Notes from Covid 19 Update 3/18/20: UCSF Grand Rounds, Infectious Disease Dept
Brian Schwartz, MD
Jennifer Babik, MD, PhD
Deborah Yokoe, MD, MPH
Adrienne Greene, MD
- SARS-CoV: Severe Acute Respiratory Syndrome Corona Virus (from the SARS outbreak of 2002)
- SARS-CoV2: what’s happening now, similar but not identical to past SARS outbreak
- Covid-19 is the clinical presentation/pathology of SARS-CoV2
- How did it spread to humans?
- Coronaviruses are a RNA virus w/ spike-like surface proteins. Some coronaviruses cause human URI.
- Some coronaviruses have animal origin, i.e. 2002 SARS in China, MERS-CoV in 2012 in Arabian peninsula. Coronaviruses don’t require a lot of mutation to cross from another animal into humans (i.e. from bats, camels, cats, etc), so we can anticipate seeing this recur.
- Why is it spreading so fast?
- Does it stay on surfaces longer than SARS? No.
- Does it stay on aerosols longer than SARS? No.
- What about viral shedding?
- There is high level early viral shedding from the upper respiratory tract, which is very different from the 2002 SARS. Peak viral shedding happens at onset of symptoms, we’re not sure how much shedding happens before symptom onset
- How does it cause respiratory failure (ARDS)?
- Infects epithelial cells and binds ACE-2 receptor in small airways
- We don’t know how it progresses to ARDS
- Elevated serum IL-6
- T-cell dysregulation
- Pathology at autopsy: diffuse alveolar damage
- Viral titers decrease as the disease gets worse. Which makes us wonder if this is an immune-mediated process instead of progression caused by the virus itself.
- Late Dec 2019, pneumonia of unknown cause ID’d in Wuhan, exposure at a seafood market
- Jan-Mar: ID’d as SARS CoV2, global spread
- Mar 11: declared pandemic
- “R0” is a basic reproduction number which describes the contagiousness of the virus
- R0 of SARS-CoV2 = 2.24-3.58. That means one infected person will infect 2-3.5 people. The seasonal flu has a R0 of 1.3, MERS has an R0 of 0.8.
- 153 countries, 196,640 cases, 7,893 deaths as of today
- 22,512 cases, 1,625 deaths
- Male predominance (60% males, 40% females)
- Age: very few infected under age 18; ⅓ 51-70yo, ⅓ >70yo. Median age 65.
- All states have cases. Total 4226 cases, 75 deaths.
- 472 cases, 11 deaths.
- Age: 64% are 18-64 yo, 34% are >65 yo, 2% are <18yo
- San Francisco
“Flattening the Curve”
- We learned from 1918 Spanish Flu from different cities’ management, social distancing of 14 days implemented early on dramatically reduced deaths (Philadelphia vs. St. Louis flattened the curve of death rates)
- Main studies are from China, Singapore, and Korea on hospitalized patients. (That means we don’t have studies on mild cases, only on people who end up admitted to hospital)
- 17 case series of between 41 and 1099 patients, 6 case series of CT findings of 41-101 patients
- More data from WHO
- Disease categorization:
- 70-80% have Non-Severe Covid-19
- 15-25% have Severe Covid-19
- 5% in ICU for Covid-19
- Fever in >75% at some point, but only about 50% on admission (i.e. afebrile status when pt arrives to care is NOT a rule-out for Covid-19)
- Dry cough 45-80%
- SOB 20-40%
- Myalgia 10-50%
- Triad of fever, cough, SOB in only 15%
- Leukopenia in 17-54%, median WBC 4.7, with leukocytosis
- Lymphopenia in 33-85%
- Median platelet normal, slt decrease in <35%
- AST/ALT increase in 4-35%
- CRP inc in 61-86%
- LDH inc in 27-75%
- Procalcitonin >0.5 in 5-10% (but higher rates in severe)
- Coinfection rate (may be underestimated) is 0-6%, though there are cases of coinfection with influenza and other respiratory viruses. Presence of other infection makes Covid19 less likely but not a complete rule-out.
- CXR abn in 60% (77% for severe), chest CT abn in 86% (95% if severe)
- Bilat findings in 75-90% (can be unilat especially early/mild)
- CT might be more sensitive than PCR testing
- Septic Shock 1-20%
- ARDS 3-31%
- ECMO rarely used
- Case fatality rate
- 2.3-3.8% in China
- 7.2% in Italy
- (rate may go down as we identify more mild/asymptomatic cases)
- mortality rate dramatically increases after age 69. 70-79yo mortality rate of 8.0-12.5%, 80+ 14.8-20%
- Comorbidities that increase risk: HTN, cancer, DM
- RT-PCR for now, in future serology will probably be used. For now running 80 samples/day. Soon 200-500 samples/day thanks to new donated machines.
