UC San Diego Health Sciences comprises the region’s only
academic health system, one of the nation’s top research-intensive schools of medicine, the Herbert Wertheim School of Public Health and Longevity Science and the Skaggs School of Pharmacy and Pharmaceutical Sciences.
In March 2020, our response to pandemic SARS-CoV-2 and the disease it causes, COVID-19, demanded dramatic changes to teaching and learning.
It quickly became apparent that the community public health efforts necessary to mitigate rapid spread of the virus, hospitalizations and deaths would require students from the schools of pharmacy, public health and medicine to transition to remote teaching and learning for the remainder of the Spring 2020 quarter.
Evolving science and availability of protective tools would improve clinical care, reduce deaths and ease the burden on health care and public health systems. But we would also learn a lot about living with the virus. Under extraordinary circumstances, UC San Diego became a trailblazer in efforts to provide a place of refuge for students facing unforeseen challenges, from food and housing insecurity to physical and emotional abuse. The campus became a refuge and respite, albeit one filled with the promises and perils of being a pioneer.
In May 2020, Return to Learn debuted, a bold initiative to return students to campus and learning during the pandemic. It was designed to be adaptive and responsive to changes in the local epidemiology of COVID-19. It focused on risk mitigation, viral detection and public health intervention. Every sector of the campus was engaged in preparations for mass testing, delivery of student health services, housing, dining, isolation and quarantine resources, symptoms monitoring, wastewater surveillance and reporting our daily status on a public dashboard. These efforts transcended everyone’s routine job assignments. It was service to an educational mission bigger than oneself.
By Fall 2020, students were presented with the option to return to campus or continue to learn remotely. We welcomed back almost 10,000 students, roughly two-thirds of whom lived on campus. Inside and outside of classrooms, our students, staff and academics demonstrated extraordinary resilience, creativity and commitment.
The new Herbert Wertheim School of Public Health and Human Longevity Science (founded in 2019) partnered with the San Diego County Department of Public Health for contact tracing among those ages 18 to 24 years. A great deal of the success for any public health program relies on human behavior that considers the needs of others. Our students’ behaviors were exemplary.
For much of the fall and winter seasons, the highest prevalence of COVID-19 in San Diego (and across the region and country) was in persons 18 to 24 years old, yet there were very few outbreaks on campus — and none traced to our classrooms. Our students adhered to rigorous testing, isolation, quarantine and monitoring protocols, and their dedication showed.
UC San Diego’s educational programs attract students from all over the world. Meeting these diverse needs requires flexibility. During the pandemic, some classes were in-person in rooms modified to maintain physical distance; some were in specially prepared outdoor settings. Some classes used a hybrid format with some students in-person and others joining lectures remotely. Yet others were fully online.
Across the campus, we emphasized proper hygiene, sanitation, face coverings and the use of other, appropriate personal protective equipment. The Teaching+Learning Commons tool assisted instructors with developing strategies for impactful remote instruction. Our faculty and staff swiftly rose to meet the challenges they faced.
Professors and instructors who, prior to the pandemic, could not have envisioned teaching students online or in hybrid formats reinvented their courses and themselves. They designed lessons that were adaptable to a range of student needs and teaching formats. They ensured high quality interactions using virtual whiteboards, chat features and breakout rooms to stimulate conversation and creative engagement.
Our response to the pandemic has perhaps permanently changed the way students will learn and faculty will teach at UC San Diego. In a stressful time without precedent, we became even more adaptive, more considerate of student needs and more conscious of our impact as educators — regardless of setting.
I hope we continue the educational practices learned over the pandemic. They will help us reduce inequities in student access and increase the reach and impact of UC San Diego’s pharmacy, public health and medical school educational programs.
Amid Tears and Fears, determination, hope and unity of purpose
I remember when I got the initial phone call from the County inquiring if UC San Diego Health would take in the first patients flying out of Wuhan, China to San Diego.
At the time, all we knew was that Wuhan was ground zero for a spreading, previously unknown viral infection. People were dying and there was no existing medical literature, nor any test, for the virus that would be called SARS-CoV-2.
Nonetheless, Marine Corps Air Station Miramar would soon receive a military plane containing multiple Wuhan evacuees; some of whom were possibly infected by the mysterious coronavirus.
Knowing our advanced capabilities as an academic medical center, particularly in the relevant areas of infection prevention and control, public health and respiratory disease, it was actually an easy decision. “This is what we are meant to do,” I thought.
We quickly opened our Hospital Command Center (HCC) and mobilized. Typically, an HCC event lasts roughly a week, maybe two. In this case, weeks became months, then months became more than a year. Time blurred. Zoom calls and masking became as routine and commonplace as handwashing. It would be 412 days between our first case of COVID-19 and the first day when we recorded no new infections.
The pandemic has been the most extraordinary event of my career, and likely for many others. Every single employee of UC San Diego Health was impacted, from custodians, nurses and nutritionists to supply chain managers, screeners, administrators and physicians. Everyone played a role in slowing or stopping the virus and saving lives.
We worked the same hours as COVID-19, which was constantly, day and night, weekends too. It was a coordinated effort of monumental proportions that led to formations of new teams and new levels of trust and innovation that propelled us forward, out of fear and into a new normal.
I cannot write about the pandemic without acknowledging those who died from the virus and whose families were devastated by the loss of loved ones. These tragedies happened disproportionately in many of our underserved and under-reached communities, a historical condition and injustice that shall remain a focus of UC San Diego Health, even as COVID-19 hopefully recedes into the background and our memories.
I’m often asked what about our response I am most proud. There is no single answer. We were first in the region to treat patients with COVID-19; first to open vaccine clinical trials; first to offer a mobile ECMO (extracorporeal membrane oxygenation), a type of machine that pumps and oxygenates a patient’s blood outside the body; first to vaccinate our employees and first to open a vaccination superstation to the public.
We led the way on CA Notify, a mobile solution to identify new exposures of COVID-19 in the community and state. Our nurses and specialists travelled to other hospitals in the United States and Mexico to teach new lessons and insights in the art of critical care; they returned to help vaccinate too. What all of these achievements have in common are unbounded compassion, brilliance and determination that characterizes the people of UC San Diego Health.
For every article in this magazine, I know there were hundreds more unwritten that could tell story of bravery, drive and connectedness during the pandemic. I thank all of my team members for their selfless contributions. I am so very proud of you and grateful for your service and kindness.
I would also like to express a deep and sincere gratitude to our donors, who stepped up at the same time to help us meet so many challenges. Their contributions of time and funding helped us rapidly expand and sustain our efforts to build testing capacity, acquire ventilators and surge supplies and launch multidisciplinary research efforts into new diagnostics, therapies and ways to monitor the virus. Their generosity saved lives and will help us in the future.
With lessons learned, I believe we move forward together, unified, a better and stronger organization.
This is a special issue, a focused look at how UC San Diego scientists, doctors, students, staff and others responded to the COVID-19 pandemic, and how they continue to rise to its many challenges.
The magazine you hold is called Discoveries, an apt name that encompasses the overarching missions of the University of California San Diego, from research that reveals and explains the mysteries of our world to the education of new doctors, artists and engineers who serve our communities to the development of therapies, art and technologies that shape our everyday lives.
You might call this issue Recoveries.
