diagnostics – Prof. Klapperich et al.

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 (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.

To pulse ox, or not to pulse ox?

Another day, another COVID-19 discussion…

With each passing week, we are learning more and more about how to deal with this pandemic, both individually and as a community. We are now well-versed with preventative measures like washing our hands frequently and wearing masks, but what happens if you actually start feeling sick? While the symptoms of this viral infection are varied, they usually include high body temperatures, dry cough, and shortness of breath. Most of us have a thermometer at home, with which we can easily diagnose abnormal temperatures. But, is that enough to detect the early stages of a COVID-19 infection?

Pulse oximeters (pulse ox) are getting a lot of attention right now. If you have ever had surgery or if you have a respiratory condition like asthma, you likely know that a pulse oximeter is the little medical device that clips onto your finger and informs your doctor of your heart rate and how much oxygen is in your blood. Monitoring blood oxygen levels has been critical for COVID-19 patients because a drop in the amount of oxygen in your blood indicates the need for more aggressive interventions. Since you can buy a pulse oximeter at the drugstore, many people are wondering if they need one at home. So why exactly do respiratory issues warrant the use of a pulse oximeter?

When your lungs are functioning properly, around 95% – 98% of the blood in your arteries should be “oxygenated,” or carrying oxygen. Your blood carries oxygen with the help of hemoglobin, a protein that has the ability to bind to oxygen molecules. Hemoglobin is what makes blood a great transporter of oxygen from your lungs to the other organs in your body. Without oxygen, your organs cannot function because they rely on a process called oxidative phosphorylation, which uses oxygen to produce the energy that drives all organ functions. When your lungs are compromised, like they are during a COVID-19 infection, they are unable to efficiently take oxygen in from the air and pass it into your bloodstream. As a result, your other organs don’t get enough of it to do their jobs. This condition is called hypoxia.

*The circulatory system. Red vessels are the ones that carry oxygenated blood.*

Now, let’s get back to the pulse oximeters. A pulse oximeter measures the percentage of oxygen saturation in your blood by shining both a red light and an infrared light into the top of your finger. The bottom of the device has a sensor that detects the amount of light that passes all the way through your finger. You can visualize this mechanism by doing a quick little science experiment on yourself. Turn on your cell phone flashlight, put your finger on it, and see what happens. If red light shines through, your blood is probably not deprived of oxygen. Good for you! Oxygenated blood absorbs every wavelength of visible light except red, which is why the red light can go all the way through your finger. Deoxygenated blood, however, is really good at absorbing red light. Now, we can see how the pulse oximeter takes advantage of these properties of blood to give a measurement of oxygen levels.

So, why is infrared light also necessary? Blood vessel width varies from person to person, making the volume of blood in the vessels vary as well. Only using red light would result in misleading oxygen levels because the readings would be affected by these varying blood volumes in different people. For that reason, infrared light is used alongside red light to normalize the measurement and adjust it to each user’s body. Infrared is not well-absorbed by either oxygenated or deoxygenated blood, so it is a good baseline comparison measurement. The pulse oximeter calculates the ratio of absorbed infrared light to absorbed red light to get the percentage of blood saturation. In oxygen-rich blood, the low level of infrared absorption divided by the similarly low level of red absorption results in a ratio close to 1, which is equivalent to a percentage close to 100%. As blood oxygen levels decrease, this ratio also decreases because the red light absorption (the denominator) increases while infrared absorption stays relatively constant. Readings below 92% indicate the beginning of a hypoxic state.

The ability to detect hypoxia is what makes pulse oximeters critical for COVID-19 patients. Healthcare professionals who are currently treating these patients are finding that oxygen levels can drop well below 92% before patients have any trouble breathing. When a patient does finally go to the doctor complaining of shortness of breath, their infection and hypoxia may be very advanced. Often, symptoms like fever and fatigue can also mask early hypoxia symptoms. It is easy to get used to the mild shortness of breath or pass it off as fatigue while blood oxygen levels continue to drop. For these reasons, some doctors are suggesting that everyone should get a pulse oximeter to use at home so the onset of hypoxia can be caught early.

A big disclaimer that many physicians are making however, is that pulse oximeters should be used at home along with thermometers and calls to your doctor. There are still many cases in which COVID patients do not present with any hypoxia, but have high fever and the telltale dry cough. So, blood oxygen level, while helpful, is not the only metric used in diagnosis.

So, should you buy a pulse oximeter? To put it plainly, it’s really up to you. If you are sick, you called the doctor, and they said you’re not sick enough to go to the hospital, it may be helpful to have one and monitor your own blood oxygen so you know if you ever do need to go in. You may want one in that situation just to keep your peace of mind. Even if you aren’t sick, and just want to be prepared, it definitely can’t hurt to get one. However, all the stories about hypoxia going unnoticed paint a scary picture. It’s important to remember that, if you can’t get your hands on a pulse oximeter right now since the demand is high, it’s not the end of the world. The vast majority of COVID patients are able to get diagnosed and get to the hospital in time if necessary just by calling a doctor. So, you really don’t need to buy that $200 pulse oximeter you found on Amazon. You can find them for about $30 at your pharmacy, but if they’re sold out, don’t panic! Just keep washing your hands, keep that 6-foot distance, and if you are sick, call your doctor. Here at the blog, however, we are device geeks – so any opportunity to have a new medical device around the house we’ll take!