COVID – Prof. Klapperich et al.

The Long Sunsetting of COVID Testing

As is usually the case in the American healthcare system, there are some groups of people in Massachusetts who have had cheap and free on demand PCR testing nearly the entire pandemic, with turnaround times well under 24 hours. How was this possible?

Subsidized and free COVID-19 testing, vaccines, and treatment will soon be gone. Frequently reported is the fact that a PCR test, previously free, but often not easy to get, will cost roughly $120. At this price, the number of people able to access reliable testing will drop significantly.

And it’s not like that $120 is getting you a better or faster test than you got before. In January of 2022, Quest was reporting 2-3 day turnaround times, and LabCorp 1-2 days. These times do not include the time to get an appointment or the time it takes to ship the sample to the testing facility, resulting in real turnaround times that are highly variable across the country. In rural areas, people typically wait 5-7 days to get results. Getting COVID test results back more than 24-48 hours after giving your sample makes this expensive test useless for both individual and public health objectives.

Several local universities set up some version of surveillance testing either independently or with the help of the Broad Institute. Because these community testing sites were local, high throughput, and paper free, they consistently achieved turnaround times significantly less than 24 hours from sample collection. As a result, we have been able to blunt the impact of virus spread on our campuses and maintain in person teaching for much of the past two years – and we didn’t spend $120 per test.

In the lab that I helped build, we process 5-8,000 PCR tests a day at peak capacity with an average turnaround time of 14 hours. At 18 months of operation, our cost all in with overhead, is about $5 per test. This is much lower than the even the price of less sensitive over-the-counter rapid diagnostic tests, which retail between $12-$15 each. A better test at a cheaper price.

PCR testing is old technology. It’s such an integral part of scientific research that it was optimized, automated, and commoditized years ago. With technologies like PCR, there are economies of scale. COVID-19 testing is just one small application of this powerful technology. It is underutilized in the context of other infectious disease challenges, most notable for the detection of antibiotic resistance and to augment good antibiotic stewardship. That we are not using this technology at scale to improve diagnostics and healthcare outcomes is inexcusable.

But ultra-modern testing facilities like the one we built still operate within a fragmented healthcare system where different payers are not connected electronically, and we were unable to easily offer our services outside of our university setting. We were hamstrung by outdated and incompatible software at other institutions, regulations on sharing healthcare data, and a longstanding national neglect of the public health infrastructure.

Beyond renewing the funding for subsidized testing now expiring, we have a real opportunity now to make inexpensive PCR testing available to everyone. The PREVENT Pandemics Act, introduced in January by Senators Patty Murray (D-WA) and Richard Burr (R-NC) of the Senate Health, Education, Labor, and Pensions (HELP) Committee seeks to “tak[e] common sense steps to act on lessons learned from the pandemic response and improve the nation’s preparedness for future public health emergencies.”

At this point, the bill contains no language to incentivize entrepreneurs, academic institutions, and other entities to build modern molecular testing facilities at the state and local levels. Sites like these could protect students in K-12 public schools, police, firefighters, teachers, healthcare workers, and essential workers. We would be able to protect everyone, not just the fortunate few.

Building a COVID-19 Lab (3/n)

The “I swear, I am not trying to kill you edition.”

So that shopping post I promised last time? Yeah, life intervened. I had to get back to teaching the class that originally led to this blog fall semester and help put out the fires that kept popping up with the testing project all semester! Anyways, let’s get back to it.

I want to take a look back at one of the more controversial parts of this project: communication. Communicating with a large, interdisciplinary team is always difficult. Much trickier is communicating with a large, interdisciplinary community of stakeholders.

We have an incredibly diverse university community. We have students who just graduated from high school who were showing up on our campus in their first foray into independent living, and we have faculty who have served the institution for decades. There are teachers who were facing the prospect of standing in front of large lecture classes, and facilities workers dealing with all matter of new protocols and work changes to most safely deal with the pandemic.

My role was straightforward, to design and build a COVID testing facility on our campus. That work was done, and was running smoothly as the first students moved onto campus in early August. Our rates of positivity have been low (more on that in a future post), and the university launched a student led campaign to get students on board with the new protocols. Contact tracing was in effect, and the cases we identified in incoming students had been isolated.

Sharing information with the community was part of my objective all along. I spoke to a number of local and national media outlets and continued to field questions to my email box every day.

