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Clinical Laboratories Prepare for SARS-CoV-2 Variants


NEW YORK – As new variants of SARS-CoV-2 continue to emerge, clinical labs are having to develop new and evolve existing approaches to test for the virus.

While existing molecular tests appear to be capable of detecting the new UK and South Africa SARS-Cov-2 strains that have been the focus of much recent attention and concern, the appearance of these and other variants could require changes in labs' testing processes and the development of better tools for monitoring the presence of relevant variants in the patients they serve.

The most immediate concern from a lab's perspective is that the mutations that characterize major SARS-CoV-2 variants may make molecular or antigen tests for detecting the virus less effective by altering the regions of RNA or protein these tests target.

Last month, the US Food and Drug Administration said that it was working with test developers to determine if existing assays were able to effectively detect variants of the virus. Also last month Laboratory Corporation of America noted that it has been monitoring the emergence of SARS-CoV-2 variants and has determined that it has "not seen any impact" on the sensitivity of its molecular test from the variants.

"I'd say there is relative comfort in the [lab community] that we can still detect at least the known variants" using existing assays, said Jeffrey SoRelle, a clinical pathologist at University of Texas Southwestern Medical Center. He added that most of the molecular tests that the medical center uses target multiple portions of the SARS-CoV-2 genome, which makes it unlikely that they would miss a variant, even if it were to contain a mutation in one of the targeted areas.

In a recent commentary in Clinical Chemistry by SoRelle and several of his colleagues at UT Southwestern, the authors noted that as of January 13, 2021, 152 of the 192 molecular SARS-CoV-2 tests with US Food and Drug Administration Emergency Use Authorization used more than one target for detection.

SoRelle said that many vendors have also done in silico analyses of the primers used in their tests to demonstrate that mutations in a given variant should not impact the performance of their assay. He noted, however, that for most tests "it still hasn't been proven experimentally that RNA from a B117 variant [the UK variant] is being detected by all of these platforms."

SoRelle said that one challenge to experimentally validating that existing tests work on new variants is obtaining reference material, a bottleneck for test development at the beginning of the pandemic, as well. He said nucleic acid-synthesis firm Twist Bioscience was offering synthetic validation material for the B117 variant but noted that his lab had not yet evaluated it.

He said that based on his lab's initial validation work at the outset of the pandemic, synthetic reference material had one disadvantage compared to an actual specimen – "Synthetic RNA doesn't go through the extraction process as well as [real viral RNA], and so there are issues with the extraction phase decreasing sensitivity."

He said that his lab at UT Southwestern is currently developing PCR-based tests it will use to detect the presence of different variants. It will then use the identified variant specimens to confirm experimentally that the molecular assays it is using still detect them effectively.

The lab is starting with assays to four targets and plans to increase that number as new important variants arise, SoRelle said. He noted that one challenge to developing such assays is achieving good specificity with as few targets as possible.

"For instance, the British variant has this S-gene drop-out that occurs in the [Thermo Fisher Scientific] TaqPath assay, but it also occurs in some US variants, and only a small portion of those have been found to actually be the B117 variant," he said. "So you might want to have two markers on that test, one that easily identifies the S-gene dropout and another one that is more specific to the [B117] variant."

Carey-Ann Burnham, medical director of clinical microbiology at Barnes Jewish Hospital in St. Louis, said that "most of the clinically relevant variants we're hearing about are [affecting] the spike protein," which she noted is good news from a testing perspective in that few molecular assays target the SARS-CoV-2 spike protein.

She said that her lab was in regular communication with its vendors about the potential impact of variants on their test. She added that while variants like the B117 were receiving a large amount of attention due to their potential public health significance, mutations are a common and expected consideration for clinical microbiologists.

Burnham said that her lab planned to continue testing using the same mix of tests and platforms it has been. "We're not shifting anything around," she said. "We really don't have any concerns about our platforms and also we have so many different redundant platforms."

Her lab is also doing antigen testing for the virus, which she said has also remained effective at detecting the existing variants.

Susan Butler-Wu, director of clinical microbiology at the LAC-USC Medical Center, said that she was concerned about the lack of visibility her lab has into the question of how variants could impact test performance. She noted that while labs at large academic medical centers like UT Southwestern have the resources to develop in-house tests for detecting variants and validating the performance of their assays, her lab, which serves a public hospital, isn't typically able to do this work.

"Where I work is more like a very large community hospital, and we have no ability to do anything other than what comes in the box," she said. "We are entirely sample-to-answer. So, we are completely dependent on the vendor of the cartridge that we use to tell us, yes, we have checked in silico that our assay should work. But we have no ability to [confirm that]. We don't even know exactly what part of the sequences is targeted by the assay because it is all proprietary."

She noted that her lab's situation is representative of the majority of hospital labs around the country. "These are not labs that have the ability to do lab-developed tests, that can add on a new target that is designed to detect the different variants," she said.

Butler-Wu said the variant situation felt to her very similar to the conditions her lab faced at the outset of the pandemic.

"I have a very big sense of déjà vu, where people like me are completely dependent on vendors to come up with the solutions, and then we can't get anything to validate it in our hands," she said. "It's exactly like almost a year ago when we were depending on companies to develop these tests and we would ask public health for samples to validate the assays and we couldn't get them."

Butler-Wu said she was also anticipating requests from public health officials for her lab to submit patient samples for sequencing as part of variant surveillance efforts. She said that while this kind of surveillance was useful and necessary, the lack of a streamlined and well-developed system for handling it presented additional challenges for labs.

"I have to go into my lab, which is already very short-staffed and under tremendous pressure and be like, oh, can you box these [samples] up for shipping," she said. "Because labs like ours don't have an integrated pathway where we are part of a network where sequencing just happens. I could be sitting on a whole bunch of variants here, and I would have no idea."

Beyond monitoring the impact of variants on test effectiveness, some labs are also beginning to think about how reimbursement might work for variant testing.

"If doctors want to order this, what would the reimbursement be, and who would pay for it?" asked Robert Boorstein, medical director at Brooklyn-based Lenco Diagnostic Laboratory.

He said that in his experience thus far, doctors are interested in variant information, but more out of curiosity than because such information could guide patient care.

Butler-Wu likewise noted that the different variants don't appear to call for different decisions regarding patient management, but she said that if, in the future, they do appear to be relevant for patient care, that could change the role of labs in variant testing.

"There is no targeted therapy like, say, a specific monoclonal antibody that has been designed to target a variant, but when that starts to happen, then it becomes a very different conversation," she said.

Burnham said that while in normal times winning reimbursement for new testing is a slow process, payors could be particularly incentivized to cover testing that allows doctors to better target monoclonal antibody treatment given the expense of these therapies.

Test regulation is also a potential question. For instance, SoRelle said, with regard to the PCR tests his lab is developing to detect different variants, that the decision on whether to take them through the regulatory process would depend in part on whether they were providing information that "gets reported in the patient's chart."

"At this time there isn't really any clinical action that can be made on it. It is more from an epidemiological standpoint," he said, adding that there isn't yet an established EUA path for variant testing.

SoRelle noted, though, that his lab has begun receiving questions from the hospital's infectious disease doctors, particularly about patients who are testing positive for the virus after being vaccinated.

"They are curious if the variants are playing a role in this at all," he said.