CEO SUMMARY: Clinical labs are working with haste to test for the novel coronavirus, also called nCoV and SARS-CoV-2. Their efforts to prepare for high capacity testing for viral respiratory illness include validating molecular tests for the newly-identified virus and making those tests available for testing patients who may have the COVID-19 illness. At Northwell Health, the lab team has been validating the CDC’s manual test and a multi-test panel for respiratory diseases that will include the novel coronavirus.
Following the outbreak of a novel coronavirus in China at the end of December, clinical laboratories have faced multiple significant challenges.
Among the challenges they face are validating a diagnostic test for the virus that has the sensitivity and specificity to make it useful for physicians treating patients and working with public health officials to manage a rapidly evolving epidemic.
Another of these challenges is to develop the ability to perform these tests at high volume levels and with a fast turnaround time for results. While seeking to meet all of these challenges, clinical labs also must comply with federal and state regulations that govern the use of these assays.
In mid-January, scientists in China released the genetic information for this novel virus. At that time, the leaders and staff in the clinical laboratories of Northwell Health in Lake Success, N.Y., recognized the need to be able to validate a test that the federal Centers for Disease Control and Prevention (CDC) would release, and then be able to run that test in enough numbers to meet an unknown level of demand.
As one of the nation’s biggest health systems, Northwell has 23 hospitals and a central reference laboratory serving both Northwell and other hospitals in the greater New York metropolitan area, making Northwell’s lab one of the largest in-system clinical laboratories in the United States, according to Stefan Juretschko, PhD, D (ABMM), Northwell’s Senior Director of the Division of Infectious Disease Diagnostics. Juretschko is leading the systemwide efforts to increase the labs’ capacity for testing for the novel coronavirus that causes the coronavirus disease (COVID-19).
The virus was unknown before late last year when it was identified in patients in Wuhan City, in Hubei Province, China. At the time, the virus was named 2019-nCoV, and by early March it was named SARS-CoV-2, the federal Food and Drug Administration (FDA) said. As of the end of the first week of March, the illness had spread to 93 other countries, infected more than 101,927 people (including 80,813 in China), and caused more than 3,486 deaths (including 3,073 in China), according to a World Health Organization (WHO) report on March 7.
Shortly after scientists in China made public the genome sequence of the novel coronavirus on Jan. 12, and public health officials began reporting the number of infected patients and deaths, federal and state health authorities began inquiring about the capacity of hospital and health system labs to identify the virus in patients. Such inquiries combined with daily and hourly breaking news about the virus created a dynamic working environment in labs nationwide.
As soon as the test kits arrived from the CDC and from the New York State Department of Health (NYSDOH), Juretschko, other lab directors, and the lab staff began the steps required to validate and run the test in Northwell’s labs. Also, the lab began acquiring new analyzers, testing supplies, and reagents from vendors nationwide to support their efforts to run large volumes of tests for patients and their physicians.
Working Day and Night
During an interview with The Dark Report on March 4, Juretschko outlined those processes and said he was confident that Northwell Laboratories would be capable of testing patients in large numbers by the end of March. Since the middle of January, Juretschko and other lab staff have worked night and day to scale up testing for the virus, he said. During this time, events in other countries and in the United States began to unfold quickly.
For example, on Jan. 21, officials from WHO conducted a field visit to Wuhan, when Chinese scientists released the primers and probes for test kits that labs in other countries would use to detect the virus.
On Feb. 4, Alex Azar, the Secretary of the federal Department of Health and Human Services, issued an emergency use authorization (EUA) saying that the coronavirus created a significant potential for a public health emergency that could affect national security or the health and security of U.S. citizens. That same day, the FDA issued an EUA allowing the emergency use of the CDC’s 2019-Novel Coronavirus (2019-nCoV) Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel.
Under this EUA, testing was limited to qualified, CDC-designated, and CLIA-certified laboratories to perform high-complexity tests. The clinical labs at Northwell Health meet these criteria.