- NP (nasopharyngeal swabs) sensitivity is ~75-80%. Sensitivity increases if you also do an oropharyngeal swab (NP/OP).
- BAL (Bronchoalveolar Lavage) and Sputum samples have highest positive testing rate (93% and 72% respectively), i.e. highest quality (highest sensitivity) samples for testing.
- Shedding lasts 12-20 days, culture positive in ~10 days. Can also find viral shedding in feces, not in urine. Only 1% of cases have had viral shedding found in blood.
- Immune-mediated vs Viral mediated: we don’t know yet
- Trying use of Antivirals:
- Remdesivir (RCT-NIH): UCSF will be trialing this for treatment use
- (Pts have high IL-6 levels, maybe this could help?)
- We don’t know what the right treatment is, there is no standard of care yet, we are running trials to get more data.
Prevention & Clinical Workflow
- Goal of algorithms: prevent spread between patients and protect healthcare workers. Ambulatory and Peds can be found online (not discussed here). Changing as we learn more.
- Novel Respiratory isolation
- Contact precautions plus
- N95 w/ eye protection or PAPR (cover w/ face shield)
- Negative pressure if available
- Contact + Droplet (surgical mask w/ eye protection)
- Standard private rooms
- UCSF Algorithm for Adult ED:
- DON’T test asymptomatic patients (test is not as sensitive as we’d hope, can get false negatives)
- Test for any of these resp complaints:
- New cough
- Flu-like illness
- Who gets Novel Respiratory Isolation (first major decision point)?
- Continuous respiratory intervention, i.e.
- Trach in place
- High-flow nasal cannula
- Non-invasive ventilation
- COVID-19 RNA test (qualitative), in-house lab
- Person collecting specimen: N95 + eye protection + contact
- Priority questions:
- inpatient/pending admission
- HCW or first responders
- Anyone living in congregate setting (i.e. senior living, dorms, incarceration, etc)
- NP swab or pooled NP/OP swab (use 2 swabs for NP/OP only if there’s 2 swabs in the kit since there’s a shortage of supplies, i.e. don’t open a second kit just to get a second swab)
- Tip sheet w/ clinical pearls at UCSF medical center website (listed above)
- CBC w/ diff
- Test results back in ~12h
- Pt with very high risk/probability of positive test, contact ID and may initiate more accelerated testing (i.e. lower respiratory tract sample, etc)
- What if pt needs aerosol-generating procedure (i.e. nebulizing meds)?
- Use meter-dosed inhalers instead of nebs whenever possible!
- Place caution sign on door and maintain precautions for 1hr post procedure
- Why is this approach safe?
- Primary mode of transmission is via droplet particles (from data to date from households, planes, ships, hospitals, etc)
- R0 would be much higher if it were airborne, the R0 of 2-3 indicates droplet spread
- Taking airborne precautions instead of droplet precautions is not necessary and would waste needed supplies, also using more commonly-used PPE decreases risk of provider contamination while removing PPE.
- Most academic medical centers and UC campuses are taking a similar approach
- PPE for OR for pts with NO respiratory infections
- Standard surgical mask, eye protection (goggle/face shield), gown
- N95 and PAPR is not needed
- PPE for OR w/ COVID19 infx
- Avoid surgical procedures unless medically urgent
- Minimize # people in OR during aerosol generating procedures (i.e. intubation, extubation)
- Standard surgical PPE + N95 and PAPR
- Bring pt directly to and recover in OR, don’t bring to pre-op holding or PACU (limit exposure)
- Clinical management guidelines will be available later today
Public Health Response Tools
- Isolation for + cases, Quarantine for contacts, Infection control at healthcare facilities, Public education for respiratory hygiene and hand washing
- Exclude non-essential personnel, visitor restrictions, consider alternative roles (like being diverted to giving ICU care)
- Social distancing, event cancellation, community quarantine, and border closures
UCSF Health response
- Early planning saved our butts (in January developed screening protocols, PPE training, designated areas for potential COVID19 pts)
- Priority work right now:
- accelerated care units (negative pressure facilities), respiratory symptom clinics, respiratory isolation unit (transformed one unit into a respiratory unit and all made negative pressure), reduction in elective procedures/surgeries/admits.
- New respiratory symptom clinic will be opened this week at Mission Bay.
- SFDPH Public Health Order: screening visitors and healthcare workers
- Current capacity 80-100 test per day, about to increase
- Coordinating PPE supply & conservation
- Expand occupational health (small department, not prepared for this surge in need)
- The best way to keep eachother safe is to practice social distancing. If you see people crowded in an area please acknowledge and ask people to distance themselves.
- In weekly newsletters there’s a section for where there is greater need and where providers might be redeployed to.
There will be another Zoom webinar tomorrow, 3/19 12-1:30pm: “COVID-19: Understanding the Science, Epidemiology and Clinical Manifestations”