One year later, life in labs remains a juggling act

Heather Dawson, I hope you’re going to tell us that there’s a silver lining in that you haven’t been struggling with flu in Minneapolis at a time when you would have been.
Heather Dawson, VP of laboratory services, Allina Health, Minneapolis (now with Philips): No, we are not struggling with the flu. We’ve had so little of it that we had to check to make sure we were right.

Our positivity rate and testing volumes continue to drop. We’ve had a lot of antibody conversations but not a significant increase in testing. Dr. [Lauren] Anthony [system lab medical director] did a fantastic job helping our clinicians understand the different test types and the clinical utility or not of such an endeavor.

We’re about 60 percent vaccinated in the lab. We take a hit every time day two rolls around with a number of people who are out because the immune response can be intense.

Lauren Anthony, MD, system laboratory medical director, Allina Health, Minneapolis: Yes, we’ve been trying to educate our physicians about monitoring for vaccine response. There is no recommendation at this point, and no value of titer. So we are navigating that and trying to educate physicians on the difference between antibodies to the nucleocapsid and the spike protein. We perform the nucleocapsid protein antibody assay on Architect. The spike assay we would send out, and we deliberately chose a test with qualitative reporting because we don’t want to get into semiquantitative numbers. Numerical results aren’t actionable at this point and would just create confusion if we decided to bring different spike antibody tests in-house. There are multiple add-on studies to the vaccine trials in progress to define titers that would have clinical decision points after vaccination. But at this point we’re just trying to manage that.

There’s not a large demand for antibody testing, but there were tons of questions, and we needed to get the education out there about when to order which test and what would be the appropriate indications. We’ve leveraged our electronic medical record system to give them just-in-time education when they order a test. They’re getting pop-ups and alerts and having to answer order questions, and it’s deserved in this situation so we have clinical support to have all those interruptive alerts.

My biggest frustration is that in the media there is no distinction between testing people who are in a high-risk situation who could have an adverse outcome if they have undiagnosed COVID versus surveillance testing for people who just want to know or are planning to travel and aren’t going into a super high-risk situation like a surgery. There’s confusion about what the purpose is of the testing or who it’s appropriate for, and the various risk stratifications for the levels of testing—the least sensitive tests for the lowest-risk situations and the most sensitive tests for the highest-risk situations. We’re in a hospital where people with COVID and people with vulnerable conditions and people at high risk of bad outcomes are gathering. And we have to protect the integrity of the health care system, and it’s important to have the best test when they enter our environment. Now we have the capacity to say they must have those tests at Allina so we can be sure of their status when they enter our hospitals.

Johan Otter, can you comment on how things are going at Scripps?
Johan Otter, DPT, assistant VP, Scripps Health, San Diego: It’s been interesting being as close to the border as we are. One of our hospitals, in the South Bay area, until about 10 days ago was still running a more than 30 percent positivity rate. Our ICUs last week were at 118 percent, and you wonder how that’s possible. It’s because we open other beds and get them temporary licenses as ICUs.

From a testing perspective, we report twice a week and we can see what’s going to happen next. When we see a high outpatient positivity rate come through, we know it’s going to hit the hospitals the next week, and then the ICUs. But in the last week and a half we dropped. We’re down at seven percent overall now. Our outpatient is way down. We send about 120 positive samples for sequencing to the Scripps Research Institute weekly. From our side, we’ve not seen variants yet, but we have them in San Diego. We’ve had a couple of people who tested positive after both vaccine shots, and that makes the providers think it’s the variant. We have to do a lot of education daily that you can still get COVID even after full vaccination.

What has it been like trying to get lab staff vaccinated?
Dr. Otter (Scripps): We couldn’t line up fast enough. I don’t know of even one employee who has refused the vaccine at this point.

Joe Baker, let’s hear from you.
Joseph Baker, VP of laboratory, Baylor Scott & White Health, Dallas: As a system we’re at about 60 percent having been vaccinated, with about 82 percent of our physicians having been vaccinated.

