NEW YORK – Despite intense scrutiny and criticism of the diagnostic testing rollout in the US for the SARS-CoV-2 virus, the emergency regulatory process may actually be proceeding at a much more rapid pace than past emergencies, which did not involve newly-emerged pathogens.
Commercial tests in development to date have faced bottlenecks in test validation, but the logjam now appears to be clearing with new US Food and Drug Administration feedback and the availability of control materials.
The coronavirus disease COVID-19 outbreak began in Wuhan, China, with the first cluster of cases uncovered Dec. 31, and the virus sequenced and viral genome publicly available on Jan. 5. When the US emergency was declared on Jan. 31, there were 11 known cases, mostly related to travel. The US Centers for Disease Control and Prevention submitted its SARS-CoV-2 real-time reverse transcriptase PCR test to FDA on Feb. 3 and was granted emergency use authorization on Feb. 4.
Historically, emergencies have involved pathogens that were already on the radar from prior outbreaks. In the current case, SARS-CoV-2 is a novel pathogen, and diagnostics had to be developed from scratch.
Offsetting this challenge, however, is the fact that the EUA application process has been streamlined. Diagnostics makers interviewed for this story estimate that it will take them about two months to complete the regulatory process, but they are well on the way with tests they have created.
In the past, there have been declared infectious disease emergencies in the US for H7N9 influenza, Middle East Respiratory Syndrome, Ebola, EV-D68, and Zika virus. The CDC or the Department of Defense were always the first to get emergency authorization from FDA, usually within a few days of the emergency being declared.
Opening up EUA accelerates the path through FDA by lowering the thresholds and requirements, but it also essentially shunts all tests through a regulatory process, since labs are typically no longer permitted to run lab-developed tests after the EUA is issued. In the case of COVID-19, however, high-complexity CLIA certified labs are now allowed to develop tests, so long as they apply for EUA as well, according to new guidance issued Feb. 29. Public health labs in NY State achieved EUA that same day. This is in part a reaction to a now-resolved issue with a reagent that slowed roll out the CDC test to public health labs, and also part of an effort to disseminate testing more broadly.
Commercial EUA timelines
Historically, the fastest time for a commercial test to obtain EUA has been about two months after an infectious disease-related public health emergency was declared.
After the Ebola emergency was declared on Aug. 5, 2014, the DoD was able to get its test authorized Oct. 10 of that year. Two tests from BioFire Diagnostics that were being developed using DoD funding were then granted EUA 81 days after the emergency was declared, on Oct. 25 that year, and a test from Altona Diagnostics was granted EUA on Nov. 26.
A declared Zika emergency issued Feb. 26, 2016 resulted in a test from CDC receiving EUA that same day. A lab test from Quest Diagnostics followed on April 28, while Altona got EUA for a commercial test kit 77 days after the emergency was declared, on May 13, and Hologic got EUA for a test on its automated instrument on June 17. Many other commercial test developers followed suit the following year.
In contrast, a MERS emergency was declared on May 29, 2013, with a CDC test subsequently granted EUA June 5, and the emergency then reissued the following year. The only commercial MERS test to get EUA was from Altona Diagnostics, granted on July 17, 2015.
Unlike these historical cases, SARS-CoV-2 is a newly emerged pathogen that bloomed from local to global spread very quickly.
Indeed, "For the other tests, we had a test ready for quite some time and CE-IVD marked before the EUA was opened," Stephan Ölschläger, Altona's head of marketing, said in an interview.
The Ebola Zaire strain was known since the 1970s, he said, and the Zika virus had been circulating in the South Pacific for a year prior to the outbreak in the Americas, and the company had tests well in advance of a US emergency being declared.
"For MERS, it was similar. At first there were only a few cases directly transmitted from camels to humans, and there were only small infection chains in Saudi Arabia, but nevertheless at that time we already designed, developed, and marketed a kit," Ölschläger said. Subsequent nosocomial outbreaks in Jetta and South Korea led to the US initiating its emergency, and by that time Altona had a test ready to go.
Wade Stevenson, senior vice president of global marketing at BioFire Diagnostics, a BioMérieux subsidiary, said that in the case of Ebola BioFire also had its test already made when the emergency was issued. "It cuts down on the development time," he said in an interview, but in the current case, "this is a novel coronavirus, and it has never before been seen in the world, and as a PCR company, you can't develop a PCR assay until someone out there has published the sequence."
