3B.

Special Topic:
Coronavirus Disease 2019 (COVID-19)
Basic Information as of April 2020

Andy ND Nguyen, MD, MS

4/23/2020
Outline of This COVID-19 Talk

Epidemiology
Clinical presentation
Testing for COVID-19 (RNA, Antibodies)
Current treatment/Clinical trials

***Information is rapidly changing; some of the materials

in this talk would be outdated as more is known
 INTRODUCTION
On February 11, 2020 the World Health Organization
announced an official name, COVID-19, for the disease that is
causing the 2019 novel coronavirus outbreak, first identified in
Wuhan, China. The virus causing coronavirus disease 2019, is
not the same as the coronaviruses that commonly circulate
among humans and cause mild illness, like the common cold.
It was formerly known as SARS-CoV-2
This COVID-19 is a novel coronavirus that has not been
previously identified.

Transmission electron microscope:

spikes on the surface of the virus
('crown’), binding to the host cell’s
surface receptor, angiotensin
converting enzyme 2 (ACE2)
Pathogens 2020, 9, 231
 INTRODUCTION
Coronaviruses are a large family of viruses that are common in
people and may different species of animals, including camels,
cattle, cats, and bats.
Rarely, animal coronaviruses can infect people and then spread
between people. This occurred in pandemics in the last 2
decades with severe acute respiratory syndrome (SARS, 2002-
2004, bat-> human) and Middle East respiratory syndrome
(MERS, 2012-2018, bat-> camel-> human), and now with the
virus that causes COVID-19.
It is believed that COVID-19 started in bats in Wuhan,
transmitted to human (animal-> human), then spread though
other human (human-human)
 Coronaviruses

Pangolin?

Ref: Viruses 2019, 11, 210

 World-wide, as of 4/22/20
https://coronavirus.jhu.edu/

- USA: 5% infection rate (may be lower)

- Vietnam: 180,067 tested; detected just 268 cases, or 0.15% [Reuters 4/22/20]
 Death Statistics (as of 4/22/20)
USA: 45,638
Italy: 25,085
Spain: 21,717
France: 20,829
UK: 18,147
Belgium: 6,262
Iran: 5,391
Germany: 5,127
China: 4,636
…
Vietnam: 0
 Model by U of Washington
https://covid19.healthdata.org/

Peak on 4/15/20
COVID-19 and Age Groups
❑ CDC:
65-74 y/o
-If infected with covid19
->30% needs admission to hospital
-If get admission ->30% go to ICU
-If go to ICU ->30% death

Chance of death with covid19 infection

= 0.3 x 0.3 x 0.3= 0.027 (~3%)

❑ Chinese CDC: 80% of all deaths

occurred in people aged 60 and above.

❑ WHO: estimates that the global fatality

rate at 3.4% and the CDC’s current
estimate for the U.S. is 1.8%.
 How COVID-19 is spread

COVID-19 is thought to spread mainly from person to person,

mostly through respiratory droplets produced when an infected
person coughs or sneezes. These droplets can land in the
mouths or noses of people who are nearby or possibly be
inhaled into the lungs. Spread is more likely when people are in
close contact with one another (within about 6 feet).
Currently, there is no evidence to support transmission of
COVID-19 associated with food.
COVID-19 seems to be spreading easily and sustainably in the
community (from asymptomatic patients, live longer outside
body)
 How long does COVID-19 live
The coronavirus can live for (2) hours to (5) days on surfaces
outside bodies; the survival depends on the surface material

Metal (doorknobs, jewelry) 5 days

Wood ( furniture, decking) 4 days
Plastics (milk containers and detergent bottles) 2 to 3 days
Stainless steel (refrigerators, pots and pans) 2 to 3 days
Cardboard (shipping boxes) 24 hours
Copper (pennies, teakettles) 4 hours
Aluminum (soda cans, tinfoil) 2 to 8 hours
Glass (drinking glasses, measuring cups) up to 5 days
Ceramics (dishes, pottery) 5 days
Paper: time varies, up to 5 days.
 Risk of COVID-19 Infection