Our main problem as a system is on the staffing side. We’re struggling to find staffing—phlebotomists and technologists. We’ve had to use agency staffing for the first time on the phlebotomy side. We’re looking into market assessments for MTs, MLTs, and phlebotomists.

We’re losing staff to agencies; they’re going out to do traveling so they can get better hours, better pay, whatever it may be. Some folks are just leaving the profession. Some are retiring probably a little sooner than planned. We’re investigating if we need to look at retention bonuses in key sites.

Retention bonuses have been used by many of the Compass Group members in the past few years. We have a fundamental shortage that the pandemic is exacerbating.
Joe Baker (Baylor Scott & White): It is. We worry about the health of our team because without them, nothing else functions. Team members are getting burned out and there’s only so much we can do to recognize them and try to lessen the stress, but we’re ever mindful of that.

On the testing side, we’re averaging about 2,500 tests a day for our system. Five weeks ago, our positivity rate was about 28 percent, and now we’re at about 15 and a half percent.

What is the antibody test demand like?
Peter Dysert, MD, chief, Department of Pathology, Baylor Scott & White Health: Not much test demand, but we have a lot of interest in using it in some of what we’ll call our strategic patient populations, our transplant and cancer patients, to study their response to vaccine, to develop clinical protocols that line up with those particular patients as we follow them after they’re vaccinated. We’re in the process of finalizing research protocols mainly in that domain. We have a lab-developed antibody test that has nucleocapsid; it also has total spike S1, S2, and RBD. We’re proposing to follow those vaccinated immunocompromised patients. That’s where the major interest is now. On the clinical side, there isn’t much demand for antibody testing.

We’re sending about 20 samples a day out of our facility, randomly chosen, to our state lab for sequencing, for surveillance purposes. We’ve had a couple of specific requests for patients who clinically look like they might have become reinfected, or we had a test result called into question.

We have two assays in-house that have the spike antibody in them—one is an LDT using Thermo Fisher and the other is the BioFire assay. So we have the ability, like some of you, to look for a spike dropout as an indirect assessment for those variants. We’ve been retesting the questionable samples on our Thermo Fisher LDT.

A question for the group: Are your organizations considering, or do you think they will consider, vaccination status as a deferral for requiring RT-PCR as part of preprocedural testing, and, second, vaccination status allowing the organization to get back to face-to-face meetings?

Stan Schofield (MaineHealth): Face-to-face meetings are still not allowed even with vaccination, and there is no procedural exclusion of PCR testing because you’ve been vaccinated. So there is no immunity passport today based on COVID vaccination.

Dr. Dysert (Baylor Scott & White): We’re in the same position.

We would also like to figure out a way to get a version of the South African variant that we could add to that multi-target assay and just follow the individual vaccine response relative to what we can quantitate or semiquantitate. The target we have now was built against the original and dominant strain of COVID. We’re interested in following a group of individual patients to see, given the same vaccine, if their relative coverage of the South African variant is the same or significantly different. Does anybody know a vendor that could provide such a target?

Stan Schofield (MaineHealth): The sources and availability of information from South Africa are limited. The country is shut down and almost incapable of functioning because of this. It’s going to be a while before we get any real scientific and commercial exchange, to start building these kinds of products. I don’t think anybody has it except maybe the World Health Organization and a couple of other highly esoteric groups at the moment. The CDC probably has it, but I don’t know that they’re going to share it.

If no one else has a different answer to Peter’s question, I’ll move on and ask Mike Quigley at Scripps to comment on any of our topics today.
Michael Quigley, MD, medical director, Scripps Health core laboratory, San Diego: My comment is related to the variants. The populations most of interest are likely to be those that have developed COVID after vaccination, those who have reinfections, and the chronically infected, and those are the ones to watch for the new variants. Do you do searches of your EMRs to try to identify those patients? Is there a plan or program in your public health system to look at those?

Dr. Crawford (Northwell): The current New York State Department of Health approach is for hospital-based laboratories around the state to send positive PCR samples of Ct counts less than 30, and that’s not too far off from the CDC’s request to send positive samples with Ct counts less than 28.