Indeed, initial development of a real-time reverse transcriptase PCR test is considered to be straightforward, once the pathogen sequence is available, and Altona is selling a research-use-only SARS-CoV-2 test kit now, as are a number of other firms.
Both Altona and BioFire are also working through the EUA process with the FDA, even as guidelines and requirements seem to be evolving. "It is a quickly moving landscape these days," Stevenson said.
Sven Cramer, Altona's head of regulatory and quality affairs, said that the company was actually contacted by FDA about submitting for EUA, and that this was the case for Zika and Ebola as well.
BioMérieux and its subsidiary BioFire Defense are working on two tests. One is part of the Argene system and will be a standard real-time RT-PCR assay that can be run on several different instruments. The other will be made by BioFire Defense through an existing DoD contract and will use the BioFire FilmArray 2.0 and FilmArray Torch systems, Stevenson said.
The validation bottleneck
According to a list of assays published by the Foundation for Innovative Diagnostics (FIND), there are many commercial SARS-CoV-2 diagnostics assays in various stages of development — from proof-of-concept tests to full-fledged emergency use diagnostics — in different locations of the world.
However, for test validation, "it is always the same bottleneck," Altona's Ölschläger said. "It is always access to clinical samples and inactivated virus material. We don't have a [biosafety level]-3 lab, so we need to work with inactivated viruses or with partners who can use the infectious virus to validate workflows."
Stevenson concurred, commenting that access to viral materials is "a huge bottleneck."
Thus, analytical sensitivity testing is the requirement that is the most difficult to fulfill. Live SARS-CoV-2 can only be safely contained in BSL-3 labs, and most diagnostics developers only have BSL-2 capabilities.
Ölschläger also said that spiking in vitro transcribed RNA is not possible with every workflow. Mock samples made by putting naked RNA into nasal swabs from healthy patients, for example, may not be useful because RNAse in the samples will instantly chew up the spiked-in material.
In contrast, Ölschläger said that real clinical samples for a validation study might be easier to get for Hamburg, Germany-based Altona, unfortunately, because there is now an outbreak in Europe.
Furthermore, for EUA, commercial diagnostics developers historically have had to validate the test for every sample type they intend it to be used for. The recent guidance provided to US high-complexity labs developing LDTs has instructed them to validate assays on the most challenging matrix they expect to use, but it is not clear if that lower threshold will be extended to commercial entities as well, and FDA did not respond to a request for comment in time for this article.
If only one sample type is in a commercial EUA claim, the extent to which a customer can use the test on another is also unknown, but allowing suppliers to widen the claim on similar sample types might be a way to make testing more widely available. "The analytical sensitivity wouldn't differ at all if you use oral or nasal swabs and spike them with virus material," Altona's Cramer said. "The only difference is the clinical samples, and the number we currently have access to isn't high enough."
Altona launched its SARS-CoV-2 test two weeks ago and has already sold it to many labs globally. It is still a research-use-only product, however, so validation for use on patients is the responsibility of end users at this point.
Nevertheless, "it is better to use commercially available tests that are produced up to a certain standard and in a controlled way," Ölschläger said, as compared to LDTs.
Cramer said he believes other developers are facing the same issues, and ones based in areas where there is a sustained outbreak may also face trouble generating enough products to meet local needs and also for export.
Stevenson also noted that there are buffers that can inactivate RNAses, and ways to pre-treat RNA to coat it and protect it from RNAse. He said that BioFire's contract with the DoD might enable it to access viral materials that might not be broadly commercially available.
Viral material now available from vendors
Cramer noted that any labs that have clinical samples and the BSL-3 labs allowed to handle the viral material are pretty occupied with testing at the moment, so they don't have time to collaborate on validating kits.
Availability of the viral material to diagnostics developers, particularly from commercial suppliers of QC reagents, had been a sticking point until earlier this week, according to one vendor.
Shawn Smith, CEO at ZeptoMetrix, said that his company had been working for a month to obtain live virus, but had resolved the issues as of yesterday morning. ZeptoMetrix has a BSL-3 lab and is certified to keep a biobank of live virus. The company can supply BSL-2 labs with virus that it inactivates using a proprietary technology, called NATtrol, and can also provide crude heat-inactivated virus.
