AGA Family of Websites:

How we managed our GI practice during COVID-19 in San Francisco

Aparajita Singh, MD, MPH, and Lukejohn Day, MD, share their approaches to caring for patients in GI clinics and endoscopy centers during this pandemic.
Aparajita Singh, MD, MPH

Aparajita Singh, MD, MPH

University of California San Francisco (UCSF)

Lukejohn Day, MD

Lukejohn Day, MD

Zuckerberg San Francisco General (ZSFG)

What interventions did your respective GI divisions implement in response to the COVID-19 pandemic?

On March 11, WHO declared a global pandemic and the shelter in place order was instituted in San Francisco on March 17, 2020. Both UCSF and ZSFG swiftly enacted a number of similar measures to combat the spread of SARS-CoV-2. In the outpatient setting, gastroenterologists converted all their scheduled clinic patients to video visits at UCSF. This transition was immediate since our practice was already conducting video visits for some GI follow-up patients using the Zoom platform. At ZSFG, clinic visits were converted to telephone visits. As a result, no outpatient clinic visits were canceled at both sites.

For workforce preservation, at each site only two endoscopists (one general and one advanced endoscopist) took consult calls and performed urgent procedures (both inpatients and outpatients). All remaining gastroenterologists served as a backup in case of a possible surge of COVID-19 hospital admissions.

With respect to endoscopy, both practices proactively rescheduled elective, non-urgent procedures to prepare for a surge of hospitalizations and maintain physical distancing. Only urgent procedures were performed from mid-March onwards. Providers and staff who were at a higher risk for developing adverse events if infected with SARS-CoV-2 (e.g., age greater than 60 years or with multiple active comorbid medical conditions/immunosuppressed) were exempt from in-hospital clinical activities during this time.

As the COVID-19 curve begins to flatten/plateau, what is the strategy to restart endoscopy and clinic operations?

Prior to resuming elective, non-urgent endoscopy a number of factors have to be achieved in the San Francisco region: 

To prepare for resuming both clinic and endoscopic activities, both sites formed a committee to develop a comprehensive plan. A phased approach was favored to resume GI operations in order to help promote physical distancing for patients and staff.

Resuming endoscopy

In contrast to clinic visits, both sites had a large backlog of endoscopic procedures. In the first four weeks, UCSF canceled 1,320 endoscopic procedures and only 196 urgent tier 3 endoscopic procedures were performed. The ZSFG endoscopy center operated at only 10% capacity during this time period. At both institutions, a committee will review rescheduled endoscopic procedures and perform a tier assignment based on a modified Elective Surgery Acuity Scale (ESAS) from the American College of Surgeons as below:

Tier 1

Low priority/elective

(example- screening/surveillance for colon cancer/intestinal metaplasia, motility testing, endoscopy for non-alarm symptoms, EUS for intermediate risk cyst)

Tier 2a

Tier 2b

Intermediate priority, should be scheduled within 3 months

High priority, possible adverse consequences with delay >1 month

FIT/Cologuard positive

Significant iron deficiency anemia

Unintentional weight loss

Variceal surveillance for banding

Active IBD restaging

Hereditary cancer surveillance

Tier 3

Urgent, possible adverse consequences with delay >7 days

(GI bleeding, cholangitis, imaging suggestive of malignancy/infection, significant acute GI symptoms)

Using these tier assignments, the endoscopy schedule will be organized as follows:

  • Phase 1: Only tier 3 cases and inpatients (~25%) (implemented during the San Francisco shelter in place order).
  • Phase 2: Tiers 3 and 2b cases = ~50% of the schedule will be reopened during the first two to three months once the San Francisco shelter in order is relaxed.
  • Phase 3: Tiers 3, 2a, and 2b cases = ~75% of the schedule will be reopened if there are no additional COVID-19 hospital surges and there is a steady decrease in new COVID-19 cases (will likely be for three to nine months after the shelter in place is relaxed).
  • Phase 4: Tiers 1-3 cases = 100% of the schedule will be reopened (likely will be implemented when a vaccine is available).