The pandemic has been difficult for everyone, at times tragic. More than 792,000 Americans have died from COVID-19 and millions more became sick, some with lingering effect. These numbers echo around the world. From small villages to great cities, no place has been immune. In the 21 months since the World Health Organization officially declared COVID-19 to be pandemic, we are still working to mitigate its consequences.
UC San Diego did not escape the pandemic’s adverse effects. In this issue, we recall not only what happened, but also how we responded (and continue to respond) through lessons learned. There have been many remarkable achievements, unplanned perhaps, but not surprising. Our nationally recognized Return to Learn program made it possible to restore in-person instruction and research on our campus, and our innovative partnerships with regional government, the San Diego Padres and area businesses created California’s first vaccination super station. These are just two of the programs and initiatives that positively impacted public health, served our community and kept our economy moving.
As one of the world’s great research universities and academic medical centers, UC San Diego is flush with talent, expertise and resources. Confronted by a public health crisis that spanned the globe, our people and programs rose to meet the complex challenges of the pandemic head on. And throughout, our world-class health care system — UC San Diego Health — has shined brightly, a nimble and innovative leader within our state and across our nation.
UC San Diego continues to be an exemplar. In a changing world, we are changing too. We continue to learn, evolve and fulfill our goals to not only make the world better, but also better prepared for the future.
Life is change. It’s about adapting to new situations and circumstances that ensure not just survival, but a presumably better, stronger future.
Virusesare especially good at this, mutating constantly and continuously, often at dizzying rates, for billions of years.
The coronavirus known as Severe Acute Respiratory Syndrome Coronavirus 2 of the genus Betacoronavirus, or slightly more colloquially, SARS-CoV-2, isn’t new at this game of life. It likely existed in other forms in other animals before jumping species, but it was new to us.
Now, we are painfully familiar. The unexpected debut of SARS-CoV-2 in late-2019 and the pandemic that followed have provoked all manner of subsequent change in all manner of ways. Like the virus and its variants, life as we knew it will never be the same.
We are changed and changing, often in ways that have made us wiser, stronger and better. Nowhere is that more evident than in the response of faculty, students and staff at UC San Diego, who pivoted their attentions, expertise, talents and resources to confronting and combatting this highly infectious, often deadly virus festooned with trademark spikes of protein on its surface.
The scope of these efforts and contributions are astounding, from helping pin down the virus’ origins in China, Europe and North America to parsing the threat of aerosolization and understanding the critical performance of neutralizing antibodies.
While much of society necessarily shut down, research at UC San Diego continued, affected but unabashed, even expanding in some cases. For example, we built from scratch a new biosafety level 3 lab capable of handling highly infectious pathogens and pop-up labs for measuring viral loads in patients. We created high-throughput systems to process daily thousands of COVID-19 test samples, including wastewater from our buildings, and to sequence and analyze all viral genomes. We developed a cellphone-based technology to alert users when someone close to them had tested positive.
Researchers shifted priorities, moving robots and equipment around to create new programs in a matter of days when the norm is more often measured in years. It was hard, often exasperating, work. A working scientist might get only one scheduled day in the lab each week, part of vital and exacting safety protocols. It might be only enough time to do a bit of “wet work,” then go home to analyze the data. Zoom calls multiplied like, well, viruses. People grumbled, but they carried on and important work was done.
Perhaps nowhere was the depth and breadth of our expertise more obvious than in our participation in three of the four first and biggest clinical trials for a COVID-19 vaccine: Moderna, AstraZeneca and Johnson & Johnson. UC San Diego Health scientists and the thousands of San Diegans who volunteered in these trials were players in the development of these vaccines. With critical help from the Altman Clinical and Translational Research Institute, they moved the needle. We have learned a lot. We have earned a lot: To date more than $30 million in new grants specifically funding COVID-19-related projects, with more in the works. And from these lessons and efforts, we prepare to change even more with an aptly named project called PREPARE, which will bring together people, programs and infrastructure to be ready for pandemics to come.
“When you are finished changing, you are finished”
— Ben Franklin
The pandemic changed everything, but not our research mission to make the world a better, healthier place. That remains unchanged and our work unfinished.
During the pandemic, innovation and adaptability became virtual realities.
By Yadira Galindo
March 2020
In March 2020, rumors and uncertainty plagued Betial Asmeron, then a third-year student at UC San Diego School of Medicine who was, by nature, optimistic and assured.
With three classmates, Asmeron now crowded anxiously around a computer monitor to watch a virtual town hall in which school leadership would reveal how their education would be impacted by COVID-19 and the growing pandemic.
Prior to the pandemic, Asmerom’s routine was the same, day in and out: Wearing hospital scrubs and coffee in hand, she would arrive at 5 a.m. for a rotation at UC San Diego Health to check on the welfare of patients under her watch.
“As medical students, we have the gift of time in the hospital. We get to know our patients on a deeper level, which allows us to better help with their medical and emotional needs,” said Asmerom.
With consent from patients and under the supervision of resident and attending physicians, third-year medical students interview and examine patients, write notes in their electronic medical records, present findings to their team for review and are part of hands-on care, such as surgery or labor and delivery.
After a full day in the hospital, Asmerom would return home by 7 p.m. for a late night of studying for shelf exams — national standardized exams that evaluate competency over each core rotation or clerkship — before repeating the routine the next day.
Wuhan to WELCOME
UC San Diego Medical Center in Hillcrest was among the first hospitals in the nation to provide care to patients with COVID-19, notably evacuees from China.
Steven Garfin, MD,
interim dean of UC San Diego School of Medicine.
Time Stands Still
Asmerom was beginning a six-week rotation in obstetrics and gynecology (OBGYN) when the pandemic struck with full force. The world shuddered, and then shuttered. Everything and everybody seemed to shut down and withdraw behind closed doors, except where she worked. As a provider of essential services, UC San Diego Health opened its doors wider. One of the first hospitals in the United States to care for patients sickened by SARS-CoV-2, UC San Diego Health’s infectious disease experts recognized the expanding pandemic that would require all available hands to care for the millions of people who would eventually become infected and the millions more who would die, close to home or far away.
“We pursued medicine because we wanted to help people, and even though we knew that there was some risk to our own health by being in the wards, we really wanted to be there,” said Asmerom. She and her classmates eagerly offered to become contact tracers, to serve as symptom checkers or help patients sign up for the MyUCSDChart electronic patient portal that would allow access to telehealth visits. They wanted to do anything and everything to help during the crisis and to continue their education. But there were immediate challenges: School of Medicine leaders were forced to make a difficult decision: Are medical students essential on site or should they be learning safely from home?
Standing before the computer monitor, a practice that would soon become very familiar, Asmerom and her classmates heard their fate echoing over the speakers. Rotations or clerkships were indefinitely suspended.
“A hurricane is devastating. The residual is terrible, but it sweeps through and it is over. There is a finite period when things turn around with enough resources, but with this pandemic, we had no clue when it was going to let up. If it would let up,” said Steven Garfin, MD, interim dean of UC San Diego School of Medicine. And just like that, Asmerom’s cherished time and connectedness with patients vanished, like a leaf in a hurricane.
“For the safety of our faculty and students, and to ensure our students had a way forward through this difficult time, we made tremendous changes over a very short period of time in a highly collaborative way.”
— Carlos Jensen, PhD
Virtual Class Rooms
Stephanie Jed, PhD,
professor of literature, works at a community farm. During the pandemic, farm visits became virtual.
