This document provides an overview of COVID-19 including its epidemiology, agent, host factors, environmental factors, transmission, incubation period, pathophysiology, diagnosis, laboratory tests, clinical guidance, control measures, and vaccination. It discusses SARS-CoV-2's structure and classification. It outlines modes of transmission and defines contact types. It also provides details on PCR, antibody, and antigen tests as well as hand washing techniques and personal protective equipment.

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COVID-19
Dr D Vignesh
(MD-AIIMS New Delhi)
Asst. Professor
ESIC Medical College & Hospital
KK Nagar, Chennai

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Pre-test
• https://forms.gle/tZT7cH28LYVx1Uoq8

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Learning objectives
Outline
• Epidemiology of COVID-19
• Agent  Host  Environment
• Burden and Risk factors
• Diagnosis and Management
• Control Measures

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Background and Current burden
• https://www.icmr.gov.in/COVIDTimeline/cindex.html
• https://www.worldometers.info/coronavirus/country/india/

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Epidemiology of COVID-19

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AGENT
• 7 human CoVs (HCoVs)
Gene sources:-
• AlphaCoVs and BetaCoVs:-Probably bats
and rodents
• DeltaCoVs and GammaCoVs:-Avian
species
• For reasons yet to be explained, these
viruses can cross species barriers and
cause illness ranging from minor URI to
Severe Diseases like MERS and SARS
• 2% of the population are healthy carriers
of a CoV
• These viruses are responsible for about
5% to 10% of acute respiratory infections.
Coronaviridae family
(Order Nidovirales)
Alphacoronavirus
229E
NL63
Betacoronavirus
OC43
HKU1
MERS-CoV
SARS-CoV
SARS-CoV2
Deltacoronavirus
Gammacoronavirus

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▪ Coronaviruses:-
▪ Single-stranded RNA viruses (+ssRNA) that can be isolated in different animal
species.
▪ Crown-like appearance (coronam is the Latin term for crown) due to the presence of
spike glycoproteins on the envelope
▪ SARS-CoV-2:-
▪ It has round or elliptic and often pleomorphic form
▪ Diameter is approximately 60–140 nm, +ss RNA is 30 kb in lenght (One of the largest
known RNA viruses)
▪ Spike Glycoprotein- S1, S2 Subunits (S2- fusion peptide)
STRUCTURE
-INTERNATIONAL PULMONOLOGIST’S CONSENSUS ON COVID-19, 2nd Edition (https://www.ncbi.nlm.nih.gov/books/NBK554776/)

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STRUCTURE
https://asm.org/Articles/2020/January/2019-Novel-Coronavirus-2019-nCoV-Update-Uncoating

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Host factors
Original illustration by Dr. William Werbel, Infectious Diseases Society of America

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ENVIRONMENTAL FACTORS
• Temperature:
• A lower environmental temperature favours persistence of virus on surfaces.
• Overcrowding:
• Enhances attack rate. Attack rates are high in close population groups eg. Ships, institutions.
• pH:
• Both high and low pH facilitates Virus reduction
• It is sensitive to ultraviolet rays, and is effectively inactivated by lipid solvents including ether (75 per
cent), ethnol, chlorine-containing disinfectants, peroxyacetic acid and chloroform except for
chlorhexidine.
•
-INTERNATIONAL PULMONOLOGIST’S CONSENSUS ON COVID-19, 2nd Edition
(https://www.ncbi.nlm.nih.gov/books/NBK554776/)

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SOURCE/RESERVOIR
• The persons infected by the novel coronavirus are the main
source of infection.
• Suspect, probable or confirmed.
• Mild, moderate or severe

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DEFINITION OF CONTACT
• Providing direct care without proper personal protective equipment
(PPE) for COVID-19 patients
• Staying in the same close environment of a COVID-19 patient
(including workplace, classroom, household, gatherings).
• Travelling together in close proximity (1 m) with a symptomatic
person who later tested positive.

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HIGH RISK CONTACT
▪ Touched body fluids of the patient (Respiratory tract secretions, blood, vomit,
saliva, urine, faeces)
▪ Had direct physical contact with the body of the patient including physical
examination without PPE.
▪ Touched or cleaned the linens, clothes, or dishes of the patient.
▪ Lives in the same household as the patient.
▪ Anyone in close proximity (within 3 ft) of the confirmed case without precautions.
▪ Passenger sitting in close proximity (within 3 ft) with a symptomatic person who
later tested positive for COVID-19 for more than 6 hours.

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LOW RISK CONTACT
▪ Shared the same space (Same class for school/worked in
same room/similar and not having a high risk exposure to
confirmed or suspect case of COVID-19).
▪ Travelled in same environment (bus/train/flight/any modeof
transit) but not having a high-risk exposure.

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Modes of transmission
• Droplet
• Droplet Nuclei
• Fomite

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FAECO-ORAL ROUTE
▪ SARS CoV 2 virus is enveloped ; unlike other enteric viruses like
adenovirus, novovirus, rotavirus and hepatitis A.
▪ Presence of envelope makes it unstable in the environment
compared to non-enveloped human enteric viruses with known
waterborne transmission.

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PETS:
▪ Several dogs and cats (domestic cats and a tiger) in contact
with infected humans have tested positive for COVID-19.
▪ In experimental conditions, both cats and ferrets were able to
transmit infection to other animals of the same species, but
there is no evidence that these animals can transmit the
disease to human and play a role in spreading COVID-19.

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#breakthechain

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INCUBATION PERIOD
• The median incubation period is 5.1 days (range 1–14 days).
• The precise interval during which an individual with COVID-19 is infectious is
uncertain.
• As per the current evidence, the period of infectivity starts 2 days prior to onset of
symptoms and declines rapidly within the first week of symptom onset.
• The duration of RT-PCR positivity generally appears to be 1-2 weeks for
asymptomatic persons, and up to 3 weeks or more for patients with mild to
moderate disease.
• In patients with severe COVID-19 disease, it can be longer.

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PATHO-PHYSIOLOGY
• Predominantly have a respiratory tract infection
• a small proportion can progress to a more severe stage : dysregulated immune
response with hyper-inflammation with subsequent development of ARDS.
• Hypoxemia, secondary to ARDS may also activate the coagulation cascade thereby
creating a vicious circle.
• Autopsy findings:
• endothelial damage of pulmonary vasculature (Endothelialitis)
• microvascular thrombosis
• extensive alveolar and interstitial inflammation (known as diffuse alveolar damage,
DAD)
• pulmonary intravascular coagulopathy
• ventilation perfusion mismatch
• right to left shunt and refractory ARDS.

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TYPES OF DIAGNOSTIC TESTS
FOR COVID-19
1. Tests to detect the
virus
2. Tests to detect
antibodies to the
virus
3. Antigen detection
tests
Preferably these samples should be obtained as early as symptom onset, since it
yields higher virus concentrations.

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LABORATORY DIAGNOSIS

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Test to detect virus: PCR TEST
▪ Advantages of PCR
tests
▪ Highly specific(100%
specificity)
▪ Tests becomes positive
in the early phase of the
disease
Disadvantages of PCR tests
• Complicated, expensive, and is thus
mainly suited to centralized reference
laboratories.
• Sensitivity may be as low as 50-70%.
• Reasons: Number of viral particles may
not be large in some infected patients.
• PCR can become negative in the later
phases of disease as the patients
immunity builds up.

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TESTS TO DETECT ANTIBODIES
TO THE VIRUS
These are mainly of two types.
• ELISA (Enzyme linked immunosorbent assay).
• Rapid tests can be done at the point of care without highly trained
personal.
Two types of antibodies are tested :
• IgM antibody which rises first after infection and it is an indicator for
an active infection.
• IgG type of antibody rises later and is an indicative of past infection.

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ANTIBODY BASED TESTS
Advantages
• Used for the rapid screening
• Qualitatively detects IgG and
IgM Ab
• Cheaper & faster results
Disadvantages
• Negative in the early phase of
the disease. IgM titers starts to
rise only 3-7 days after the
onset of symptoms
• The specificity of the test can
also be a concern when it is
used primarily as a standard
diagnostic test.

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ANTIGEN BASED TESTS
Minimum acceptance criteria of sensitivity and specificity of Rapid Ag
Test Kits:
• Validated as a Point of Care Test (POCT) without transport to a
laboratory setupSensitivity: 50% and above; Specificity: 95% and
above
• Validated in a laboratory setup with samples collected in Viral
Transport Medium (VTM)- Sensitivity: 70% and above; Specificity:
99% and above

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Clinical guidance
• Keeps changing
• Refer to latest clinical guidance document
• Scan this for latest home isolation guidelines

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Control and disease
prevention

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“Everything we do before a pandemic will seem
alarmist. Everything we do after will seem
inadequate”
~ Michael Leavitt

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Disease prevention and control –
clinical settings
Most important in clinical settings:-
1. Hand-washing
2. Immunization (If available)
3. Use of PPE
4. Strict compliance to Infection Prevention and Control (IPC)
protocols
5. Bio-medical waste management protocol compliance

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COVID-19 ISOLATION WARDS
▪ Separate colour coded bins/bags/containers in wards and
maintain proper segregation of waste as per BMWM Rules
and CPCB guidelines –all four categories (yellow, red, white,
blue)
▪ Double layered bags (2 bags)
used for collection of BMW
so as to ensure adequate
strength and no-leaks

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Six steps for hand-washing

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5 Moments of handwashing

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Personal Protection Equipments

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BMW DISPOSAL – YELLOW
BAGS
▪ Collect used masks (triple
layer mask & N95 mask),
head cover/cap, shoe-
cover, disposable linen
gown, non-plastic or
semi-plastic coverall

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COVID 19 vaccination
• Coverage as of today (31-mar-2023) :-
• About 104 Crore people have received 1st dose
• About 92 Crore people have received 2nd dose
Vaccines available:-
• Covaxin, Covishield, Corbevax

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Some MCQs on COVID
• Corbevax
• Biologicals E. Limited, India produces it
• Adolesceents 12-14 years
• Receptor binding domain recombinant subunit type of vaccine
• 2 doses 0.5 ml i.d 4 weeks apart
• Cold Chain 2 – 8 degree
• When did vaccinations started in India – 16th Jan 2020
• Duration by which COVID 19 vaccine has to be deferred after recovery from illness – 3
months Which vaccine can be given to lactating mother – COVISHIELD and covaxin both
• 2 Deoxy D-Glucose – Emergency Use Authorization – Anti metabolite – suppresses viral
multiplication
• VIRAFIN – pegylated INF-Alpha 2b for moderate COVID – Increase Antibody production

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Some MCQs on COVID
• BBV-154 – Nasal Vaccine, Viral vector vaccine by bharath
biotech
• Novovax – spike protein binder (protein sub unit), 2 doses, 3
weeks apart
• mRNA – Gennova, moderna , Pfizer
• Viral vector based: Astra Zeneca (Covishield), Sputnik V,
Gamaleya
• Whole virus – Sinovac, Covaxin

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Some MCQs on COVID
• Sputnik V – Powdered form!!! But still has to be stored in 2-8,
>=18 years of age, 0.5 ml 3 weeks apart
• Sputnik Light – one dose vaccine, 70% Vaccine efficiency
• Portals: COWIN, evin, rtPCR,
• Minimum gap between covid 19 vaccine: 14 days

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