February 2021—Variants and vaccines were in the news when Compass Group members spoke with CAP TODAY publisher Bob McGonnagle for the first time in the new year, on Jan. 5. “This is something we all need to stay close to,” Julie Hess, of AdventHealth, said of the variants. “We need to know if it’s going to impact our ability to detect.”
It was the fifth Compass Group roundtable McGonnagle led since August last year (see CAP TODAY: September, November, December 2020 and January 2021 issues).
With McGonnagle and Hess on the Jan. 5 call were Dwayne Breining, MD, and James Crawford, MD, PhD, Northwell; John Waugh, MS, MT(ASCP), Henry Ford; Stan Schofield, MaineHealth; Gregory Sossaman, MD, Ochsner; Peter Dysert, MD, Baylor Scott & White; Steven Carroll, MD, PhD, Medical University of South Carolina; Heather Dawson, Allina; Janet Durham, MD, ACL; Daniel Ingemansen, Sanford Health; Ericka Olgaard, DO, MBA, University of Arkansas for Medical Sciences; Sterling Bennett, MD, MS, Intermountain; and Judy Lyzak, MD, MBA, Alverno.
The Compass Group is an organization of not-for-profit IDN system lab leaders who collaborate to identify and share best practices and strategies. Here is what they said.
Dwayne Breining, what impact has the variant had on your laboratory and your system?
Dwayne Breining, MD, executive director, Northwell Health Laboratories, New York: We started working with the New York State Department of Health to refer positive samples to them for increased surveillance. We just heard that the first cases in New York were identified in the Saratoga Springs area. I’ll be surprised if we don’t find more of it in the New York City area knowing that travel has been essentially open. In the U.K. roughly five percent of cases are sequenced routinely for new strains. In the U.S. we’re probably sequencing between 0.1 percent and 0.01 percent on a regular basis. Now everybody is stepping it up because of the need.
We’re running just about every commercial assay out there, portable cartridge-based tests and high-throughput tests, on Hologic, Roche, and other analyzers. We received confirmation from everyone that they don’t think there’s any issues and they verified that these tests will detect the U.K. B.1.1.7 variant.
We are not running any specific tests ourselves, although we might have stumbled across one in one of our laboratory-developed tests, which we haven’t deployed. It looks for a spike protein epitope that’s right in the middle of one of the mutations in this variant. So we’re toying with the idea of maybe using the absence of that detection in combination with another positive test to do our own surveillance. But it is not something we’re going to do now because other than the public health need, there’s not going to be any additional clinical management instruction based on this variant.
Now we’re hearing about the South African variant, which has more and different mutations. They’re unlike the U.K. variant for which the expectation is that the vaccines and the tests will be just as effective. For the South African variant, there is concern that there are more accumulated mutations in those spots, and that potentially impacts detection and vaccine effectiveness.
John Waugh, are you confident that we do know that the SARS-CoV-2 tests are going to be efficacious in detecting what I assume will be an ever-increasing percentage of variant cases?
John Waugh, MS, MT(ASCP), system VP, pathology and laboratory medicine, Henry Ford Health System, Detroit: This is an area of interest and concern to all of us and one we feel we needed to get out in front of because we will get questions from clinicians who are curious about whether our test platforms and the systems we’re using are competent and reliable enough to pick up the variants as they appear.
We asked all of the suppliers we’re using for statements on their assurances that the test platforms will be reliable and won’t be fooled by these variants. We’re receiving those now and would like to get that messaging in front of clinicians to give them a level of confidence before they begin to ask the questions. Right now they’re just wondering. But we’ll put it out there as a formal laboratory update along with other guidance.
Has anyone heard anything from laboratories in the United Kingdom about the efficacy of their tests against these variants? Stan Schofield, have you heard anything yet? And do you think labs will be able to cope with these variants or do we have to wait and see?
Stan Schofield, president, NorDx, and senior VP, MaineHealth: Not a word yet, and I think we will have to wait and see. And we’ll have to see if the CDC will come out with probes and primers—most of us standardize on the CDC’s technology as the reference point—and if they can come up with a variant where the S drops out at a late cycle, at 60 and 70 cycles. That’s an awful lot of ifs. If the CDC comes out with a new package of standards, controls, and calibrators, that will help drive the adoption and detection process for many of us.