All levels of education — from elementary schools to universities
— found themselves grappling with unprecedented challenges posed by a highly contagious virus that did not discriminate by age, gender, ethnicity or even health status.
Once lively campuses emptied as schools and districts took early or extended spring breaks to plan for online instruction and to implement safety protocols to bring staff and students back, when it was safe to come back.
UC San Diego faculty, program directors, course directors and information services scoured online resources to build and shift to virtual learning on a campus-wide scale.
“For the safety of our faculty and students, and to ensure our students had a way forward through this difficult time, we made tremendous changes over a very short period of time in a highly collaborative way,” said Associate Vice Chancellor for Educational Innovation Carlos Jensen, PhD.
“The way that administration, faculty and senate came together, because it was the right thing to do, is a tremendous testament to the kind of community that we are. We’ve shown that we can really change education if we want to.”
— Carlos Jensen, PhD
For example, the Division of Arts and Humanities quickly flipped its campus-based, 12-week transfer student Summer Academy to online only. The Preparing Accomplished Transfers to the Humanities partnership with the San Diego Community College District provides hands-on resources for students to succeed at the university, as well as two full academic courses.
For the class “Politics of Food: Justice, Diversity, Community,” led by Stephanie Jed, PhD, a professor in the Department of Literature, students would normally visit multiple community farms together. For the virtual class, students instead received a produce delivery from a San Diego-based Community Supported Agriculture (CSA) program, and seeds, soil and a planter box to grow their own vegetables at home. The program staff organized an online discussion about community gardens and food deserts and cook nights to help create bonds among the students.
Bioengineering students at UC San Diego Jacobs School of Engineering completed senior design projects. They used many strategies, including creative use of Zoom for collaborative brainstorming and design; a focus on regular, precise communication with project sponsors and clients; off-campus, socially distanced outdoor work meetings; and limited use of labs following safety protocols. And, in a nod to the old days, they mailed parts and prototypes to each other.
Faculty members tapped into a wealth of resources available through the Teaching + Learning Commons. It became an important source of support for faculty, instructors, graduate instructional assistants and students. The Commons created an integrated approach that ensured educators had the tools they needed to keep teaching through partnerships with Educational Technology Services, the Library, Academic Integrity Office, Campus Privacy Office and others.
Summer session:
Under strict COVID-19 protocols, several thousand students were able to remain in or move into campus housing.
“Dealing with a new organism is the greatest challenge,” said Maria Savoia, MD, an infectious disease expert and dean of medical education at UC San Diego.
Savoia could have been talking about the novel coronavirus, which was previously unknown, but her words applied as well to teaching medical students during a pandemic.
“We did not know exactly how people would react. There were challenges and worry over access to personal protective equipment in the clinical arena. No one knew where we would end up, and what we saw happening in Italy was worrisome. People were afraid for their patients, afraid for themselves. And everything was changing almost every single day,” said Savoia.
Medical school is a minimum of four highly structured years of classes, myriad exams and countless hours of clinical experience that must be completed in a specific sequence and time.
During the first two years, students spend most of their time in classrooms. The third and fourth years are devoted to applying in a clinical setting what they previously learned. Going virtual meant trying to train medical students without access to clinics.
“We pivoted from in-person learning, where we work together in teams and take care of patients in the clinic, to deciding what could be virtual for effective student instruction. We had to implement the strategy as best we could on virtual platforms over the course of a couple of days,” said Savoia.
Julia Cormano, MD, assistant professor in the Department of Obstetrics, Gynecology and Reproductive Sciences and director of the Third Year Medical Student Clerkship, said medical school scheduling can be unforgiving, especially in the third year.
Third-year medical school students are required to learn in-person rotations in seven specialties — internal medicine, family medicine, surgery, pediatrics, obstetrics and gynecology, psychiatry and neurology — before progressing to their final year and earning their medical degree.
Unique Challenges
House rules:
To reduce exposure risk, on-campus housing density was reduced, frequent testing required and buildings’ wastewater screened for indicators of positive cases.
“It was also a big pivot for physicians. We were trying to figure out very quickly how to do remote clinical visits ourselves. We realized there were a number of different ways we could include students in this sudden increase in telehealth, including pre-interviewing the patient and observing,” said Cormano.
Case in point: A hospitalist stepped back from the clinical setting and spent his days rounding virtually with students in the OBGYN rotation. Students were able to review patient charts, interpret fetal heart-tracing data and speak with the hospitalist in real time.
“It was essentially transferring what we would do on the wards to our house, with the added luxury of having an uninterrupted hour of the physician’s time. Something like that never happens in the hospital. I probably learned more pathophysiology doing this at-home rotation,” said Asmerom.
“Still, it’s not the same as being in the hospital and being with patients and I think that was the part we really yearned for.
“We wanted to be able to see our patients, interact with them, and really just feel like we were making some sort of impact or difference in their lives and in their care.”
In addition to the unique challenges of medical school, faculty and students across the entire campus were faced with a lack of at-home workspace or proper equipment. Some found that having multiple people working or studying from home affected their bandwidth and therefore their productivity.
“We tried hard to mitigate that by giving people resources as much as we could. I think the university was very good about trying to help and we opened up spaces for students to be able to find a quiet space to learn and to study,” said Savoia.
Campus-wide virtual instruction was never intended to be long-term or permanent at UC San Diego.
From day one, a multidisciplinary team of leaders began formulating a plan to safely welcome back students, faculty and staff.
Through its transformative, adaptive and multilayered Return to Learn plan, which launched in May 2020, the university was able to bring students back to campus in a safe and strategic manner. Among the first to return were medical students.
“None of the national requirements or dates changed so we could not select 10 students to come back. The whole class had to follow a pattern to get into the next year’s program. There is just no way to catch up in medical school without losing potentially a whole year,” said Garfin.
Guided by risk mitigation, virus detection and intervention, Return to Learn kept positive case rates low compared to regional and national case rates.
UC San Diego maintained a median campus-wide infection positivity rate of 0.28 percent throughout the fall 2020 quarter, while San Diego County’s median was 8.1 percent.
“We see students as being integral parts of medical teams. So we wanted to introduce them back into the clinic as soon as we could, and we did that safely,” said Savoia.
“In addition, we did a lot of hands-on training in the Simulation Training Center. We broke classes into much smaller groups and had students mask and take COVID-19 tests. Many of our anatomy professors and the people in the simulation lab thought that the educational experience was better in smaller groups because it was more one-on-one.”
The number of students returning to campus increased with each subsequent quarter. With access to COVID-19 vaccines for faculty, staff and students, as well as continued mitigation and virus detection efforts, the plan is to return to full, on-campus operations for fall 2021.
Teaching is primarily delivered through in-person instruction in campus classrooms. Appropriate remote learning options are available for students who are unable to arrive from abroad due to visa delays or travel restrictions.
Betial Asmerom
Asmerom is in her fourth year of medical school after taking a year to pursue a master’s degree in public health.
A School Tested
Shelter-in-place began in March 2020. It took approximately six weeks for medical students to return to clinics and hospitals and yet seniors still needed to complete rotations in order to graduate in May.
While medical students were ready, patients were not.It took a while for hospitals to have the resources to return to regular operations, but it took patients even longer to feel comfortable resuming routine screenings and active health care, affecting some clerkships and residency programs.
“We worked to find the right spots for students who still had requirements that needed to be met so that they could meet their graduation requirements. This necessitated adaptability and a lot of individual work with students. For example, surgeons who could not be in the operating room instead helped in the intensive care units putting in central lines to help their overworked colleagues,” said Savoia.