Resuming clinic

The clinic appointment schedules will also resume in-person visits in a phased approach but that would be a later priority. Currently, until the end of May, all clinic patients will be seen via telemedicine only. We will continue to monitor the COVID-19 hospital admission curve and plan accordingly from June onwards using a phased approach of increasing clinic appointments to 25%, 50%, 75% and 100% of schedule capacity that will consider physical distancing requirements and San Francisco health officer orders. 

What precautionary measures need to be taken during those rescheduled procedures and clinic visits?

Until a vaccine is developed a number of precautionary measures must be undertaken to stem the spread of infection to both staff and patients once elective endoscopic procedures resume. A number of interventions will include:

  • Daily symptom-based screening with temperature screens for endoscopy staff entering the campus. At both sites a web-based questionnaire (that can be completed on one’s mobile device) was used for staff to complete within four hours of their shift start time to expedite the entrance screen.
  • Both sites implemented universal surgical mask policy and all individuals including the endoscopy staff wear a mask at all times while at work.
  • Staff are asked to change into and out of laundered scrubs that are provided to them.
  • Nurses conduct a confirmation call one week prior to a patient’s scheduled procedure. At this time, patients will undergo a symptom-based screening to determine if they may be at risk of having COVID-19. A similar symptom-based screening will occur on the day of the patient’s scheduled procedure. Patients that screen positive at any time will be referred to their primary care provider and their endoscopy will be rescheduled.
  • With increased availability of testing, May 1 onwards, all patients will also be scheduled for a nasal swab PCR based testing within 72-96 hours before their scheduled endoscopic procedure.
  • No visitor would be allowed with the patient and the staff will escort the patient from the hospital entrance if assistance is needed.
  • Patients are scheduled in one hour blocks to ensure adequate physical distancing will be maintained.
  • It remains unclear about colonoscopy but upper endoscopy is considered an aerosol generating procedure. Until we await further data, each site will use similar personal protective equipment (PPE) for all endoscopic procedures. Health care personnel (including physician, nurse, technician) involved in any endoscopic procedure will wear: 1) N-95 mask, 2) eye-protection/face-shield, 3) gown, 4) double gloves, 5) shoe cover and 6) head cover.
  • Procedural staff wear PPE including (labeled with name and date) face-shield on top of N95 masks. If not soiled, the face-shield is wiped with hydrogen peroxide wipe after each use. N95 masks are being stored in a labeled brown bag in a designated area and reused for the shift and beyond if not being soiled/damaged or fit not being maintained.
  • Care should be taken to minimize the number of essential health care personnel in each procedure room. Maximum of five individuals allowed in any procedure room. As of now, attendings have done urgent outpatient cases without the presence of a fellow in the room but we plan to lift this personnel restriction as we test all the patients before endoscopy.
  • At both sites all endoscopy rooms are negative pressure rooms. At the conclusion of a procedure a 30 minute air turnover/air exchange time will be allowed prior to room cleaning. A sign is posted on the endoscopy room door showing when the room is ready for the next patient.
  • Outside of procedure rooms, endoscopy staff should practice preventive measures such as: 1) frequent hand hygiene (for > 20 seconds), 2) avoiding touching eyes, nose and mouth, 3) practicing respiratory hygiene, 5) not attending work if one is sick, especially if evidence of a fever is present, and 6) maintaining physical distancing (at least 2 meters or 6 feet apart).
  • No changes in the endoscope reprocessing process are anticipated.


Lei S, Jiang F, Su W, et al. Clinical characteristics and outcomes of patients undergoing surgeries during the incubation period of COVID-19 infection. EClinicalMedicine. April 2020:100331.

Aminian A, Safari S, Razeghian-Jahromi A, Ghorbani M, Delaney CP. COVID-19 Outbreak and Surgical Practice: Unexpected Fatality in Perioperative Period. Ann Surg. March 2020:1.

AGA and colleague societies issue clinical insights for COVID-19

AGA Institute Rapid Recommendations for Gastrointestinal Procedures During the COVID-19 Pandemic

New York Society for Gastrointestinal Endoscopy Guidelines for Endoscopy Units during the COVID-19 Pandemic March 16, 2020

AGA news and updates on