Ericka Olgaard, DO, MBA, laboratory medical director, Department of Pathology, University of Arkansas for Medical Sciences College of Medicine: I have a little more information about the variants that might be helpful. The B.1.1.7 that we’re seeing from the U.K. is asparagine replaced for a tyrosine at position 501. As was said, that’s not affecting any of the assays. I think Thermo Fisher has one for the spike protein. However, Thermo Fisher users are finding there is a co-mutation that is seen with some of the B.1.1.7 variants. That is a codeletion at codon 69/70 and it is causing some drop-out of the spike protein in those assays. I think it’s a three-target assay so they’re still seeing the other two targets come through and they’re not worried about it.
Greg Sossaman, what kind of concerns have you heard around the vaccines and their efficacy against these variants?
Gregory Sossaman, MD, system chairman and service line leader, pathology and laboratory medicine, Ochsner Health, New Orleans: We haven’t yet had any specific questions related to the vaccine and variant. We just started yesterday with communication about vaccinating patients and the response was huge. We’re getting questions from our infectious disease colleagues, with whom we meet regularly, about antibody testing post-vaccination, but no significant questions around variants yet.
Pete Dysert, would you like to tell us what’s going on in Dallas now?
Peter Dysert, MD, chief, Department of Pathology, Baylor Scott & White Health: We were asked, because we have an LDT that contains spike protein, whether the vaccines will cause a false-positive. Because it is an LDT and we own the performance of that assay, we have a QA project in which we’re following our vaccine recipients to see if anybody turns up positive as a result of the Moderna or Pfizer vaccine. About the role of variants impacting our assays, again we had one LDT with spike in it and we’re depending there on the supplier of those reagents to keep us informed.
I have to believe variants are also occurring in the other portions of the virus and they’re not being reported or followed carefully because they’re basically not linked to transmissibility. So it’s entirely possible that at some point we might even see mutations in those thought to be highly conserved areas that could impact the performance of our assays and not be aware of it unless we are sequencing the virus.
The other project we’re going back and forth on—whether a research project or a quality assurance project—has to do with profiling the immune response on the vaccine. Given the number of logistical steps involved, the way the vaccine is reconstituted, the issue of five versus seven doses from a single container on the Pfizer side has left a lot of unanswered questions. So we started recruiting volunteers whom we’ve been profiling before and after dose one and we’ll follow them after dose two—in a QA-like fashion. There’s a larger-scale interest on behalf of many people to use their antibody response as a surrogate for immunity.
Having independent third-party entities validate the immune response and the antibody profile might help encourage people who are hesitant to get vaccinated. In addition, given the complexity of storage requirements, think of this as quality assurance on the logistical and distribution process once the vaccine leaves the manufacturer. It would be a way of doing a final clinical outcomes quality check on the distribution process if the way it’s being handled in your facility was in some way compromising those doses. So we think it addresses a number of issues and see it potentially as a QA project. But also I think it has public interest from a research perspective to know what happens because, as you look at the data submitted by both vendors, it’s vague between the first and second dose about the antibody response. And they don’t go into a great deal of granularity on profiling the immune response over weekly intervals, for example.
Dr. Sossaman (Ochsner): I have looked superficially at the data. They measured antibody response against the spike protein, and they also did real neutralization titers in those in the Pfizer study; I’m not sure about the Moderna vaccine. But I find the argument about splitting the doses, or only using one dose at least, not supported by the current data because if you look at the time interval when they showed antibody response, at least at Pfizer, you don’t have much of an antibody response over the placebos until day 28. There may be some T-cell mediated immunity generated there initially, but it looks like there’s not much of a response you can count on unless you get the two doses and until after that second dose, about day 28.
Steve Carroll, would you like to jump in here with comments of your own?
Steven Carroll, MD, PhD, chair, Department of Pathology and Laboratory Medicine, Medical University of South Carolina: In terms of vaccinations we’ve been looking at it more from a practical perspective. I’m worried in particular about protecting our laboratory staff who are handling the virus. One of the things that has surprised me is even though we’ve had the vaccine available for a while, we still have not seen as many people vaccinated in some of our hospitals as we would like. I’m concerned we’re seeing vaccine hesitancy, which may place our workers at risk. In our Charleston division, 62 percent of health care workers have been vaccinated. But the worst infection rate is in our Florence and Lancaster hospitals and there only 40 percent of personnel have chosen to be vaccinated so far. That has been a big concern for us moving forward. It could have a major impact on some of our hospital operations.
