Caring for COVID-19 Patients:
Department of Medicine Comes
Together to Serve Community
Impacted by COVID-19

From the beginning of the COVID-19 pandemic, through two surges, and now during a “new normal,” one thing has never changed: The Stanford Department of Medicine staff and faculty have provided the best care possible to their patients, offering hope during a dark time.

Doctors, trainees, and staff held patients’ hands, arranged Zoom calls to family members, and performed clinical trials to find drugs to treat the virus.

Dedicated members from the infectious diseases, pulmonary and critical care medicine, and hospital medicine groups worked together to provide inpatient care for their COVID-19 patients, bolstered by Department of Medicine leadership and volunteers from other divisions and departments.

They found meaning in providing this necessary care and are proud to have come together to serve their community during this unprecedented time.

Infectious Disease at the Forefront

When the novel coronavirus started spreading within and beyond China in early 2020, people throughout Stanford Medicine began making plans for handling infected patients. According to laboratory tests, COVID-19 patients began showing up at Stanford clinics in late February and early March. By mid-March, elective surgeries were put on hold, visitors were temporarily barred, and medical students paused their clinical rotations. A few days later, the governor of California announced a statewide lockdown.

When COVID-19 patients arrived, infectious disease (ID) doctors were ready. They created a consult service specifically for COVID-19 patients at the Stanford Hospital. “We were very much at the forefront of providing care from the very beginning at Stanford,” says Upinder Singh, MD, professor and division chief of infectious diseases. “Even early in the pandemic, we were comfortable with infection control practices, and we have experience seeing patients with new emerging infections.”

Early on, with so little known about the virus, there was much anxiety about how it spread, how to protect patients and staff, and the best way to treat the infection. No one knew the right time to intubate a struggling patient or which drugs could be repurposed for treatment.

In that first month, new study results appeared daily, sometimes with conflicting results. Shanthi Kappagoda, MD, clinical associate professor of infectious diseases, sorted through the information to develop clinical care, education, and treatment guidelines, in concert with colleagues in hospital medicine and pulmonary and critical care medicine.

“When we saw our first hospitalized COVID-19 patients at Stanford, there were almost no clinical trial data on how to treat COVID-19 and no national guidelines,” says Kappagoda. “At the same time, there was a flood of anecdotal information from colleagues in Seattle, Boston, and New York, which changed from day to day.”

Kappagoda and David Ha, PharmD, infectious diseases pharmacist, worked with a committee of clinicians to develop evidence-based treatment guidelines and present them in a simple, easy-to-disseminate format.

“We are fortunate in the ID division to have a deep bench of virologists, immunologists, and data scientists who helped us assess the early data—in vitro, preclinical, and clinical—and sift out what could help us improve our care and what experimental therapies were likely to cause harm,” says Kappagoda. “As chair of the ID COVID-19 treatment guidelines committee, I am proud of how our division stepped up to support the Department of Medicine.”

Infection Control

Another key role of the ID division is keeping patients and staff safe through infection control. Lucy Tompkins, MD, PhD, Lucy Becker, professor of medicine and microbiology and immunology, and the hospital epidemiologist for Stanford Health Care, has carried the enormous burden of halting the spread of infections within the hospital, including COVID-19. “It’s been a nonstop job,” she says—the hardest of her 38 years at Stanford.

Along with a team of nine infection preventionists, including Sasha Madison, administrative director of infection prevention and control at Stanford Health Care, Tompkins decides, implements, and enforces infection control policies, covering correct testing and quarantine protocols and the use of proper personal protective equipment (PPE) for each medical procedure.

“The infection control group was dealing with changing guidelines that were morphing on a daily basis,” says Marisa Holubar, MD, clinical associate professor of infectious diseases, who was also involved in infection control efforts. She says it was challenging to take in and communicate that information effectively to the thousands of staff members at the hospital and clinics. “Our efforts really minimized the exposure of health care workers to COVID-19 in the hospital. We armed them with information so they could protect themselves.”

A swab awaits testing for COVID-19 in the Clinical Virology Laboratory

Benjamin Pinsky, MD, PhD

Stanford Hospital and the clinics were fortunate to have adequate PPE supplies throughout the pandemic to keep staff and patients safe. The single occupancy rooms at the new hospital helped with patient isolation.