There’s an interesting wrinkle to that because if your workhorse machine is the TMA Hologic Panther, it doesn’t generate a Ct count. The GenMark cartridge, which is one of our two platforms for in-hospital near-patient testing, also buries its data deep inside its electronic brain. So it’s only the Cepheid cartridge that spits out a Ct test, but that is at least satisfying our need to send off samples to the state. That doesn’t constitute targeted populations. So in response to my question in a New York State call earlier today about what we are looking for—is surveillance good enough?—at least for today, the goal is to identify variant entry into the state early, so it can be tracer confined.

That makes me uneasy because we proved to ourselves a year ago that the virus may already have outpaced our testing strategies. That’s why John Tomaszewski [MD, University of Buffalo] and I are riffing on the possibility of hyper agile multiplex PCR to identify S dropout and/or known sequence variants. You want to design your hyper agile LDTs to have clinically licensed lab surveillance done by labs like ours, uplinking to the sequence competent public-health–oriented labs.

That’s the conversation we’ll be having in a state call later today—whether we could bring back to the state as a regional response a hyper agile hybrid of surveillance non-CLIA or just public health, or some combination of sequencing with clinically competent labs out in the field, targeting patients. But the corollary question is, should we be targeting cases of interest? The danger of skewing sequencing prioritization of “patients of interest”—however accurately or not—is that the public health data is then skewed. I’m not smart enough yet to get my head around that. But if there’s either lab data or clinical data to identify patients of interest, for variant sequences, then there may be medical reason for obtaining sequence information. To date there is insufficient evidence for identifying SARS-CoV-2 variants on the basis of proxy patient data.

I’ll be interested to see how this develops in the state. Linda Mirkes, would you like to comment?
Linda Mirkes, MBA, MT(ASCP), assistant VP, core laboratory and integration, Atrium Health, Charlotte, NC: Our experience is similar to that of others in that we were seeing a demand for up to 4,000 tests per day and we’re down now to closer to 2,000. We’re able to perform 1,500 tests per day in-house.

Our positivity rate was in the mid- to high 20s, and we’re now down to around 12 percent. Staffing continues to be a challenge in Charlotte—phlebotomy staff and techs are in short supply. We’re exploring bringing in resources from other countries.

Judy Lyzak, the last time we spoke you were worried about supply chain. How are things faring there?
Judy Lyzak, MD, MBA, VP of medical affairs, Alverno Laboratories, Indiana and Illinois: Things have settled down nicely. We’re doing well with our ID Now kits. We have them moved out into all of our family practice network offices, and they now procure their own kits independent of the laboratory.

I am one of the vaccine ambassadors for the laboratory. It’s a remarkably clinical role for a pathologist to be in. I get daily emails from lab staff with questions or concerns. It’s concerning to me that there is still residual politicization of vaccination and concerns expressed around that, some of which are more reasonable, such as those of our patient-facing phlebotomists, who are also often of reproductive age. They have a lot of concerns. Misinformation circulated on social media about impact on fertility. We’re trying to talk staff members through that—what are the realistic concerns about fertility, about breastfeeding. They always have an ear and we can connect them with our ID experts so that they have multiple sources of opinion, and we can help them make an informed decision. Even if they decide against vaccination temporarily, we’re giving them as much information as they need to make a good decision.

John Waugh, tell me about your experience with getting adequate vaccinations for lab staff and lab staff’s attitude toward getting vaccinated.
John Waugh, MS, MT(ASCP), system VP, pathology and laboratory medicine, Henry Ford Health System, Detroit: We’ve had a good response to the vaccine. We had reluctance initially and had to address it organizationally.

Our testing is down substantially. We’re probably under 1,500 tests per day in the past several days. And there is no draw for antibody testing at this time.

Do you think the variants will be the next big story?
John Waugh (Henry Ford): We’re living in an interesting time, aren’t we? Every week there’s some new thing out there. I’ve been telling our people worry is a growth business. With the prevalence of the U.K. origin, the spike dropout in those areas, I think there’s concern. And I’m not sure that people are accepting of the fact that the current testing and the current vaccines will be unaffected by these mutations. That’s just my gut. They’ve heard a lot of things that have turned around in the last year.