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Calm before spring storm? Compass on COVID

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GROUP’S MEMBERS CONSIDER VARIANT SIGNIFICANCE, STRATEGY

April 2021—Test volumes and positivity rates were down and vaccinations and interest in variants were up on March 2 when Compass Group laboratory leaders met with CAP TODAY publisher Bob McGonnagle for another in a series of calls about SARS-CoV-2.

Also in the discussion: antigen and serologic testing, school and sports team testing, and testing for travel. Pre-procedure testing, too: “That’s a new struggle in trying to figure out how we can keep everybody happy,” said Janet Durham, MD, of ACL Laboratories and president, Great Lakes Pathologists, West Allis, Wis.

With McGonnagle and Dr. Durham were Judith Lyzak, MD, MBA, Alverno; Modena Henderson, MHA, MT(ASCP), Atrium Health; Dan Ingemansen, Sanford; James Crawford, MD, PhD, Northwell; Michael Quigley, MD, Scripps; Walter Henricks, MD, Cleveland Clinic; Sterling Bennett, MD, MS, Intermountain; Tony Bull, AdventHealth; Clark Day, Indiana University Health; Steven Carroll, MD, PhD, Medical University of South Carolina; Mike Black, MBA, MT(ASCP), DLM, Avera; Lauren Anthony, MD, Allina; Diana Kremitske, MS, MHA, MT(ASCP), Geisinger; and Stan Schofield, MaineHealth.

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’s what they shared in March.

The first thing I will ask for is a reaction to the title for today’s conversation: “COVID’s March Anniversary—No Longer a Wolf but Not Yet a Lamb.” How apt is that title at this time?
Judy Lyzak, MD, MBA, VP of medical affairs, Alverno Laboratories, Indiana and Illinois: The decline in positivity rates, hospitalizations, and deaths is encouraging. And yet a note of caution and a bit of prudence would be wise given the warnings we’re hearing from the CDC director about the plateau in the decline, the small bump they have seen, and the worrying circulating variants.

In my organization we are concerned about a surge in April and spring break. That age group has not been vaccinated nor are they eligible to be vaccinated.

Dr. Lyzak

What’s going on now in your lab, Judy, as regards testing and positivity rates?
Dr. Lyzak (Alverno): We have capacity to do 4,000 to 5,000 tests a day and our volume now is about 1,300 a day. We’ve been fortunate to see a decline in the positivity rate, and we separate our preprocedure asymptomatic population from our symptomatic population. Our symptomatic population on average across our 26 hospitals is down to about seven percent to a high of 10 percent, which is great compared with what we saw in the fall and winter. Our asymptomatic rate on March 1 was 0.5 percent. There was a collective shout of joy from all of our ID physicians.

Henderson

Modena Henderson, how do you see the current environment in your laboratories across Atrium Health?
Modena Henderson, MHA, MT(ASCP), VP of laboratory services, Atrium Health, Charlotte, NC: Thankfully, we’re seeing a decrease in test volumes and in positivity rates across the communities we are privileged to serve. At this time we’re optimistic that the more than 250,000 doses of the vaccine we have administered at our many vaccination events are having a great impact, and we continue to monitor for a possible surge in the March-April time frame because of the variants.

Dan Ingemansen, have your positivity rates and test demand continued to fall?
Dan Ingemansen, senior director, laboratory, Sanford Health, Sioux Falls, SD: Our positivity rate across our system has decreased. We’re running about 11 percent now. We’ve continued to see volumes sharply decrease since Thanksgiving, but they remain at about 1,000 tests a day in our health system.

Jim Crawford, are you getting a lot of demand for variant testing, and are you seeking answers to do that?
James Crawford, MD, PhD, professor and chair, Department of Pathology and Laboratory Medicine, and senior VP of laboratory services, Northwell Health, New York: Demand is an interesting word because demand suggests it’s coming from the providers. I’ve spent a good portion of the past month trying to understand what the New York State region and New York City approach and strategies are for variant testing. And my brief version after countless conversations is that New York City is working with New York City Health & Hospitals for coordination and—through the NYC Economic Development Corporation—with the Manhattan-based Pandemic Response Lab, PRL, to provide public health data for detecting variants. In turn, the state public health laboratory, the Wads­worth Center, has achieved its target of 600 genomes sequenced per week based on hospital and other laboratories around the state sending them samples with Ct counts of less than 30. The sampling the state does is on the basis of geographic diversity using zip codes as a guide.

The remainder of variant testing in New York State is through the university community, which is providing key regional information because a lot of variants are identified by such university-based laboratories as Columbia and Cornell. But what I’m going to pressure test in the 4 PM meeting of the New York State SARS-CoV-2 Testing Consortium, which I moderate, is the question: Is it true that the university-based variant testing is funded either by repurposed or other extramural funding from NIH and/or commitments from institutional funding?

Every time I’ve asked the question so far, the answer is yes, the university is funding it themselves or repurposing other research funding. Yet I can’t help but conclude from publicly available information that a substantial portion of the information we are getting regionally as well as nationally is from university labs.