Emergency Use Tests
The FDA then issued two EUAs on Feb. 29. One outlined the policy-specific guidance that public health laboratories needed to follow to contain the public health emergency. The second EUA allowed two public health laboratories in New York to expedite the availability of diagnostic testing. The two public-health, CLIA-certified labs were the Wadsworth Center at the NYSDOH and the New York City Department of Health and Mental Hygiene, Public Health Laboratories.
“The EUA required labs to follow specific procedures when seeking to produce assays and test kits for identifying the virus, a process that slowed Northwell’s efforts,” Juretschko said. For individuals who meet the CDC’s criteria for such testing, the FDA’s instructions called for collecting upper and lower respiratory specimens (such as nasopharyngeal or oropharyngeal swabs, sputum, lower respiratory tract aspirates, bronchoalveolar lavage, and nasopharyngeal wash/aspirate or nasal aspirate).
Since then, Northwell’s lab staff has made significant progress in drafting plans for the tests, and to have the equipment and supplies in place to test an unknown, but presumably large number of patients.
By March 7, lab leaders were deep into validating the test kits received from the CDC and preparing to validate test platforms from commercial companies such as GenMark Diagnostics in Carlsbad, Calif., and Cepheid in Sunnyvale, Calif., Juretschko explained. He expected the lab to complete validating multiple platforms for identifying the virus by March 15 or so. “We did all of this preparation work without getting any material or fund-ing whatsoever from the CDC or NIH,” Juretschko said.
“But we did get a visit from New York Sen. Chuck Schumer,” he noted. “And New York Gov. Andrew Cuomo has promised to make some capital available to us in some fashion. Plus, we learned recently that we will shortly get some quality control material from NYSDOH that is not infectious. It is contrived material that we will use for quantitative analysis.
Testing at Scale
“We are developing a three-pronged approach to do testing on a large scale,” Juretschko reported. “The first approach is to implement the original assay that the CDC and all public health laboratories use, along with controls and detailed directions.
“The second approach is to use a device, similar to a commercially-available respiratory pathogen panel to test for the novel coronavirus,” he added. “This panel allows for more mobility and flexibility in testing because we can provide the assay directly to the hospital laboratories.
“The ability to apply for an EUA opened up opportunities for labs like ours to do research on how to get these tests running on a larger scale,” Juretschko explained. “For example, we used the EUA to have conversations with three vendors to get the tests and the equipment we need to serve our health system.
“The approach would entail an even more automated process for testing on several big-footprint instruments,” he continued. “These analyzers are already placed at the core laboratory and can be ‘fed’ with the original patient samples, processed internally by robot arms, and thus allow for extremely high throughput testing of 1,000 to 2,000 patients per day. The actual assays and reagents have yet to be designed and validated, but we expect to launch those assays and reagents within the next several weeks.”
Before going into detail about the second approach (using the respiratory pathogen panel), Juretschko outlined the first approach: validating and running the test from the CDC. “The CDC has its own validated assay,” he explained. “It’s distributing this assay to all departments of public health across the United States. That assay includes all details about probes and primers and the entire standard operating procedure for the test.”
During the interview on March 4, Juretschko said the lab team was at the end stage of the validation process to run that test in the lab. Via email, he con-firmed that the process was completed on March 7.
While CDC validated the test itself, the Northwell lab staff needed to validate the CDC assay on its own equipment and in the laboratories in which it will run, he said. That validation includes ensuring that physicians can order the tests electronically, and also that the results can go back to ordering physicians.
“Plus, we want to make sure that physicians can read and understand what the results mean,” Juretschko added.
The lab team’s multi-pronged strategy, as Juretschko described, is to scale up the novel coronavirus testing by first using the assay from the CDC. In a parallel effort, the lab will use an automated respiratory pathogen panel from GenMark and other vendors. As Juretschko explained, the work the Northwell lab team is doing to prepare to do high-volume testing for the novel coronavirus provides an excellent example for other labs in hospitals and health systems of the benefits of having a highly-integrated in-system laboratory network.