Tompkins oversees contact tracing within the hospital in the event of an outbreak. Only once was there an exposure event where a patient infected staff members—resulting from a false negative COVID-19 test at another facility. She reviews each hospitalized COVID-19 patient’s chart to determine when the person can leave isolation, using a diagnostic test developed by Benjamin Pinsky, MD, PhD, associate professor of pathology and infectious diseases, and medical director of the Clinical Virology Laboratory for Stanford Health Care.

Family visitation falls under Tompkins’ purview. She has been instrumental in enacting protocols for safe visitation, which resumed in March 2021. “I think that is the only humane thing to do, especially for patients who are truly ill and when they’re going to be in the hospital for any length of time,” says Tompkins.

Making Progress through Clinical Trials

ID faculty began enrolling patients in clinical trials early on—the first on March 14, 2020. Aruna Subramanian, MD, clinical professor of infectious diseases, and Philip Grant, MD, assistant professor of infectious diseases, participated in trials for remdesivir, which is now the backbone of patient treatment. They were involved in the National Institutes of Health (NIH) Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV-1) trial, which evaluated several immune modulators for their ability to tamp down an overactive immune response in COVID-19 patients. They collaborated with hospital medicine and pulmonary, allergy, and critical care medicine teams. Grant led the Johnson & Johnson vaccine trial at Stanford.

“It’s unbelievably gratifying to be involved in trials that were effective,” says Subramanian. “Patients were so interested in getting treatment, you could see the gratitude on their faces.”

With support from the Dean’s Office, Catherine Blish, MD, PhD, professor of infectious diseases, set up a state-of-the-art biosafety level 3 lab space so that researchers could safely study cultures of the virus—an improvement over their previous smaller space.

“There was just an amazing amount of work they did behind the scenes,” says Subramanian. “I feel like the entire ID group was involved in so many aspects of COVID-19, not always known to the world.”

Hospital medicine faculty members also participated in clinical trials from the earliest days of the pandemic, under the leadership of Neera Ahuja, MD, clinical professor of medicine, and Kari Nadeau, MD, PhD, Naddisy Foundation Professor of Pediatric Food Allergy, Immunology and Asthma.

At Stanford Hospital, Nidhi Rohatgi, MD, clinical associate professor of hospital medicine; Jessie Kittle, MD, clinical assistant professor of hospital medicine; Andre Kumar, MD, MEd, clinical assistant professor of hospital medicine; Rita Pandya, MD, clinical assistant professor of hospital medicine; and Jeffrey Chi, MD, clinical associate professor of hospital medicine, participated in the NIH Adaptive COVID-19 Treatment Trial (ACTT) that led to the approval of remdesivir and the granting of emergency use authorization for the anti-inflammatory drug baricitinib. This clinical trial was the first ever conducted at ValleyCare, Stanford Health Care’s sister hospital located in the East Bay’s Tri-Valley region, through the efforts of Evelyn Bin Ling, MD, clinical assistant professor of hospital medicine; Minjoung Go, MD, clinical assistant professor of hospital medicine; and David Svec, MD, MBA, clinical associate professor of hospital medicine. “When COVID-19 hit in March, we had a sense of urgency to bring more COVID-19-related studies to the university and to ValleyCare, and to make that available for patients,” says Ling.

This clinical trial was the first ever conducted at Stanford ValleyCare

Minjoung Go, MD reviews procedures

Stanford ValleyCare faculty and staff on the first day of clinical trial enrollment

Rohatgi enrolled the first Stanford patient in the ACTT trial. “It was heartwarming to see how much our patients trust us,” she says. “They were willing to contribute to science just based on that trust so we could find an answer for other patients.”

Rohatgi was also the site principal investigator on the COVACTA clinical trial for tocilizumab, a monoclonal antibody that modulates the immune response, which is now part of the treatment algorithm for patients with worsening COVID-19 symptoms, and on the NIH ACTIV-5 trial. She and her colleagues worked with others in emergency medicine to investigate the combination of monoclonal antibodies with remdesivir. “With the question of resistant strains coming up all across the world, we want to be prepared with more therapeutics,” says Rohatgi. “We don’t know what the next few years of our life are going to bring.”

