What It's Like to Get Breakthrough Omicron Covid: A Scientist's Story
What Happens When a Student of Viruses Gets a Virus She's Been Preparing For Her Whole Career
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Dr. Piraye Yurttas Beim is one of those people we all know who appears to do it all. She’s a wife, a friend, the mother of three children under eight, as well as an entrepreneur, a scientist, and a pioneer in women’s health. With a B.A. in Biology from the University of Texas at Austin and a Ph.D. in Molecular Biology from Cornell University, she founded Celmatix in 2009 to empower women to be more proactive and informed about their health through better data, including genomics.
In recent weeks, she became something new: a patient with breakthrough Omicron COVID-19. Since Piraye is someone who has spent her career at the intersection of public health and virology, and is a great science communicator as well, I asked if she would be willing to share her experiences with The Nonlinear Life. I’m delighted that she said yes and am thrilled to share this exclusive and timely report.
1. You’re a scientist, an entrepreneur, as well as a mother of three children under 8, which gives you such a unique point of view on the entire pandemic. Can we start with how you viewed COVID-19 from the start? So many women, in particular, struggled to balance everything. In your case, you fled your home, wiped down groceries for months, homeschooled, and continued running your company. How did you manage?
I’ve spent much of my life anticipating this pandemic. When I was a child in the 80s, the AIDS epidemic made a huge impact on me. In high school, it was the Ebola outbreaks in Africa. Then as an undergrad, I was fascinated by the story of the Manhattan Project and felt that, in my lifetime, the equivalent would be a viral pandemic that required scientists around the world to drop everything and save humanity. I passed on an opportunity to do my Ph.D. in virology at Harvard Medical School. My early Ph.D. research at Cornell’s medical school in New York was focused on decoding the atomic structure of a Human Papillomavirus (HPV) protein to aid in drug discovery for what was, at the time, a leading killer of women globally.
In the first weeks of the pandemic, I told my husband that at the beginning, everyone would think I was crazy and over-reacting, and at the end, everyone would think I was crazy and under-reacting. As a scientist, I have become used to everyone considering themselves an “expert” because of a YouTube video or something they saw on social media. So even though the first few months of the pandemic felt like watching a train collision in slow motion, I focused my energy on ensuring that my family was safe and that my community had my support.
When the first case was reported in Washington state, I knew it was either already in New York City or would be within days. The first cases seemed to track back to a worker at a shipping facility, so I assumed the virus was being spread through surfaces. We started stocking alcohol wipes and gloves and dedicated a corner of the apartment to mail and packages, which I would carefully open and decontaminate after a “quarantine period.”
The day the first case of community spread was reported in New York State, I informed employees that they had 48 hours to gather whatever they needed from the office because we would be shifting to remote work immediately. Two days later, our kids were sent home from school. This was when the CDC was claiming that handwashing was the best protection, but I knew it was a respiratory virus, so I started trying to find masks. Like many families with small children, we left New York City for a rented home. My husband asked me how long; I told him it could be two years. This was in March 2020.
I stocked up on first aid supplies and, after seeing the chaos and food shortages at the grocery stores, also planted a vegetable garden in the backyard. Having been raised in small-town Texas and survived 9/11 in NYC, I’ve always been a bit of a “prepper,” and those first few months very much felt like showtime for pulling up the drawbridge and going into survival mode. I recognize what a luxury our resources and desk jobs afforded us to do this, of course.
In addition, overnight, I found myself homeschooling a 2nd grader, a 1st grader, and a three-year-old. We didn’t celebrate our daughter’s third birthday for weeks after she actually turned three because I was so overwhelmed. She kept asking me, “Mommy, how much longer will I be 2?” I also had to try to keep spirits high with my team at work, as they were all also navigating many of the same challenges of lockdown and school disruptions. We had weekly Zoom meetings where we did everything from pandemic bingo to learning how to dance the Macarena. Children made frequent appearances in meetings.
We did our best to offer flexible hours, time off, or a shift to part-time for the working moms on our team who were concerned that they couldn’t shoulder the extra burden the pandemic presented for them. It was so painful to read about how many of the jobs that were lost were women exiting the workforce in droves because of the crush of new responsibilities as support structures collapsed around them. One thing that kept me sane during those difficult first months was walks in nature. A silver lining of the pandemic for my family and me was that we had the opportunity to engage with nature in a way that likely would never have happened otherwise. Our kids were scared of the smallest bug at the beginning of the pandemic, and by the end, they were chastising me when I killed a spider instead of capturing it and setting it free outside.
2. You also did something else remarkable that is a tribute to your scientific background—you volunteered to be part of the vaccine trial. Why did you do that, what was your experience like, and what did you learn about the public role of science?
As I mentioned, I spent a good deal of my childhood and early adulthood thinking about viruses and the big pandemic that would come one day. When that day did come, I felt a strong sense of regret that I hadn’t stayed in virology. I longed to rush into the lab and help find a cure or vaccine. When I saw that the first vaccine studies were starting to enroll, I felt this was my opportunity to contribute. I had spent my scientific career enrolling thousands of patients in clinical studies and benefiting from the valuable data they shared. Now it was my turn to be the patient, the data source.