“Our core lab serves our very large health system and an additional 11 area hospitals as the reference lab,” he said. “And in our own system hospitals, the clinical labs are already equipped with the Respiratory Pathogen (RP) Panel from GenMark. This means that, if we success-fully validate the GenMark platform, we can deploy such testing throughout the health system, not just at the core lab. “The RP panel is a sample-to-answer test, which means the sample is put in a cartridge and that cartridge is then put into the analyzer.
The operator can walk away and go do something else for 90 minutes or so,” he added. “Once the analysis is complete, the results are available without additional labor or input.
“Thanks to the usual needs for respiratory virus testing, we have one of these instruments in every one of our hospitals,” Juretschko reported. “In one cartridge, the panel can test for influenza, including influenza A and influenza B, and for respiratory syncytial virus (RSV).
“In addition, we have a more complex panel in some of our largest hospital labs that test for more than 20 targets, including flu A and its subtypes, H3N2 and H1N1; flu B; the four types of coronavirus that were identified in earlier epidemics; the 2009 swine flu; RSV; and others,” he said. “About four to six companies make these larger test panels.
“Our immediate goal is to get a test for the novel coronavirus under the EUA, and then work with the NYSDOH and the FDA to add the novel coronavirus testing to the panels these companies already offer,” Juretschko explained. “We expect to get validation of the test panels going soon, because they have been designated for research use only (RUO) and some are available for use already.
“It’s important to note that the testing reagents in the panel are based on the virus’ RNA structure, meaning the tests are similar to what the CDC assay offers,” he added. “The key difference is that CDC sent us the primers and probes needed mainly for manual testing, whereas the panel kits enable automated testing.
“Using the panel kits has a lot of advantages,” he commented. “First, auto-mated cartridge-based testing provides an answer within 80 to 90 minutes, with very little manpower needed. Second, deployment to all the hospitals that have that analyzer can be done immediately.
Third, a technologist can run the updated panel with very little in-service training, since they are already familiar with the testing platform,” he said. “And, fourth, we can further expand our system capacity by acquiring additional machines.
“We’re already talking to the vendor about whether we should buy some of the smaller instruments and put them in all of our hospitals,” he added. “We haven’t made a decision yet, but that’s an approach we’re considering.”
Instruments in All Hospitals?
“Having full capacity for local hospital testing would shorten turnaround times tremendously because samples would not need to be sent to the core lab for testing,” Juretschko explained. “Such rapid resulting—within two hours—would have significant value for managing patients, triaging in emergency departments, and in managing the healthcare workforce.”
With sufficient testing capacity, using the complex test panel will give Northwell an important advantage for any patient who goes to a doctor with flu-like symptoms, he said. That patient would be tested for a wide variety of viruses and get an answer quickly. “Many of those patients would be in the clear, and others would learn if they have the novel coronavirus and can take appropriate steps,” he noted.
This multi-pronged strategy enables Northwell to achieve a quick launch with the CDC assay, while simultaneously gearing up for high testing capacity using commercially-available automated platforms. Since the end of January, at least two companies announced that they would offer tests for such analyzers.
On Feb. 10, Cepheid said it was developing an automated molecular test for the qualitative detection of the novel coronavirus for its GeneXpert Systems, and that the tests could deliver point-of-care results in about 30 minutes. On March 2, GenMark announced it shipped RUO test kits to detect the SARS-CoV-2 virus and that it would submit an EUA to the FDA for this test.
After working with these vendors and validating the tests, Juretschko predicted that by about the middle of April, Northwell labs would be ready to test large numbers of patients with fully-validated assays.
“By that time, I expect that the whole picture will be turned around so that we’re no longer validating and working to get the right equipment and test kits here, but we are at the point of testing a lot of patients quickly and efficiently,” he said.