Looking to the future of post-COVID-19 surgeries, Rohatgi is involved in research on surgical co-management, a system where hospitalists partner with surgeons to prevent postsurgical complications. The coronavirus can wreak havoc on multiple organ systems, so Rohatgi and colleagues are investigating whether surgical patients who had COVID-19 have different outcomes compared with patients who didn’t contract the virus.

Lisa Shieh, MD, PhD, clinical professor of hospital medicine, led multiple quality improvement studies to institute stronger safety protocols, leading to better patient outcomes. In one study, her team sent each patient home with a pulse oximeter, which measures the blood oxygen saturation level. “I always worry about patients when we discharge them,” says Shieh. The oximeter results were vital for follow-up telemedicine visits and informed patients if their symptoms had worsened and they needed to return to the hospital.

Through these diverse studies, the hospital medicine faculty endeavored to learn more about the novel coronavirus to provide the best possible care for COVID-19 patients, now and in the future.

Hospital Medicine Faces the Pandemic Head-On

The hospital medicine division saw the majority of COVID-19 patients throughout the pandemic, providing care as case numbers waxed and waned.

“All of the non-ICU symptomatic COVID-19 patients were admitted to our general medicine wards,” says Ahuja. The hospitalists quickly adapted to caring for these patients, protecting themselves with proper PPE and working with IT to develop “Zoom rooms” to connect with patients’ family members. In collaboration with ID and the ICU, they established the protocol for patient care early on, and Ahuja was frequently asked to share their clinical COVID-19 guidelines.

The hospital had braced for an influx of patients at the pandemic’s start, but thanks to the state lockdown, that spring surge never happened. In fact, the hospital was eerily empty, with elective surgeries paused and many non-COVID-19 patients staying away for fear of the virus. This was a stark change from the new hospital’s opening in late 2019, when it was filled with patients and family.

The first surge finally hit in July. Chief residents organized surge teams for the general COVID-19 wards, staffed primarily by volunteer internal medicine residents. Cases dropped off again, and the surge teams ended in early fall. In hindsight, this small wave was a warm-up for the larger surge that hit in November.

The Winter Surge

As in many parts of the country, COVID-19 cases ramped up quickly in mid-November. At the peak of the surge, the general wards held more than 100 patients, about half of them with COVID-19. Chi organized faculty to staff the surge teams. “People were going two weeks, or in some cases even three weeks, straight without a day off,” he says.

“Seeing that spirit of camaraderie, and the willingness to serve, was just heartwarming for me,” says Ahuja. “Some of my faculty are young and have small children at home. Some were actually pregnant themselves, and they never said no. They just showed up time and time again, ready to serve our patients.”

Other divisions loaned their faculty to staff the surge teams, adding to the spirit of collaboration.

Ultimately, about 20% of patients from the general COVID-19 wards were transferred to the ICU, but some returned and recovered. Overall, the COVID-19 mortality rate at Stanford Hospital reached just 6%, far lower than the average U.S. in-hospital mortality rate of 13.6%.

The sacrifices of the hospitalists were perhaps most acute during the holiday season. Physicians often work holidays, but staff couldn’t even gather at work to celebrate during the pandemic. Many faculty and staff decided to isolate from their families for fear of bringing the virus home.

Poonam Hosamani, MD, clinical associate professor of medicine, was not yet vaccinated during the winter surge, so she sent her husband and 4-year-old daughter to live with her elderly parents. She celebrated Christmas and New Year’s with her family over Zoom.

Of course, the holidays were more difficult for the patients. Hosamani was shocked by how many patients had multiple relatives also hospitalized due to COVID-19.

Underserved Communities

Throughout the pandemic, suffering concentrated within families. People with multiple infected family members often were Latinx and lived in multigenerational households where strict quarantining wasn’t possible. Many of these patients were essential workers. At one point, a mother and son were in adjacent rooms. The mother went home, but the son didn’t recover.

“It was patients that were otherwise underserved or didn’t have easy access to the health care system that were most dramatically hit by COVID-19 infections,” says Mita Hoppenfeld, MD, internal medicine chief resident, who organized residents on the surge teams in the general wards. “That was really tough to see because you knew that their recovery would be rough and that they didn’t have the financial means to make that recovery easier.”