In the end, all students passed their tests and met the requirements to move on to the next stage in their medical education or career.
“Given the situation and how many unknowns there were, I think we adequately prepared students to be able to have the clinical information that they needed to move forward to their fourth year and to their future careers. Their test scores reflected that readiness,” said Cormano.
Charley Coffey, MD, associate professor in the Department of Surgery, who published three papers on student perspectives of remote learning during the pandemic, said that although first- and second-year students spend minimal time in clinics, they too felt the loss of clinical interactions.
“For many students, working with patients is one of the most gratifying things that they do. It is one of the things that keeps them motivated through sitting in lecture halls for hours and years on end,” said Coffey, co-director of the Third Year Surgery Clerkship.
“There were very creative and innovative things done to involve students in telemedicine and to rounding remotely on the surgical floor and labor and delivery floor. Those were things that students responded well to, ways to reconnect with those aspects of patient care that were so easily lost when we shifted to remote learning modalities.”
Students did appreciate the flexibility of learning at their own pace and working virtually in smaller groups, said Coffey. However, digital fatigue set in after one hour.
“It is nearly as easy for a professor to stand up in front of a lecture hall of students as it is to stand in front of a computer and similarly for students to be able to just sit in front of their computer.
”On the other hand, when it came to anatomic dissections, it is impossible to do that without being in person. It is nearly impossible to replicate during an overnight transition to remote learning and it is among the things that preclinical students missed most,” said Coffey.
Fellows are physicians who have already completed their residency and are now in specialty training. Because fellowships are entirely dependent on caring for patients, fellows were dramatically impacted during the pandemic. Thankfully, by this point in their training most fellows had met the required number of surgeries.
“The concern that many trainees had at that time was how they would transition into the working world. A lot of the hiring, or the interviewing process, or both, were put on hold due to the pandemic,” said Coffey.
Lessons Learned
Challenges met:
Maria Savoia, MD, dean of medical education, said everything about teaching during the pandemic was new.
Prior to the pandemic, some lectures were available virtually. COVID-19 forced the entire campus, from dance instruction to chemistry labs, to find alternative instruction options.
“We have learned a lot about how diverse our student population is, and their diverse needs, and how some of the small changes that we make in the classroom have a tremendous impact on student well-being, success and retention. We have learned to become comfortable with remote and hybrid teaching in a way that we were not before and it has made us think differently about classes,” said Jensen.
“This post-pandemic period is going to be an exciting time when we start thinking about what are the right pedagogical tools. It forced faculty to challenge their assumptions and learn new skills.
“I wish we could have learned these skills under better circumstances, but I think we need to take the good that has come out of this and take that forward. They are valuable skills.”
For the School of Medicine, small groups for hands-on learning has been one of the most touted changes by students and faculty alike. Cormano recognizes that less time in the labor and delivery ward may actually be a more productive and immersive experience if it allows for individualized teaching.
“I think one of the real take-homes for educators is to be critical in determining the modalities and the resources that are going to be most useful to students. How do we make those accessible, digestible and useful for student learning without just throwing a lot of information at them?
“Part of that comes with experience and listening to what students said worked and what did not.”
For Asmerom, who will start her fourth year of medical school in the fall after taking a year to pursue a master’s degree in public health as part of the UC San Diego School of Medicine Program in Medical Education – Health Equity program, remote learning was an effective experience. Still, she is not advocating to make medical school virtual.
“Remote learning is not how you learn to be a doctor. It’s really like an apprenticeship model where you have to go there in person, work with patients, residents and attendings, review labs, and develop your differentials. You have to do it over and over again in order to cultivate your clinical decision-making skills. You can’t do that very well from home,” said Asmerom.
“And I really missed seeing and interacting with patients, meeting their families and being able to bear witness to some of their hardest moments or laugh with them. Relationships are the heart of medicine and I really craved and missed that when we switched to remote learning. And, of course, I missed morning burritos from the Hillcrest cafeteria.”
Frontline staff at UC San Diego Health recollect the first days of the pandemic, a time marked by fear, uncertainty and endless acts of kindness
By Michelle Brubaker, Jackie Carr and Jeanna Vazquez
On a cold morning in February, seven stainless steel electric tea kettles, filled with hot water, are delivered to patients’ rooms at UC San Diego Health Medical Center in Hillcrest. The tea kettles are not typical, but neither are the times.
The COVID-19 pandemic had begun in earnest, and the kettles represented an early act of comfort and humanity in a time that would soon demand an outpouring of both.
On February 5, 2020, UC San Diego Health activated the organization’s Hospital Command Center (HCC), the central location where in-house experts gather to develop and implement a response to an emergent and urgent situation. In this case, it was the growing crisis surrounding the novel coronavirus, SARS-CoV-2, then rapidly spreading in Wuhan, China.
Five days later, UC San Diego Health received its first patient with diagnosed COVID-19, an evacuee from Wuhan, who had previously been airlifted to and quarantined at Marine Corps Air Station (MCAS). The patient was officially the 13th case of COVID-19 in the United States and would soon be followed by others from MCAS.
They arrived via ambulance, escorted by law enforcement vehicles and greeted by medical staff, security officers and officials from the Centers for Disease Control (CDC), all wearing masks, face shields, gloves and other personal protective equipment (PPE).
Seven new tea kettles were purchased, filled with hot water and served with sides of lemon and ginger to the first patients from Wuhan.
There were more questions than answers
The virus was largely unknown, as was the plan of treatment. There were more questions than answers.
“One question raised in the HCC was ‘Does anyone here speak Mandarin?’” recalled Lily Angelocci, transformational health care lead coach at UC San Diego Health. “From there, I spent the next two weeks at the bedside of the patients in our intensive care unit, helping to meet their physical and emotional needs.”
Four evacuees were eventually transferred from MCAS to UC San Diego Health for care. Most spoke little or no English. Translators were found.
Angelocci was always nearby, intent on addressing their physical needs or easing their emotional concerns. It wasn’t yet clear who was infected with the SARS-CoV-2 virus and who was not, but all of the patients were far away from home, away from loved ones and afraid of a disease no one yet understood.
“At the time, we had to wait days to receive test results from the CDC in Atlanta to confirm if the patients from Wuhan were actually positive with the virus,” said Angelocci. Two were.
“What initially struck me was the delicate humanity of the situation,” said Francesca Torriani, MD, program director of Infection Prevention and Clinical Epidemiology at UC San Diego Health. “In the patients’ faces, I could simultaneously see fear and gratitude: fear of rejection and gratitude for us accepting and welcoming them.
“Can you imagine being evacuated from Wuhan on a windowless airplane, not knowing if you had the virus, or if you would live or die; of being targeted because of bringing a new disease into a country? My heart went out to them.”
Even with the language barrier, the patients’ concerns and fears soon became apparent.
Comfort Food
Chef Bo-Kai Liao learned about the Wuhan patients’ food preferences; food and nutrition service staff members Buddy Cacatian, Jill Martin, Alejandra Cazares and Xavier Garcia helped speed recovery with healthy meals and a side of humanity.
Comfort Food
“We realized that they were not eating,” said Jill Martin, director of food and nutritional services at UC San Diego Health. “We needed to devise a plan to make sure these patients were fed and felt supported. Our role is not just to provide food on a tray. Providing healthy meals is a significant part of the recovery process. That was our main priority.”
