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UC San Diego Health Sciences

Article Type: Q&A

— Research

“We must all get on the same page”

A Q&A with David Pride, MD, PhD, associate professor of pathology at UC San Diego School of Medicine and director of the Clinical Molecular Microbiology Laboratory at UC San Diego Health

— By Scott LaFee with David Pride, MD

Q&A

  • Question

    In the beginning of the pandemic, there was much concern and angst regarding COVID-19 testing in terms of accuracy of results, capacity and timing. You were deeply involved in developing and advancing testing throughout the pandemic. How would you describe that experience, the highs and lows?

    Answer:It was very difficult for clinical laboratories like ours early in the pandemic. We are accustomed to evaluating tests much more deeply than we were able to do before we started offering some of the tests we did earlier in the pandemic. It was also very problematic not to be able to give physicians definitive answers when they asked about the sensitivity and specificity of our tests. They simply hadn’t been studied well enough for us to have those answers. It was also quite problematic for laboratories like ours to have so many different tests simultaneously that all checked for the same virus. In general, we evaluate all the available tests and choose the one that works best or that best suits our institutional needs. Because there was such a limited supply of testing available, we often had to choose tests, even before we were able to evaluate how well they worked. This was, in essence, a lab director’s worst nightmare. In retrospect, we are relieved that most of the tests we chose work really well, and most importantly, are still available on the market because of their superior performances.

  • Question

    There is talk of an almost instantaneous breath test for COVID-19. Do you think that might happen, maybe before the next pandemic?

    Answer:It will be difficult for a COVID-19 breath test to rival the sensitivity/specificity that we have with our assays based on quantitative PCR. We find for many of the more rapid antigen assays the sensitivity would likely be too low to have a performance that would give us confidence in telling people they are not infected.

  • Question

    One observation you’ve made is that, even if a person isn’t infected by SARS-CoV-2, they are not virus-free. Quite the contrary: Bacteria residing in and on each of us outnumber human cells, and viruses outnumber bacteria — we each carry an estimated 380 trillion viruses. Your point is that most of these viruses are not dangerous, but simply part of the human virome. What is a virome and what’s currently known about it?

    Answer:Regardless of whether we are healthy or sick, we’ve all got viromes, which essentially are just collections of viruses that inhabit the human body. Many of these viruses infect the many bacteria that also live in the human body, and thus, we probably need to think about ourselves slightly differently than we probably do. That is, that we are collections of microbes that vastly outnumber our own cells, and that our bodies are fertile hunting grounds for viruses to attack their bacterial hosts. All of this goes on pretty much every second of every day, and we have very little insight into the fact that this is happening. We know that most, if not all human body surfaces, are inhabited by viruses. This competition for space and resources in the human body probably plays a role in our homeostasis, but this hasn’t been borne out so well by studies yet. We know that these viruses can change the bacterial communities and that these viruses can be readily shared with our close contacts. We believe that, because our bacterial microbiomes can be involved in helping determine healthy and disease phenotypes among us, the fact that viruses can attack these bacteria suggests that they may be involved in this process as well.

  • Question

    You’ve said the development of COVID-19 vaccines, and the underlying research, was the top scientific breakthrough of 2020. Why?

    Answer:Simply put, science doesn’t typically move at the speed that was observed earlier in the COVID-19 pandemic. Not only were vaccines developed in record time using existing technologies, but they were also tested in thousands of people to ensure they were safe and effective prior to being rolled out to millions across the world. This will go down as one of the top scientific breakthroughs, perhaps of all time, and we have to thank the scientists who developed the vaccines, the people who were willing to participate in these clinical trials without having foreknowledge of the potential beneficial or deleterious outcomes, and the regulatory agencies that worked closely with scientists to make all this happen. I don’t think the average person realizes how much everyone involved had to set aside their own personal biases, difficult working relationships, and even political disagreements to work together to do the most beneficial thing that they could to benefit the health of everyone.

  • Question

    Like many of your colleagues, you have cautioned about the dangers of antibiotic resistance, which you say is here to stay. But you also argue that there is much that can be done to mitigate antibiotic resistant bacteria, a public health challenge that the World Health Organization predicts might kill 10 million people annually by 2050. Antibiotics don’t work against viruses, which have different structures and methods of replication compared to bacteria. Apart from developing vaccines to prevent viral infections or reduce transmission, what is the remedy?