Hoppenfeld also cared for patients—many from the same underserved populations—who put off necessary care for fear of the virus. One patient had suffered a heart attack but waited five days to seek help. Three of her patients were recovering from opiate use disorder but relapsed or suffered from withdrawal when they couldn’t access necessary medication through methadone clinics or pharmacies. “It was really sad to see people who are on the path to recovery having this issue,” says Hoppenfeld. “There was no good safety net for these patients.”

COVID-19’s disproportionate socioeconomic impacts were especially apparent in the patient demographic data collected by William Collins, MD, clinical assistant professor of hospital medicine. He began these efforts in spring 2020 to help with pandemic planning and put a human face on the suffering caused by COVID-19. “One thing that was very apparent from our data from early on was disparities—certain communities were obviously more affected than others,” says Collins. He frequently presented his data to the larger Stanford Health Care community during virtual grand rounds, organized and hosted by Errol Ozdalga, MD, clinical associate professor of hospital medicine. These conferences sometimes attracted more than 800 viewers.

One elderly Latinx man who was a former physician was cared for by Ahuja. When it became clear that he would not survive, he requested to go home to be in hospice. Soon after his death, his wife sent a thank-you card.

“It’s so heartbreaking, and it almost brings tears to my eyes remembering this,” says Ahuja. “She should have been focusing on her grief and her family, but she took the time to reach out and thank us for listening to their request.”

The Pandemic’s Sickest Patients

Throughout the pandemic, the pulmonary, allergy, and critical care medicine division cared for COVID-19 patients with the most severe infections in the ICU. Besides respiratory symptoms, patients presented with kidney problems, strokes, blood clots, heart conditions, and metabolic issues that interfered with blood sugar control.

To address these complex issues, Angela Rogers, MD, associate professor of pulmonary and critical care medicine, chaired a multidisciplinary Stanford COVID-19 Critical Care Task Force. In the early days, it met for three hours each week and numbered up to 50 people. Members came from hospital medicine, anesthesia, emergency medicine, surgery, infectious diseases, neurocritical care, respiratory therapy, nutrition, and other divisions to weigh in on patient treatment. The group also announced new clinical trials being held at Stanford.

“Stanford’s response was amazing,” says Rogers. “Just the way people came together to take the best care of their patients was really remarkable.”

Angela Rogers, MD (left), reviews treatment guidelines for patients with COVID-19 with a colleague

When the pandemic started, there were few COVID-19 patients but a huge need for clinical trials to understand how best to care for them. Like colleagues in hospital medicine and ID, Rogers; Joseph Levitt, MD, assistant professor of pulmonary and critical care medicine; and Jenny Wilson, MD, clinical associate professor of emergency medicine, recruited sick patients into numerous NIH multicenter clinical trials, for therapies including hydroxychloroquine and multiple monoclonal antibodies and anticoagulants.

Stanford’s multidisciplinary teams also enrolled more than 500 patients into a Stanford COVID-19 biobank, led by Blish; Samuel Yang, MD, associate professor of emergency medicine; Andra Blomkalns, MD, professor of emergency medicine and the Redlich Family Professor; Nadeau; Rogers; and Ruth O’Hara, PhD, senior associate dean of research and Lowell W. and Josephine Q. Berry Professor of psychiatry and behavioral medicine. O’Hara was instrumental in instituting the research infrastructure necessary for biobanking and conducting trials.

“Stanford, from its earliest days, has really tried hard to enroll people into as many clinical trials as we can to quickly improve the care of our patients,” says Rogers. “The vast majority of patients admitted to Stanford with COVID-19 have been approached to participate in biobanking and potential clinical trials. We have worked hard to use all of Stanford’s resources to try to learn from our patients.”

Isolation in the ICU

Christopher Thomas, MD, a chief pulmonary and critical care medicine fellow, said that among all the challenges of treating COVID-19 patients in the ICU, the hardest was communicating with family at home over the phone or Zoom, especially when discussing end-of-life care. “Normally, if someone were dying, you would have the family come in and have a conversation—you’d have 10 people in the room—and they could spend as much time as they wanted,” says Thomas. “It made a particularly tough thing that much harder.”