People in places where ongoing community spread of the virus

Healthcare workers caring for patients with COVID-19
Close contacts of persons with COVID-19
Travelers returning from affected areas and countries
Risks of severe illness: older adults (>60 y/o) and people of any
age who have serious underlying medical conditions
 How to prevent infection:
1.Quarantine
Quarantine is usually established for the incubation period of the
communicable disease, which is the span of time during which
people have developed illness after exposure.
For COVID-19, the period of quarantine is 14 days from the last
date of exposure because the incubation period for this virus is
around 2 to 14 days (infection-symptoms).
44% of secondary cases were infected during the index cases’
presymptomatic stage (Nature Medicine, 4/15/20,
https://www.nature.com/articles/s41591-020-0869-5)
Someone who has been released from COVID-19 quarantine is
not considered a risk for spreading the virus to others because
they have not developed illness during the incubation period.
 How to prevent infection:
2.Wahing / Mask
Frequent washing your hands with soap and water for at least
20 seconds. Throughout the day use a tissue to cover your
coughing or sneezing, and wash your hands after blowing your
nose, coughing or sneezing.
It may be possible that a person can get COVID-19 by touching
a surface or object, that has the virus on it, and then touching
their own mouth, nose, or their eyes.
Wearing mask in public place
 Flattening the curve and time span
Time span for Flattening the curve:
-Infection until getting seriously ill with ICU admission:
typically 2 weeks
ICU admission until death: typically 2 weeks on ventilator
-> Time span from social distancing to flattening the curve (stop
infection until death rate peaks): up to 4 weeks
 COVID-19 Symptoms

First Case of 2019 Novel Coronavirus in

the United States.
N Engl J Med 2020;382:929-36.

LAB TESTS:
Leukopenia, thrombocytopenia,
coagulopathy, elevated levels of
creatine kinase, elevations in
hepatic function tests (AP, ALT,
AST, LDH), typically negative
blood cultures
 Testing for COVID-19:
RNA detection by PCR
❑ The COVID-19 RT-PCR test is a real-time reverse transcription
polymerase chain reaction (rRT-PCR) test for the qualitative
detection of nucleic acid from COVID-19 in upper and lower
respiratory specimens (such as nasal, nasopharyngeal,
bronchoalveolar lavage, and nasopharyngeal wash )

❑ The test uses primer and probe sets to detect RNA regions in the
COVID-19 nucleocapsid gene and
Ribonuclease P in a clinical sample.

❑ RNA is reverse-transcribed to cDNA and

subsequently amplified using PCR system

❑ Advantage: detect viral RNA in patient

Disadvantage: long turn-around-time, hours to days
COVID-19
RNA
detection
by PCR

for nucleocapsid and

Ribonuclease P
COVID-19 RNA detection by PCR

Heat/Cool
cycles

+ Primers
+ DNA polymerase
 Sensitivity and Specificity of a Test
❑ Sensitivity is the percentage of persons with the disease who
are correctly identified by the test.
Sensitivity = TP/(TP + FN)
❑ Specificity is the percentage of persons without the disease who
are correctly excluded by the test.
Specificity = TN/(TN + FP)
❑ Clinically, these concepts are important for confirming or excluding
disease during screening. Ideally, a test should provide a high
sensitivity and specificity.
❑ For FDA approval, a clinical test has to be rigorously validated with
sound technical performance, including excellent sensitivity,
specificity.
In the current CODID-19, there is no time to do this
-> emergency use authorization (EUA) with less rigorous validation

***Abbreviations: TP, true positive; TN, true negative;

FP, false positive; FN, false negative.
 Testing for COVID-19: RNA detection by PCR
Positive and Negative Agreement

❑ Positive samples were comprised of 40 NP swabs and 40

BALs spiked with quantitated live COVID-19
❑ No sensitivity and specificity data available at this time with
EUA
 Faster COVID-19 RNA Detection
Cepheid (SUNNYVALE, Calif)
announced on 3/21/20 it has received
Emergency Use Authorization (EUA)
from the U.S. Food & Drug Administration
(FDA) for rapid PCR test for qualitative
detection of COVID-19. The test has been
designed to operate on any of Cepheid’s
more than 23,000 automated GeneXpert®
Systems (PCR) worldwide, with a detection
time of approximately 45 minutes.
On Mar 27 2020, Abbott received EUA
from the FDA for the Abbott ID NOW
COVID-19 for the detection of COVID-19;
delivering positive results in as little as five
minutes and negative results in 13 minutes.
It runs on Abbott's ID NOWTM platform-a
Light-weight box (6.6 pounds and the size
of a small toaster). It detects COVID-19 by
identifying a small section of the virus’
genome, then amplifying that portion (at one
temperature, or isothermal amplification)
for detection (not a PCR test).
 Abbott ID NOW COVID-19
Positive and Negative Agreement