I gave presentations to students, parents, faculty, and staff over zoom. A side effect of all of this one on one science communication is that I became, for a short time, the public face of an effort that was not welcomed by everyone on campus. Many believed that attempting to go back to residential learning was misguided, that it was too dangerous. Still others pointed out how going back to campus would impact our surrounding neighbors. Inequality of risk was a major concern.

I shared many of these concerns. The pandemic had become far worse in the United States than I thought it would be. Leadership at the federal level was virtually nonexistent. At best, the federal government abdicated its responsibility, at worst, it spread false information that made people more anxious and upset and resulted in more illness and death than we would have seen had we had a coordinated effort from the top down from the start. I do hope better days are ahead of us in that respect.

Given the year of no federal leadership, I decided that if I could help increase the testing in my state, I was going to lend my expertise to that effort. But, after I thought we were off to a good start, a lot of people started getting really snarky on Twitter.

Some of the comments were thoughtful. Some expressed real fears. I tried at first to answer them to the best of my ability. Answering questions about science is my job after all. But then a subset of folks came after me in ways that felt personal. And I started to get defensive. I swear, this widespread testing effort is not an evil plan to kill you or your students! After a couple of weeks of engagement, my husband quietly suggested that perhaps Twitter was not a good use of my time or that great for my mental health. And I took a step back. However, I think it is worth looking back at the main arguments from that time, because they are still important today.

There were two conflicting arguments being made by my colleagues online. The first held that no matter what we do in terms of testng, tracing, and mask wearing enforcements, that undergraduates will never comply and we will all get sick in the end. The second argument warned against the university “blaming undergraduates” for failures resulting from the administration’s choice to bring students back to campus. We focused on the undergraduates because they were the largest group of people coming to campus from other places. Almost all of these other places had higher COVID-19 positivity rates than we had, so it was justified to keep our eyes closely on this group.

Interestingly, in the end, neither of these things came to be. Nearly everyone, undergraduate to faculty, complied with protocols, and spread of the virus in the fall semester was much lower than in the surrounding communities. Ongoing analysis by my colleagues is forthcoming that will put numbers to this assertion. I also think that the overall communication coming from the university administration has greatly improved over the past 6 months as we have hit our stride. We start spring semester with similar fears and higher community numbers almost everywhere in the USA. We will continue to look at the on campus numbers daily, enforce testing compliance, and strive to keep our community safe.

For me, I have learned to use the block feature on Twitter. However, I have also opened new avenues of conversation via email and direct message with several colleagues who definitely disagree with our approach, but who also value ideas and reasoned arguments. These have been very rewarding interactions. I am still learning from this project, and will continue to be open to your comments and suggestions. I continue to remind myself that everyone is scared, and most are acting in good faith.

Building a COVID-19 Test Lab (2/n)

Last time we talked about how I got into this mess! Now let’s define the mess.

Ever had a great idea only to find out that someone else did your thing years ago? The high of thinking up something new is dashed by the realization that it wasn’t that new at all. Google has greatly increased the speed of this mental rollercoaster ride. I used to feel this disappointment acutely – but over time, I reframed it. Now when I see someone else doing my thing I think, “Damn, I’m not actually insane, that was a good idea!”

Step one of this undertaking was to make sure that I was not insane. My first calls were to my colleagues at Boston Medical Center (BMC) who had started up an expansion lab to test more people at their site. The generosity of these folks cannot be overstated. Back in April they were still in the throes of the Boston surge, yet they gave me all the information, explanation, and time that I needed. They laid out the challenges ahead and linked me to the answers to my questions.

I then followed up with some very close reading of a preprint put out by the Berkeley team that outlined all of the hurdles they overcame to make their lab a reality. As I read through that paper, I was soothed. It was a blueprint with clear metrics for success – things I could get done. Then, I got to the last page of the preprint. It had an acknowledgements list of people who had helped the lab team get up and running. There were about 50 people on that list, and around 15 organizations. The magnitude of this endeavor became clear.

When a job is this big, you should first ask “can I just buy this?” In other words, can I pay money to leverage the invested time and expertise that others have already put in and get all of or most of what I need? It’s the difference between buying a fixer upper that requires a huge remodeling project, and just buying something move-in ready that you like well enough. The former may allow you to get every detail the way you want it, but the latter would be a whole lot easier in terms of time and aggravation.