Properly documenting the material transfer of the inactivated virus between commercial entities seemed to have been the main issue, but Smith said on Wednesday that his team got the necessary clarification on the paperwork requirement and had placed the order for live SARS-CoV-2 from BEI Resources.
BEI is the repository to which CDC sent the virus samples it was able to grow in culture from US patients. Rebecca Bradford, the senior director of government programs at BEI Resources and ATCC Federal Solutions, said in an email that currently BEI Resources has no shortage of live virus product and it does not anticipate any shortage for qualified BSL-3 laboratories working on the SARS-CoV-2 efforts.
"For inactivated material, it is imperative to perform inactivation method validation and subsequent testing on the product to ensure no residual live virus remains," Bradford noted. "This prevents live virus from being distributed to laboratories who cannot handle infectious SARS-CoV-2." Furthermore, testing of inactivated SARS-CoV-2 is currently in process at BEI. "Once confirmed, the inactivated material will be available through BEI Resources [and] SARS-CoV-2 RNA is currently available and can be worked with in a [BSL-2] laboratory," she added.
Zeptometrix also makes constructs that incorporate synthetic viral RNA into Escherichia coli, which are typically used as positive controls for diagnostic testing, and may also have some utility for test validation in the SARS-CoV-2 context as they can be handled more safely but won't be degraded by RNAses in the samples. That product will be available within a week, he said.
Smith also estimated that the firm will get live SARS-CoV-2 virus within the week, grow it in culture in the BSL-3 lab, and be able to supply heat-inactivated viral material in about two weeks, and refined chemically inactivated virus in about four weeks. Even "heat-inactivated material will allow people to use it in BSL-2 labs and start to make progress in assay development," Smith said. The firm is in continuous contact with about 10 large national and multinational firms who are seeking reagents as soon as possible, he said.
A simpler FDA template
The submission for EUA is reportedly different now than in past emergencies. Currently, it is a rolling process involving an electronic template. The FDA has said it engaged with more than 70 diagnostics developers, and the initial conversation is apparently the first step in the application.
"When we did the first EUA for Ebola, there was no template available," Cramer said, adding that "since then, from EUA to EUA the template has become more specific, with more specific requirements and guidance."
Also, there has been room for negotiation with FDA, so that the process is more of a back-and-forth.
"FDA is very open," Cramer said, and Altona and FDA have been continuously negotiating the parameters of validation. This was also the case historically in past emergencies. "It is a lot of back-and-forth until finally everything is agreed upon, and then the data are entered into the form sheet, and it is usually a week until the EUA is granted," he said. For Ebola it was only two days from the moment the form was finally submitted to the EUA being granted, he added.
Ölschläger noted that by the end of the process, FDA essentially knows what is coming in the final document because the agency has been reviewing it all along.
Richard Montagna, senior VP of scientific and clinical affairs at Rheonix, is also working through the template for a SARS-CoV-2 assay on the firm's automated, closed test system. Montagna said he has been working with FDA for 35 years and is currently in the late stages of the process of applying for clearance for Rheonix's Encompass MDx along with a multiplex sexually transmitted infections test. In that case, the FDA had reviewed a 1,500-page submission and provided feedback within six weeks, which in itself was remarkable, he said.
For EUA, Montagna said that Rheonix reached out to FDA shortly after the World Health Organization issued its public health emergency of international concern. He said he went through his usual regulatory contact, was put in touch with the EUA administrators, and got the template sent to him within an hour. Montagna said his company is almost finished filling in the template, after about one week of work.
"It basically looks like a submission that anyone would send to them, with yellow highlighted areas where they want me to fill in the blanks," Montagna said. "They've done all the work, and they even gave us the cover letter that they want, and said, 'Cut and paste it on your letterhead.' They couldn't have made it any easier."
Montagna said Rheonix is also applying for funding through the Office of Biomedical Advanced Research and Development Authority (BARDA), and the EZ-BAA template that is used in that case is also incredibly simplified, and only 20 pages.
