Animal Reservoirs, Immunocompromised Hosts: COVID Dangers Ahead

Animal Reservoirs and Immunocompromised Hosts: COVID Dangers on the Road Ahead

; Abraham Verghese, MD; Benjamin Pinsky, MD, PhD

Disclosures

April 21, 2022

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This transcript has been edited for clarity.

Abraham Verghese, MD: Welcome to another episode of Medicine and the Machine. It's a great pleasure to be here with my co-host, Eric Topol. Today we have as our guest someone I've looked forward to listening to every Wednesday morning without fail when he gives the COVID update to us at Stanford. He's been a linchpin in our abilities to respond to this epidemic locally, in Stanford, and also all over California.

Our guest is Benjamin Pinsky. He's an associate professor at Stanford, the medical director of the clinical virology lab for Stanford Health Care and Stanford Children's Health, and the medical co-director for Point of Care Testing. He got his MD/PhD at the University of Washington, and he was at the Fred Hutchinson Cancer Research Center in Seattle before coming to Stanford, where he trained in pathology and molecular pathology. His focus of interest is molecular infectious disease testing, and he has done a lot of great work on dengue and Zika, among all kinds of other infectious diseases. I can't think of a person better situated to address COVID testing. Welcome to the program, Ben.

When did you first hear about COVID? How did you get your head around it and anticipate what was coming?

Benjamin Pinsky, MD, PhD: First, thank you so much for having me on the program. This is a great honor to be able to share my story.

Initially, like most other folks in the world, I saw the outbreak occurring in China in early 2020 with the news reports on television. As you mentioned, I'd had experience with the Zika outbreak, which was not so concerning for the United States. And as a resident, I had been involved in our laboratory response to the 2009 H1N1 pandemic, which was almost as concerning as the COVID pandemic was initially but turned out to be not as severe. At that point, I saw that testing was very important in all those different outbreaks. And I realized quite early on with COVID that we were going to need testing and we were going to need it rapidly.

Verghese: I remember how cumbersome it was to get the Centers for Disease Control and Prevention (CDC) to do the tests because they were the only ones approved to test. But meanwhile, if I recall, you began to conduct testing here and then marshal resources from all over Stanford and do the tests for all of Northern California. Can you talk about those early pioneering days?

Pinsky: Those early days were quite challenging and exciting at the same time. I saw reports about this novel coronavirus on the news and was concerned that this was going to be coming to the United States sooner rather than later. The sequences from the virus were published very early on in January 2020, and then a number of groups published, on the World Health Organization (WHO) website, primer and probe sets for detection of the novel coronavirus. That, I believe, was in maybe the second week of January. Shortly thereafter, my laboratory — I have a small research laboratory that does translational infectious disease diagnostics development — ordered the primers and probes, got those into the lab, and started validating the test at that point with synthesized nucleic acids.

We couldn't get our hands on actual clinical specimens at that time. We had a test based on the test from Christian Drosten's group in Germany, which targets the envelope gene. We had that up and running by early February of 2020. At that point, we started retrospectively screening our samples because, as you mentioned at that time, testing at the CDC and local public health labs was limited. There were significant requirements that changed over time depending on whether someone was a returning traveler or had contact with someone who was known to be infected with SARS-CoV-2. So, we started looking back and seeing if we could find community transmission that was going unnoticed, because in addition, that was in the midst of our standard respiratory virus season and lots of folks were coming in with respiratory illnesses that were similar to SARS-CoV-2.

We started doing retrospective screening and then prospective screening after we caught up, and that was throughout the month of February, before widespread testing was available. We captured two cases of very early community transmission of SARS-CoV-2 by this method. Unfortunately, at that time, we weren't allowed, as a clinical laboratory and based on the regulatory requirements, to provide that testing for clinical purposes. That changed when the US Food and Drug Administration (FDA) and the CDC recognized that there was a deficiency in testing available throughout the United States. On February 29, the FDA came out and said, with their guidance, clinical laboratories able to perform high-complexity testing could now start to perform testing and then submit applications for emergency use authorization. We immediately did that and had a test up and running by early March; I believe ours was one of the earliest clinical laboratories able to offer testing in the United States and certainly in the Bay Area.

Eric J. Topol, MD: It's amazing how you were out in front of the virus. But some of the academic centers that tried to do what you did were shut down by CDC and FDA — for example, University of Washington and one of the Harvard sites — because not only did CDC and FDA not have a test, they didn't like the idea that academic centers like yours would go ahead with this. Did you ever get threats to desist during this stretch?

Pinsky: I did not get threats to desist from any of the public health authorities — local, state, or CDC. I had some interesting conversations when trying to get some samples tested. That was challenging because the samples did not meet the requirements, as I mentioned before, for their current rules about testing. We never used the CDC assay, which I think was fortunate. It turns out this envelope gene assay works quite well and has maintained its performance throughout the pandemic, despite all the different variants. I didn't get any cease-and-desist comments from CDC. I kind of flew under the radar a bit and just got it up and running and asked for forgiveness later.

Topol: So, on February 29, you got the go-ahead from FDA. On March 6, at a historic meeting of the press, the CDC, and the triumvirate of Donald Trump, Robert Redfield, and Alex Azar, Trump said anyone can get a test. Anytime. They're beautiful. But there were no tests and the virus was spreading like wildfire throughout the entire country because of the lack of testing. It's just incredible, the lies that we're being told to the public throughout this time. It's how we got so far behind. I don't know if we had further thoughts about that, because you were watching what you were doing and what the government, including the top leadership, was telling us, which were blatant lies. Were you thinking about that?

Pinsky: At the time, I knew that we needed tests, from my past experiences dealing with how tests get rolled out during epidemics or pandemics. I knew that it was on the clinical laboratories to pick up some of the slack and that the public health authorities could only do so much, particularly in those circumstances. So we were focused on getting our testing up, making sure we could first provide testing for the Stanford patients and the Stanford community, but then also provide testing for what turned out to be the entirety of the Bay Area for approximately 6-8 weeks, in those very early days. We were getting samples from UCSF, from Kaiser Health, and from the various counties and other hospital and clinic facilities. We were also trying to make sure we had enough reagents. That was a huge problem throughout the first year of the pandemic, and it has popped up occasionally since then, during the last surge and the Delta surge last summer.

Verghese: I'm struck by your curriculum vitae showing how active you've been, with papers just rolling out on SARS-CoV-2 — incredible stuff, both on the antibody side and on surveillance testing, and the nasopharyngeal tests. Step back for a moment as a virologist speaking to our audience, which comprises largely nonvirologist, non–infectious disease types. What are your thoughts on this virus compared with some of the other viruses you've focused on, from influenza to dengue to Zika? What makes this virus special? Some thoughts about the enemy.

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