LIMS and COVID-19 Testing & Reporting

Posted on March 24, 2020 By LabLynx Blog

Known variously as coronavirus, COVID-19, novel coronavirus, 2019-nCoV and SARS-CoV-2, the current global pandemic has been reported in 191 Countries and Territories around the world as of March 23, 2020, with over 350,000 confirmed cases and more than 15,000 deaths. These figures are being tracked in real time by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University.

Here’s the straight info on getting the name right, before we go any further:

1. The term “coronavirus” refers to the type of virus in question. It’s slightly vague, only indicating it belongs to subfamily Orthocoronavirinae, a group of RNA rhinoviruses (viruses that prefer the cool moist environment of the nose and sinuses) that are spherical in shape, with projections making them look quite like the old sea mines used in World War 2, that cause upper respiratory infections in animals or humans or both, and some various other symptoms in animals.
2. “COVID-19” is an abbreviation of “coronavirus disease”, with the year it first turned up added (December 2019).
3. “Novel coronavirus” is simply using the word “novel”, which means “new”. This is a new coronavirus.
4. “2019-nCoV” is one way scientists include all of the above information in a shortened designation.
5. “SARS-CoV-2” is another scientific shorthand that includes more information. It stands for “Severe Acute Respiratory Syndrome Coronavirus 2” – the 2nd coronavirus to cause “severe, acute” respiratory symptoms (you may remember the first SARS emerged in 2003).

A brief history of covid19 and the importance of testing

This new RNA rhinovirus is commonly thought to have originated from a bat/rodent coronavirus that jumped to humans in Wuhan, Hubei Province, China and began spreading at a fresh seafood market there. It is, however, similar to the SARS and MERS (Middle East Respiratory Syndrome) coronaviruses that emerged in 2003 and 2012, respectively. Its more contagious than the flu, probably due to its ability to live on various surfaces for hours or days and the fact that its victims are contagious even before they display any symptoms, according to a recent study by US-based scientists. Additionally, because it is a new virus previously only known in animals, human immune systems have no history to help identify it as a threat.

The fact that COVID-19 spreads so quickly is what makes the need for quick and plentiful testing so urgent. Detecting the disease allows for early quarantine, reducing the rate of new infections significantly – thus “flattening the curve” of new cases.

The evolving state of testing and various innovations in testing

The current priorities for dealing with the outbreak are to

1. Adopt practices that limit its spread and
2. Detect cases quickly so that they can be quarantined and, if necessary, treated.

The first part consists of things that by now everyone is familiar with: frequent handwashing, sanitization and “social distancing”. The second part is the main focus of this article: the need for the fastest possible implementation of sufficient patient sampling and specimen submission and rapid and accurate testing and reporting by laboratories.

An unprecedented private industry effort, encouraged and facilitated by the federal government, is now underway, with new testing protocols being produced specifically to address the crisis and existing tests being deployed as widely and quickly as possible. For now the testing is still limited to health workers and the most at-risk patients displaying symptoms. But as tests become much more available and the pandemic progresses, more and more labs will be called on to provide analysis and reporting services.

The availability of testing and the challenges

Companies are responding to the challenge of developing better and faster protocols and test kits. Some examples:

• TaqPath COVID-19 Multiplex Diagnostic Solution
• Cepheid Receives Emergency Use Authorization from FDA for Rapid SARS-CoV-2 Test
• Abbott Labs Test approved for EUA (Emergency Use Authority)
• New Oxford test simple and 3 times faster
• Aid to COVID Diagnosis

As new assays appear and are made available, the push is on for labs to support them. That means having the capability to not only do molecular diagnostics (mostly PCR), but also provide ease of submission, quick TAT (Turnaround Time) and federally-mandated reporting to the FDA and CDC as well as to client physicians. The issue has recently become more complicated, however, as a relaxing of federal requirements has led to fake home tests appearing from overseas in the US, which can inundate labs with spurious throughput that will interfere with bona fide work. That’s not to say that genuine home tests won’t play a part. Home telehealth companies Everlywell, Nurx and others say their home kits follow the recently modified federal EUA regulations. On Monday, March 23, Everlywell is set to ship 30,000 home test kits.

However it all plays out, it is clear that labs have an important part to play in the current crisis, and should be looking at ways to provide COVID-19 testing and reporting. However, this is severely challenged by outdated systems in many labs:

“Something like 2 to 5 million Coronavirus tests are going to show up and most public health departments are going to have to relay the results to CDC via paper faxes and/or phone calls”, according to Open Health News publisher Roger A. Maduro.

Preparing for meeting the submissions, testing and reporting challenges may involve more than adding a test or two.

LIMS and COVID-19 testing & reporting

All of this comes just as the ONC has released its final rule on interoperability. As is so often the case, tech is central to finding ways to meet public health challenges, just like any other industry. The problem is that the health industry and many laboratories in it have been slow to embrace the technology that passes for baseline even at home and among our kids.

Laboratories may have a lot of money tied up 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 ahead. Hospitals, clinics and practices may or may not have EHRs, and even where they do, 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, and a modern LIMS (or LIS) to provide the necessary speed and accuracy in their workflows and reporting that is also compliant with HIPAA and CLIA.

If your lab expects to participate in COVID-19 testing in any meaningful way, but doesn’t have such a system, it will be important to be able to adopt one that is COVID-ready. That is, it needs to be able to be operational within days, not weeks or months, and contain the necessary features. Moreover, this may just be the beginning, with some experts believing animal-to-human pathogen jumps will increase:

“I am not at all surprised about the coronavirus outbreak,” he says. “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 feature set needed from a LIMS for COVID-19 or any 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:

• Unique IDs for samples
• Barcoded labels and scanning capability
• Pre-loaded assays and workflows
• Flexible, easily-configured new assays and workflows. Adaptable.
• Secure, HIPAA-compliant access and data management
• 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
• Federal and CDC reporting
• Integrates to instruments, agencies
• Integrated client web portal
• Can be live and operational inside a week
• Training provided
• Fully supported
• Preferably cloud-based for ease of maintenance, access, with full data protection and security

How to get your lab set up to perform COVID-19 testing & reporting

Use the FDA’s policy guide in ensuring you qualify to provide testing services. You can begin this even before you have your LIMS in place. As we touched on earlier, recent relaxation of the requirements allow extra time to supply supporting documents.

Beyond that, of course 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.

Finally, 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.

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

For information and help in ramping up to provide COVID-19 testing services, contact LabLynx, Inc. or call 866-522-5969.

by LabLynx