Due to the disparities in the most affected populations, many of those tough conversations took place in Spanish, Mandarin, or Tagalog, usually through a translator. Thomas recalls one young patient in his mid-30s who had been in the ICU for a week, struggling despite being on high-flow oxygen. Thomas communicated to his wife through a Spanish translator that intubation was the best course of action. He could hear the man’s two small children in the background. While some patients never came off the ventilator, Thomas’ patient ultimately went home to his family.

When the surge hit the ICU in November, more and more physicians were pulled onto the surge teams to care for patients. Rogers and Arthur Sung, MD, clinical associate professor of pulmonary, allergy, and critical care medicine, gathered faculty members to staff teams. Paul Mohabir, MD, clinical professor of pulmonary, allergy, and critical care medicine, and Ann Weinacker, MD, professor of pulmonary, allergy, and critical care medicine, were also instrumental in coordinating the response. As patient numbers grew, two teams grew to four, with teams caring for 15 patients each. The ICU even received overflow patients from as far away as Imperial County, on the border with Mexico.

Internal medicine residents, pulmonary and critical care medicine fellows, and critical care medicine fellows performed the bulk of the ICU care, along with hardworking respiratory therapists and the nursing, transportation, and environmental staff. Members of the departments of surgery, anesthesia, and emergency medicine also contributed to patient care in Stanford’s multidisciplinary ICU.

At its peak, the ICU held about 45 COVID-19 patients, but modeling predicted that case numbers might rise to 80 or 90. The task force had contingency plans to convert inferior spaces into hospital rooms, assign extra patients to each nurse, and reduce time off. Fortunately, after the winter holidays, the caseload flattened and the ICU was never overwhelmed, as occurred elsewhere in the country.

“We were able to give our full care to every patient,” says Rogers. “We’re proud, we’re tired. But it never got as bad as we feared.”

Small Victories

There were some bright spots in the ICU during the pandemic. While many critical care patients never leave the ICU, large numbers of COVID-19 patients recovered. Staff rang bells and cheered as long-term patients were wheeled off to rehab.

“Seeing people get better in the ICU was really encouraging and really something that made me interested in doing pulmonary and critical care,” says Kyle Fahey, MD, a resident who gave up two of his rotations to volunteer in the ICU. “There was a really strong sense of camaraderie in the COVID-19 ICU. I think that was a big part of what made it so bearable, even given the difficult circumstances.”

Carrie Cao, MD, a second-year resident, initially had selected a different specialty, but her time volunteering in the COVID-19 ICU ward crystallized her interest in pulmonary medicine and critical care, and she has now switched her focus

“Every COVID extubation was really emotional,” says Cao. “It felt like a victory.”

Despite the utter exhaustion that many physicians have felt after caring for COVID-19 patients in the last year, Rogers and others said that it was an honor to serve their community and it brought them a deep sense of fulfillment.

“I’ll have this experience for the rest of my life as I take care of people,” says Thomas. “Overall, it’s confirmed that this is where I’m meant to be.”

Residents and Fellows—the Foundation of COVID-19 Patient Care

The pandemic touched everyone, but it especially disrupted the lives and education of residents. “The residents and fellows have really stepped up to provide care for these patients in every single way,” says Hosamani, who serves as an associate program director of the Stanford Internal Medicine Residency Program.

In mid-March 2020, leadership within the residency program took steps to protect their trainees. They moved the Morning Report meetings and the Daily Core Curriculum Conference—the residency program’s main educational components—to an online format. Initially, they feared this was an overreaction, but soon they realized it was the right decision.

This transition to online interaction was especially difficult for the first-year residents who arrived in June 2020 during the pandemic. Their orientation was remote, and they lost out on the bonding and in-person social events that balance the many demanding aspects of residency.

Residents also saw patients remotely, and Hosamani was impressed by how quickly they adapted. “Knowing that telemedicine and telehealth initiatives are probably the way of the future, it’s been wonderful to see them learn those strategies and implement them as they enter the clinical setting.”