    Answer:Unfortunately, bacteria respond to what we do to them by developing resistance to antibiotics. It’s remarkable how bacteria will develop resistance specifically to antibiotics that are used in a particular hospital, but not some of those antibiotics that are used in other hospital systems. This reveals a key feature of bacteria: that they continually evolve to solve the problems that they are faced with, such as antibiotics. It is interesting to see that this is exactly what we are observing in the current virus pandemic. We responded by rapidly developing vaccines that had the potential to significantly reduce, if not eradicate, SARS-CoV-2. Instead of simply going away, the virus has evolved specific means to respond to what we have done. The virus has chosen to infect largely those who are unvaccinated and has even mutated to become clever enough to infect some who are vaccinated. This persistence despite our best efforts is real-time proof that this virus will continue to try to respond to what we do to eliminate it. It also strongly suggests that we must all get on the same page and have a coordinated response if we expect to eliminate it. If we do anything less, SARS-CoV-2 has proven that it will seek out refuge, mutate, and then potentially come roaring back

— Research

“We must all get on the same page”

A Q&A with David Pride, MD, PhD, associate professor of pathology at UC San Diego School of Medicine and director of the Clinical Molecular Microbiology Laboratory at UC San Diego Health

— By Jackie Carr with Francesa Torriani, MD

Q&A

  • Question

    When did you first become aware of COVID-19 outside of the United States?

    Answer:I happened to be in Switzerland at the time and was with friends with whom I had graduated from medical school. We were reading in the news what was happening in China and discussing whether the illness was a global threat, whether this could be the next SARS or the next epidemic.

  • Question

    Were you afraid in the early days?

    Answer:No. As a health care epidemiologist, you’re always thinking about what could be. Always in the back of your mind, you think, “What should I be worrying or thinking proactively about? Could this virus come to the U.S.? How should we prepare?” As epidemiologists, we are engineered to think ahead. It’s really a question of how do you detect or how do you prevent infection. For example, what PPE (personal protective equipment) should you use? What are the needed diagnostic tests? Ventilation systems? Etcetera.

  • Question

    When did you start to realize that a global threat was emerging?

    Answer:Toward mid-January 2020, we started hearing about something unusual going on in Italy. Within weeks, it was clear that the situation was remarkable and dangerous. Illnesses started appearing in the region of Bergamo in northern Italy. That was when my attention became very narrowly focused and I started thinking about San Diego and a need for a headquarters of local operations. Then, in late-January, we got the phone call that planes would be arriving from Wuhan. That was our unified call to action at UC San Diego.

  • Question

    What prepared you for the patients’ arrival from China?

    Answer:Every infectious disease that came before COVID-19 prepared us. In 2014, we prepared for Ebola and even designed and built an infectious disease unit to care for potential patients. Before that, there was SARS, H1N1, and avian flus. All of the lessons learned came into play. While there was no test for COVID-19 early on, we already had intense safety protocols to prevent disease transmission, plus the CDC team was onsite for consultation. We knew that this was a respiratory virus, so if we had good protection, and we knew how to doff (or remove) our PPE without contaminating ourselves. We would have appropriate layers of defense.

“It’s inevitable there will be another pandemic. Hopefully, this lesson learned stays with us and is implemented quickly in the future.”

— Francesca Torriani, MD
  • Question

    What did you see in the patients’ faces when you entered their rooms?

    Answer:For me, one thing that struck me about the patients from China was the fear. The fear of being targeted because of the perception of bringing a disease into a new country? The racism, the inherent fear of being targeted, the abrupt separation from family all became factors. All of the patients had a connection to the U.S and so were allowed to get on that plane, but their fear was real. When I saw them, I observed how isolated they were. I felt the pure humanity of it all. Very few of the patients actually tested positive. One happened to be a grandmother and nurse bringing her grandson to the U.S. She had to be separated from him to be hospitalized and how heart-wrenching that was to see. In the grandmother, in all the patients, was this fear of rejection, and this feeling of guilt. Survivor’s guilt. But at the same time, a lot of gratitude towards us, who were willing to take care of them, and welcome them.

  • Question

    What was the game-changer in altering the course of the pandemic?

    Answer:One of the things I greatly appreciated was a leadership team deeply grounded in reality. They were very keen on learning from a wide variety of experts and polling them on a regular basis to guide the health system forward. They made hard decisions to protect the integrity and the survival of the health care ecosystem, especially our CEO. It was gutsy to stop all surgeries because we wanted a safe environment for all employees and patients, knowing that there would be economic consequences. Our C-suite was among the heroes in this community. We took in the first patients, launched the first clinical trials and vaccinated the first community members. None of this would have been possible with leaders who were not nimble and present every single day.

  • Question

    What traits about UC San Diego Health helped us survive the pandemic?

    Answer:One of the things I greatly appreciated was a leadership team deeply grounded in reality. They were very keen on learning from a wide variety of experts and polling them on a regular basis to guide the health system forward. They made hard decisions to protect the integrity and the survival of the health care ecosystem, especially our CEO. It was gutsy to stop all surgeries because we wanted a safe environment for all employees and patients, knowing that there would be economic consequences. Our C-suite was among the heroes in this community. We took in the first patients, launched the first clinical trials and vaccinated the first community members. None of this would have been possible with leaders who were not nimble and present every single day.