Many of the patients could not digest certain foods being offered. With assistance from Angelocci, Martin’s team visited specialty grocery stores to purchase more familiar fare. It brought patients and staff closer together. “One of our chefs, Bo-Kai Liao, speaks Mandarin and was integral in those early days, making sure there was a strong line of communication. He would call the patients in their rooms several times a day, find out about their food preferences and customize their meals,” said Martin. Favorites were wonton soup, egg and seaweed soup, congee (a type of rice porridge), spicy Mapo tofu and a Taiwanese basil omelet.
Meals were served using only disposable materials, to reduce the risk of virus transmission. Some foods, such as meats, were cut into bite-sized portions in the kitchen before delivery.
“We are all human, but different things comfort and heal us,” said Martin.
“We found a balance of caring for these patients while still following all the safety measures.”
“Normally, loved ones are in the rooms to help with the meals, but that was not the case for these patients. Sometimes, patients were too weak to cut their own food, so we did that for them to make sure we were doing everything we could to help them eat and heal.”
The seven tea kettles were part of that process.
“In Chinese tradition, they do not drink cold or room temperature water, only hot water. In talking with the patients, we realized they were being served cold water,” said Angelocci.Tea kettles were purchased. Patients soon received their water hot, served with sides of lemon and ginger. Patient Experience staff added to the efforts, delivering floral arrangements to brighten up rooms and power cords, chargers and coloring books to help patients stay connected to the outside world and pass the time.
“We always teach our staff one word: the Japanese term, ‘gemba’,” said Angelocci.
“It means ‘the place where value is created.’ In practical terms,” said Angelocci, “it means to ‘see, show respect, and ask why.’ It meant the world to patients and staff.”
“We needed to devise a plan to make sure these patients were fed and felt supported. Our role is not just to provide food on a tray. Providing healthy meals is a significant part of the recovery process. That was our main priority.”
— Jill Martin
Summer session:
Under strict COVID-19 protocols, several thousand students were able to remain in or move into campus housing.
Counceling Patients
The unpredictable nature of COVID-19 first struck Kevin Kwak, MD, a hospitalist at UC San Diego Health, when he walked into the room of a 30-something patient with the disease.
“When I had seen the patient earlier in the day, he seemed stable overall. He did have some shortness of breath, but he was able to communicate. Later that evening, he was on six to seven liters of oxygen,” said Kwak.
“Seeing a patient decline like that in only about 12 hours was eye-opening. He did have some co-morbidities, but that moment stands out as when I truly realized how serious this virus is, and that it does not discriminate.”
Kwak was among the first health care workers on the scene when patients from Wuhan were admitted to a dedicated, isolated COVID-19 unit at UC San Diego Medical Center in Hillcrest. The unit was the product of multiple departments collaborating, and was staffed by physicians and nurses who volunteered to care for the patients.
“I remember that night vividly,” said Kwak. “I was asked if I would be willing to take care of the patients coming from MCAS because we were not sure of the associated risks. I am relatively young. I am healthy. I live alone. I quickly answered yes. It was definitely something I wanted to do.”
He said most of the Wuhan patients’ symptoms were mild, but he spent considerable time trying to alleviate their uneasiness.
“As physicians, we were still learning about the trajectory of the virus. We were trying to address the patients’ questions, even though we didn’t know all the answers. The main questions were: Am I going to be okay? When will I be able to go home? I could only tell them with confidence that we were working around the clock to provide the highest quality of care. We were gathering as much information as possible and adapting.”
All of the Wuhan patients were discharged a week or so after admittance to continue their recoveries with family and friends. By then, however, COVID-19 cases were appearing among local residents. At Hillcrest and Jacobs Medical Center in La Jolla, long-term COVID-19 units were set up for patients from the San Diego community.
“Back in February 2020, all we knew about the virus was that it was respiratory, but we weren’t sure how it was being transmitted,” said Dante Segundo, RN, MSN, nurse manager at UC San Diego Health.
The rising number of local cases prompted massive organizational changes.
“We transitioned from a relatively contained situation with the patients from Wuhan to one that was now affecting the community at large. Our entire hospital system had to pivot.”
Processes, from testing and treatment plans to managing huge volumes of lab work, were refined daily, often spurred by evolving CDC guidelines.
“We were all learning about the swab tests, waiting three to four days for test results (from the CDC in Atlanta) and understanding what PPE we should be wearing,” said Kwak. “There were so many uncertainties at that time, but we were all incredibly focused while collaborating, coordinating and communicating.”
It Takes a Medical Center
Everyone Helped
From the first day and the first patients, staff across all disciplines and departments at UC San Diego Health stepped up to provide exemplary care, 24/7.
Conquering COVID-19 required a team effort, from university researchers to practicing physicians, nurses and the staff that keep hospitals functioning.
“I must give credit to the pulmonary critical care group for the daily care and management of the patients. I saw how their team, under the leadership of Dr. Jess Mandel, fine-tuned the treatments and turned the care of patients with COVID-19 into an art,” said Torriani.
“Based on their observations, they developed strategies for steroid use, ventilation management and other necessary lifesaving interventions that were eventually taught to other hospitals in the United States and Mexico.”
In the beginning, only physicians and nurses were permitted inside rooms with COVID-19 patients. It was a matter of prudence and safety, but it also “provided the opportunity to work closely together, which strengthened our working relationship during such a stressful moment in time,” said Segundo.
“It was all hands on deck,” added Kwak. “We were all in the same boat, learning about this disease together. We were supporting each other and had a deep understanding of what we were all going
through and feeling. We were holding each other up through all of the exhaustion. We became like family during this time, and those strong relationships remain.”
COVID-19 changed work streams throughout the hospital. It impacted the hospital’s Environmental Services Department (EVS), who needed to assess and revise cleaning and disinfection protocols.
It Was All Hands On Deck
There was a steep learning curve when the first patients arrived from MCAS Miramar, and initially Environmental Services (EVS) staff did not clean the rooms when patients were to avoid any unintentional contraction of the virus. Instead, nursing staff kept patient rooms clean; EVS crews prepared rooms before and after patients were admitted or discharged. When community spread surged in April 2020, EVS teams transitioned to cleaning rooms with patients to better support over-taxed nurses and doctors.
Throughout the pandemic, Segundo said the tripartite mission of UC San Diego Health — outstanding patient care, groundbreaking research and inspired teaching — was tested, but rose to the challenge.
“As an academic medical center, we had patient care, research and education all happening in one space at the same time. That idea of lifelong learning was an everyday normality for our unit,” Segundo said. “I’m most proud of our resilience. We found ways to be joyful, caring and critical thinkers all at the same time.”
A synergistic effort that helped keep the UC San Diego campus, local schools and community safe.
By Heather Buschman, PhD
Concern for his pregnant wife and soon-to-be-born twin girls prompted one scientist’s obsession with COVID-19 testing,
ultimately leading to a collaborative effort that helped keep the UC San Diego campus, local schools and community safe, and made numerous research projects possible.
Spring
2020
Expecting twin girls, Gene Yeo and Corina Antal thought it would be fun and meaningful to hold their baby shower on International Women’s Day.
The couple was “beyond excited,” but also anxious. They were expecting not just identical twins, but monoamniotic-monochorionic (MoMo) twins, which means the fetuses shared a single placenta and amniotic sac. It’s an extremely rare type of pregnancy, occurring in just one in 60,000 pregnancies. Pregnancies with MoMo twins are considered very high-risk because of heightened dangers of umbilical cord entanglement.