Will you employ mandates for health care workers to be vaccinated?
Dr. Carroll (MUSC): We’ve had a lot of discussion about that, but the concern is that since this is under an EUA, making it mandatory is going to be problematic.
Heather Dawson, what’s going on in your neck of the winter woods?
Heather Dawson, VP of laboratory services, Allina Health, Minneapolis: The volumes fell off a cliff. The positivity rate dropped to where it looked more like it was in May, which is wild because it was so high and volumes were so high in late November and early December.
There have been geographic pockets of acceptance for the vaccine. Close to our metro hospitals we are vaccinating at high rates. In some of the community hospital areas, acceptance is a mixed bag. Our phlebotomists were in the first round and a high percent of them took the vaccine.
We’re communicating with our vendors about the variant.
Julie Hess, does the report from Minnesota sound like a dream? What’s going on in Orlando?
Julie Hess, executive director, laboratory services, AdventHealth, Orlando, Fla.: We’re up to 25 percent positivity just in the past few days and volume has doubled what we had in early December. As far as the supply chain goes, we’re getting enough for the testing demand.
We’ve been working with our vendors the past few days to understand the variant. I have about a dozen methods across AdventHealth at all of our sites, and only one of our vendors includes the S protein. We were told by that vendor that primers included in the assay are outside of the 69/70 region impacted by variant B.1.1.7. Because the target of the S gene primer is outside of the S gene mutation region, we should expect to see alignment and amplification of the S gene. So we expect no change in detection from the U.K. strain, but this is something we all need to stay close to. We need to know if it’s going to impact our ability to detect.
Someone earlier mentioned Hologic—in our documentation, we showed that the Hologic test is detecting the ORF1 gene. With the U.K. variant being in the spike protein, we didn’t think it would be a problem.
There has been some vaccine hesitancy. Our physicians had a high adoption rate, and most of our professionals also have a pretty high adoption rate. But in some of the populations that need it the most, there is more hesitancy. Until it is fully FDA approved, we’re not comfortable mandating that health care professionals get it.
Janet Durham, what’s going on in Wisconsin and Illinois?
Janet Durham, MD, medical director, Wisconsin operations, ACL Laboratories, and president, Great Lakes Pathologists, West Allis, Wis.: We are seeing about five percent increase from last week in our testing volume, and our positivity rate is about 14.7 percent. This is systemwide, Wisconsin and Illinois. We have a handle on supplies now. We’ve brought everything in-house; we previously had been outsourcing.
There was some hesitancy here locally about vaccination, but this is our way out so we’re hoping we can promote it.
What, if any, foothold has rapid antigen testing gained within the ACL system? If it has, are you more comfortable now with how it fits into an overall testing strategy?
Dr. Durham (ACL Laboratories): We’re using rapid antigen for employee health—the state provided BinaxNow. We’re using that for some of the pre-monoclonal antibody testing, too, because they wanted a fast answer. Yes, I’m a little more comfortable—as comfortable as you can be.
Dan Ingemansen, we hear a lot about South Dakota—up, down, doing well, doing poorly. What’s the latest?
Daniel Ingemansen, senior director, laboratory, Sanford Health, Sioux Falls, SD: The positivity rate for our COVID testing is averaging around 18 to 20 percent, so we’ve recovered from the 30 percent I reported a month ago. We’re averaging 1,000 to 1,500 PCR-based tests per day, so we’re down significantly and have reached the point where it almost feels like a routine test. We have capacity to do about 4,000 tests.
As of yesterday we had deployed about 8,000 vaccinations, 3,000 of which were to our rural communities.
What, if any, niche or role is antigen testing playing in your system?
Daniel Ingemansen (Sanford Health): We have the BinaxNow cards deployed to more of our rural hospital and clinical systems. We’re using it in the outpatient world. We worked with several of the Compass Group members on the LumiraDx product, and we rolled that out in one of our markets before Christmas. We’ll have it available at 50 to 60 locations by the end of January.
Julie Hess, it appears you have a question about using antigen testing for qualification in emergency departments.