By Jackie Carr — Executive Director of Communications and Media Relations

— Education

THE PANDEMIC TEMPORARILY CLOSED CAMPUS, BUT OPENED OPPORTUNITIES AND MINDS

A Q&A with James C. Nieh, PhD, professor of biological sciences, and graduate student Sumedha Ravishankar

— By Scott LaFee with James C. Nieh, and Sumedha Ravishankar

Q&A

  • Question

    How did your roles as teacher and student change during the pandemic?

    Answer:NIEH: Moving to fully remote education was challenging, especially during Spring Quarter 2020, when everyone was embarking on this experiment, and there were many aspects that we were unsure about. For many years, I have created video podcasts for my Animal Behavior course (BIEB 166). All notes, lectures slides, lecture readings and exercises were also available online. Thus, my biggest change was to only interact with students via Zoom and to give online exams.

    RAVISHANKAR: As PhD students, our lives revolve around our lab experiments. When the world went remote, I lost a core component of my livelihood. Unlike many of my friends, I couldn’t work from home in the same way they could. I couldn’t bring my bacteria or zebrafish home (that’s a MAJOR safety violation!). When we got the news that California was going into lockdown, I remember going into the lab for the last time to clean up and throw away bacterial cultures, effectively halting months of research. My role as a graduate student went from a full-time laboratory researcher to a work-from-home scientist. At first, I didn’t even really know what a work-from-home scientist looked like. I went from doing hours of infection research and imaging per day to zero. I used my time at home to read, write and do further analyses on my existing data. I was able to take a deep dive into the literature to get a better understanding of the state of the field, and how my work could further it. I was also able to write my thesis proposal and focus on developing a plan for the next four (or five or six) years of my PhD program. Instead of working on developing my research skills, I was able to hone my writing, public speaking and experimental design skills. Around June 2020, we were able to re-enter the lab and resume research part-time. Now, I try to ensure I make enough time for both in-person research and at-home reading and writing, as both are essential to being a successful scientist.

  • Question

    What were your biggest concerns at the beginning of the pandemic when the campus closed and education went remote?

    Answer:NIEH: I was not sure how the systems would handle the internet load of essentially all students in the United States going remote at the same time. There were concerns about our Canvas software crashing, and about the local networks at UC San Diego. I tried to prepare for this with multiple backups, mirroring all course materials and lectures onto separate cloud servers approved by the campus. However, this was only needed for a few days, and everything else went quite smoothly, a remarkable achievement for the campus and its hardworking staff. My second concern revolved around how the instructional assistants (IA) and I could provide equitable access for students in multiple, different time zones. How could we ensure that everyone could attend office hours and sections? We were fortunate to have several IAs and came up with a system to accommodate students who were at home across the globe.

    RAVISHANKAR: The severity of the pandemic became abundantly clear the day UC San Diego shut down. Thousands of students, myself included, were left uncertain about how they would graduate or continue with school, or when they’d next see their friends. My main concern was for my safety, and the safety of my peers. I was terrified to be around other people and out in public. But my anxiety over graduate school was constantly nagging at me. Would I still be on track to finish graduate school? What would happen to my research that was already in progress? So much of my scientific development comes from discussing science with others and learning from my colleagues. I work in an open lab space with five other labs, where collaboration occurs daily. This synergistic environment was gone, and I felt isolated. In terms of my education, I was primarily concerned with falling behind, losing the precious time I had to make discoveries in the lab, and missing out on working with my fellow graduate students. Remote learning can only go so far, especially when the majority of what I needed to do had to be in person.

Life lessons: Sumedha Ravishankar is a fourth-year PhD student studying bacterial infections that affect the nervous system.

“At the end of Spring Quarter 2020, we saw a huge increase in student stress as they grappled with the important issues brought up by the racial justice movements around the country.”

— James C. Nieh, PhD
  • Question

    How did your expectations of teaching and student performance change? Was the school year better, worse or about the same?

    Answer:NIEH: At the end of Spring Quarter 2020, we saw a huge increase in student stress as they grappled with the important issues brought up by the racial justice movements around the country. Because of the pandemic, my expectations had already shifted to focus more upon what students were able to achieve and learn, given the pandemic. I think the concept of advancement within opportunity, evaluating what individuals are able to achieve and thinking more broadly about what constitutes achievement, was very helpful. Essentially, having honest conversations with students about learning and grading is necessary. For example, like many other instructors, I adopted a “no fault” final exam policy in which students could raise their grades via the final, without penalizing them. I think that it will take time to better understand the impact on learning, but I hope that shifting the focus away from grades toward learning through opportunities gave students the breathing space they needed during this difficult time.