98.7% concordance between the rapid Abbott NOW COVID-19

test and the Real Time PCR tests
Important points in fast RNA detection

Advantages: detect infection rapidly for health care workers and

patients in the hospital-> isolation for prevention of spreading
COVID-19; decrease personal protection equipment (PPE)
Disadvantage: small number of samples in each batch-> less
efficient for less critical testing (asymptomatic outpatients)
Recovered coronavirus patients test positive again ?
Korean health officials reported that 91 patients thought to have
been cleared of the virus had tested positive again, up from 51
people 4 days earlier (The Telegraph, April 10, 2020)
Some of the patients testing positive again showed no
symptoms, while others were suffering from fevers and
respiratory issues.
The prospect of people being re-infected with the virus is of
international concern, as many countries are hoping that
infected populations will develop sufficient immunity to prevent a
resurgence of the pandemic.
At this time it is unclear whether: (a) virus may have been
“reactivated” in previously infected people, (b) the patients being
re-infected, (3) false positive test results
Points to take home with COVID-19 RNA testing
For positive result, quarantine is a must to prevent spreading
infection. Note that 44% of infection are caused by
asymptomatic patient. Repeated testing is needed later on to
assure that the infection is over. About 18% of infected patients
have no symptoms.
The RT-PCR test performed with nasal swabs is only reliable in
the first week of the disease. Later on the virus may go down the
throat and continues to multiply in the lungs. For infected people
tested in the second week on, alternative sample material can
then be taken from the deep airways by suction catheter, or BAL
It is logistically difficult to test a large part of the population
quickly enough. In the US only 120,000 tests are done each day
as of 4/18/20. The incidence of positive cases was likely under-
reported
It is estimated that detectable viral load is only present after 3-4
days of infection
 COVID-19 Antibody Test

Antibodies against the virus, known as serological tests, identify

who has already been exposed and theoretically become immune.
Unlike molecular diagnostics that detect viral RNA, serological
tests can’t be used to diagnose COVID-19 or determine whether
people are at risk of infecting others or advancing to severe
disease
Instead, the antibodies are to identify people (with IgG) who may
safely return to work, especially in front-line healthcare settings;
determine how and where COVID-19 is spreading, which could
guide resource allocation decisions; and identify potential donors of
convalescent sera.
 COVID-19 Antibody Test
FDA’s March 16th guide on COVID-19 rapid antibody tests opened
the runway for serological tests to launch in the U.S. without FDA
review under certain conditions. Such tests had already been
made available by Chinese, Korean, Singaporean and European
regulators weeks before.
FDA’s rationale for not requiring regulatory review is that the tests
can’t be used to diagnose disease (need confirmation), are less
complex than molecular diagnostics, and are needed as soon as
possible.
In its March guidance, FDA said it “does not intend to object to the
distribution and use of serology tests to identify antibodies to
COVID-19,” so long as the developers have validated the tests and
included language saying the tests have not been reviewed by
FDA and should not be used “as the sole basis to diagnose or
exclude COVID-19 infection or to inform infection status.”
 COVID-19 Antibody Test
Cellex Inc, Ortho, Abbott, and Mount Sinai received EUA from FDA
in April 2020 for COVID-19 antibody testing.
The tests by Ortho, Abbott, and Mount Sinai are enzyme-linked
immunosorbent assay (ELISA) tests that takes 1–5 hours to give
results. The Cellex test is a rapid test (10-30 min) that is based on
Lateral flow chromatographic immunoassay
They use venous blood to detect IgM and IgG antibodies to
COVID-19.
Anti-COVID IgM, IgG are detectable in serum starting at the
earliest 5 days after onset of symptoms. Since incubation is 2-14
days, IgM and IgG are positive 1-3 weeks after infection (IgM then
IgG about 7 days later)
IgM is expected to drop within 10 weeks after infection
IgG is expected to last much longer (unknown length of time at
this time)
 COVID-19 Antibodies: Time Spans
Infection: day 0
.
1 week . Incubation:
. day 2-14 .
IgM appears:
2 weeks .
. 1-3 weeks
.
3 weeks . IgG appears:
.
4 weeks 2-4 weeks