That much Yeo and Antal knew. Now, a new danger loomed.
The baby shower was March 8, 2020. Earlier that week, California Governor Gavin Newsom had declared a state of emergency due to the spread of a novel coronavirus that had only recently been formally named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the cause of coronavirus disease-2019, or COVID-19.
At their baby shower, Yeo and Antal prudently asked everyone to wash their hands as they arrived. Guests laughed at the novelty of elbow bumping instead of hugging or shaking hands, still becoming accustomed to the new public health recommendation intended to help prevent the spread of COVID-19.
Over the next few days, the first local community case would be reported in San Diego County, the World Health Organization would officially declare a COVID-19 pandemic and schools throughout San Diego County would close.
“As scientists, we were not only reading all the studies we could find on MoMo twins, but now we were also learning all we could about COVID-19,”
said Yeo, PhD, a professor of cellular and molecular medicine at UC San Diego School of Medicine. Antal, PhD, is a postdoctoral researcher at Salk Institute for Biological Studies.
Yeo leads a research team focused on RNA, how cells translate the genetic material into proteins, how these processes are regulated and how they can go wrong in diseases like adult-onset muscular dystrophy and ALS. But the COVID-19 pandemic was a crisis of global proportions, and Yeo felt he needed to do something, to help make the world safer for his growing family.
Summer session:
Under strict COVID-19 protocols, several thousand students were able to remain in or move into campus housing.
A few days after the baby shower, Yeo logged into Slack, where many other local researchers were also eager to help.
With their own research programs paused, conferences cancelled, lab teams working remotely and a lot of leading-edge technology shut down and gathering dust, these bored, anxious, smart people were keen to use their time and talents to at least help blunt the coming waves of COVID-19 cases.
What started as a small online discussion for local researchers — a support group of sorts — exploded into a round-the-clock frenzy of activity. Within a few months, nearly 1,000 scientists were sharing information, forming research collaborations, offering available research reagents, technology, sourcing materials and volunteers. (The community later became screencovid.info.)
1000 Scientists Sharing Information
At the time, SARS-CoV-2 was not yet highly prevalent in San Diego. The main and pressing concern was personal protective equipment (PPE) for health care workers. Sudden, high demand worldwide for surgical masks, N95 respirators, paper gowns and gloves produced alarming shortages.
In California, health systems had some wiggle room to shore up supply chains and implement emergency plans, but in places like New York City, hit by one of the first and worst surges of cases in the U.S., some health care workers were forced to repeatedly reuse masks, or even wear trash bags instead of medical-grade gowns. The Slack community of San Diego scientists zeroed in on the PPE problem with unprecedented clarity and cooperation. Yeo helped facilitate that effort, but he had other worries too.
“Due to the difficulty of the pregnancy, we had to go to the hospital often for checkups. I was worried about people around us being masked, about our physicians and nurses getting masks and about getting tested. All of that made me push for more testing for everyone.”
But in this moment, COVID-19 testing capacity was very limited. Until late-February, nasal swabs collected from patients in the U.S. suspected of having COVID-19 needed to be shipped to the Centers for Disease Control and Prevention (CDC) in Atlanta for testing. Getting results took days. Eventually, the U.S. Food and Drug Administration (FDA) allowed hospital laboratories that meet federal regulations for clinical diagnostic testing (CLIA certification) to develop their own in-house tests for COVID-19. That included UC San Diego Health’s Center for Advanced Laboratory Medicine, which ramped up quickly. In mid-March, UC San Diego Health was performing just 20 COVID-19 tests per day; a month or so later, it was performing thousands daily, a rate that continues.
With severely limited supplies, instrumentation and staffing, most testing labs prioritized patients with symptoms of COVID-19, but emerging data suggested the coronavirus was also being spread by asymptomatic people — those who carried and spread the virus without any signs of illness.
“At that time, I wished we had had a better idea of how prevalent the virus was in the community,” Yeo said.
“I knew I’d sleep better if we knew that people, even those without symptoms, were being regularly tested and that those testing positive were being appropriately isolated and treated. That’s what they were doing in Singapore, China, Taiwan and other places. But here we had this silent spread.”
— Gene Yeo
Yeo reached out to a friend and colleague who also knows RNA, Rob Knight. Knight had pioneered the use of bacteria-specific RNA as a “barcode” to read what’s living in a mixed sample, whether soil, ocean water, human stool or just about anything. Over the past decade, he and his team figured out how to scale up the approach. Now, in a global effort known as the Earth Microbiome Project, researchers worldwide are cataloging which bacteria and viruses live where, and determining how the makeup of each of those unique communities, called microbiomes, influence human and environmental health.
The lab of Rob Knight, PhD,
(left) re-deployed staff and resources to help build the EXCITE testing platform, screen wastewater from campus buildings for the presence of SARS-CoV-2 and test surfaces for the virus.
Knight was sheltering in place at home with his partner, a bioinformatician, and their eight-year-old daughter, struggling to balance two work and one school Zooms simultaneously, in a small house not intended for it. Knight is originally from New Zealand, a country known for handling the COVID-19 pandemic differently — and very successfully. Yet even early on, he recognized that his home country’s ability to enforce stricter lockdowns and the advantage of being an island made his family’s situation a bit different than the one he faced in the U.S. Because the COVID-19 case rate was always low in New Zealand, they didn’t need to invest in as much technology to solve the problem.
“It’s the difference between setting your toast on fire, in which case you just need a cup of water to put it out, versus your whole house is on fire and you need a fire truck,” said Knight, PhD, professor at UC San Diego School of Medicine and Jacobs School of Engineering and director of the Center for Microbiome Innovation.
“So we decided to build the fire truck.”
Yeo and Knight Slack-messaged and emailed everyone they could think of in San Diego to ask how many thermal cyclers they had.
“We had this crazy plan to bring them all together in one spot to run tests,”
— Gene Yeo
“And then Louise chimed in on Slack and said that she not only had the instruments, she’d been miniaturizing the COVID test and it’s all in her lab, just one floor up from mine.”
Thermal cyclers and PCR:
How SARS-CoV-2 is detected.
The entirety of SARS-CoV-2 genetic code is contained in just one small length of RNA. (In contrast, the human genome is comprised of double-stranded DNA that needs to be transcribed into RNA, then translated into proteins.) SARS-CoV-2 doesn’t need to carry around much else because once it enters a human cell, it relies on host machinery to do all the work of translating viral RNA instructions into proteins that ultimately result in making more viral particles. A COVID-19 test is considered “positive” when it detects unique bits of SARS-CoV-2’s RNA. One of the most reliable tests uses quantitative polymerase chain reaction (qPCR), a common laboratory technique used to detect and amplify genetic material of all types. Lab technicians isolate genetic material from a nasal swab sample, mix it with special chemicals and put it into a machine called a thermal cycler. The thermal cycler repeatedly heats and cools the mixture. If the coronavirus’s RNA is present, the tell-tale genes are amplified, making many more copies of them. During this amplification process, one of the special chemicals is converted into a fluorescent molecule that is detected by the thermal cycler.