Validation of the COVID-19 Test Requires Lab to Undertake Numerous and Complex Logistics
To validate the CDC’s test for the novel coronavirus that causes the coronavirus disease (COVID-19), the lab team at Northwell Health found that it “had numerous and complex logistics to work out, such as the positive controls and negative controls, the limit of detection, sensitivity, specificity, and so on,” said Stefan Juretschko, PhD, D(ABMM), Northwell’s Senior Director of the Division of Infectious Disease Diagnostics.
“As one example, when we look at sensitivity of these tests, we want to know the number of copies of the virus per milliliter of sample,” explained Juretschko. “In terms of specificity we want to know if it can actually detect the virus itself or whether it’s accidentally detecting something that it shouldn’t detect. And here we want really high specificity, such as in the upper 90% or better range.
“Inactivated samples of the virus in different concentrations can be ordered through the CDC and sent to us via courier. We tested those samples side by side with real patient samples here at the core laboratory,” he explained. “Those are the technical aspects of the tests, but there are other aspects to be decided about these tests as well.
“For example, how can physicians order the test, who can order it, and is there a restriction on ordering?” he asked. “We need to know if the test detects the one virus—meaning the novel coronavirus—or also detects influenza A and B, RSV, and other viruses. Also, what is the test’s negative predictive value?
“We are working with the NYSDOH to have a batch automated test kit. This means we’ll be able to run a number of those tests all at once,” he reported. “When each test batch is done, we’ll load another batch of tests on that same machine, and so on.”
Batch processing enables Northwell to test as many patient samples as the number of wells (96) that the machine can handle at one time, he said. Although that batch number is still a limiting factor, this automated processing will vastly increase testing capacity at Northwell Laboratories, he added.
“The test from the CDC is an “old-fashioned,” but very reliable and precise polymerase chain reaction (PCR) test, where you have to extract the nucleic acid, which in this case is the RNA,” he explained. “A reverse transcriptase will follow along with the actual detection of the virus, which happens in a different instrument.
“Extraction takes place in the first machine, and that process runs for about an hour,” he added. “The extracted material is then combined with the testing reagents and run on a different machine for about an hour-and-a-half to two hours. The whole process from start to finish takes about three-and-a-half to four hours.
Core Lab Testing
“This batch test will be done in our core lab, which serves all the hospitals that do not have testing in-house, including affiliated hospitals that use us as a reference lab,” he reported. “Our core lab has two instruments for this test and each instrument can test a plate with 96 wells. Every patient sample requires four wells, meaning we can run about 24 patients per batch, thus the two machines can handle 48 samples about every three to four hours.
“We plan to double our capacity by adding two more PCR analyzers. With four machines, we’ll be able to run 96 samples every three hours. Then, because these machines will run 24 hours per day, we can analyze up to 768 samples per day at full capacity, which is more than 23,000 samples per month,” he said.
Origins of the Novel Coronavirus
AT THE CENTERS FOR SYSTEMS SCIENCE AND ENGINEERING (CSSE) AT THE JOHNS HOPKINS WHITING SCHOOL OF ENGINEERING, researchers tracked the novel coronavirus since the pathogen was identified. On the CSSE site, researchers reported that on Dec, 31, the World Health Organization learned of a case of pneumonia of unknown cause in Wuhan City, Hubei Province, in China. By Jan. 23, there were more than 800 cases of the virus confirmed worldwide, including cases in at least 20 regions in China and nine countries or territories, CSSE reported. Among the first infected individuals were some who showed symptoms as early as Dec. 8 and were stallholders from the Wuhan South China Seafood Market. That market was closed on Jan 1. On Jan. 10, gene sequencing showed the pathogen was a new Wuhan coronavirus—2019-nCoV—a betacoronavirus, related to the Middle Eastern Respiratory Syndrome virus (MERS-CoV) and the Severe Acute Respiratory Syndrome virus (SARSCoV), CSSE reported.
Contact Stefan Juretschko, PhD, at Sjuretschko@northwell.edu.