I knew that the vaccine study needed to get to a certain number of positive cases to be able to report outcomes, so my rationale was that if I did get COVID, at least it would benefit my children by accelerating the trial. I also wanted to set an example for the kids. Participating in the trial required me to be quarantined away from them, so we spent time talking about the importance of volunteering so they could understand why I was away. We also found creative ways to stay in touch, like bedtime books and stories over Zoom.
Dr. Piraye Yurttas Beim participating in the Pfizer trial.
I had the opportunity to participate in the Pfizer study, which was my first choice for a number of reasons. First of all, I knew that mRNA is intrinsically a highly unstable molecule. Therefore, I wasn’t worried that the molecule being injected into my arm would persist. Second, the two biggest potential risks for a novel vaccine were unlikely based on Pfizer’s preliminary data. Finally, having immigrated to the US from Turkey as a child, I was inspired by the story of the Turkish immigrant scientists who developed the vaccine.
People have thanked me for volunteering, but I am so grateful for having had the opportunity.
3. Then, after all, that, just when you started venturing out (to a concert, no less!), you came down with a breakthrough case of COVID-19. Do you know where you got it? How did you learn? And how did it affect your health?
Yes! My friends, colleagues, and family know that I have adhered to much more strict protocols than the average American, so it was initially surprising that I tested positive. The weekend that I was infected, my husband and I attended an LCD Soundsystem concert at Brooklyn Steel. The venue was very disciplined about following the protocols. They were so careful in checking proof of vaccination that it took over 2.5 hours to admit the 1,400 people who showed up for the concert. That was reassuring. However, we did become concerned when we entered the venue and realized that fewer than 5% of people were masked (masking was voluntary). We were wearing KN95 masks and never removed them.
We were hearing reports about how quickly the Omicron variant was spreading in the UK, so we started testing daily with rapid home tests after that weekend. On Tuesday evening of that week, I developed cold symptoms but was still testing negative, so I assumed it was not COVID. On Wednesday, I had a painful inflammatory attack that almost sent me to the ER (I have a condition called endometriosis). The cold symptoms continued to worsen, and on Thursday, I tested positive for the first time. My cold symptoms and fatigue lasted for ten days, which was still considered a “mild disease” for COVID because I didn’t get pneumonia.
On day 8 of my quarantine, I got a message from a contact tracing app saying I had been exposed to someone with COVID while out running errands the day after the concert, so it’s not clear where I got it. My husband got it from being exposed to me that Thursday before realizing I was positive, not at the concert. No one I was exposed to in the days leading up to my positive result tested positive.
4. Both you and your husband quarantined—I assume for ten days. Among other inconveniences, you had to reschedule Christmas for the kids. How comfortable are you with the new CDC guidelines that drop self-quarantines to five days?
Yes, we each quarantined away from the kids for ten days, respectively, over the holidays. One important thing we didn’t know until we were sick is that the first day of symptoms is considered Day 0 (not Day 1). We tested to exit, and fortunately, both finally had negative tests on our respective Day 10s. We tested positive each day before that. We canceled a family trip planned to the UK. Every person we had planned to meet in the UK turned positive for Omicron that week. We told the kids that Santa was making delayed house calls for families with COVID and ended up celebrating on December 29.
As for the new CDC guidelines, they are about preventing economic collapse, not about personal risk. That’s an Important point because people find the CDC guidelines to be confusing. Public health is not about individual health. Also, there is some important fine print in the guidelines that don’t fit in the “5-day” headline. First of all, the 5-day guideline is for people who don’t have any cold symptoms (sorry, a cough or scratchy throat is a symptom!) or have improving symptoms, and it is advised that they test before exiting. If they are positive, then they recommend staying in quarantine and testing again on Day 10 to exit. Also, they recommend strict mask wearing for people who do exit quarantine before Day 10 and ideally avoiding high-risk, unventilated indoor environments where you might encounter unvaccinated or immunocompromised people.
5. There’s an emerging view out there that with Omicron so transmissible but less lethal that we’re all going to get it sooner or later, and we should come to accept that. What’s your view of that?
First, I would clarify that the lower lethality is on a population level because of the high degree of recovered COVID patients or vaccinated people that we have. For the average vaccinated family in New York City, at least, an Omicron infection will be a bad cold at worst and will give them a natural “boost” to their immunity. But some families have unvaccinated small children or immunocompromised family members. Those families have to take the same precautions that they would take with any serious infectious disease (flu etc.).
While I don’t think vaccinated, healthy individuals need to live in fear of being infected with the Omicron variant, I do think everyone has the responsibility to quarantine and take precautions to avoid spreading it to vulnerable members of the community once they test positive. Hospital occupancy has already outpaced the Delta variant wave in many parts of the US, and the Omicron wave has not yet passed.
6. Thank you for sharing your story. What advice would you give people now—both about what to do if they get the virus and how to approach their lives in the coming months?
First, there is no stigma in getting COVID if you’ve taken all the precautions you can, including getting vaccinated and boosted if you’re eligible. Unlike the previous waves, there is no protocol short of complete lockdown that will keep you from being infected with this highly transmissible variant. It’s a numbers game. Not everyone will get it, of course, but most people who are living their lives (going to work, running errands, using public transport, attending school) in urban areas will get it.
If you fall into the category of having young children or immunocompromised family members, then it probably makes sense to wait for this wave to pass. That should be by mid-February, in most places. If not, then live your life. I probably got it running an errand, but I like to think I got it having the time of my life at the LCD concert!
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