Louise C. Laurent, MD/PhD Vice-Chair for Translational Research and Director of Perinatal Research for the Department of Obstetrics, Gynecology, and Reproductive Sciences
At the time, Louise Laurent already had what sounds like multiple jobs:
As a perinatologist, she cares for women with high-risk pregnancies. She runs a research lab focused on understanding the molecular mechanisms involved in human development and looks for molecular clues that could help predict or diagnose pregnancy complications. She’s also a mother of four: two in high school and two in college.
“I’ve long been interested in the process of fetal development, labor and birth — something we all go through, yet we don’t understand all that well. Women’s reproductive health has always been a little bit of a second-priority type of thing when it comes to research and funding,” said Laurent, MD, PhD, professor of obstetrics, gynecology and reproductive sciences, vice chair for translational research and co-director of the Center for Perinatal Discovery at UC San Diego School of Medicine
The due date for Yeo and Antal’s twins was fast approaching. At one of the couple’s hospital visits, they were pleasantly surprised to see Laurent, the on-call perinatologist, walk into the room. She went over the monitoring and birth plan with them.
“It was so funny to suddenly see this person that I’d been talking to professionally by email about thermal cyclers, here to help us take care of our twins, too,”
— Gene Yeo
In early April, Antal was admitted to Jacobs Medical Center at UC San Diego Health for observation.
On April 14, at 32 weeks gestation and via Cesarean section, Antal and Yeo welcomed their MoMo twins, Emilleen and Emabelle, who each weighed approximately three pounds.
MoMo Twins
Monoamniotic-monochorionic (MoMo) twins share a single placenta and amniotic sac. It’s an extremely rare type of pregnancy, occurring in just one in 60,000 pregnancies.
Monoamniotic
Despite their umbilical cords being knotted together, there were no critical complications at birth. But because both twins were high-risk and born a bit prematurely, the girls were admitted to the neonatal intensive care unit (NICU) for observation. Yeo and Antal visited their “California burritos,” as they called them, in the NICU every day, masks on. “I always looked around just to make sure that all the nurses and doctors had their masks on as well,” Yeo said.
“And it was scary, and almost surreal, that we just had these fragile babies in the middle of what felt, at times, like an apocalypse.”
Between NICU visits, the quest to test helped Yeo channel his anxious energy. RNA is a notoriously finicky molecule that easily degrades. Yeo, Knight, Laurent and their teams countered with experience and resources.
Knight’s lab had something most academic labs do not: Automated lab machinery that can extract RNA from many distinct samples simultaneously. Laurent’s lab was already running concurrent qPCR tests on RNA as molecular clues to predict pregnancy complications and working out how to miniaturize the process so they could run even more tests with fewer materials. Yeo’s lab had experience with computational biology. They introduced an information management system to keep track of samples, experiments and data.
“We glued all the pieces together, and had an idea of how we could track samples all the way through the workflow from extraction to qPCR to result,” Yeo said. “But the problem was still that we’re not virologists or epidemiologists.”
Yeo, Knight and Laurent teamed up with Slack community members Kristian Andersen, PhD, whose lab at nearby Scripps Research was known for using genomics and computational biology to investigate emerging infectious diseases, such as Zika and Ebola, and Lauge Farnaes, MD, PhD, assistant medical director at Rady Children’s Institute for Genomic Medicine. The team set up an experiment: A drive-through site near Rady Children’s Hospital-San Diego, where they could collect nasopharyngeal swabs from study participants, all of whom were invited health care workers and firefighters.
In the first two months, the team screened more than 10,000 participants, mostly asymptomatic, and found that an average of two participants per every 1,000 carried SARS-CoV-2. In addition to looking for the virus itself (sign of an active infection), the researchers tested participants who hadn’t been diagnosed with COVID-19 to see if they had antibodies against the virus (a sign of a past infection), to better gauge the extent to which SARS-CoV-2 was spreading undetected.
Summer
2020
In mid-May, Emilleen and Emabelle were ready to graduate from the NICU.
“When we finally got home, it’s probably an understatement to say that I was a bit distracted by them,” Yeo said. “There were so many meetings, even when I was chairing a session or giving a talk, where one of the babies was screaming and I had to go grab her and hold her before I could continue.
“There were so many times I had to text Rob and Louise to say that I couldn’t make a meeting, but they have kids too, so they get it. Everyone has been so understanding. I even learned to delegate, to give more freedom and independence to the people in my lab, and they’ve done amazingly well.”
The COVID-19 screening study at Rady continued to hum along, boosted by a donation from philanthropists Gary and Jean Shekhter, but it wasn’t an easy or simple operation.
Volunteers and lab staff transported samples around town, from the drive-through to Yeo and Laurent’s labs on one side of UC San Diego’s La Jolla campus, to Knight’s lab on the other, to Andersen’s lab down the street.
The collection and testing process was not CLIA-certified, so any positive samples needed to be sent back to the clinical laboratory at Rady Children’s Hospital for re-testing, confirmation and communication to the participant.
“Everything we did was considered part of a research study, not a clinical diagnostic test,” Knight said. “The drive-through worked, but it wasn’t the most efficient or cost-effective process. We tweaked and optimized, learning everything there is to know about running a large-scale viral testing facility.”
In early July, COVID-19 cases surged in San Diego and the drive-through site closed down so staff could be redeployed to patient care. But soon after, the team’s original dream of “everything in one place” was realized, and a new COVID-19 testing facility was born: Expedited COVID IdenTification Environment, or EXCITE.
The Department of Pathology at UC San Diego School of Medicine had two small laboratory spaces they had been reserving for new faculty, but with hiring and onboarding delayed due to the pandemic, the empty space was offered to EXCITE.
Laurent submitted the paperwork to extend an existing CLIA license, previously granted to the Biochemical Genetics Lab in the Department of Pediatrics, to include EXCITE in late-August; approval came September 4. Eleven days later, the team completed clinical validation of their COVID-19 qPCR test.
EXCITE runs COVID-19 tests in a mostly-automated assembly line, from intake to RNA extraction to qPCR and detection. Samples to be tested are barcoded so technicians don’t handle private patient information. Everything is tracked by the laboratory information management system and, depending on the source, test results are reported directly to patients’ electronic medical records or the physician leading a partner program. All positive results are also reported to San Diego County’s public health office.
A bonus is redundancy. The lab runs COVID-19 tests on a different platform than the Center for Advanced Laboratory Medicine at UC San Diego Health, which Yeo says helps safeguard against shortages. If one site is down for some reason, the campus will still have the other.
Laurent says one of the upsides of the pandemic has been the opportunity to work with so many different people. Before EXCITE, she had worked with Knight on a few small projects to study changes in the gut microbiome during pregnancy. Yeo’s research lab is in the same building as hers.
“But it’s a lot different when you actually have to start a lab with someone — buy equipment, hire people and all that,” she laughs. Yeo calls the group his “COVID buddies.”
“We routinely run about 3,000 tests a day without really breaking a sweat,” Laurent said, “and we could double that without too much trouble if we had to.”
While the Center for Advanced Laboratory Medicine at UC San Diego Health continued to be the health system’s primary testing facility for tens of thousands of staff, patients and other community members, EXCITE played an integral role in UC San Diego’s Return to Learn program, a science-informed approach that allowed the university to continue to offer on-campus housing and in-person classes and research opportunities throughout the pandemic. Largely because EXCITE could provide regular asymptomatic testing of all students, staff and faculty, the university hosted approximately 10,000 students on campus in the fall of 2020, maintaining a positivity rate of less than 1 percent, generally 10 to 15-fold lower than the surrounding community.