Julie Hess (AdventHealth): We are primarily using the Roche Liats in our ED location and they expect the demand to go up because of the positivity in our area. We’re not sure we would be able to support that much more volume based on our weekly allocation. I was asked if we could use antigen testing and that concerned me because we have seen what we suspect are false-positives with the antigen. What are others doing?
Judy Lyzak, MD, MBA, VP of medical affairs, Alverno Laboratories, Indiana and Illinois: We’re using the ID Now as our rapid screen for eligibility. But if that supply chain fails we would fall back to a rapid antigen.
Judy Lyzak, has the ID Now supply improved from the problem you described a month ago?
Dr. Lyzak (Alverno): It has greatly improved. We’re now facing unfortunate news that the supply chain might be compromised for some of our high-throughput analyzers at our central facility. For a long time we had no problems with that supply chain. Now we’re being told it’s day to day on delivery for Abbott m2000s and Alinity m.
Now that we have sufficient ID Now kits, we’re discussing a scenario in which if we had insufficient reagent to do high-throughput testing at the core lab, we could push some of that back to hospital-based testing with the ID Now and then the rapid antigen tests as the backup. One of the lessons this pandemic has taught us is to try to anticipate bad scenarios and plan for them as best we can given the tools we have in hand.
Daniel Ingemansen (Sanford Health): We’ve experienced a shortage of core tips for sample handling. And for the Abbott Alinitys we’ve experienced issues with the lysis buffer. The challenge for these high-throughput manufacturers is they all build their automation using core products from Hamilton or Tecan, and they have their set supply in inventory. Now they’ve depleted it and are fighting over the same raw materials. Dr. Lyzak, can you add to that or bring context to what we’re seeing?
Dr. Lyzak (Alverno): That sounds as reasonable as any other explanation I’ve heard. It makes sense. It’s one of our lessons learned—a failure to prepare or failure of imagination. It’s stunning to me that we’re having the same supply chain problems today that we had last February.
Would anyone like to make predictions around what might happen in this pandemic fight with a new administration in Washington?
James Crawford, MD, PhD, professor and chair, Department of Pathology and Laboratory Medicine, and senior VP of laboratory services, Northwell Health, New York: There is going to be respect for science, which has not been a strong suit of the past year, and I’m hoping that out of that will come communication with a broader community of people who can lend expertise from their respective perspectives. But I remain concerned about the ability of the laboratory to be properly voiced at the national level. Based on reporting from around the Compass Group and the Association of Pathology Chairs, there’s reasonable evidence that at the state level, laboratories have had good access to the halls of power. But it’s an insufficient structure because it doesn’t bring the manufacturers into the conversation. That’s a maypole that is not well connected laterally. And it doesn’t connect the 50 stripes on the maypole, which are the 50 states. My deep concern is that we’re going to have sloshing around in 2021 the way we did in 2020.
To me the optimistic upside is that the communities we have—and my national communities are the Compass Group and APC—are fantastic communities. We should lean into them as much as we possibly can because we’re going to need each other.
Sterling Bennett, can you, as president of the Compass Group, comment, too, on the future under a new administration?
Sterling Bennett, MD, MS, medical director, Intermountain Healthcare central laboratory, Salt Lake City: I echo Jim Crawford’s comments. I think we’ll see what I consider to be better role modeling out of the incoming administration than we saw out of the previous administration. We’ll see a higher reliance on and more credibility given to the science behind it. Some of it may not be attributable to the new administration, but it will happen anyway. We’ll see better coordination and communication at the state and federal level.
Stan Schofield, look in your crystal ball for the balance of 2021 on this same topic.
Stan Schofield (MaineHealth): This past year has been a disaster politically, scientifically, medically, and healthwise for the communities we serve, and it can only get better. I’m looking forward to better communication and probably more cooperation between the state and the feds, and the feds are going to try to take more of a leadership role. The feds dumped everything on the states in the past year and said, “Figure it out.” The states figured it out 50 different ways, and some do it well and others do it less well. Coordination and symmetry at the federal level will go a long way to improving things.
Ten to 20 years from now, historians will look at the U.S. federal government and the state response as being just short of disastrous. We’re picking ourselves up by our own bootstraps and having to recover and learn from it. I’m hoping the new administration will put more structure in place and provide the states with more guidance and leadership.