5 weeks
…
10 weeks

…
 Rapid COVID-19 Antibody Test:
Lateral flow chromatographic immunoassay

Serological tests expose

FLOW → patient blood to target
antigens on nanoparticles,
Covid-19 ag/
Gold colloid with the goal of trapping
antibodies against the
antigens. The trapped
Human Anti- antibodies are detected by
Rabbit IgG Covid IgG
anti-gold
applying monoclonal Abs
that recognize the Fc portion
Anti-human
IgG
Anti-rabbit
IgG
of patients’ IgM and IgG
-> Pos for
antibodies.
Human Anti- -> Pos control
Covid IgG
Rapid COVID-19 Antibody Kits

https://cellexcovid.com/
 Rapid COVID-19 Antibody Kits
-Interpretation:
(A) If both are neg: not infected or during the
first 1-3 weeks after infection
(B) If only IgM is pos: being actively infected
(C) If both IgM and IgG are pos: being infected
and IgG started to be produced
(D) If only IgG is pos: active infection stops or in
the last phase; IgG was produced to
maintain immunity

-Be aware: many kits are available and sold on

internet with questionable accuracy!
Put blood Positive
Sample/ control
diluent here
 COVID-19 Antibody Test
Sensitivity and Specificity

Cellex’s FDA-authorized test has a sensitivity of 93.8% and a

specificity is 95.6%
These were obtained at two hospitals with a total of 128 positive
patients and 250 negative patients based on COVID-19 results
by RT-PCR.
Points to take home with COVID-19 antibody results

Note that if both IgM and IgG are negative, we still cannot rule
out infection since IgM takes 1-3 weeks after infection to show
up and patient may be asymptomatic early on or throughout
infection
Since FDA allows for the use of rapid antibody kit without review
(only self validation) and it is not a complex test to produce, one
has to take caution in using rapid test kits on the market with
potentially low accuracy
In some kits, positive results may be due to past or present
infection with non-COVD-19 coronavirus strains, such as
coronavirus HKU1, NL63, OC43, or 229E
Some notes on current treatment (as of 4/18/20)
The mainstay of treatment is supportive care (airway with
oxygen, ventilator, or extracorporeal membrane oxygenation
(ECMO)
No FDA-approved medications for COVID-19 are available at
this time
For patients with respiratory compromise, medications are often
tried as last resort:
(a) Medications already FDA-approved for other diseases (off-
label use), such as antivirals for virus including HIV, chloroquine
for malaria
(b) Medications under clinical trials or compassionate use, such
as Remdesivir
Different institutions have their own treatment protocols
In general, for severely ill patients on ventilators/ECMO, only 20-
50% patients survive
Typical treatment
protocol at
MHH-TMC
on 3/20/20:

Medications include:
Chloroquine/
Hydroxychloroquine,
Azithromycin, Ribavirin,
Lopinavir, ritonavir,
Ribavirin, Remdesivir
Updated protocol at
MHH-TMC
on 4/9/20

Medications include:
Chloroquine/
Hydroxychloroquine,
Azithromycin, Remdesivir,
and Tocizilumab
 Waiting for potential solutions to the COVID-19 Pandemic
(All currently under clinical trials; Data shown for non-randomized studies only)
Chloroquine/Hydroxychloroquine +/- Azithromycin
(in-vitro antiviral activity against COVID-19, anti-inflammation):
-Professor Didier Raoult, in Marseille: 26 patients got the drugs,
1 died (3.8%), they were cleared of the virus (tested negative)
more rapidly than the control group
[Antimicrobial Agents, 3/17/2020]
-Another French study with 181 patients, 84 receiving
chloroquine with 20.2% deaths, 97 not receiving chloroquine
with 22.1% death
[MedRxiv, doi: https://doi.org/10.1101/2020.04.10.20060699]
-May prolong QT interval causing cardiac arrhythmia
Remdesivir (RNA polymerase inhibitor, originally tried on Ebola):
- 53 severe patients, 68% had an improvement, only 13% died
[April 10, 2020, New England J of Med]
-125 people at the University of Chicago in Phase 3 clinical
trials; 113 with severe forms; only 2 died [Reuters, April/16/20]
 Waiting for potential solutions to the COVID-19 Pandemic
(All currently under clinical trials)
Tocizilumab (immunosuppressor, a monoclonal antibody against
the interleukin-6 receptor)
Antibodies from convalescent patients: multiple on-going trials
Synthetic antibodies: Distributed Bio Co.
Vaccines: multiple trials going on (most optimistic estimate: in
12-18 months)
 Current Medicine Trials
https://www.visualcapitalist.com/every-vaccine-treatment-covid-19-so-far/
 Current Vaccine Trials
https://www.visualcapitalist.com/every-vaccine-treatment-covid-19-so-far/
 Selected References

CDC: https://www.cdc.gov/coronavirus/

Model by U of Washington: https://covid19.healthdata.org/

John Hopkins University: https://coronavirus.jhu.edu/

WebMD: https://www.webmd.com/lung/