So the question I remain with, four weeks from our last conversation, is how does this roll up to a national strategy? Is it true that every state is taking its own approach? California with UCSD, Michigan with Michigan State and the University of Michigan, New York with the Wads­worth Center laboratory, New York City with PRL, and the university labs are operating independently but staying in touch through the reporting systems for their state? And how many other 47 different versions do we have of variant reporting partially subsumed by the CDC’s feeding of samples to LabCorp?

This is reminiscent of what we were going through a year ago when we didn’t have a good broad-based strategy for the labs. Mike Quigley, what do you think about this variant situation as it relates to Scripps?
Michael Quigley, MD, medical director, Scripps Health core laboratory, San Diego: I agree completely about the lack of a federal, central strategy for variant testing. So basically it’s the same story as a year ago. It’s unfortunate, but it’s something we have to live with and have to figure out locally. In San Diego, the county is working with health care systems and sequencing partners. The goal for the region is to test 20 percent of the positives for variants; overall they are running about 17 percent now.

Walter Henricks, MD, vice chair, Pathology and Laboratory Medicine Institute, and laboratory director, Cleveland Clinic: Our state health department is aiming to partner with us, with The Ohio State University, and with two other labs to obtain sequencing information. And we have done some sequencing at Cleveland Clinic on a research basis and we’re looking to expand that out, for public health purposes, not for patient reporting.

To my knowledge, no one is reporting for clinical decision-making, nor have we had significant demand for variant sequencing for clinical decision-making. We’ve received questions about whether our nonsequencing tests will detect cases with the variant, and they do. We’ve also been asked, can you tell us if a given patient has the variant? The answer is not at this time.

Dr. Henricks

Do you, like others, lament the fact that there doesn’t seem to be a national coordinated strategy on the variant testing?
Dr. Henricks (Cleveland Clinic): If we knew it was tied to an immediate patient care need, I’d be more concerned. We do need tests, and variant testing is important for public health and research purposes. I don’t know that a national strategy by itself is going to put tests that can identify the variants quickly into clinical labs in a way that is relevant for patient care decisions. There are other reasons a national testing strategy would be helpful, as have been described.

Sterling Bennett, let’s hear from you on this topic.
Sterling Bennett, MD, MS, medical director, Intermountain Healthcare central laboratory, Salt Lake City: Things are better here, and the Intermountain experience is the same as that of the others. With variant testing we’re seeing the same pattern we’ve seen with many other things COVID-related: We wouldn’t know yet what to do with the results even if we had them.

Our state has told us that it has a shortage of pipette tips for its sequencing methods and it has turned around a lot fewer genomes than we anticipated. We know there is a variety of variants in the state, but we don’t have any real sense of frequency. With the rates falling, we’re uncertain about the significance.

So within your system, the infectious disease physicians and other clinicians are not yet a source of demand for test results on patients for the SARS-CoV-2 variants?
Dr. Bennett (Intermountain): They would love to see testing for variants, but they’re not beating down our doors and demanding that we have the testing available. They’re not going to bat with our system executives saying we must have high-throughput sequencing capabilities so we know what’s going on in terms of variants. We’re not seeing that level of demand, but there is interest.

We’re exploring Thermo Fisher’s primers for some of the mutations and trying to get that in and at least take a look to see if it provides useful information to us about the number of variants. The reason we’re looking at a PCR option is that we don’t think we’re going to get the timeliness or the number of sequencing tests done by the state that we wish we could.

Bull

Tony Bull, what is your situation in Florida?
Tony Bull, executive director, AdventHealth, Orlando, Fla.: We’re seeing an easing of demand for testing and an easing of the number of hospitalizations. We’re proceeding cautiously in light of the variants in Florida and spring break visitors.

We’re sharing samples with some manufacturers to help make sure tests are accurate for variants. We’re also working with the Florida Department of Health and providing them with specimens. There’s a focus with the state on patients who are PCR positive 14 days after a second vaccine. We hope to understand if these are variants or patients for whom the vaccine was not effective.

Clark Day, what’s going on at Indianapolis, particularly with regard to variant testing?
Clark Day, VP of system laboratory services, Indiana University Health: We were asked to incorporate variant testing into the positives we might detect in the course of testing for the NCAA tournament of 68 teams. We are partnering with a separate entity to perform testing for variants on any positives we might detect over the course of the tournament.

Our weekly testing volume has been down lately by as much as 20 to 30 percent. The capacity we gained is allowing us to perform the testing for this national tournament without affecting care for our own patients.

Dr. Carroll

Steven Carroll, what’s going on in South Carolina?
Steven Carroll, MD, PhD, chair, Department of Pathology and Laboratory Medicine, Medical University of South Carolina: We’re seeing declines in viral infection rates and testing. We started sequencing genomes; so far we’ve identified only the South African variant, but it’s something we’re devoting resources to because of the public health implications. We’ve been working in partnership with our public health lab and reporting the data to them because there is worry that we’re going to have some of the more rapidly spreading variants put the brakes on our decline.

There is also discussion, and it’s come up several times, about whether we need to look at wastewater out of some communities as a means of monitoring. We have not gone there yet; we’ve been mainly looking at individual genomes.

We have individuals who have been vaccinated but still become infected with COVID, so we’re sequencing their variants to see if known mutations or new mutations might be accounting for why the vaccine was not effective in them.

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