How Labs Can Get Involved in COVID Screening Programs
Organizations, Businesses, Schools and Colleges Everywhere Need Testing Programs
Data-driven decision making has put laboratories squarely in the center of the COVID-19 pandemic response. Unfortunately, even CLIA-certified clinical diagnostic labs can’t contribute unless they have the resources to conduct COVID-19 molecular diagnostics testing. But now there may be a way that they too — and in fact anyone who wants to start up a clinical lab — can become involved in COVID testing.
Bringing the pandemic under control requires diagnostic testing on a scale and frequency that today’s PCR-based testing programs cannot deliver. The time required to perform each test combined with the sheer volume of samples molecular diagnostic labs must process has stretched turn-around times from days to weeks.
An NPR-commissioned study by the Harvard Global Health Institute estimated that the United States must conduct more than 14 million tests per day to fight the coronavirus’ spread. This level of testing requires screening programs in colleges, schools, retail locations and businesses.
Rapid Tests Enable More Screening Programs
The recent FDA Emergency Use Authorizations for the use of rapid antigen tests means that screening programs are much more practical. These tests receive provisional CLIA-Waived status since they are simple to perform and present a low risk of harm or inaccurate results. These minimal requirements let labs process tests without a big expense.
The logistics of basing daily or weekly screening programs on PCR tests have meant that they are largely impractical because of the slow turnaround time for results. The tests themselves take time to process. And the sheer number of samples labs are processing have stretched turnaround times — anywhere from a few days to a couple of weeks. But with these new assays delivering onsite results within minutes, any business, facility or organization could potentially test their staff/members/students frequently enough to resume near-normal operations.
There is still, of course, an important role for the “gold standard” PCR testing labs. The rapid antigen tests are generally prone to false negatives, but positive results are about as accurate as PCR tests. So standard precautions such as social distancing, masks and handwashing stay in place. But anyone testing positive is immediately quarantined and monitored for symptoms. They can return to the workplace or school only until they return two successive negative results from lab PCR tests and show no symptoms.
These rapid antigen tests will create new opportunities for labs to partner with businesses and other organizations that want to establish screening and follow-up programs. But crucially, this depends on the availability of these new rapid antigen tests.
Rapid Assay Availability
The US federal government has been expediting approvals for new rapid tests. For example, it contracted with Abbott Laboratories to produce the high-profile antigen test BinaxNOW with 150 million kits to be delivered to state public health departments by the end of 2020. Other tests becoming more widely available include Access Bio CareStart, Quidel Sofia SARS 2, LumiraDx lateral flow assays, as well as others like the BD Veritor system. Innovative rapid PoCT PCR tests recently received EUAs including Cepheid Xpert® Xpress SARS-CoV-2/Flu/RSV and Roche’s Cobas SARS-CoV-2 & Influenza A/B Test.
Unfortunately, BinaxNOW and other in vitro diagnostic (IVD) tests authorized for the COVID-19 pandemic are only available to CLIA-certified labs. None are over-the-counter or generally available for businesses or schools to use themselves. As Jackie Lustig, Director of Public Affairs for Rapid Diagnostics at Abbott Laboratories asserted, reporting is a crucial area of COVID-19 management. As a result, the government will only allocate tests to CLIA entities bound by HIPAA-compliant public health reporting requirements.
Becoming a CLIA Lab
If controlling the pandemic requires regular onsite screening at businesses and schools, and that requires testing kits these organizations cannot buy, then we need more CLIA labs able to support general screening programs.
To help address this, the government is reducing the turn-around time for laboratory CLIA certifications, especially CLIA-waived status. The Department of Health and Human Services issued a memorandum (Ref: QSO-20-21-CLIA) with guidance for labs during the COVID-19 emergency. Among its objectives:
“…Ensuring that laboratories located in the United States wishing to perform COVID-19 testing that apply for CLIA certification are able to begin testing as quickly as possible during the public health emergency”
Any entities starting a lab or seeking CLIA certification for their existing lab must fulfill state laboratory requirements first. Of course, these vary from state to state. For instance, Georgia’s requirements include:
- Lab or Specimen Collection Station — You can be one or the other of these
- License application
- Category — Single lab/multiple locations, etc.
- Status — POL, private health care facility, non-profit public health entity, etc.
- Lab Director
- Fees — These depend on the details of the type of lab you are proposing.
Labs in Georgia can get the Clinical Laboratory Licensure Application Packet and CLIA Certification Instructions from here. In other states, similar instructions are available from state public health regulators.