    RAVISHANKAR: UC San Diego shut down in March of 2020. I started my PhD program in September 2018, so I was just wrapping up my second year and my first year in my thesis lab. I was just getting ready to begin conducting research in earnest, after having found my bearings in the lab. I had pretty high expectations for the year, and was hoping to make significant progress in my research. However, after the school shut down, I was forced to take a step back from lab work. I had no idea what the timetable for our return to the lab would be, and watching the cases exponentially increase, it seemed like we were in the pandemic for the long haul. Around this time, there was a resurgence of civil rights advocacy and awareness, galvanized by the brutal murder of George Floyd. Re-energized, I shifted my focus to science outreach and co-founded an organization that is geared toward increasing underrepresented minority retention in STEM (Science, Technology, Engineering and Math) and creating a safe community for our minority students. Along with my fellow graduate student, Tara Spencer, and biological sciences faculty member Dr. Sonya Neal, we co-founded the Biology Undergraduate and Master’s Mentorship Program (BUMMP). Our primary aim is to ensure that our undergraduate and master’s students at UC San Diego, who are underrepresented in science, are reminded that they belong in STEM by providing them with a scientific mentor and funding to do research. I am so thankful for the amazing work we’ve been able to accomplish with BUMMP. We have raised more than $150,000 to award scholarships for our undergraduate and master’s students. This year ended up being far more successful than I had anticipated when the pandemic began.

“The following Monday, UC San Diego went into lockdown and our labs shut down. I will never forget the pure confusion, fear and hopelessness that I felt. A little over a year later, we’ve made it through, but that moment still feels fresh.”

— Sumedha Ravishankar
  • Question

    What would you do differently if you had to do 2020 all over again?

    Answer:NIEH: think I would have taken a more relaxed approach. I wanted everything to work out and so we spent a lot of time and energy creating backups and worrying about online exams and how to ensure that students could learn and perform in the same way as they did in person. In retrospect, this was not a realistic expectation. Given the pandemic and the racial reckoning, it now seems that I should have relaxed a bit and dedicated that extra time and energy to conversations with students, including how events outside of the classroom were affecting their lives. The mantra “keep calm and carry on” perhaps should have shifted to “keep calm and carry on, but recognize that that this is a very difficult time and the same expectations cannot not apply.”

  • Question

    Was there any particular moment/ conversation/ event from the pandemic that you think will stick in your mind forever?

    Answer:NIEH: For me, there was no striking moment. But I will always remember the first few weeks of class when everyone was still adjusting to this new Zoom world. There were a lot of blank screens in the beginning and reluctance to talk. Students mainly texted questions. But in the third to fourth week, this began to break down and students actually showed their videos and asked questions in person: a wonderful small step forward!

    RAVISHANKAR: The week before we went into lockdown, my lab mate and I were talking about all the news articles that were circulating about a flu-like infection that was taking over China. There was so much information that we really didn’t know what to believe. We were in our lunchroom, eating and chatting, talking about how we thought people were overreacting and that it was just like the flu: no big deal. The next night, we were with a few friends for our weekly The Bachelor (the TV show) viewing night. We suddenly got a notification that the NBA was stopping its season. That’s when we realized that we were about to live through a historic event. The following Monday, UC San Diego went into lockdown and our labs shut down. I will never forget the pure confusion, fear and hopelessness that I felt. A little over a year later, we’ve made it through, but that moment still feels fresh.

  • Question

    What changes do you hope will continue beyond the pandemic?

    Answer:NIEH: Multiple aspects of remote learning are here to stay. I think that many more instructors will now feel more comfortable about video podcasting, putting their lecture materials online and generally increasing access. There are small but significant changes that will help students. For example, several students have told me that automatic, closed captioning of video-recorded lectures was very helpful. I hope that most instructors will adopt this for the future. Open-book exams and writing tests that evaluate knowledge, not only memorization, are also important legacies of the pandemic.

    RAVISHANKAR: This year was tough for so many, with countless lives lost and a lack of much-needed human interaction. Despite that, there were positives to come out of the pandemic that I hope we continue to see in the future. There was an emphasis on mental health for graduate students this year, and I hope we continue to prioritize our well-being above our daily grind. Additionally, having meetings on Zoom allowed me to attend more seminars than I would have before the pandemic. Scientists from all over the world were able to give talks that anyone could join. I hope we continue to use Zoom as a platform for various meetings and conferences to encourage greater attendance. Finally, I hope we all continue to wash our hands and practice clean habits! I haven’t gotten sick in over a year, so I hope we maintain this level of mindfulness.

Proof is in the pooping: