CORONAVIRUS

DISEASE 2019
(COVID 19)

Dr. Rohit Gupta

St. George’s University
Department of Microbiology,
Immunology, and Pharmacology
Nature.com
 What is a Coronavirus??

• Family - Coronaviridae
• Largest positive strand RNA viruses
• Characteristic surface - virions appear as a crown under EM
• Latin word ‘corona’ means 'crown' or 'halo‘
• Single molecule of linear, +ve ssRNA
• Helical nucleocapsid; enveloped

Diameter 80-160 nm 2
 Coronavirus – What do we already know

• Well known human and animal pathogens

• Second most common cause of common cold
• Usual transmission usually via airborne droplets (minor – fomite, fecal oral)
• Six genera: alpha, beta, gamma, delta, bafinivurus, toroviurs
• Human coronaviruses (HCoVs’) are of the genera:
• alpha coronaviruses
• HCoV-229E and HCoV-NL63
• beta coronaviruses
• HCoV-HKU1, HCoV-OC43, Middle East respiratory syndrome
coronavirus [MERS-CoV], Severe acute respiratory syndrome
coronavirus [SARS-CoV], SARS-CoV-2
3
 Coronavirus – What do we already know
• Identified in the mid-1960s
• known to infect humans and a variety of
animals (including birds and mammals)
• Epithelial cells in respiratory and
gastrointestinal tract are the primary target
cells
• Coronavirus evolution and dissemination:
• It appears that bats and birds are ideal hosts
for the coronavirus gene source
• Bats for Alphacoronavirus and
Betacoronavirus, and
• Birds for Gammacoronavirus and
Deltacoronavirus
Photo: https://www.newscientist.com/
4
 Coronavirus – What do we already know

• Unique aspects:
• Causes infection of respiratory epithelium
• Reinfection can happen in the presence of
serum antibodies
• Antibodies appear after initial infection and
wanes
• Glycoprotein “corona” helps survive GI tract
• Also linked to gastroenteritis in adults and
children

Virus Survival time

Coronavirus Up to 9 days 5
https://www.cell.com/trends/microbiology/fulltext/S0966-842X(16)00071-8

Coronaviruses HCoV-229E, -NL63, -OC43, and -HKU1 continually

circulate in the human population and cause respiratory infections in
adults and children world-wide
7
 Severe Acute Respiratory Syndrome (SARS)

• SARS-associated coronavirus (SARS-CoV)

• Originated in Guangdong Province Southern China
• Infections reported in 26+ countries 8
 Severe Acute Respiratory Syndrome (SARS)

• Case Definition (WHO):

• H/O fever or documented fever AND

• One or more symptoms of LRTI (cough, dyspnea/SOB) AND

• Radiologic evidence of pneumonia/ARDS or autopsy confirmation

without identifiable cause

• Lab diagnostics: Abs by ELISA or IFA; Viral DNA by RT-PCR

9
 Severe Acute Respiratory Syndrome (SARS)
• Reservoir: Bats

• Intermediate hosts: animals eaten

as culinary delicacies in China e.g.
civet cats.
Image: http://www.npr.org/sections/health-shots/2012/09/28/161944734/

• Transmission:

• Respiratory droplets (major

route); Person to person

• Also suggested are airborne,

feco-oral, fomites

• Incubation period: 2-10 days Image: https://www.pinterest.com/pin/266556871665188263/10

 Middle East Respiratory Syndrome (MERS)

• Coronavirus – MERS CoV

• Index case: Saudi Arabia June 2012

• Since April 2012: >1900 lab-confirmed

human cases

• Majority cases - Saudi Arabia http://a.abcnews.com/images/Health/ap_britain_two_diseases_ml_130513_ms.jpg

• All cases outside Arabian Peninsula has travel

history or through close contact with MERS
patient

• Animal Host: Dromedary (Arabian) camels

• Incubation Period: 2-14 days

11
https://www.arabamerica.com/the-importance-of-that-splendid-beast-the-camel-to-the-arab-world/
 Middle East Respiratory Syndrome (MERS)

• Case Definition (WHO) –

• Confirmed case: Laboratory confirmed
• Probable case:
• Febrile acute respiratory illness with clinical, radiographic, or
histopathologic evidence of pulmonary parenchymal disease AND
• Direct epidemiologic link with a confirmed MERS-CoV case AND
• Testing for MERS-CoV is unavailable or inconclusive
• Laboratory confirmation:
• sequence-specific real-time reverse-transcriptase polymerase chain
reactions (rRT-PCRs) OR
• acute and convalescent serology.
Ref: World Health Organization. Revised case definition for reporting to WHO – Middle East respiratory syndrome coronavirus - Interim case definition as of 14 July 2014. 12
http://www.who.int/csr/disease/coronavirus_infections/case_definition/en/ (Accessed on March 06, 2015).
 CORONAVIRUS DISEASE 2019
(COVID 19)

https://www.cdc.gov/coronavirus/index.html

An Ongoing Outbreak
Public Health Emergency of International Concern
 New Outbreak

• Late December 2019: cluster of

pneumonia cases in Wuhan, a city
in the Hubei Province of China
• Cases of pneumonia detected in
Wuhan, China, are first reported to www.the-sun.com
the WHO
• Cause was unknown
• Cases occurred between December
12 and December 29, according to
Wuhan Municipal Health
• Live animals sold at Huanan
Seafood Wholesale Market thought
to be the source

http://shanghaiist.com
 COVID 19
• Respiratory illness
• Rapid spread, epidemic throughout China
• Currently, cases reported globally in all continents except Antarctica
• A novel coronavirus identified as the cause
• Initially called 2019-nCoV
• 30th Jan. 2020 – Declared as public health emergency of international
concern
• 11th Feb. 2020 –
• Named “coronavirus disease 2019” (COVID-19)
• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
 Situation – 3/2/2020, 12:33:02 PM
Confirmed Cases – 89, 254; Deaths – 3,048;
Countries with Cases – 67; Recovered – 45,393

Source – WHO, Johns Hopkins Global Cases

https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6
From: Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in
China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention

JAMA. Published online February 24, 2020.

Copyright 2020 American Medical Association.
Date of download: 3/2/2020
All Rights Reserved. doi:10.1001/jama.2020.2648
 Coronavirus genome has been completely
sequenced

https://www.nejm.org/doi/full/10.1056/NEJMoa2001316
Phylogenetic analysis: Orthocoronavirinae subfamily
 SARS-CoV-2
Betacoronavirus
(photo: Wikimedia Commons) https://time.com

Intermediate
Natural Hosts Hosts
Bats ?Snakes,
HUMANS
?Pangolins
https://www.wcs.org
http://www.china.org.cn

https://www.dailymail.co.uk/
 Transmission
• Current understanding is based on other coronaviruses
• Person to Person (main mode of transmission)
• Close contact with one another (within 6ft)
• Through respiratory droplets from an infected person coughs or
sneezes
• Contact with infected surfaces or objects
• Possible; but not major route
• Patient is most contagious when they are the sickest (most
symptomatic)
• Some reports suggest transmission occurs before symptoms appear
(not main route)
• SARS-CoV-2 thought to be
• Highly contagious
• Community spread
Ref.: US CDC
 Visualization of SARS CoV-2 (formerly 2019-
nCoV) with Transmission Electron Microscopy
Size approx. 125 nm

N Engl J Med 2020; 382:727-733

DOI: 10.1056/NEJMoa2001017
? Entry Point – Human ACE2 Receptors

DOI https://doi.org/10.1038/s41564-020-0688-y
Cytopathic Effects in Human Airway Epithelial
Cell Cultures after Inoculation with 2019-nCoV

N Engl J Med 2020; 382:727-733

DOI: 10.1056/NEJMoa2001017
 COVID 19
Case Definition (ECDC): As of 25th Feb. 2020
• Patients with acute respiratory infection (sudden onset of at least one of
the following: cough, fever, shortness of breath) requiring hospitalization
or not,
• AND
• 14 days prior to onset of symptoms have met at least one of the following
epidemiological criteria:
• close contact with a confirmed or probable case of COVID-19 infection
OR
• having stayed in areas with presumed community transmission
• Probable case
• Suspected case with inconclusive testing for virus (SARS-CoV-2)
• Confirmed case
• Person with laboratory confirmation of virus (SARS-CoV-2)
27
https://www.ecdc.europa.eu/en/case-definition-and-european-surveillance-human-infection-novel-coronavirus-2019-ncov
 SYMPTOMS
• Illnesses ranges from mild symptoms to severe illness and death
• Thought to appear 2-14 days after exposure
• Symptoms -
• Fever, Cough, Shortness of breath
• Gastrointestinal symptoms like vomiting and diarrhea (frequency
unknown)
• Pneumonia most common serious manifestation
• Complications Acute respiratory distress syndrome, septic shock

Recovery time around 2-weeks for mild infections; 3-6weeks for severe disease
First Case of 2019-nCoV in the US
(Holshue et. al.)

https://www.nejm.org/doi/full/10.1056/NEJMoa2001191
JAMA. Published online February
24, 2020.
doi:10.1001/jama.2020.2648

From: Characteristics of
and Important Lessons
From the Coronavirus
Disease 2019 (COVID-19)
Outbreak in China:
Summary of a Report of
72 314 Cases From the
Chinese Center for
Disease Control and
Prevention
 COVID 19 - Cases Reported in the United States
(As of February 26, 2020)

• Total 61 cases

• 46 of these were among repatriated persons from high-risk settings.

• 15 cases were diagnosed in the United States

• 12 were persons with a history of recent travel in China

• 2 were persons in close household contact with a COVID-19

patient (i.e. person-to-person spread).

• One patient no travel history or links to other known cases

(reported in California)

Ref.: US CDC
 CT CHEST FINDINGS Figure 3

The Lancet Infectious Diseases DOI: (10.1016/S1473-3099(20)30086-4)

Copyright © 2020 Elsevier Ltd Terms and Conditions
 CT CHEST FINDINGS Figure 2

The Lancet Infectious Diseases DOI: (10.1016/S1473-3099(20)30086-4)

Copyright © 2020 Elsevier Ltd Terms and Conditions
 Whom to Investigate
Person Under Investigation (PUI)

Ref.: US CDC
 Laboratory Testing (US CDC)
• Specimen to be collected as soon as possible and shipped to CDC

• Testing by US CDC or a CDC-qualified lab

• Sample - Respiratory Specimens

• Lower respiratory tract (if possible)

• Bronchoalveolar lavage, tracheal aspirate, Sputum

• Upper respiratory tract

• Nasopharyngeal swab AND oropharyngeal swab (NP/OP swab),

Nasopharyngeal wash/aspirate or nasal aspirate
• SARS-CoV-2 RNA is detected by polymerase chain reaction (PCR)
Ref.: US CDC
 https://www.ucsfhealth.org/

Treatment

• No specific antiviral treatment

recommended for COVID-19

• Patients receive supportive care

to relieve symptoms

• Severe cases provided care to

support vital organ functions
https://www.nytimes.com/

If you think that you may have been exposed to COVID-19

contact your healthcare provider immediately
 Prevention and Control
https://www.nytimes.com/
• Currently no vaccine available

• Best way of prevention is to avoid exposure

• Non-pharmaceutical measures -

• Aim is to reduce the impact of an outbreak by reducing the number of

contacts, hence reducing transmission.

• Through four main countermeasures:

• Personal Protective Equipment

https://www.aa.com.tr/
• Environmental Countermeasures

• Social Distancing Countermeasures

• Travel Related Countermeasures

https://www.express.co.uk/
https://eva.ecdc.europa.eu/mod/page/view.php?id=9676
 Prevention and Control

• US CDC always recommends everyday

preventive actions to help prevent the spread
of respiratory diseases, including:
• Avoid close contact with sick individuals
• Avoid touching your eyes, nose, and mouth
• Stay home if sick
• Cover cough or sneeze with a tissue,
appropriate disposal of tissue
• Clean and disinfect frequently touched
Photo: https://www.nasdaq.com/
objects and surfaces

Ref.: US CDC
 Prevention and Control
• US CDC recommendations -

• Does not recommend routine use of a

facemask for general public

• Facemasks recommended for patients with

symptoms and individuals with increase risk
like healthcare professionals, close contact

• Frequently washing hands with soap and

water for at least 20 seconds

• Alternative to soap and water is alcohol-

based hand sanitizer with at least 60%
alcohol Photo: https://www.businessinsider.com/

Ref.: US CDC
DO NOT BELIEVE IN RUMORS
KNOW THE FACTS

https://www.cdc.gov/coronavirus/2019-ncov/about/share-facts.html
 Some References and Useful Resources

• https://www.who.int/emergencies/diseases/novel-coronavirus-2019
• https://www.cdc.gov/coronavirus/2019-ncov/index.html
• https://www.springernature.com/gp/researchers/campaigns/coronav
irus
• https://www.thelancet.com/coronavirus
• https://www.nejm.org/coronavirus
• https://www.ecdc.europa.eu/en
• https://www.cdc.gov/coronavirus/2019-ncov/faq.html
• http://www.cidrap.umn.edu/covid-19
Thank You!