But even Return to Learn didn’t max out EXCITE’s testing capacity. Testing services were soon extended to local fire departments and schools.
“I’m proud that we’re serving populations that weren’t necessarily the first priority in the pandemic — children, students, frontline workers,” Laurent said.
“We’re serving a need that might not otherwise have been served.”
Laurent and team quickly kicked EXCITE into high gear, managing 20 people working two shifts, seven days a week.
Winter
2020
On December 15, the first COVID-19 vaccines arrived in San Diego, going first to health care workers and COVID-19 testing and research lab staff.
“After nine months of relentless bad news, the announcement that a vaccine was developed faster than for any virus before was an amazing piece of good news — even leading some to think the pandemic would be over soon,” Knight said.
Vaccine optimism helped blunt the disappointment of the holiday season. None of EXCITE’s leadership was able to see extended family: Yeo’s parents live in Singapore, Laurent’s in Kansas and Knight’s in New Zealand. One of Laurent’s daughters was unable to come home from college in Canada for fear she wouldn’t be able to return to school. Knight’s daughter hadn’t touched another child in nine months. Yeo and Antal celebrated Emilleen and Emabelle’s first Christmas quietly at home, just the four of them, opening presents with their extended family over Zoom.
Then Came the Variants
Detecting Variants
Genetic mutations are extremely common in most viruses, which replicate quickly. Most variations have no effect on disease, but scientists around the world watched for the emergence of SARS-CoV-2 “variants of concern.” One of the first to make headlines was detected in the United Kingdom. It was called B.1.1.7, a variant with more genetic changes than most, some of which affect the spike protein — the molecule the virus uses to bind and infect human cells. Based on early data, the B.1.1.7 variant seemed likely to spread from person to person more readily.
On December 28, EXCITE received an alert from the CDC to be on the lookout for an “S dropout,” a sign that a positive COVID-19 test may be the B.1.1.7. variant. In a regular positive qPCR test, three SARS-CoV-2-specific genes light up. In a positive test with S dropout, only two of the three tell-tale genes show up. What isn’t detected is the bit of RNA that codes for the spike protein (“S”) because it’s mutated in B.1.1.7.
On December 29, an EXCITE technician spotted the tell-tale “S dropout” in a test sample. The team drove the sample over to Scripps Research, where Andersen’s lab labored through the night to sequence the full genome of the virus in the sample. They confirmed the first known case of the B.1.1.7 variant in California. It was a local man in his 30s who had not recently traveled, indicating the variant was already spreading in the community.
“It’s not random chance that we were the first to detect B.1.1.7 in California. It wasn’t because it wasn’t anywhere else. It’s because we were looking for it,”
Knight said, “and because we already had highly trained EXCITE staff, sequencing built into our workflow thanks to close collaboration with Scripps Research, support from our own research lab members, as well as the cooperation of many campus administrative units that quickly turned around the various approvals we needed to be able to do this work with patient samples, between two different organizations.”
Spring
2021
More than a year into the COVID-19 pandemic, EXCITE has evolved into not just a high-throughput clinical testing lab, but also a research hub.
“We’re available to any researcher in San Diego who has a question about the virus that we can help answer through testing and sequencing. For example, how long does the virus survive on surfaces? What kills it? How does it evolve under certain conditions?” Laurent said.
Despite increasing vaccination rates, Laurent said it’s still critically important to understand where the virus lurks, who is most likely affected and how best to deploy resources.
“There are still many areas of San Diego, and the country, that are disproportionately affected by COVID-19 and experience a number of barriers to health care, testing and vaccination. We need to overcome these to reduce health disparities.”
To that end, Laurent is involved in two projects supported by Rapid Acceleration of Diagnostics (RADx) grants from the National Institutes of Health. One study seeks to maximize COVID-19 testing among pregnant women and children in an area of San Diego near the U.S.-Mexico border with the highest local incidence of COVID-19. In the other, a team is working to enhance asymptomatic COVID-19 testing capabilities at three regional community health centers in San Diego County.
Milestones:
In April 2021, Gene Yeo and Corina Antal celebrated Emilleen and Emabelle’s first birthday the same way they had all previous holidays. The four of them stayed home, Zooming with family. At one year old, the twin girls still hadn’t met their grandparents in person.
Sequencing Remains a High Priority
“We’re furiously trying to expand sequencing of positive samples so we can build phylogenetic trees — maps that help us track how the virus is evolving and when and where new variants of concern may be emerging,” Knight said.
“Fortunately, especially compared to one year ago, we have more funding and more equipment, and we are expanding sequencing capabilities rapidly.”
Sequencing SARS-CoV-2 samples also allows researchers to explore some interesting questions. For example, UC San Diego researchers are sequencing samples from patients with severe cases of COVID-19 in the intensive care unit to see if the viruses infecting them differ genetically from those causing milder disease in other people.
Another UC San Diego team is working with EXCITE to sequence SARS-CoV-2 samples repeatedly collected from the same patient over time. The patient has a blood cancer and has undergone chemotherapy, leaving him with next to no immune cells. For months, the patient has continuously tested positive for COVID-19 because his body has no way to get rid of the virus. As his physicians work to get him well enough to resume chemotherapy, researchers are sequencing his samples to keep tabs on how the virus may mutate as it replicates without restraint.
On April 12, most of San Diego’s children — including Laurent’s — were finally given the option to return to in-person learning. They had been attending school remotely via Zoom for 13 months. The same week, Yeo and Antal celebrated Emilleen and Emabelle’s first birthday the same way they had all previous holidays. The four of them stayed home, Zooming with family. At one year old, the twin girls still haven’t met their grandparents in person.
“It was hard at first, but as more testing happened and we were more reassured that the right behaviors were being adopted in our community, we realized that we’re going to be fine. The girls are thriving now,” said Yeo.
If there’s a silver lining to the pandemic, Yeo said it’s that he was able to be home all year, rather than traveling around the world giving talks, something he used to do almost on a weekly basis.
“Instead, I’ve had this once-in-a-lifetime opportunity to work with some amazing colleagues, to help keep people safe during a crisis and, most importantly, to learn how to be a father.”
Nicaragua:
A Government in Testing Denial
By summer 2020, Nicaragua’s hospitals were filled to capacity with patients suffering from respiratory infections. Doctors and nurses were dying. The nation’s health system was collapsing. For more than two years, the government had been suppressing protests on a variety of topics, often with guns and violence. Everything was fine, it insisted, downplaying the COVID-19 pandemic. Health care workers lacked personal protective equipment and other critical resources. Access to testing was rare. No one knew the true extent of the public health crisis in Nicaragua. Jorge Huete-Pérez, PhD, of the Molecular Biology Center at University of Central America in Nicaragua’s capital city of Managua, was alarmed and frustrated. He shared both with an old colleague: James McKerrow, MD, PhD, dean of Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego. The pair began collaborating to investigate COVID-19 infection rates among Nicaraguan health care workers.
They quickly discovered that a study conducted with relative ease in most countries was notably complicated in Nicaragua. A collaborator was fired for voicing concern about the failed management of the crisis. Many health care workers were afraid that they would be fired from their jobs for participating in the study. Despite these challenges, the researchers published their findings in January 2021: approximately 30 percent of participants had been infected with COVID-19. Nearly 55 percent of those who tested positive were asymptomatic and still treating patients. —Heather Buschman, PhD.