Compared to the past, the current outbreak is also much bigger than historical emergencies. "The last real pandemic we had was H1N1, and all the other outbreaks were more or less local," Ölschläger said. Ebola has been in West Africa, and MERS was in the Middle East. "Zika was kind of pandemic, but then it is a tropical virus which is transmitted by mosquitoes, so that limits the potential" for global spread, he said, as well as the number of locations that could support the virus becoming endemic.
"This is a whole different situation now," Ölschläger said. On top of the global spread, quarantines and treatment require a lot of infrastructure, and this is occurring on the backdrop of a very severe influenza season when there are already few empty beds in hospitals.
The FDA recently relaxed its requirements in order to enable highly-complex labs in the US to develop tests. It has also made the CDC's EUA almost like an umbrella authorization to cover certain kit lots from a reagent supplier, Integrated DNA Technologies, as long as the lots have been validated at CDC, and it has implied that other kits will be validated in this way in the near term.
Altona's Cramer noted that labs are also permitted to use certain RUO reagents to develop LDTs, as the new guidance states that "FDA anticipates that clinical laboratories may need to design and manufacture the individual test kit components (e.g., primers, probes, etc.), or to purchase research use only (RUO) components from third party manufacturers for the development of their assays."
This could open the use of RUO real-time PCR assays, like the one Altona is currently offering, by labs as a basis to develop LDTs.
But there is also the constraint that labs must submit an EUA application within 15 days. "EUA submission of LDTs involving commercial RUO reagents will require input from the supplier and possible disclosure of IP to the CLIA labs, which has to be evaluated on an individual basis," Cramer said. "Overall, we think that the new guideline describing workarounds for CLIA labs will enhance the capabilities to test for SARS-CoV-2, but not so much involving commercial assays."
In addition, unlike LDTs, which can use manual extraction methods if needed, makers of diagnostics are typically required to validate their tests using all the workflows a lab would use when testing patients, and this presents a real problem with automated extraction instruments, according to Altona.
The best way to spike in viral RNA is after the lysis step, but in an automated instrument this is a physical challenge. Without opening up the instrument in the middle of the process — something an end-user would never do — it is tough to get to that step in extraction, and it is unclear if FDA can relax its guidelines in a situation like this.
One solution in the future might be having a dedicated validation lab in the US, Ölschläger said. If a company could send its product to a CDC or FDA lab that had the viral material and clinical samples to generate the analytical and clinical data, that could speed up the process.
Ölschläger also said there is a limit on how many tests companies can produce, above and beyond the demands of their regular supply commitments, and having enough expert-trained staff and lab space are the limiting elements.
"We have around 200 employees, and we have the daily business to do, too," Ölschläger said. "We cannot just hire 50 people from off the street and say, 'Here, take a pipette, here is the protocol, just go for it.'" Staffing will also likely set a limit on production capacity across the industry, he suggested.
For BioFire, the company expects to have manufacturing capabilities to support SARS-CoV-2 testing once the assay has EUA. "We manufacture quite a high volume of respiratory tests, as well as other tests," Stevenson explained. BioFire has also seen an increase in sales of its respiratory panel tests in Asia Pacific so far this year, attributed to an increased clinical need right now to rule out infection with other pathogens.
Meanwhile, the business case for emergency infectious disease diagnostics at a smaller company like Altona can be more incremental. For Ebola, for example, a lab network in Europe subcontracted development of the commercial assay, and after that, Altona had it on the shelf and could sell it at a low level, Ölschläger said.
Altona's Cramer noted that CE-IVD can be self-declared for certain pathogens, with the exception of things like HIV, hepatitis B and C, and cytomegalovirus, so there are a few products that have achieved this mark to date. But, "we will not lower our standards," he said, adding that "from our point of view, this will backfire ... We don't take shortcuts."
In terms of timeline, both Altona and BioFire representatives said two months from the date they started working on the test would be a good estimate, but they could not specify exactly when work began.
Still, "the market is really waiting for something to use, and every lab needs it, from hospital diagnostic labs to private labs and public labs," Ölschläger said.
BioFire's Stevenson concurred. He has also heard the criticism of the US diagnostics response. He noted he can only speak for his company, but said that "we prioritize doing it right over doing it fast. It is a lot of work, a lot of validation, and there are issues that take time."
And, ultimatelty the FDA regulations are in place for safety reasons. "Even in EUA, they are scaled back, but it is still super important that you do that work," Stevenson said.