenMark Dx ePlex, the Cepheid GeneXpert and the Simplexa from DiaSorin) to support our ED and outpatient volumes. Implementation of the Roche cobas 6800, GenMark Dx ePlex, the Cepheid GeneXpert, and the Simplexa from DiaSorin were all relatively easy, as we already had those platforms within our laboratories. However, we had to source the reagents and verify the claims on the EUAs from these vendors.
In order to accommodate the Abbott M2000 RT-PCR instrument and other related instruments and materials into our physical space, we began converting a pathology conference room to a “COVID laboratory.” Needless to say, converting this space into a functioning lab in one week required extensive teamwork. Fortunately, we received assistance from several areas; representatives from the facilities department and external vendor reps helped with plumbing and electrical concerns, local universities provided heat blocks and a centrifuge, a hood was donated from one of our system hospitals, and our own internal laboratory staff gave ample support in moving furniture and rendering the lab operational, safe, and compliant (see FIGURE 1).
Using the previous verification protocol as a model, we worked to verify testing kits as new instruments or reagents became available. As of April 21st, we are employing two different, large automated platforms (the Abbott M2000 and the Roche cobas 6800) to perform high throughput testing, although the reagents are allocated and limited. As a supplement, we also are utilizing a trio of lower throughput (albeit faster to results), moderately complex instruments (ie, the ePlex, GeneExpert, and Simplexa).
The stated sensitivities of these assays range from 50 cp/mL (Roche cobas 6800) to 100,000 cp/mL (GenMark ePlex). Although there is a large variance in these stated sensitivities we have found that when symptomatic patients are tested early in the disease course they tend to be highly positive. The Roche cobas test has the highest capacity with reagents being supplied for 576 tests per day. It also happens to be the fastest (3.5 hours to first result; 1.5 hours per 94 samples after that point) and most sensitive method (25-50 cp/mL) we use. However, in our system, one method would not be sufficient to provide results for the number of specimens we need to process per day (at the time of this writing, we are at greater than 1500 COVID tests per day). Abbott was also very responsive in providing reagents and instrumentations to support our system. Their test is very sensitive at 100 cp/mL and can handle 470 tests per day. In addition, the moderately complex tests enable rapid, and if your laboratory does not have an existing molecular laboratory, the moderately complex instruments (eg, the GeneXpert, the ePlex, and the Simplexa) are easy to both insource and operate (see FIGURE 2 for a simple comparison chart).
This flexibility has allowed us to offer testing at system hospitals that are further away from our hub in a timely manner. Thus far, nine verifications for SARS-CoV-2 have been completed using 6 different assays on a total of 8 different PCR-based instruments throughout our system. We also have just completed a validation of the Hangzhou AllTest biotech SARS-CoV-2 IgG/IgM lateral flow assay to augment our PCR testing and to provide a more accurate assessment to our physicians of the overall clinical picture. We are continuing to be transparent to all the diagnostic companies we are working with regarding both our reagent needs as well as our current stock in order to help ensure we are not sitting on stock that could be better used elsewhere.
Early Lessons Learned
Keys to our success on-boarding SARS-CoV-2 testing included the ability to move rapidly, organized teamwork, multi-staff flexibility, and open communication. The command center structure and follow-on support have been invaluable. Most questions were diverted away from the operational laboratory to allow those staff members to focus on verifications and testing. Large organizations such as Sentara Healthcare normally require fairly substantial processes when making IT changes, initiating construction projects, contracting with new vendors, and securing funding. But given the urgency that COVID-19 has brought to our doorsteps, all red tape was removed, and we were able to quickly access the internal financial and personnel resources we needed.
Although our plan to respond to the COVID-19 pandemic has changed often (sometimes daily or hourly), we have been able to clearly communicate throughout our organization and adapt our plans to fit the availability of external resources. The teamwork seen across the entire organization has been awe inspiring. Staff from every reach of our operations have come together to ensure the molecular laboratory was performing this testing with significant support. This support extends from the highest echelon of our organization down and throughout our community. I cannot thank enough the entire village that has been required to make these endeavors a success and I have special gratitude for my molecular team and the tireless effort they have devoted to ensuring we are providing the best possible patient care.
Tabetha Sundin, PhD, HCLD(ABB), MB(ASCP)CM, is the scientific director of molecular diagnostics and serology at Sentara Healthcare. With over 10 years of laboratory experience in cancer biology and clinical molecular diagnostics, she is an active member of the Association of Molecular Pathology (AMP) and is involved with numerous efforts to support the molecular diagnostics field with American Medical Technologists (AMT) and Clinical & Laboratory Standards Institute (CLSI).
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