Residents were especially instrumental in keeping family members updated on patient care. Hoppenfeld recalls seeing the residents she oversaw staying late into the night, making calls to reassure family members that someone was looking out for their loved one. Residents also acted as IT, helping people at home to download Zoom and use the app to talk with patients.

Learning in a Pandemic

During the summer and winter surges, residents gave up their normal rotations to volunteer for the surge teams that cared for COVID-19 patients.

“It was clear that the residents were going to be a critical part of our ability to care for the community and were one of the most valuable resources at Stanford,” says Ronald Witteles, MD, professor of cardiovascular medicine and program director for the internal medicine residency program. “You’re talking about a group of people who understand the logistics of the hospital and how to get things done.”

Chief residents Andrew Moore, MD (left), and Mita Hoppenfeld, MD (right), organized residents to staff the surge teams during the height of the COVID-19 pandemic

Residents from otolaryngology (ear, nose, and throat), psychiatry, and urology—doctors who rarely treat infectious disease—stepped in to take shifts on the surge teams. Residents worked more than 80 hours per week to ensure that COVID-19 patients received the best possible care.

“It’s just been unreal. I never imagined being a trainee during a pandemic of this magnitude,” says Cao. “There were a lot of really fast-paced changes this past year, as well as really emotional moments, both in terms of caring for patients and this sense of we’re all in this together.”

The ‘COVID-19 Generation’

Andrew Moore, MD, chief resident, who helped organize and staff the surge teams, is proud of the residents for offering excellent care under the difficult surge conditions. “It’s been a tough year, and residents have really, really stepped up in ways that have been incredibly inspiring for me.”

Moore also applauds the Department of Medicine for advocating for residents and fellows to be first to receive the COVID-19 vaccine. After the algorithm used to plan vaccine distribution left out most residents and fellows due to their young ages, some Department of Medicine faculty refused vaccination until their trainees were protected. Within days, the administration included these groups, who had been so vital for patient care. “That really speaks to how much this department values their residents and how much they recognize how hard we work to keep patients safe,” says Moore.

“It’s been a tough year, and residents

have really, really stepped up in ways that

have been incredibly inspiring”

Despite—or because of—these tremendous challenges, the pandemic has been an incredible learning experience for residents and fellows.

Ralph Tayyar, MD, an infectious disease fellow, arrived during the July surge. He saw many COVID-19 patients die early on, as a resident at another hospital. “It’s heartbreaking for doctors not to be able to save lives,” says Tayyar. Thinking back to a night when he lost three patients, he says he felt like he was “carrying a mountain.” Later he realized, “I’m going into infectious diseases to help figure out a better treatment to prevent patients from dying and help their families. It pushed me to do a better job, and joining the division of infectious diseases and geographic medicine at Stanford provided me with the best support to do so.”

In the future, Hosamani says, it will be especially important to focus on residents’ mental health needs and to offer support services for post-traumatic stress disorder or other health conditions that may arise in the wake of this difficult year. She expects that, much like doctors who received their training during the HIV epidemic, physicians from the “COVID-19 generation” will remember the missteps, the successes, and the socioeconomic factors that worsened the pandemic’s impact.

“I think it’s something that they will never forget and will always shape their training,” says Hosamani. “They will truly go forward to shape medicine for the better because of the experiences they have had.”

The New Normal

With the end of the surge teams and the vaccination of medical workers, staff at the Stanford hospitals and clinics have entered a new normal, where COVID-19 may continue be a threat, much like the seasonal flu.

When asked to reflect on the pandemic, faculty and staff said they were proud to care for their community during the pandemic.

They also were impressed with the leadership displayed by Robert Harrington, MD, chair of the Department of Medicine, during this time of crisis. “Harrington did an excellent job in coordinating very complex care, with outstanding communication between the leaders of infectious disease; hospital medicine; and pulmonary, allergy, and critical care medicine, and their teams,” says Mark Nicolls, MD, professor in pulmonary and critical care medicine.

One silver lining of the pandemic is that it has engendered collaboration between faculty across divisions in the Department of Medicine, with support and encouragement from Harrington and Cathy Garzio, vice chair and director of finance and administration. These partnerships led to new research collaborations and advanced patient care—changes that will persist in the post–COVID-19 era.