Once licensed in a state, the laboratory can apply for federal CLIA certification using form CMS-116, available from the state or through CMS (get the form and guidance here). The lab must have a designated CLIA-certified physician lab director in order to apply. In addition, the lab must determine the protocols and devices it intends to use and apply for certification at an appropriate level:
- High Complexity
- Moderate Complexity
- Waived
For the purposes of this article’s premise — lab support for widespread screening programs at businesses, institutions and organizations of all kinds — the best target would be Waived, with Moderate in second place. The reason for this is that the devices and protocols capable of producing results quickly enough to support frequent screening tend to be in those categories. Confirmatory follow-up PCR testing can be sent out to other labs. Other requirements include appropriate insurance, OSHA safety and Good Laboratory Practices.
How to Get Your Lab Set Up to Perform COVID-19 Testing & Reporting
Make sure you have the equipment, qualified staff, and understanding of the assays you will be performing. Integral to the overall process will be appropriate lab safety, including protocols for handling samples and disposing of them when called for. Use the FDA’s policy guide to ensure you qualify to provide testing services. There are some specific guidelines for COVID-19:
- Laboratory testing for coronavirus disease (COVID-19) in suspected human cases: Interim Guidance, 19 March 2020
- CIDRAP COVID-19 Lab Guidance & Diagnostics
- CDC Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)
- UK Public Health COVID-19: safe handling and processing for samples in laboratories
However, the largest challenge many laboratories will face is managing the high volume of data that COVID-19 screening programs generate. The 14 million daily tests cited in the NPR report was based on regular testing of healthcare workers, essential personnel and schools. As screening programs expand into every workplace, the test rate will expand further. Of course, no single lab will be responsible for all of the tests. But labs that support screening programs must be ready to manage a high volume of patient and sample data as well as distributing reports to patients, physicians and regulators — while maintaining HIPAA and CLIA compliance.
Automation is Key
An effective data management system is among the most important good practices a laboratory will need to handle rapid, high through-put COVID-19 testing. Laboratories have invested in sophisticated instrumentation and highly qualified staff. Yet if they rely on spreadsheets, paper and faxing for their data management and reporting, they will find themselves unequipped to meet the challenges we are facing.
Take reporting as an example. Even when hospitals, clinics and practices have EHRs, their systems often are difficult or impossible for labs to interface with. The labs must offer simple and quick HIPAA-compliant web portals for sample submission and reporting. A modern LIMS (LIS) will provide the necessary speed and accuracy in laboratory workflows and reporting while ensuring compliance with HIPAA and CLIA.
If a lab doesn’t have such a system but expects to participate in COVID-19 testing in any meaningful way, then it must adopt a LIMS that is COVID-ready. That is, the new system must be operational within days, not weeks or months. The new system must contain the necessary features to support all aspects of COVID-19 testing. Moreover, the new system must be future proof. This may just be the beginning, as some experts believe animal-to-human pathogen jumps will increase:
“I am not at all surprised about the coronavirus outbreak. The majority of pathogens are still to be discovered. We are at the very tip of the iceberg.” – Disease Ecologist Thomas Gillespie, an associate professor in Emory University’s Department of Environmental Sciences
The LIMS Feature Set Needed for COVID-19 and Other Pandemic Testing
So what must the diagnostics LIMS give you to make you “COVID-ready” (or in fact ready for any pandemic)? Here’s a list of the main features:
- Able to manage high throughput
- Can be operational within a week
- Automated reporting to CDC, federal and state agencies
- Secure HIPAA-compliant access and data management
- Pre-loaded COVID-19 assays and workflows
- Easily-configurable for new assays and workflows
- Integrates existing instruments and lab systems
- Unique IDs for samples
- Barcoded labels and scanning capability
- Audit trail
- Results approval
- Out-of-range flagging, positive flagging
- Set values to report as pos/neg
- Reflexive testing
- Supports NGS, ePCR, genomics/MolDx
- Results Report approval
- Integrated client web portal
- Training provided
- Fully supported
Preferably, the solution will be cloud-based. This makes it easier to collect patient and sample data at the screening site with HIPAA-compliant data protection. A cloud solution is also easier to maintain and secure the testing data from end-to-end.
As you deploy your LIMS, you’ll want to ascertain where you anticipate receiving samples from, understand your LIMS and web portal’s registration, accessioning, processing and reporting methodologies and, importantly, determine your projected TAT and throughput capabilities.
As an industry leader in laboratory informatics, LabLynx can help you through the LIMS for COVID testing deployment process. We can tailor our COVIDLiMS solution to your lab’s unique needs in as little as a week. For more information, contact at sales@lablynx.com or call 866-LABLYNX (522-5969).
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