The major limitation to just buying from a testing service was cost. The big-box stores of laboratory testing were already struggling in April to promise COVID-19 test turnaround times of less than 3 days. On a campus like ours, with students, faculty, and staff coming and going on schedules, models showed that we were going to need 24 hour turnaround time, or it wasn’t going to make sense to test at all. So, the big testing companies were out. Other options available in the Northeast had price points significantly higher than what we knew the cost of materials to be, so we started to research in-house testing.

Turns out professors are a bit out of the loop when it comes to real-life project budgets – or at least I was! My idea of what physical things like reagents and instruments cost is usually an overestimate, since I’m usually doing one off experiments and almost never can take advantage of scale. My idea of personnel costs skewed in the other direction. Academic labs are home to extremely motivated and sharp young people who are working overtime to get their degrees at a rate significantly below what they will be earning the second they step out of our doors. For this project we needed to hire professionals with experience doing specialized testing. Same with space and overhead costs. It is often a conceit of those of us who bring in research dollars that we are “making money for the university.” Actually, most research active departments cost the larger organization money, while places like the law school bring in cash because they sell a high priced product that doesn’t take up a lot of specialized space!

To condense a lot of spreadsheets into one sentence, I am happy to say that we were able to predict a cost per test in a new facility well below what we could get from any of our other options.

Next time we will talk about procurement – or as I like to call it, shopping!

Building a COVID-19 Test Lab (1/n)

When the president of the university asked me to put together a plan for what an on campus testing site would look like for our large campus community, I said yes.

Initially, this was going to be a short little post about my experiences the past couple of months. Turns out this experience has been the most complicated and rewarding time in my career, and it will require installments! Also, in this manner I can make sure that all the info I am providing is fact-checked and that I don’t get out ahead of guidance we are giving to our campus community.

I hope you decide to follow along.

Back in late April, a couple of emails popped into my inbox about what I thought about the possibility of building an on-site COVID-19 testing lab at my university. I had watched colleagues do this at our medical school to expand their ability to test patients and healthcare workers during the early surge in Boston. Colleagues at UC Berkeley, my alma mater, were also doing the same for their campus. From afar I had admired their resourcefulness and ability to pull together these complicated undertakings in a few weeks, and even faster at Boston Medical Center!

Stock image of a large scale laboratory.

Yeah, I thought, we can do this, but we need either a lot of people to pipette, or robots. Graduate students, much to the chagrin of many in the academy, are not an infinite resource! Besides, like everyone else, they wanted to get back to their own disrupted lives and research.

I’ve always been into outbreaks. For me, they are like the true crime of science. I’ve read all the books. The villain is the microorganism. Sometimes the causative agent is a mystery or comes from a mysterious source. Sometimes we know exactly who the serial killer is, and we have to try and stop it. SARS-CoV-2 is a virus we are getting to know quite well.

One of my favorite colleagues is an honest-to-goodness card-carrying Ebola researcher. On my last sabbatical, I expressed my fascination with BSL-4 work, and how cool I thought it would be to just quit my job and train up with him to do this work. Leave everything behind and chase these mysterious villains. His immediate response was, “You are exactly the kind of person who should NOT be doing this work!” Hopes dashed, I went back to the relative safety of working on point of care (POC) tests for sexually transmitted infections.

Then COVID-19 emerged. The world seemed to start noticing POC diagnostics, or tests that can be done quickly and close to a patient. Journalists were calling to ask my opinion on how fast something like that could get to the mass market for COVID-19. The federal government started throwing money (billions of dollars, with a B) at my area of research. The little obscure molecular test system I work on was suddenly on the tips of the tongues of every Super Fancy Research University scientist.

What I worked 20 years to make myself an expert in was finally interesting to someone other than my mother! But designing and developing new tests takes time, and we do not have a lot of time with this virus. Perhaps for the next one, and there will be a next one, quick POC tests will be widely available and cost effective. For now, we have to go with the systems we have, and the fastest way to get a lot of people tested efficiently is to scale up existing molecular tests and make sample collection as easy as possible.

So, when the president of the university asked me to put together a plan for what an on campus testing site would look like for our large campus community (35 – 50,000 people, depending on how you count), I said yes.

Next time I’ll talk about steps one and two in every big engineering project: defining the problem space and consulting the experts.